MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with ' protein'. Sat, 03 Sep 2011 01:58:27 +0100 http://www.medworm.com/index.php?rid=5140183&cid=t_416261_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2011%2F08%2F17%2Fpenns-genetically-modified-t-cells-create-antitumor-effect-in-mice-with-folate-positive-ovarian-cancer-clinical-trial-pending%2F In a recent issue of Cancer Research, researchers from the University of Pennsylvania showed for the first time that engineered human T cells can eradicate deadly human ovarian cancer in immune-deficient mice. A clinical trial involving the modified T cells is expected to be announced within the next few months. In a recent issue of Cancer Research, Daniel [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=5140183 Wed, 17 Aug 2011 22:50:23 +0100 5140183 http://www.medworm.com/index.php?rid=5103337&cid=t_416261_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fhelp-my-diet-is-so-gross-do-i-have-to-do-it-this-way-insights-welcome%2F2011.08.06 I’m feeling rather nauseated today. This is my fifth day of a high-protein, low-fat, low-carb diet, and I have already developed a deep-seated hatred of egg whites. My regimen includes uncomfortable quantities of grilled chicken breast, fat-free cottage cheese, Greek yogurt, and egg protein, occasionally garnished with a lettuce leaf or perhaps a blueberry. Just yesterday I had to drink a plastic test tube of liquid protein to meet my goals (see offending product image to the left). It looked like a blood-tinged albumin sample, and tasted like orange flavor crystals with a splash of soy sauce. I know that the scientific literature (if we distill it and perhaps oversimplify it a bit) seems to suggest that there may be a short-term advantage to high-protein diets in terms of weight los... Better Health blogs http://www.medworm.com/rss/comments.php?id=5103337 Sat, 06 Aug 2011 18:36:59 +0100 5103337 http://www.medworm.com/index.php?rid=5086296&cid=t_416261_111_f&fid=38038&url=http%3A%2F%2Fcosmicwatercooler.blogspot.com%2F2011%2F07%2Fbodybuilding-protein-requirements.html Besides the free bodybuilding routine, perhaps the most prominent argument against including bodybuilding as we pump iron. To any natural bodybuilder. Just remember, your body beyond its limit, you must be ready to compete and who needs to do more work. Depending on whether you go along, doing what's necessary to get the bodybuilding supplement reviews and build the muscle mass decade.Nowadays, all this has changed and there are no miracle supplements or machines that will surely make a difference in your area. It's the bodybuilding video free with bodybuilding, because bodybuilders are not as strong as they try and stuff themselves with healthy foods to make them again. Our health depends on it, even as we pump iron. To any natural bodybuilder. Just remember, your body beyond its limit, y... Cosmic Watercooler blogs http://www.medworm.com/rss/comments.php?id=5086296 Mon, 01 Aug 2011 03:41:00 +0100 5086296 http://www.medworm.com/index.php?rid=4984721&cid=t_416261_160_f&fid=36190&url=http%3A%2F%2Fwww.skincareblog.org%2F Sonal Bahuguna: Unhealthy food that affect your skinEat healthy, stay healthy. If we eat healthy, we stay healthy. In other words, our diet affects our body. So, it is very important to take a healthy diet for a glowing skin. A healthy skin reflects back the healthy regime you are following to maintain that lovely glow on your face. There are adverse effects of unhealthy diet on your skin. Let’s figure out which food items are not good for skin: 1. Sugar: If taken in excess it can affect your health badly. Problem starts with the process called glycosylation. In this process, the sugar in the blood attaches itself to the protein and stops its proper functioning. All body cells include the component collagen and it’s a vital component of our skin. So, it badly affects the skin. ... Skin Care blogs http://www.medworm.com/rss/comments.php?id=4984721 Thu, 30 Jun 2011 06:26:43 +0100 4984721 http://www.medworm.com/index.php?rid=4968823&cid=t_416261_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2011%2F06%2F23%2Fcan-a-diet-low-in-carbs-high-on-protein-help-in-the-fight-against-cancer%2F Eating a low-carbohydrate, high-protein diet may reduce the risk of cancer and slow the growth of tumors already present, according to a study published in Cancer Research, a journal of the American Association for Cancer Research. Eating a low-carbohydrate, high-protein diet may reduce the risk of cancer and slow the growth of tumors already present, [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=4968823 Fri, 24 Jun 2011 05:21:02 +0100 4968823 http://www.medworm.com/index.php?rid=4952952&cid=t_416261_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fscience-across-the-spectrum.html Penrose, Escher, back – M.C. Escher‘s famously paradoxical illustration of 1960 depicting a stairway atop an “impossible” building, and made famous recently in a dreamscape of the Hollywood movie “Inception“, that seems to ascend or descend interminably is a good example of how projecting our 3D world into two dimensions in artwork can be exploited to manipulate our perceptions. The stairway was originally conceived by father and son team Lionel and Roger Penrose in 1959. Now, Japanese chemists have reconstructed the illusion using a single molecule. Yet another source of antioxidants, in the trees – Researchers in France explain how several species of poplar tree have been used in traditional medicine for their anti-inflammatory properties. They h... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4952952 Fri, 17 Jun 2011 07:16:06 +0100 4952952 http://www.medworm.com/index.php?rid=4934029&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2011%2F06%2Ffirst-contaminated-heparin-case-verdict.html In February, 2008, we first posted about the case of the deadly adulterated heparin.  (A case summary is appended to the end of this post, and nearly all our posts are here.)  The case is of fundamental importance because it involves the failure of pharmaceutical companies to fulfill their core mission, to supply pure, unadulterated drugs.  It is also of fundamental importance because it may be about how this failure to fulfill core mission was not due to accident, or even simple incompetence, but due to putting financial goals ahead of patient safety.  The latest event in the very slowly unfolding aftermath of this case was the first verdict against the sellers of the heparin in a civil trial in a US court room.  As reported by the Chicago Tribune,A Cook Coun... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4934029 Mon, 13 Jun 2011 19:26:00 +0100 4934029 http://www.medworm.com/index.php?rid=4921751&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FSl0FiwryeeY%2F An Illinois jury has awarded $625,000 to the estate of a man who was given a dosage of the heparin blood thinner that contained a contaminated ingredient, The Chicago Tribune writes. The verdict is the first against Baxter International and its supplier, Scientific Protein Laboratories, among hundreds of such lawsuits. Three years ago, the FDA determined the heparin contained fake ingredients from China. The heparin scandal, you may recall, focused a harsh light on the pharmaceutical supply chain, notably poorly supervised manufacturing in China and the inability of the FDA to perform sufficient oversight. The episode led to Congressional hearings and significant pressure on the agency to upgrade its supervision (see here, here and here). Attorneys for the estate of Steven Johansen of Oak ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4921751 Fri, 10 Jun 2011 12:41:17 +0100 4921751 http://www.medworm.com/index.php?rid=4921429&cid=t_416261_87_f&fid=39261&url=http%3A%2F%2Fvactruth.com%2F2011%2F06%2F10%2Fpart-3-of-3-an-interview-about-vaccines-with-helen-v-ratajczak-phd%2F Dr. Ratajczak was or remains a member of Sigma Xi; American Thoracic Society; American Association of Immunologists; International Society of Chronobiology; Society of Toxicology Immunotoxicology Subspecialty Section; North East Chapter of Society of Toxicology and the Autism Society of America.   Now, to the last of my interview questions.   Q. 15. Why do vaccines increase blood histamine levels? Vaccines activate the immune system that responds in a specific way to the antigen in the vaccine, but, in the process, the vaccines also cause inflammation, which is a defense mechanism in which there is increased vascular permeability and release of mediators. Mast cells and basophils have receptors for both C3a and C5a, components of the complement cascade, which is intimately involv... vactruth.com blogs http://www.medworm.com/rss/comments.php?id=4921429 Fri, 10 Jun 2011 06:53:18 +0100 4921429 http://www.medworm.com/index.php?rid=4709237&cid=t_416261_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Frecent-science-news-roundup.html Optical catapulting for explosive fingerprint detection – Optical catapulting-laser-induced breakdown spectroscopy has been used to successfully detect residues of common explosives in human fingerprints, according to researchers from Egypt and Spain. Unsettling enzymes – Millisecond oscillations can massively impact how an enzyme functions, a new NMR spectroscopic study in the US reveals. The study suggests that finding ways to control such movements, without altering the overall structure of an enzyme might be useful in disabling an enzyme in disease. Proof of principle was demonstrated with an enzyme from Escherichia coli. Melanoma lead – Cheminformatics has helped researchers home in on a single compound that could lead to a new approach to treating malignant melanoma... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4709237 Thu, 14 Apr 2011 09:00:34 +0100 4709237 http://www.medworm.com/index.php?rid=4676317&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FYgb2d_p5qu4%2F This week’s addition to the virology toolbox was written by Chris Upton Sequence Searcher is a Java program that allows users to search for specific sequence motifs in protein or DNA sequences. For example, it can be used to identify restriction enzyme cleavage sites or find similar sequence patterns among multiple sequences. Most searches run in a few seconds. Sequence Searcher is part of the Virology.ca suite of programs available at the University of Victoria. Help files: Quick start How-to Some of the key features of Sequence Searcher include: Searching through multiple sequences Use of regular expressions or fuzzy search patterns. Searching for patterns on both strands of a DNA sequence Graphical representation of results and ability to save search results It can run on multiple ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4676317 Mon, 04 Apr 2011 19:14:42 +0100 4676317 http://www.medworm.com/index.php?rid=4552058&cid=t_416261_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fis-turbulence-good-for-the-heart%2F2011.03.05 It’s hard to believe that turbulence could be a good thing for the heart. Consider how the word turbulent is defined: “Characterized by conflict, disorder, or confusion; not controlled or calm.” Those traits don’t sound very heart-healthy. But when it comes to heart rhythm, it turns out that a turbulent response — to a premature beat — is better than a blunted one. The more turbulent the better. No, you haven’t missed anything, and turbulence isn’t another of my typos. Until [recently], heart rate turbulence was an obscure phenomenon buried in the bowels of heart rhythm journals. What Is Heart Rate Turbulence (HRT)? When you listen to the heart of a young physically-fit patient, you are struck not just by the slowness of the heartbeat, but also by the variability... Better Health blogs http://www.medworm.com/rss/comments.php?id=4552058 Sat, 05 Mar 2011 15:00:27 +0100 4552058 http://www.medworm.com/index.php?rid=4540528&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2011%2F03%2Fvon-recklinghausens-disease-neurofibromatosis-type-1%2F Pathophysiology syndrome secondary to genetic defect marked by benign neural tumors and characteristic skin changes Signs and Symptoms 1) multiple neurofibromas 2) positive “button hole” sign (tumors invaginate into skin with pressure) 3) six or more cafe-au-lait spots greater than 1.5 cm 4) freckles in nonexposed skin areas, such as axillary and inguinal areas 5) scoliosis 6) pseudoarthrosis of tibia 7) peripheral nerve sheath tumors (Schwannomas) 8) CNS tumors (neurofibrosarcoma, glioma, malignant Schwannoma) 9) Lisch’s nodules (pigmented iris hamartomas) 10) infiltrative lung disease Histology/Gross Pathology 1) cafe-au-lait spots are flat and uniformly light brown in color 2) benign neurofibroma may convert to malignant peripheral nerve sheath tumors Associated Condit... Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=4540528 Thu, 03 Mar 2011 04:17:31 +0100 4540528 http://www.medworm.com/index.php?rid=4517139&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2011%2F02%2Fthree-years-later-congressional.html Slightly more than three years ago, we first posted about the case of the deadly adulterated heparin.  (A case summary is appended to the end of this post, and nearly all our posts are here.)  The case is of fundamental importance because it involves the failure of pharmaceutical companies to fulfill their core mission, to supply pure, unadulterated drugs.   Three years later, how the heparin was adulterated, and who was responsible are still unknown. So now, it seems, there will actually be an official investigation.  As reported by Alicia Mundy in the Wall Street Journal,The House Energy and Commerce Committee is conducting a formal investigation into the contaminated-heparin crisis of 2008, saying it wants regulators to figure out who was responsible f... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4517139 Thu, 24 Feb 2011 22:41:00 +0100 4517139 http://www.medworm.com/index.php?rid=4517202&cid=t_416261_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fsix-slick-science-picks.html Science video widget – Shortform offered me a sneak preview of their video widget, which allows users to embed a video channel into their blog. Contraceptive pill not to blame for feminized fish – Despite claims that excreted contraceptive hormones are causing endocrine disruption in aquatic animals evidence suggests that this is not the case. Dark Energy, Dark Matter – What is the difference between dark energy and dark matter? NASA explains…even though they don't know what either is. Two sides to every story – even the Lord of the Rings – What if we were to look at Tolkien's epic from Mordor's perspective? Gandalf is a war-monger intent on crushing the scientific and technological initiative of Mordor and its southern allies because scie... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4517202 Thu, 24 Feb 2011 10:00:06 +0100 4517202 http://www.medworm.com/index.php?rid=4436751&cid=t_416261_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fa-new-twist-on-food-allergies-in-kids%2F2011.02.04 The current New Yorker unfolds an engaging story on childhood food allergies. As related by Dr. Jerome Groopman, there’s a shift in how some doctors think about how these conditions  are best managed and, even better — might be prevented. The article feeds into recent discussion that medical science, and even dogma, too-often turns out to be incorrect. Groopman interviews Dr. Hugh Sampson, director of the Jae Food Allergy Institute at Mount Sinai Medical Center in New York: …“This increase in the incidence of food allergy is real,” Sampson said when we spoke recently. He cannot say what is causing the increase, but he now thinks the conventional approach to preventing food allergies is misconceived. For most of his career, he believed, like most allergists, that children are... Better Health blogs http://www.medworm.com/rss/comments.php?id=4436751 Fri, 04 Feb 2011 14:00:01 +0100 4436751 http://www.medworm.com/index.php?rid=4428968&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2011%2F02%2Ffda-to-scientific-protein-laboratories.html Per Ed Silverman on the Pharmalot blog, we hear of new concerns about a company in the supply chain that ended up with adulterated heparin and dead patients.  Before summarizing what the blog reported, let me summarize the case again.Case Summary- We have posted several times, recently here, about the tragic case of suddenly allergenic heparin. Although heparin, an intravenous biologic anti-coagulant, has been in use for over 70 years, serious allergic reactions to it had heretofore been rare. Starting in 2008, hundreds of such reactions, and now over 80 deaths were reported in the US after intravenous heparin infusions.All the heparin related to these events in the US was sold by Baxter International.- We then learned that although the heparin carried the Baxter label, it was no... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4428968 Wed, 02 Feb 2011 17:04:00 +0100 4428968 http://www.medworm.com/index.php?rid=4424441&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FrMRhvr_EIp8%2F One of the companies at the center of the Heparin scandal nearly three years ago just can’t seem to get it right. Last fall, the FDA sent an inspection letter to Scientific Protein Laboratories because the supplier of active pharmaceutical ingredients received info that additional lots were contaminated in October 2008 - months after the scandal broke - but failed to adequately investigate for a year. Now, the FDA has issued a January 20 warning letter in which SPL was upbraided for failing to consider widening its internal investigation into contamination into other lots for another eight months. This is serious; the blood thinner, you may recall, was linked to more than 80 deaths and hundreds of serious reactions in patients in late 2007 and early 2008. In the spring of 2008, an FD... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4424441 Tue, 01 Feb 2011 17:24:42 +0100 4424441 http://www.medworm.com/index.php?rid=4331094&cid=t_416261_113_f&fid=39278&url=http%3A%2F%2Fblogsite.mdbuyline.com%2F%3Fp%3D142 There is great news for cardiology: the reimbursement level for Myeloperoxidase will more than double for FY 2011. Myeloperoxidase is a protein biomarker found in the blood and is more commonly referred to as MPO.  First studied in 2003, it is an early predictor for chest pain patients who are at risk of a heart attack.  Each year, over 5 million patients seek treatment for chest pain in an ER and encounter a long list of possible chest pain causes; some causes can be ruled out with basic tests.  EKGs have been an excellent test for heart problems, but in more recent years, MPO has proven very effective as an early indicator.  When discovered early, physicians can prescribe preventative treatment before damage can occur.  However, reimbursement, in most cases was below the cost of the... MD Buyline blogs http://www.medworm.com/rss/comments.php?id=4331094 Tue, 11 Jan 2011 14:24:35 +0100 4331094 http://www.medworm.com/index.php?rid=4302851&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2011%2F01%2Fblogscan-on-device-companys-obfuscation.html On the Hooked: Ethics, Medicine and Pharma blog, Dr Howard Brody analyzed further the case of the huge royalties paid to spine surgeons by Medtronic (see our most recent post here).  He wondered why surgeons would get such sizable payments for "intellectual property" related to devices that they neither seemed to use or to research?  I would note that the lack of clarity about the reason for Medtronic's payments to these surgeons is just part of a larger lack of clarity about most of the payments made to physicians and medical and health care academics for "consulting" or serving on advisory boards.  If such professional-industrial collaboration is so important for "innovation," one wonders why the people engaged in it are almost never willing to disclose the topics of these... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4302851 Sat, 01 Jan 2011 21:19:00 +0100 4302851 http://www.medworm.com/index.php?rid=4298600&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F12%2Fspine-surgeons-reticent-about.html Starting in 2007, we posted (here, here, here, here and here) about the payments, often huge, that five manufacturers of prosthetic joints (Biomet, DePuy Orthopaedics (a unit of Johnson & Johnson), Stryker Orthopedics,a unit of Stryker Inc, Zimmer Holdings, and Smith & Nephew) revealed they made to orthopedic surgeons and various academic and other organizations. We also noted that some of the leadership of the major orthopedic societies have received substantial amounts from these companies, as have the societies themselves. In 2008, our post on this subject noted the minimal disclosure some of the surgeons receiving these huge payments made when writing scholarly articles on related topics.  In 2009, an article in the New England Journal of Medicine showed that alm... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4298600 Wed, 29 Dec 2010 21:28:00 +0100 4298600 http://www.medworm.com/index.php?rid=4294557&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F12%2Fcharcotmarietooth-disease%2F Pathophysiology 1) heterogeneous group of hereditary peripheral neuropathies 2) type 1 – most common; marked by demyelination 3) type 2 – less severe clinically; lacks demyelination 4) type 3 (Dejerine-Sottas disease) – infantile onset; severe symptoms 5) type 4 – rare; X-linked recessive 6) frequency for all variants combined is 1/2,500 Signs and Symptoms 1) onset is in adolescence with both motor and sensory deficits 2) distal extremity weakness 3) distal atrophy 4) decreased deep tendon reflexes 5) high stepping gait 6) frequent falls 7) abnormal feet (commonly pes cavus or high arches) Characteristic Test Findings EMG – 1) type 1 – decreased nerve-conduction velocity 2) type 2 – normal or only slightly decreased nerve-conduction velocity Histol... Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=4294557 Sun, 26 Dec 2010 23:37:12 +0100 4294557 http://www.medworm.com/index.php?rid=4275324&cid=t_416261_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fa-chia-pet-for-diabetes%2F2010.12.21 Like swallows returning to San Juan Capistrano in the spring, Chia Pets begin appearing every December on late-night television and in the gift aisles of many stores. (Full disclaimer: I bought one for the Yankee Swap at Harvard Health Publication’s annual Christmas party.) Water these ceramic figures and they sprout a green “fur” from seeds embedded on the surface. Silly? Sure, that’s why they are such a hit. What you might not know is that the seeds may someday be a real gift for people with diabetes. Chia seeds come from a plant formally known as Salvia hispanica, which is a member of the mint family. It gets its common name from the Aztec word “chian,” meaning oily, because the herb’s small, black seeds are rich in oils. It was a staple food for the Aztecs, and legend has... Better Health blogs http://www.medworm.com/rss/comments.php?id=4275324 Tue, 21 Dec 2010 14:00:58 +0100 4275324 http://www.medworm.com/index.php?rid=4225186&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F12%2Funreasonably-dangerous-heparin.html It is time for an update on the case of the deadly contaminated heparin sold by Baxter International, which has received much less attention than seems warranted given its human costs (81 lives).  How the heparin was contaminated, and how the contaminated heparin ended up being sold as a US Food and Drug Administration approved American product are still unknown.  Despite the fact that the outcome of this case were so bad, it received disproportionately little attention when it was first made public, and now seems to have become nearly anechoic.Case Summary Baxter International imported the "active pharmaceutical ingredient" (API) of heparin, that is, in plainer language, the drug itself, from China. That API was then sold, with some minor processing, as a Bax... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4225186 Thu, 02 Dec 2010 19:34:00 +0100 4225186 http://www.medworm.com/index.php?rid=4073991&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F10%2Fmore-contaminated-heparin-but-who-leads.html We have posted multiple times over the last two years about the deadly contaminated heparin from China. (See the case summary and link at the end of this post.) One of the key players in this case was a company called Scientific Protein Laboratories (SPL). The company that sold the heparin in the US under its logo, Baxter International, had outsourced production of the active ingredient to a long, and ultimately mysterious supply chain. Baxter got the active ingredient from Scientific Protein Laboratories, which in turn obtained it from a factory in China operated by Changzhou SPL, which in turn was owned by Scientific Protein Laboratories and by Changzhou Techpool Pharmaceutical Co. Changzhou SPL, in turn, got it from several consolidators or wholesalers, who in turn got it from numerous ... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4073991 Fri, 15 Oct 2010 20:56:00 +0100 4073991 http://www.medworm.com/index.php?rid=4073526&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FvHqbPksYzRM%2F This week’s addition to the virology toolbox was written by Chris Upton Generating multiple sequence alignments (MSA) is one of the most commonly used bioinformatics techniques. The “sequences” to be compared can be DNA (promoters, genes, genomes) or proteins. Note that the length and number of sequences to be aligned has an impact on the methods (algorithms) that can be used; what is suitable for aligning 20 proteins probably won’t work for alignment of 5 poxvirus genomes (200 kb each). Some useful links: Wikipedia: multiple sequence alignment Wikipedia: sequence alignment Wikipedia: list of sequence alignment software Protein Multiple Sequence Alignment: Book chapter by Chuong B. Do and Kazutaka Katoh Sequence alignment: Lecture notes by Per Kraulis Another list of tools So yo... virology blog blogs http://www.medworm.com/rss/comments.php?id=4073526 Fri, 15 Oct 2010 16:24:12 +0100 4073526 http://www.medworm.com/index.php?rid=3913104&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F08%2Fpromising-melanoma-drug-tested%2F A drug against melanoma being described by researchers as “phenomenal” is one step closer to being widely available to patients after results of an early study were released two days ago. The gene therapy drug acts against the BRAF protein that causes skin cells to abnormally replicate. Dr Keith Flaherty of the Developmental Therapeutics Institute at Massachusetts General Hospital and Dr. Lynn Schuchter at the University of Pennsylvania took part in the study and comment. (Source: Inside Surgery) Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=3913104 Sat, 28 Aug 2010 18:14:41 +0100 3913104 http://www.medworm.com/index.php?rid=3876592&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F08%2Fproprietary-information-confidentiality.html The case of the deadly contaminated heparin sold by Baxter International has received much less attention than seems warranted given its human costs (81 lives).  How the heparin was contaminated, and how the contaminated heparin ended up being sold as a US Food and Drug Administration approved American product are still unknown.  Our most recent post, here, noted that an investigation into the contamination of the active pharmaceutical ingredient (API - actually the heparin itself) in China failed to produce any results, apparently because the Chinese government did not see fit to pursue it.  (Note that a brief summary of the whole case is at the end of this post.)Now a new story in the Wall Street Journal by Alicia Mundy explains even more about why we do not... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=3876592 Tue, 17 Aug 2010 20:59:00 +0100 3876592 http://www.medworm.com/index.php?rid=3802326&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F07%2Fprotein-urine-risk-factor-kidney-failure%2F Dr. Morgan Grams at Johns Hopkins Hospital and colleagues have published a study that suggests that the presence of protein in the urine can be a significant prognostic sign of likelihood of later more severe kidney disease. (Source: Inside Surgery) Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=3802326 Fri, 30 Jul 2010 04:25:46 +0100 3802326 http://www.medworm.com/index.php?rid=3784215&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F07%2Fmore-about-what-we-dont-know-about.html We last blogged about the case of Baxter International's adulterated heparin here.  (For a more detailed summary of the case, look here.)In summary, Baxter International imported the "active pharmaceutical ingredient" (API) of heparin, that is, in plainer language, the drug itself, from China. That API was then sold, with some minor processing, as a Baxter International product with a Baxter International label. The drug came from a sketchy supply chain that Baxter did not directly supervise, apparently originating in small "workshops" operating under primitive and unsanitary conditions without any meaningful inspection or supervision by the company, the Chinese government, or the FDA. The heparin proved to have been adulterated with over-sulfated chondroitin sulfate (OSCS), and many ... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=3784215 Fri, 23 Jul 2010 15:13:00 +0100 3784215 http://www.medworm.com/index.php?rid=3946234&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2Fh1f6DEG1Yr8%2F A more rapid method than Western blot analysis to detect a specific protein in a cell, tissue, organ, or body fluid is enzyme-linked immunosorbent assay, or ELISA. This method, which does not require fractionation of the sample by gel electrophoresisis, is based on the property of proteins to readily bind to a plastic surface. To detect viral proteins in serum or clinical samples, a capture antibody, directed against the protein, is linked to a solid support such as a plastic 96 well microtiter plate, or a bead. The clinical specimen is added, and if viral antigens are present, they will be captured by the bound antibody. The bound viral antigen is then detected by using a second antibody linked to an enzyme. A chromogenic molecule – one that is converted by the enzyme to an easily ... virology blog blogs http://www.medworm.com/rss/comments.php?id=3946234 Fri, 16 Jul 2010 16:28:49 +0100 3946234 http://www.medworm.com/index.php?rid=3714108&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F06%2Famyloidosis%2F Pathophysiology 1) deposition of fibrous, insoluble amyloid protein in extracellular matrices of body 2) clinically ranges from benign to severe sequelae 3) classification is based on fibril-forming protein 4) most common systemic types – primary (idiopathic), secondary, and familial amyloid polyneuropathy (FAP) (Source: Inside Surgery) Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=3714108 Thu, 01 Jul 2010 00:45:16 +0100 3714108 http://www.medworm.com/index.php?rid=3687048&cid=t_416261_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2010%2F06%2F23%2Fwill-nano-publications-triplets-replace-the-classic-journal-articles%2F “Libraries and journals articles as we know them will cease to exists” said Barend Mons at the symposium in honor of our Library 25th Anniversary (June 3rd). “Possibly we will have another kind of party in another 25 years”…. he continued, grinning. What he had to say the next half hour intrigued me. And although [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=3687048 Tue, 22 Jun 2010 22:07:47 +0100 3687048 http://www.medworm.com/index.php?rid=3625802&cid=t_416261_167_f&fid=38271&url=http%3A%2F%2Frebeccascritchfield.wordpress.com%2F2010%2F06%2F03%2Fmeatless-monday-catches-on-meat-industry-sizzles%2F Carlene Helble, Elite Nutrition Intern Guest Blog Post The Washington Post ran an interesting article by Jane Black recently on Meatless Monday and the trouble it’s stirring up for the meat industry. Chef Mario Batali, most often known for his orange Crocs, has recently unveiled himself as the latest supporter, a surprising move considering at least 3 of his 14 restaurants are named for meat. All of his restaurants will now offer two vegetarian entrees every Monday.  However, Batali is by no means on the forefronts of this movement. The Post article also cited that Baltimore City Public Schools launched Meatless Mondays for its 82,000 students in October of 2009 and 32 US hospitals have also signed on to the ‘Balanced Menu Challenge’ which aims to reduce meat purchases by 20 percent... Balanced Health and Nutrition Rebecca Scritchfield's Blog blogs http://www.medworm.com/rss/comments.php?id=3625802 Thu, 03 Jun 2010 10:41:02 +0100 3625802 http://www.medworm.com/index.php?rid=3614496&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F05%2Frespiratory-syncytial-virus-rsv%2F Pathophysiology 1) respiratory tract disease with the most severe clinical conditions seen in newborns and infants 2) cause is infection with a virus in the Paramyxoviridae family 3) exists in types A and B with the antigenic difference owing to differences in the G protein Signs and Symptoms Infants and young children – 1) fever 2) rhinorrhea 3) cough 4) wheezing 5) rhonchi 6) rales 7) can progress to dyspnea, tachypnea, hypoxia Adults – 8) headache 9) sore throat 10) malaise Elderly – 11) pneumonia 12) bronchiolitis 13) tracheobronchitis Characteristic Test Findings Radiology – 1) hyperexpanded lung fields 2) infiltrates (can range from diffuse infiltrates to lobar consolidation) Laboratory – 3) definitive diagnosis is made by isolating the virus from respir... Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=3614496 Sun, 30 May 2010 16:05:02 +0100 3614496 http://www.medworm.com/index.php?rid=3614522&cid=t_416261_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fbrush-up-on-heart-health%2F2010.05.30 The British Medical Journal reported on a study of toothbrushing and found that people with poor oral hygiene had an increased risk of cardiovascular disease and heart attack. We’ve known for the last two decades that inflammation plays an important role in atherosclerosis. Markers of low-grade inflammation like C-reactive protein are also shown to be higher in heart disease. The Scottish Health researchers looked at the general population and followed a large subset with questions about their oral health. They asked about frequency of dentist visits, toothbrushing, and controlled for many co-variables such as general activity, hypertension, smoking, height and weight. They also collected blood for studies of C-reactive protein as a marker of inflammation. They removed from the... Better Health blogs http://www.medworm.com/rss/comments.php?id=3614522 Sun, 30 May 2010 16:00:00 +0100 3614522 http://www.medworm.com/index.php?rid=3542906&cid=t_416261_167_f&fid=38576&url=http%3A%2F%2Fwww.drbriffa.com%2Fblog%2F2010%2F05%2F07%2Fhigher-protein-diet-with-resistance-exercise-best-for-fat-loss%2F There are a myriad of ways to lose weight, but I lean generally towards diets relatively low in carbohydrate and rich in fat. This is on the basis that such diets consistently out-perform diets explicitly low in fat in terms of weight loss. Also, such diets tend to, generally speaking, bring about desirable changes in [...] (Source: Dr John Biffa's Blog) Dr John Biffa's Blog blogs http://www.medworm.com/rss/comments.php?id=3542906 Fri, 07 May 2010 16:12:50 +0100 3542906 http://www.medworm.com/index.php?rid=3526355&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV080.mp3 Hosts: Vincent Racaniello, Alan Dove, Rich Condit, and Michael Bouchard Vincent, Alan, and Rich speak with Michael Bouchard about hepatitis B virus discovery, replication, and pathogenesis. This episode is sponsored by Data Robotics Inc. Use the promotion code TWIVPOD to receive $75-$500 off a Drobo. Win a free Drobo S! Contest rules here. Download TWiV #80 (58 MB .mp3, 80 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email. Links for this episode: The enigmatic X gene of hepatitis B virus Tableau public (thanks Ricardo!) Molecular phylogeny of Archaea from soil (thanks Etienne!) Habitats of Archaea (thanks Cedric!) Timer remote controls (thanks Bill!) Letters read in episode 80 Weekly Science Picks Rich PBS Frontline: The Vaccine War Alan ... virology blog blogs http://www.medworm.com/rss/comments.php?id=3526355 Mon, 03 May 2010 00:39:31 +0100 3526355 http://www.medworm.com/index.php?rid=3524115&cid=t_416261_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fmcdonald%25e2%2580%2599s-vs-dash-two-days-two-diets%2F2010.05.01 This week I’ve been trying to eat according to the DASH guidelines for lowering blood pressure. It actually hasn’t been too difficult — partly because I’m not following their strictest guidelines, which call for just 1,300 milligrams of sodium and 16 grams of saturated fat a day. I’ve been shooting for 2,300 milligrams of sodium and 22 grams of saturated fat. In 2003, I tried a somewhat different “diet,” which in some ways was more difficult to follow, even though it only lasted one day. My son Jim (then age 11) and I ate every meal at McDonald’s for an entire day (yes, this was before Super Size Me). We recorded the experience on the Web. I thought it would be interesting to compare my day at McDonald’s to a typical day on DASH. (more…) *This blog p... Better Health blogs http://www.medworm.com/rss/comments.php?id=3524115 Sat, 01 May 2010 16:00:38 +0100 3524115 http://www.medworm.com/index.php?rid=3490830&cid=t_416261_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2010%2F04%2F20%2Fexpression-of-proteins-linked-to-poor-outcome-in-women-with-ovarian-cancer%2F Scientists have established the presence of certain proteins in ovarian cancer tissues and have linked these proteins to poor survival rates in women with advanced stages of the disease. Scientists have established the presence of certain proteins in ovarian cancer tissues and have linked these proteins to poor survival rates in women with advanced [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=3490830 Wed, 21 Apr 2010 00:09:14 +0100 3490830 http://www.medworm.com/index.php?rid=3362486&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fwww.molecularbrain.com%2Fcontent%2Fdownload%2Fsupplementary%2F1756-6606-3-5-s3.mov Atsushi Miyawaki’s lab has developed a series of neat tools for visualizing cell cycle progress. For zebrafish, the zFucci system consists of two fluorescent proteins, mKO2 and mAG, that are fused to Cdt1 and geminin genes.  Cell cycle- regulated proteolysis of these fusion proteins causes each cell to display orange fluorescence in G1 phase nuclei and green fluorescence in both the nucleus and cytoplasm of S/G2/M phase cells. Video of cell cycle transitions in culture. Click for the video. The last time I saw Atsushi give a talk, he showed an incredible time lapse video from the zebrafish cleavage stage that I haven’t been able to find online.  However, here is a video from later in development of the zebrafish that is still pretty remarkable. Development of a zebrafish visu... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3362486 Sat, 13 Mar 2010 16:08:39 +0100 3362486 http://www.medworm.com/index.php?rid=3354459&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F03%2F10%2Fcnifers-of-acetylcholine%2F “If you find yourself needing to reread this paragraph, perhaps it’s not that well written. Or it may be that you are low on acetylcholine.” Acetylcholine (ACh) is a major modulator of brain activity in vivo and its release strongly influences attention. If we could visualize when and where ACh is released, we could more fully understand the large trial to trial variance found in many in vivo recordings of spike activity, and perhaps correlate that to attentional and behavioral states mediated by ACh transmission. Back in grad school, when I was desperately trying to figure out what biological question to answer with my GluSnFR glutamate sensor, I ended up in a meeting with Kleinfeld, his grad student Lee Schroder and Palmer Taylor. We plotted a strategy to make a FRET... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3354459 Thu, 11 Mar 2010 05:53:24 +0100 3354459 http://www.medworm.com/index.php?rid=3318691&cid=t_416261_167_f&fid=38576&url=http%3A%2F%2Fwww.drbriffa.com%2Fblog%2F2010%2F03%2F01%2Fcinema-popcorn-highlighted-as-a-nutritional-hazard-and-how-to-avoid-it%2F Over the weekend the radio was on and I caught an item about the apparent hazards of popcorn. The Food Standards Agency in the UK has, it seems, launched a bit of a blitz against the snack foods and drink available in cinema foyers (see here for a report regarding this) and popcorn is [...] (Source: Dr John Biffa's Blog) Dr John Biffa's Blog blogs http://www.medworm.com/rss/comments.php?id=3318691 Mon, 01 Mar 2010 10:25:20 +0100 3318691 http://www.medworm.com/index.php?rid=3301988&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Fwww.virology.ws%2F008_W3310_10.mp4 Download: .wmv (298 MB) | .mp4 (65 MB) My apologies for the poor audio in this lecture: I neglected to turn on my lapel mic and the entire session was recorded on the microphone in my laptop – which was across the room. Visit the virology W3310 home page for a complete list of course resources. (Source: virology blog) virology blog blogs http://www.medworm.com/rss/comments.php?id=3301988 Tue, 23 Feb 2010 21:58:11 +0100 3301988 http://www.medworm.com/index.php?rid=3290769&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F02%2Fhuntingtons-chorea%2F Pathophysiology 1) progressive neurodegenerative disease with selective neuronal loss – caused by an excessive repeat of the CAG nucleic acid sequence in the gene on chromosome 4 that codes for the Huntington protein 2) unclear how altered Huntington protein contributes to the specific symptoms 3) the protein HAP-1, which binds to the Huntingtin protein, possibly contributes to the pathogenesis 4) usual duration from onset of symptoms to death is about 15 years 5) marked by involuntary movements, progressive dementia, striking emotional changes Signs and Symptoms 1) the greater the expansion, the earlier the onset of disease 2) onset is earlier by 3-4 years if condition is inherited from father 3) usual presenting signs – emotional and cognitive deficits (often by years) 4) mos... Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=3290769 Sat, 20 Feb 2010 03:19:44 +0100 3290769 http://www.medworm.com/index.php?rid=3276115&cid=t_416261_167_f&fid=38576&url=http%3A%2F%2Fwww.drbriffa.com%2Fblog%2F2010%2F02%2F16%2Fhigher-protein-diet-plus-resistance-exercise-aids-weight-and-fat-loss-in-type-2-diabetics%2F Where weight and fat loss is concerned, I favour a relatively low-carbohydrate, high-protein diet on the basis that such diets generally outperform low-fat, carb-rich diets traditionally advocated for weight loss. A lower-carb diet I think may have particular advantages for diabetics because, well, they have difficulty handling carbohydrate as a result of impaired insulin function [...] (Source: Dr John Biffa's Blog) Dr John Biffa's Blog blogs http://www.medworm.com/rss/comments.php?id=3276115 Tue, 16 Feb 2010 12:12:51 +0100 3276115 http://www.medworm.com/index.php?rid=3251431&cid=t_416261_167_f&fid=38576&url=http%3A%2F%2Fwww.drbriffa.com%2Fblog%2F2010%2F02%2F08%2Fmy-friends-son-reminds-me-how-important-blood-sugar-control-is-to-energy-and-mood%2F I was talking to a son of a friend of mine over the weekend. Mark (not his real name) is 18 and has been finding his energy and motivation can flag at times. Some of the time he can be energised and motivated. Other times he feels lethargic and “can’t be bothered with life”. Naturally, [...] (Source: Dr John Biffa's Blog) Dr John Biffa's Blog blogs http://www.medworm.com/rss/comments.php?id=3251431 Mon, 08 Feb 2010 10:29:53 +0100 3251431 http://www.medworm.com/index.php?rid=3236046&cid=t_416261_136_f&fid=36162&url=http%3A%2F%2Fwww.myelomablog.com%2F2010%2F02%2F02%2Fmyeloma-treatment-test-results%2F Here are my latest results. Specific Proteins Test Name Result AB Normal Range Units IGG 466 L 600-1700 MG/DL IGM 31 L 35-290 MG/DL IGA 408 H 40-400 MG/DL Electrophoresis The SPE pattern demonstrates two bands of restricted mobility in the gamma region. Immunofix, Serum Monoclonal component typed as IgA Lambda. Concentration of monoclonal protein determined by serum protein electrophoresis is 0.4 g/dL. Monoclonal component typed as IgA Lambda. Concentration of monoclonal protein determined by serum protein electrophoresis is 0.3 g/dL. *Suggestive of a monoclonal component typed as IgG Kappa. Concentration of monoclonal protein is too low to accurately quantify. * This is new! Previously, I’ve only ever had just two m-spikes. That’... beth's myeloma blog blogs http://www.medworm.com/rss/comments.php?id=3236046 Tue, 02 Feb 2010 20:43:21 +0100 3236046 http://www.medworm.com/index.php?rid=3224805&cid=t_416261_83_f&fid=34856&url=http%3A%2F%2Finsidesurgery.com%2F2010%2F01%2Fcreutzfeldtjakob-disease%2F Pathophysiology 1) degenerative disease of CNS caused by presence of infectious protein called a prion 2) presents with myoclonus and dementia; relentlessly progresses to death, usually within 1 year 3) in the past decade new-variant CJD has been described that is a human infection by the etiologic agent causing bovine spongiform encephalopathy (”mad cow” disease) Signs and Symptoms 1) in one third of cases a prodrome of malaise, fatigue, sleep problems, headache, and weight loss occurs 2) myoclonus 3) dementia 4) choreoathetoid movements 5) vision deficits Characteristic Test Findings EEG – 1) early in disease can be normal or show only scattered theta activity 2) as disease progresses episodic triphasic and polyphasic spikes are seen Histology/Gross Pathology 1) affecte... Inside Surgery blogs http://www.medworm.com/rss/comments.php?id=3224805 Sat, 30 Jan 2010 20:39:48 +0100 3224805 http://www.medworm.com/index.php?rid=3223443&cid=t_416261_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F30%2Fphosphogrid%2F I no longer work on protein kinases but when I did, PhosphoGRID is the kind of database that I would have wanted to see. It features: A nice clean interface, with good use of Javascript Useful information returned from a simple search form Data for download in plain text format with no restrictions or requirements for registration All it lacks is a RESTful API, but nothing is perfect :-) Published in the little-known but often-useful journal Database: PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. doi:10.1093/database/bap026. Filed under: bioinformatics, publications, web resources Tagged: database, phosphory, protein kinases (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3223443 Sat, 30 Jan 2010 04:10:45 +0100 3223443 http://www.medworm.com/index.php?rid=3201695&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV067.mp3 Hosts: Vincent Racaniello, Alan Dove, and Marc Pelletier Vincent, Alan, and Marc talk about chronic wasting disease of deer caused by prions, blocking the semen-derived enhancer of HIV infection with surfen, and making green transgenic rabbits using a lentiviral vector. This episode is sponsored by Data Robotics Inc. Use the promotion code VINCENT to receive $50 off a Drobo or $100 off a Drobo S. Download TWiV #67 (64 MB .mp3, 88 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email. Links for this episode: Chronic wasting disease in West Virginia Chronic wasting disease alliance and CDC webpage Semen-derived inhibitor of viral infection (SEVI) Surfen inhibits the action of SEVI Making green transgenic rabbits using simian immunodeficiency vir... virology blog blogs http://www.medworm.com/rss/comments.php?id=3201695 Sun, 24 Jan 2010 14:44:22 +0100 3201695 http://www.medworm.com/index.php?rid=3083071&cid=t_416261_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F12%2Fsky-rocking-graphics-in-new-moe-release.html Have you seen the new graphics functionality in the new MOE (Molecular Operating Environment) of the Chemical Computing Group (CCG)? No? You need to look at some examples in their image gallery! The graphics engine is by-far the best I have seen since a long time, even without using 3D shutter glasses.Besides, the release has not only an improved look-and-feel, but also (as usual) a lot of high-level algorithm improvements. Here an overview about the new features of the 2009.10 release:Real Time Ray-traced GraphicsProtein/Antibody ModelingLowModeMD Conformational SearchSynthetic Score DescriptorScaffold Replacement/Fragment Linking MOE/web SOAP ServerFinally, for those being interested in using Schrodinger's or CCG's tools in combination with KNIME, there is good news. After a long perio... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=3083071 Sun, 13 Dec 2009 13:57:00 +0100 3083071 http://www.medworm.com/index.php?rid=3052346&cid=t_416261_136_f&fid=36162&url=http%3A%2F%2Fwww.myelomablog.com%2F2009%2F12%2F03%2Fmy-two-m-spikes%2F I wanted to post my results, and got a little behind! Here it is: SERUM PROTEIN ELECTROPHORESIS: COMPARED TO 6/1/09, NO SIGNIFICANT CHANGE IN PREVIOUSLY CHARACTERIZED (2) IgA-LAMBDAS FROM 0.25 TO 0.26 G/dL AND FROM 0.19 TO 0.15 G/dL. The two m-spikes have been staying this way for several months now. The complete bone survey report says, “No aggressive lytic or sclerotic osseous lesions.” Good, eh? Possibly Related Posts: Dr. Brian Durie to host a teleconference H1N1 flu that’s resistant to Tamiflu International Myeloma Foundation’s 3rd Annual Comedy Celebration for the Peter Boyle Memorial Fund If you’re sick, please stay home! Flu Preparedness Advice (Source: beth's myeloma blog) beth's myeloma blog blogs http://www.medworm.com/rss/comments.php?id=3052346 Thu, 03 Dec 2009 13:41:46 +0100 3052346 http://www.medworm.com/index.php?rid=3029868&cid=t_416261_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2009%2F11%2F25%2Fcan-therapy-really-change-your-brain%2F In this study they used Interpersonal Psychotherapy (IPT) which looks through the lens of both cognitive and interpersonal issues. It would be interesting to know how other theoretical orientations would fare. There is a lot known about the power of oxytocin (the hormone of love) to bond people together but oxytocin can also be an ally to encourage therapeutic change. According to Linda Graham, MFT and trainer on the integration of relational psychology, mindfulness and neuroscience, it is “the neurochemical basis of the sense of safety and trust that allows clients to become open to therapeutic change.” It was a class I recently took with Linda, “The Neuroscience of Attachment,” that left me feeling so inspired about the implications of this in my practice. As a therapist, it’s ... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=3029868 Thu, 26 Nov 2009 03:25:33 +0100 3029868 http://www.medworm.com/index.php?rid=2977425&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F11%2F09%2Fthree-cheers-for-gcamp%2F Three papers are out online in Nature Methods that show big improvements in calcium imaging with genetically encoded sensors.  They are are based on the fluorescence intensity indicator, GCaMP.   GCaMP, first developed by Junichi Nakai, consists of a GFP that has been circularly permuted so that the N and C termini are fused and new termini are made in the middle of the protein.  Fused to one terminus is calmodulin and the other is a peptide, M13, that calmodulin (CaM) binds to in the presence of calcium. The name is supposed to look like GFP with a CaM inserted into it, G-CaM-P.  Normally the GFP is dim, as there is a hole from the outside of its barrel into the chromophore.  Upon binding calcium, this hole is plugged and fluorescence increases. The first paper, A genetically encod... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2977425 Mon, 09 Nov 2009 23:54:11 +0100 2977425 http://www.medworm.com/index.php?rid=2966802&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F11%2Fepstein-barr-virus-leader-protein.html Epstein-Barr virus (EBV) efficiently infects and immortalizes human B lymphocytes through expression of at least 12 viral genes, which include the EBNA-LP protein. Recent work discusses the current state of knowledge about how EBNA-LP contributes to EBV biology. EBNA-LP is an enigmatic protein comprised largely of 22 and 44 amino acid repeated sequences. Elucidation of EBNA-LP functions has been guided by identification of interacting cellular and viral proteins. The functions of these cofactors implicate EBNA-LP as a potential modulator of apoptosis, cell cycle processes, and transcriptional pathways. Recent studies have linked EBNA-LP with Sp100, a protein associated with promyelocytic nuclear body proteins (PML NBs), which mediate intrinsic cellular defenses against viral infections. Al... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2966802 Fri, 06 Nov 2009 09:18:00 +0100 2966802 http://www.medworm.com/index.php?rid=2954213&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F11%2Fpathobiology-of-lyme-disease-borrelia.html Lyme disease Borrelia are host-dependent, tick-transmitted, invasive, nontoxigenic, persistent pathogens that cause disease in humans and other mammals primarily through the induction of inflammatory reactions. During transmission from the infected tick, the bacteria undergo dramatic changes in gene expression, resulting in adaptation to the mammalian environment. (Samuels and Radolf, 2010)Expression of outer surface protein C (OspC) is essential during these early stages of colonization, although the mechanism by which OspC promotes spirochetal infectivity is unknown. Organisms multiply and spread locally and induce an inflammatory response that in humans results in an erythema migrans, the hallmark lesion of localized infection. The spirochetes enter the bloodstream during the primary in... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2954213 Tue, 03 Nov 2009 09:07:00 +0100 2954213 http://www.medworm.com/index.php?rid=2886206&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F10%2F1918-pandemic-influenza-virus.html The pandemic influenza virus of 1918 was extremely virulent and caused significant morbidity and mortality to millions of people worldwide. The extinct virus caused severe pathology in both the upper and lower respiratory tract, resulting in fatal respiratory complications and bacterial pneumonia. The pathology associated with 1918 influenza virus infections is thought to be the result of the exposure of an immunologically naive host population to an unusually virulent virus. Using reverse genetics, the 1918 pandemic virus has been studied in an attempt to determine which viral genes contribute to the increased virulence. Studies to date point to the role of the hemagglutinin, neuraminidase, and the polymerase basic protein 1 genes as the virulence genes responsible for the high pathogenic... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2886206 Mon, 12 Oct 2009 15:46:00 +0100 2886206 http://www.medworm.com/index.php?rid=2886210&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F10%2Finfluenza-non-structural-protein-1.html The non-structural protein 1 (NS1) of influenza virus is a potent antagonist of the cellular antiviral interferon (IFN) response. It is a multifunctional protein with two domains, a dsRNA binding domain (RBD) and an effector domain (ED) which interacts with various cellular proteins. Although, initially sequestration of dsRNA was considered the primary mechanism for countering IFN, subsequent studies have shown that the interactions of ED with various cellular proteins are likely involved. NS1 is shown to be a virulence determinant, especially in the highly pathogenic H5N1 viruses that are currently a threat for another influenza pandemic. Among various influenza virus strains, NS1 is relatively well conserved with major differences occurring in the linker region and the C-terminus, where... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2886210 Mon, 12 Oct 2009 15:34:00 +0100 2886210 http://www.medworm.com/index.php?rid=2886211&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F10%2Fns1-protein-of-influenza-viruses-is.html The NS1 protein of influenza A viruses is a small (230-237-amino acid), multi-functional dimeric protein that participates in both protein-RNA and protein-protein interactions. It is comprised of two functional domains: N-terminal (amino acids 1-73) RNA-binding domain; and C-terminal (amino acids 74-230/237) effector domain. Here we focus on several of the best-characterized functional interactions of the NS1 protein. A major role of the NS1 protein is to counter host cell antiviral responses. Thus, the RNA-binding domain binds double-stranded (ds) RNA, thereby inhibiting the dsRNA activation of the antiviral oligo A synthetase/RNase L pathway that is induced by interferon-α/β (IFN-α/β). A region of the effector domain binds the protein kinase PKR, thereby preventing ... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2886211 Mon, 12 Oct 2009 15:31:00 +0100 2886211 http://www.medworm.com/index.php?rid=2876295&cid=t_416261_134_f&fid=36012&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBattleDiabetes%2F%7E3%2Fxs1a1rzLhyg%2F Whey protein is a natural product, produced as part of the cheese making process. It is probably most renowned for being a supplement used for bodybuilders and weight trainers as it is an excellent source of protein. Whey protein is not only of benefit to bodybuilders and weight trainers but also to sufferers of conditions such as cancer sufferers, people who are overweight and to Diabetic sufferers. How can it benefit Diabetic sufferers? As mentioned already, whey protein is the best natural source of protein. Protein can become an element lacking in some Diabetic’s diets, as a result of their dietary alterations. Whey protein also lowers levels of blood glucose and this is thought to happen because higher protein levels stimulate Insulin production from the Pancreas. This particular e... Battle Diabetes Blog blogs http://www.medworm.com/rss/comments.php?id=2876295 Thu, 08 Oct 2009 23:04:41 +0100 2876295 http://www.medworm.com/index.php?rid=2862083&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F10%2Fretroviral-restriction-factors.html Over the course of the retrovirus replication cycle, viral cDNA is inserted into host chromosomal DNA to establish the provirus. This process results in a permanent insertion mutation in the host cell genome. Host cells have evolved intracellular factors that block the spread of retroviral infection. Some of these antiviral factors act prior to integration and therefore also block the mutagenic potential of infection. Several such factors have been identified, including Fv1, the APOBEC3 complex, and TRIM5. These host factors potently block HIV-1 and other retroviruses from establishment of the provirus. Here we will review current understanding of Fv1, APOBEC3, and TRIM5 proteins, with particular emphasis on TRIM5.Further reading: Retroviruses: Molecular Biology, Genomics and PathogenesisF... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2862083 Mon, 05 Oct 2009 11:17:00 +0100 2862083 http://www.medworm.com/index.php?rid=3016943&cid=t_416261_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FLCpPTwJRsoY%2F The classical complement pathway begins when the initiator protein C1q binds directly to the surface of a pathogen, or to an antibody that is bound to a microbe. There is a binding site for C1q on the Fc portion of antibody molecules. C1q can also recognize molecular patterns characteristic of pathogens, much like the Toll-like receptors. C1q binding to antibody or a pathogen surface initiates an unusual protease cascade with one or more members of a set of seven activating enzymes. This set of cleavages, which occurs on the surface of the microbe, leads to the formation of the membrane attack complex that produces holes in membranes of cells and viruses. Other products of the cascade include mediators of inflammation, which recruit white blood cells to the site of infection. Still mor... virology blog blogs http://www.medworm.com/rss/comments.php?id=3016943 Fri, 02 Oct 2009 02:37:04 +0100 3016943 http://www.medworm.com/index.php?rid=2812460&cid=t_416261_111_f&fid=36048&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAHeartyLife%2F%7E3%2F5TGcdTrdQmw%2F Losing weight is a good idea for any of us. But a new study says that if you have kidney disease, it’s even more important to get rid of excess baggage. An article in the Clinical Journal of the American Society of Nephrology said “dieting and exercising cut down on proteinuria — the increased output of protein in the urine — while also preventing kidney function from worsening.” Surgery that brings about weight loss is also a benefit to kidney patients as it reduced high filtration rates. Image: sxc.hu. Post from: Blisstree Kidney Disease Patients Should Lose Weight (Source: A Hearty Life) A Hearty Life blogs http://www.medworm.com/rss/comments.php?id=2812460 Sun, 20 Sep 2009 12:50:33 +0100 2812460 http://www.medworm.com/index.php?rid=2809765&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F09%2F18%2Foptogenetic-induction-of-memory-recall%2F Speaking of reactivating specific memories, at the 2009 Society for Neuroscience meeting, Matteo Rizzi of Michael Häusser’s lab is presenting the realization of an idea that has been floating around in some research proposals I’ve read over the last year.  Express channelrhodopsin-2 under control of the immediate early gene c-fos, induce a strong memory formation via fear conditioning, and then drive the recall of that memory by stimulating the neurons that are expressing ChR2. Immediate early genes are activated shorty after high levels activity in neurons, though the precise patterns are different depending on which promoter (c-fos, Zif268, etc) you use, making precisely HOW they reflect recent neuronal activity patterns unclear.  Nevertheless, the activation of the c-fos ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2809765 Fri, 18 Sep 2009 19:40:52 +0100 2809765 http://www.medworm.com/index.php?rid=2800550&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F09%2F16%2Flight-switchable-protein-interactions%2F A fully genetically-encoded approach to light-activated transcription is getting closer now that a new, generalizable method of light-switchable protein interactions has been published.  In Nature’s advance online publication, Spatiotemporal control of cell signalling using a light-switchable protein interaction, Anselm Levskaya of the Voigt lab at UCSF and co-authors demonstrate inducible, reversible control of protein binding, localization and signalling in mammalian cells.   apo-PhyB covalently binds to the chromophore phycocyanobilin (PCB) to form a light-sensitive holoprotein. PhyB undergoes conformational changes between the Pr and Pfr states catalysed by red and infrared light, reversibly associating with the PIF domain only in the Pfr state. This heterodimerization interac... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2800550 Wed, 16 Sep 2009 16:06:58 +0100 2800550 http://www.medworm.com/index.php?rid=2766213&cid=t_416261_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F2BEtNQ7gafI%2F Through the wonders of genetics, we might have a wonder drug that let us eat anything we want -without ever gaining a single pound! We can eat fatty and sugary food and we won’t even need to exercise to lose all those calories.   I’m not sure that’s such a good idea but that drug may exist in the near future, with the recent discovery of the so-called “obeso-genes”. The key lies in a gene called IKKE that acts as a master switch that control obesity, by producing a protein kinase that turns other proteins on or off. When a body is fed a high fat diet, the IKKE kinase slows down metabolism and burns less calories, and weight increases. When the gene IKKE (and thus the kinases) are deleted, metabolism speeds up and the body burns more calories. Knock-off mice that didn’t c... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2766213 Fri, 04 Sep 2009 15:16:24 +0100 2766213 http://www.medworm.com/index.php?rid=2699587&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2009%2F08%2Fwho-investigated-case-of-deadly.html A year and a half ago, we posted quite a bit about the case of the deadly contaminated heparin. In retrospect, what is most amazing is how quickly this case fell off the radar screen.Summary of the Case of the Deadly Contaminated HeparinHere is a summary:- We have posted several times, recently here and here, about the tragic case of suddenly allergenic heparin. Although heparin, an intravenous biologic anti-coagulant, has been in use for over 70 years, serious allergic reactions to it had heretofore been rare. Starting late last year, hundreds of such reactions, and now 21 deaths were reported in the US after intravenous heparin infusions.All the heparin related to these events in the US was made by Baxter International.- We then learned that although the heparin carried the Baxter label,... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=2699587 Thu, 13 Aug 2009 17:39:00 +0100 2699587 http://www.medworm.com/index.php?rid=2645408&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F07%2F27%2Fvoltage-imaging-with-sub-millisecond-single-action-potential-resolution%2F I have been itching to post about this work since David DiGregorio presented it at a meeting at Janelia last year. His group’s results, Submillisecond Optical Reporting of Membrane Potentials In Situ Using a Neuronal Trace Dye, were published in the Journal of Neuroscience last week.  Their method of optical voltage sensing is the first one that looks like its ready for “prime-time” action outside of the labs of developers of these sorts of techniques.  It has sufficient speed (<1 ms resolution), sensitivity (25% dF/F per 100mV), and limited membrane perturbation to see single action potentials, without dramatically altering the shape of these currents.     Membrane depolarization causes DPA to rapidly partition to the inner membrane leaflet, quenching DiO.   Like... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2645408 Mon, 27 Jul 2009 15:28:54 +0100 2645408 http://www.medworm.com/index.php?rid=2469888&cid=t_416261_136_f&fid=36162&url=http%3A%2F%2Fmyelomablog.com%2F2009%2F06%2F10%2Fserum-protein-electrophoresis-mutliple-myeloma%2F Lab Report: Final    06/01/2009 14:36 SERUM PROTEIN ELECTROPHORESIS                                                              Reference SPE INTERP COMPARED TO 2/10/09, NO SIGNIFICANT CHANGE IN PREVIOUSLY CHARACTERIZED (2) IGA-LAMBDA COMPONENTS FROM 0.21 TO 0.25 AND 0.14 TO 0.19 G/DL. "I have personally performed the interpretation". Dr. S. Pizzo, MD,PhD SPE TOTAL PROTEIN 6.8 g/dL [6.0-8.0] SPE ALBUMIN % 65.6 % SPE ALBUMIN 4.46 g/dL [3.97-5.34] SPE ALPHA 1 % 2.9 % SPE ALPHA 1 0.20 g/dL [0.11-0.32] SPE ALPHA 2 % 10.5 % SPE ALPHA 2 0.71 g/dL [0.40-0.88] SPE BETA % 11.3 % SPE BETA ... beth's myeloma blog blogs http://www.medworm.com/rss/comments.php?id=2469888 Wed, 10 Jun 2009 17:06:09 +0100 2469888 http://www.medworm.com/index.php?rid=2456788&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F06%2Fbook-review-secreted-proteins.html Bacterial Secreted Proteins: Secretory Mechanisms and Role in PathogenesisPublisher: Caister Academic PressEditor: Karl WooldridgeISBN: 978-1-904455-42-4"This collection of expert reviews provided the reader with a detailed insight into the exotic world of secreted proteins and their role in bacterial metabolism and pathogenicity. The text is well referenced throughout with many chapters being especially up to date. There is liberal use of tables and figures are used to illustrate the complex mechanisms described throughout the book. Dr Wooldridge is to be complimented on assembling such a knowledgeable group of lucid authors who review a rapidly advancing and complex field in an easy to read manner." (Expert Review of Anti-infective Therapy, August 2009)from Joni Tillotson and Glenn S Til... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2456788 Thu, 04 Jun 2009 10:51:00 +0100 2456788 http://www.medworm.com/index.php?rid=2417147&cid=t_416261_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2009%2F05%2F18%2Fmesothelin-a-potential-new-target-for-ovarian-cancer-immunotherapy%2F Researchers have generated altered immune cells that are able to shrink, and in some cases eradicate, large tumors in mice. The immune cells target mesothelin, a protein that is highly expressed, or translated in large amounts from the mesothelin gene, on the surface of several types of cancer cells. The approach, developed by researchers at [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=2417147 Tue, 19 May 2009 04:51:22 +0100 2417147 http://www.medworm.com/index.php?rid=2423182&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F05%2Fbacterial-secreted-proteins-book-review.html "This is a good overview that will be of interest to scientists interested in protein secretion as well as individuals studying bacterial pathogenesis ... The diagrams are very helpful in understanding how the bacteria control the process of secretion ... This well designed book will provide a clear understanding of how bacterial protein secretion occurs. These different mechanisms appear to be common in a variety of different bacteria and thus understanding of one system will assist in the study of various organisms."from Doodys Book Review Service (2009) Further reading: Bacterial Secreted ProteinsMetagenomics: Theory, Methods and ApplicationsEnvironmental Molecular MicrobiologyABC Transporters in MicroorganismsPili and FlagellaBacterial PolysaccharidesMicrobial ToxinsBiopolymersFull ran... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2423182 Mon, 18 May 2009 11:33:00 +0100 2423182 http://www.medworm.com/index.php?rid=2398985&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F05%2F08%2Finfrared-fluorescent-proteins%2F Hunting for new fluorescent proteins in the coral reefs of the Caribbean and Australia is a task that a lucky few researchers have managed to get funding for. Scuba diving in some of the world’s most beautiful places; it’s not a bad gig, if you can get it.  Most fluorescent protein scientists are confined to a lab, mutating existing fluorescent proteins from jellyfish and coral. Shifting their excitation and emission spectra has allowed multiple fluorescent proteins to be used as molecular highlighters at the same time, since their colors are distinct from each other. Some members of this palette are shown in Brain Windows top image bar.  After over a decade of research, the spectrum is pretty well covered.  Except for one area…  The infrared. The near-infrared band i... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2398985 Fri, 08 May 2009 19:33:12 +0100 2398985 http://www.medworm.com/index.php?rid=2390180&cid=t_416261_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F1012 In the article Conservation and Variability of West Nile Virus Proteins published in PLoS this April, August et al., applied a bioinformatic approach in examining a large number of West Nile Virus (WNV) sequences available from public databases. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2390180 Tue, 05 May 2009 00:42:03 +0100 2390180 http://www.medworm.com/index.php?rid=2364981&cid=t_416261_87_f&fid=34825&url=http%3A%2F%2Fwww.wesleyjsmith.com%2Fblog%2F2009%2F04%2Flead-into-gold-protein-induced.html This is potentially huge: Induced Pluripotent Stem Cells, which permit tailor made, patient specific pluripotent stem cell lines to be created ethically without the use of embryos, can now be made without using genetic material. From the story, "Purely Protein Pluripotency," in The Scientist (no link):Researchers have attained the holy grail of cellular reprogramming: inducing pluripotency without using any DNA-based materials. Using only a cocktail of purified proteins and a chemical additive, investigators have generated induced pluripotent stem (iPS) cells that don't carry the potential burden of unexpected genetic modifications, according to a new study published online today (Apr. 23) in Cell Stem Cell."This new advancement is both exciting and startling," Huck-Hui Ng, a stem cell res... Secondhand Smoke blogs http://www.medworm.com/rss/comments.php?id=2364981 Thu, 23 Apr 2009 23:24:00 +0100 2364981 http://www.medworm.com/index.php?rid=2321724&cid=t_416261_129_f&fid=36038&url=http%3A%2F%2Fwww.everydayhealth.com%2Fblog%2Ftrevis-life-with-multiple-sclerosis-ms%2Fnext-generation-interferons-for-ms%2F Oral drugs are the hottest topic among people living with multiple sclerosis.  We are all tired of daily, weekly injections (sometimes thrice weekly!), monthly or quarterly infusions.  “If only a pill for this” seems to be a mantra. The thing is: no drug is without potential (and in the case of MS, serious) side effects. Then you may ask, “what about the people who are stable on their current meds?”  If you are doing “well” on your current drugs, is it even a good idea to switch for the simple reason of convenience? I attended a meeting a few weeks ago where I learned about the next generation of “injectables” and it seems pretty interesting. This particular drug was a new version of the Interferon Beta drugs.  Unlike the current formulat... Life with MS blogs http://www.medworm.com/rss/comments.php?id=2321724 Fri, 03 Apr 2009 22:02:41 +0100 2321724 http://www.medworm.com/index.php?rid=2323795&cid=t_416261_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F985 ProteinShader is a free, open-source molecular visualization project written primarily in Java by Joe Weber. The ProteinShader program, is a new tool for macromolecular visualization, it uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2323795 Thu, 02 Apr 2009 02:47:03 +0100 2323795 http://www.medworm.com/index.php?rid=2287184&cid=t_416261_109_f&fid=35671&url=http%3A%2F%2Fwww.anxietyinsights.info%2Fabstract_depression_and_creactive_protein.htm Conclusions: Depressive symptoms may be partly responsible for inflammatory processes, and inflammatory processes may induce depressive symptoms in men. (Text has been reformatted for visual clarity; ed.) Source... © 2009 by American Psychosomatic Society (Source: Latest entries from www.anxietyinsights.info) Latest entries from www.anxietyinsights.info blogs http://www.medworm.com/rss/comments.php?id=2287184 Fri, 20 Mar 2009 07:33:00 +0100 2287184 http://www.medworm.com/index.php?rid=2268014&cid=t_416261_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2009%2F03%2F15%2Fcan-fda-approved-hiv-drugs-treat-chemoresistant-ovarian-cancer%2F Two recent in vitro studies conducted in the U.S. and Europe raise a provocative question:  Can FDA-approved human immunodeficiency virus (HIV) drugs be used to treat chemoresistant ovarian cancer?  Both studies were based upon the fact that HIV patients taking antiretroviral inhibitors have a lower incidence of infection-associated malignancies.  Based upon that fact, the researchers [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=2268014 Mon, 16 Mar 2009 04:26:23 +0100 2268014 http://www.medworm.com/index.php?rid=2259405&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F03%2F12%2Fbackground-perceval-the-atpadp-sensor%2F Recently, Brain Windows mentioned the report A genetically encoded fluorescent reporter of ATP:ADP ratio. We invited Dr. Jim Berg, the lead author of the study to provide additional background to our readers. Below, Jim provides a fascinating look at rationale behind sensor development.  I really like that they came at this problem with a biological question in mind, something I would recommend before anyone start the development of a genetically encoded indicator.   A pixel-by-pixel ratio of the 490 nm excitation image by the 430 nm excitation image from two cultured HEK293 cells expressing Perceval during control conditions (left) and after 40 min of metabolic inhibition with 5 mM 2-deoxyglucose (right)   Here’s a little insight into why we decided to develop a fluorescent sens... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2259405 Thu, 12 Mar 2009 19:52:55 +0100 2259405 http://www.medworm.com/index.php?rid=2243024&cid=t_416261_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F952 The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.  UniProt provides the scientific community with a protein knowledgebase (UniProtKB), sequence clusters (UniRef), sequence archive (UniParc), and supporting data consisting of literature citations, taxonomy, keywords and more. (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2243024 Sat, 07 Mar 2009 02:16:04 +0100 2243024 http://www.medworm.com/index.php?rid=2227533&cid=t_416261_134_f&fid=36049&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FDiabetesNotes%2F%7E3%2FlI2JVSG06U8%2F var iamInit = function() {try{initIamServingHandler(320,480,674723,"http://cdn.pis.picapp.com/IamProd/Resources/Css/css2.css")}catch(ex){}}() Lots of us want to lose weight, and when it’s all sad and done it really isn’t that difficult to do. Let me amend that…. losing weight takes effort and time, and IS hard to do… but the formula to lose weight isn’t rocket science. As if we needed even more convincing, a new study has determined that eating “heart-healthy, low-calorie foods and exercising is the key to losing weight regardless of levels of protein, fat or carbohydrates.” Make sense, doesn’t it? Eat a balanced diet that is less in calorie than you eat now. Work out. The pounds will come off. It might not be right away, but they will. Tag... Diabetes Notes blogs http://www.medworm.com/rss/comments.php?id=2227533 Sun, 01 Mar 2009 11:12:06 +0100 2227533 http://www.medworm.com/index.php?rid=2212776&cid=t_416261_167_f&fid=38271&url=http%3A%2F%2Frebeccascritchfield.wordpress.com%2F2009%2F02%2F24%2Fclearing-up-protein-misinformation-interview-with-dr-nancy-rodriguez%2F I was very lucky to grab a few minutes with Nancy Rodriguez. She is an authority on protein and human nutrition. Check out what she had to say about protein minsinformation and the latest research. Rebecca: When you’re teaching your students about protein, what do you think is critical they understand about the importance of protein in the diet and how the body uses protein. Nancy: Absolutely.  I make sure the students understand how protein differs from carbohydrate and fat, and that using it for energy is ‘last resort’ so to speak. Rebecca: What are the most interesting outcomes you found in your research on the relationships between exercise, protein intake, and protein utilization in athletes and physically active adults? Nancy: One of the most significant findings is the cr... Balanced Health and Nutrition Rebecca Scritchfield's Blog blogs http://www.medworm.com/rss/comments.php?id=2212776 Tue, 24 Feb 2009 23:27:05 +0100 2212776 http://www.medworm.com/index.php?rid=2196280&cid=t_416261_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F929 David Leader and James Milner-White, of the Faculty of Biomedical and Life Sciences in the University of Glasgow have built a freely accessible web application called Motivated Proteins.  This web facility was designed for protein scientists in mind to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.  Their study has been published in BMC Bioinformatics, February 2009, entitled Motivated Proteins: A web application for studying small three-dime read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2196280 Thu, 19 Feb 2009 04:47:05 +0100 2196280 http://www.medworm.com/index.php?rid=2195053&cid=t_416261_134_f&fid=36049&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FDiabetesNotes%2F%7E3%2FJb2hXvV0Bw4%2F var iamInit = function() {try{initIamServingHandler(320,215,624956,"http://cdn.pis.picapp.com/IamProd/Resources/Css/css2.css")}catch(ex){}}() Well this is exciting news for diabetics everywhere! Scientists have isolated a protein called CXCL10 that “induces inflammation that can trigger the destruction of insulin-producing beta cells in the pancreas.” This may be the cause of Type 1, and perhaps Type 2 diabetes. This research could help predict Type 2 diabetes in certain individuals, and has the potential to lead to get us closer to the ultimate goal: a cure. Tags: beta cell loss, cause of diabetes, cxcl10, protein, ResearchShare This (Source: Diabetes Notes) Diabetes Notes blogs http://www.medworm.com/rss/comments.php?id=2195053 Wed, 18 Feb 2009 03:22:32 +0100 2195053 http://www.medworm.com/index.php?rid=2182654&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F02%2F11%2Fsymposium-a-revolution-in-fluorescence-imaging%2F This coming Tuesday and Wednesday (Feb 17th & 18th) at UCSD, there will be a symposium honoring Roger Tsien, featuring presentations from 32 former and current members of the Tsien Lab. The topics are quite diverse, concentrated in genetically-encoded indicators, but also featuring fluorescent cell penetrating peptides for cancer therapy, photophore ligases for imaging synaptic development, and even a radical new design for the internal combustion engine. The quality of speakers and subjects looks to be outstanding.  Here is a complete schedule.  You may notice that at 11:15 AM on Tuesday in Price Center East Ballroom, I will be presenting recent progress we have made in the development of genetically-encoded calcium indicators and their application to in vivo imaging.  Don’t... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2182654 Thu, 12 Feb 2009 04:45:42 +0100 2182654 http://www.medworm.com/index.php?rid=2163589&cid=t_416261_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fdo-you-really-mean-what-you-think-you-mean.html%3F_c%3Dfeed-rss ...Or, on defining a protein. If you take away just one thing from this post it is this: a single word means different things to different people (especially in biology: "gene" and "protein" are two examples), and as long as you can agree on a ... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2163589 Thu, 05 Feb 2009 12:25:51 +0100 2163589 http://www.medworm.com/index.php?rid=2092629&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F01%2F09%2Fbrainstorm-1-the-calcium-memory-sensor%2F As mentioned in the previous post, this is the first installment of BrainStorm, a section of ideas I have under development, but don’t have the time to physically work on.  This section will contain organically developed ideas, organized by project.  Reader feedback is encouraged. How can we identify the group of neurons that encode a particular thought?   I don’t want to simply see correlations of in activity of a few scattered neurons with a given thought, but identify the entire neuronal ensemble.  Which neurons are active at a precise moment in a task?  How are they wired together? Which are the drivers of activity? Existing technology is inadequate to identify the entire neural ensemble that encodes a thought. Immediate early gene expression  patterns have not been s... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2092629 Fri, 09 Jan 2009 19:06:39 +0100 2092629 http://www.medworm.com/index.php?rid=2033252&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F12%2F12%2Ffluorescent-proteins-in-scholarpedia%2F This article is an excellent review of all fluorescent proteins that contains both classic and very current references.  I recommend it as the first place to go to learn about fluorescent proteins in detail. It makes my contributions to the GFP page of wikipedia look quite primitive. The author, Rob Campbell, is relatively famous in the field of fluorescent proteins for his monomerization of dsRed, the brilliant red fluorescent protein from coral. Many of the fluorescent proteins in Brain Windows title bar were derived from mutations of this monomeric red fluorescent protein. Less well known is that he taught me how change restriction sites on plasmid DNA via overlap extension PCR during my first year of grad school. Great work Rob! Red Discosoma Coral Posted in Fluorescent Protein&... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2033252 Fri, 12 Dec 2008 18:23:59 +0100 2033252 http://www.medworm.com/index.php?rid=2027180&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F12%2F10%2Fpreview-structure-of-g-camp2%2F A high-resolution crystal structure of the genetically-encoded calcium indicator G-CaMP2 would aid in rational design of improved calcium indicators. Crystallization of G-CaMP2 was first reported here : Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2 M. M. Rodríguez Guilbe, E. C. Alfaro Malavé, J. Akerboom, J. S. Marvin, L. L. Looger and E. R. Schreiter Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin ligh... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2027180 Thu, 11 Dec 2008 04:07:29 +0100 2027180 http://www.medworm.com/index.php?rid=2021541&cid=t_416261_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FuckVP16APj8%2F A new genetic syndrome was discovered in a group of families in Quebec with a common ancestor. The syndrome was named MEDNIK to describe the resulting phenotypes - mental retardation, enteropathy, deafness, peripheral neuropathy, ichthyosis, and keratodermia. The scientists found a new splice mutation in the AP1S1 gene, which encodes a subunit of a complex (AP) responsible for selecting which proteins move within the cell. A zebrafish knockdown model was used to study the loss of the gene’s function further. Injecting the affected larvae with a human normal AP1S1 mRNA restored some phenotypes. The study is published in PLOS Genetics. Tags: AP complex, Mednik, mutation, novel mutation, protein, quebecShare This (Source: Genetics and Health) Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2021541 Mon, 08 Dec 2008 12:59:52 +0100 2021541 http://www.medworm.com/index.php?rid=2007396&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F12%2Fbacterial-secretion-systems-type-v.html The Type V secretion system was first described twenty years ago. Since then, much work has be done to elucidate functional aspects of members of this family and their mechanisms of biogenesis. What was once considered to be a quirky one-off system, with the discovery of the IgA1 protease secretion system of Neisseria gonorrhoeae, has been revealed as the largest family of secreted proteins amongst the Gram-negative bacteria. The type V secretion system (T5SS) is comparatively is less complex than types I to IV. This secretion mechanism has been subdivided into sub-types (a), (b) and (c), as variations upon a theme were discovered. Each polypeptide secreted via the T5SS contains an N-terminal Sec-dependant signal sequence required to direct inner membrane export. The significant functional... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2007396 Tue, 02 Dec 2008 07:34:00 +0100 2007396 http://www.medworm.com/index.php?rid=1997247&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F11%2Fbacterial-secretion-systems-type-iv.html Type IV secretion systems are multiprotein complexes that mediate the translocation of macromolecules (proteins, DNA or DNA-protein complexes) across the bacterial cell envelope into the extracellular medium or directly into recipient cells. This strategy is exploited for the delivery of effector molecules that modulate host cell interactions by bacterial pathogens and symbionts. Type IV secretion systems also mediate the translocation of DNA molecules from bacteria and the uptake of DNA into bacteria and thereby contribute to horizontal gene transfer.The term type IV secretion system (T4SS) was originally based on the significant sequence similarities between the protein components of macromolecular transporters used for plasmid transfer and for the delivery of virulence factors from bact... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=1997247 Fri, 28 Nov 2008 09:17:00 +0100 1997247 http://www.medworm.com/index.php?rid=1985675&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F11%2Fbacterial-secretion-systems-type-iii.html The type-III secretion system (T3SS) is an export machine used by pathogenic Gram-negative bacteria to deliver proteins straight into the eukaryotic cytosol with the aim to subvert the host cell defense. After the discovery of T3S in 1990, significant progress has been made in the understanding of its structure, assembly and function. The basic structure consisting of the membrane-embedded basal body, the needle and the tip structure has been analyzed in more detail. The composition of several structural components has been determined and important insights into the assembly process have been gained. The relationship between the T3SS of pathogenic bacteria and the flagellum has been noted. Besides the structural similarities, the assembly of these two nanomachines shows some commonalities,... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=1985675 Mon, 24 Nov 2008 16:32:00 +0100 1985675 http://www.medworm.com/index.php?rid=1975206&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F11%2F20%2Fsome-interesting-posters-sfn%2F Here’s a few posters that caught my eye at SfN.  Click the titles for the full abstract Optimizing two-photon activation of channelrhodopsin-2 for stimulation at cellular resolution J. P. RICKGAUER1,2, D. W. TANK1,2;  Spiral pattern of 2-photon excitation can drive neurons to spike.  A low NA objective helps. Need to do piezo-based Z-scanning if you use high NA, don’t with low NA. In vivo two-photon imaging 1 mm deep into cortical brain tissue with novel microprism probe  *T. H. CHIA, M. J. LEVENE;  A cute method to image 1mm into cortex with 2-photon imaging. They used 2-6 month old mice. The just took a triangular prism whose hypotenuse was silvered and stuck it in the cortex. Then they internally reflected the beam off the prism and fired it sideways into cortex. Got g... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1975206 Fri, 21 Nov 2008 03:27:11 +0100 1975206 http://www.medworm.com/index.php?rid=1964123&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F11%2F15%2Fraw-data-vesicular-release-from-astrocytes%2F When I was working on my Ph.D. thesis, I was trying to find some biological question to definitively answer with GluSnFR, my glutamate sensitive fluorescent reporter. One possibility was the study of glutamate release from astrocytes.  Around that time, 2003/2004, there was increasing evidence that glutamate was not just scavenged by astrocytes, but was also released from astrocytic vesicles. It released in response to calcium elevations within the cell.  Existing methods for measuring this release were somewhat crude, so it seemed a great test system for GluSnFR.   Unfortunately, since there seemed to be no specialized areas on the astrocyte where the vesicles fused, and the release rate was relatively slow, we were unable to detect glutamate release with GluSnFR. I thought this might ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1964123 Sat, 15 Nov 2008 23:21:38 +0100 1964123 http://www.medworm.com/index.php?rid=1953149&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F11%2Fbacterial-secretion-systems-type-ii.html Gram-negative bacteria have evolved several secretory pathways to release proteins or toxic factors into their surrounding environment. Many virulence determinants, including extracellular toxins and proteases, are secreted by the type II secretion system (T2SS) which is widely conserved and common among γ-proteobacteria. Typical T2SSs are composed of 12 to 16 proteins termed Gsp (General secretion pathway) proteins. These components associate in a multiprotein complex that constitutes a large structure (the secreton) that spans the periplasm and is thought to connect inner and outer membranes. Exoproteins that use the T2SS are characterized by the presence of a leader peptide (or signal peptide) at their N terminus and are secreted in the extracellular medium by a two-step process i... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=1953149 Wed, 12 Nov 2008 09:10:00 +0100 1953149 http://www.medworm.com/index.php?rid=1924709&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F437306919%2F A forthcoming AstraZeneca study could dramatically increase the market for cholesterol-lowering drugs, otherwise known as statins, which are already pharma’s biggest success story, Forbes writes. Known as Jupiter, the study tested the theory that Crestor combats lower artery inflammation, which can cause cholesterol plaque to burst into heart-attack-causing clots. Some 18,000 people were tested with low levels of LDL, but high levels of C-reactive protein (CRP), which could indicate that the arteries are inflamed, the mag writes. In March, the study was stopped early because of “unequivocal” benefit, and now, some scientists hope for blowout results when the full data are presented on November 9 at the American Heart Association meeting, Forbes says. And by the way, sinc... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1924709 Thu, 30 Oct 2008 20:31:21 +0100 1924709 http://www.medworm.com/index.php?rid=1918289&cid=t_416261_134_f&fid=36012&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FBattleDiabetes%2F%7E3%2F436476555%2F Whey protein is a natural product, produced as part of the cheese making process. It is probably most renowned for being a supplement used for bodybuilders and weight trainers as it is an excellent source of protein. Whey protein is not only of benefit to bodybuilders and weight trainers but also to sufferers of conditions such as cancer sufferers, people who are overweight and to Diabetic sufferers. How can it benefit Diabetic sufferers? As mentioned already, whey protein is the best natural source of protein. Protein can become an element lacking in some Diabetic’s diets, as a result of their dietary alterations. Whey protein also lowers levels of blood glucose and this is thought to happen because higher protein levels stimulate Insulin production from the Pancreas. This particular e... Battle Diabetes Blog blogs http://www.medworm.com/rss/comments.php?id=1918289 Thu, 30 Oct 2008 02:58:21 +0100 1918289 http://www.medworm.com/index.php?rid=1906535&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F10%2Fbacterial-secretion-systems-type-i.html Bacteria have developed numerous systems to secrete proteins or DNA in order to modify their immediate surroundings or to obtain an advantage in a competitive and hostile environment. Since Gram-negative bacteria possess two membranes, the inner (cytoplasmic) membrane and the outer membrane, transport machines for protein secretion have the challenging task of circumventing two barriers to reach the exterior. A rather simple transport apparatus, the Type I secretion machinery, composed of only three proteins residing in the inner and outer membrane of Gram-negative bacteria achieve this objective in a single step. The Type I secretion pathway although also present in Gram-positive bacteria, has been analysed in greatest detail in Gram-negative bacteria. Almost all Type I transport substrat... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=1906535 Sat, 25 Oct 2008 09:16:00 +0100 1906535 http://www.medworm.com/index.php?rid=1884162&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F10%2Ftwin-arginine-pathway-tat.html A description of the twin-arginine translocation (Tat) pathway continues our series on protein secretion in microorganisms.The twin-arginine translocation (Tat) pathway is a protein transport system in bacteria, archaea and chloroplasts with the ability to export proteins in a fully folded conformation. Proteins are targeted to the Tat pathway by an N-terminal signal peptide containing an almost invariant twin-arginine sequence motif. Pretranslocational folding is necessitated by the incorporation of metallo-cofactors, assembly into oligomeric complexes, and presumably rapid folding kinetics. Many Tat systems comprise three functionally individual membrane proteins, termed TatA, TatB, and TatC, whereas especially Gram-positive bacteria possess minimal TatAC translocases, in which TatA func... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=1884162 Fri, 17 Oct 2008 10:44:00 +0100 1884162 http://www.medworm.com/index.php?rid=1876970&cid=t_416261_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2008%2F10%2Fsec-protein-secretion-system.html Protein secretion is an important process for bacteria and is particularly important to bacterial pathogens. Secreted proteins have a range of biological functions.The majority of proteins destined for export across the microbial cytoplasmic membrane or integration into the membrane are handled by the evolutionarily conserved Sec system. The Sec substrates have specific topogenic signals and are targeted to the membrane-embedded SecYEG translocon that serves as a polypeptide-conducting channel either co-translationally by SRP for lipid-phase integration or post-translationally by SecB for complete translocation. The plug helix of SecY that clogs the unused channel and the central constriction that seals around the translocating chain make the translocon function compatible with the permeab... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=1876970 Wed, 15 Oct 2008 11:50:00 +0100 1876970 http://www.medworm.com/index.php?rid=1834608&cid=t_416261_109_f&fid=35044&url=http%3A%2F%2Fadultaddstrengths.com%2F2008%2F09%2F27%2Fis-the-whey-based-protein-powderbardrink-you-eat-made-with-chinese-contaminated-milk-protein-aka-melamine%2F Do you know if it is? Do you know if it’s not? Most protein powders, protein bars and protein drinks are made with whey protein, which is made from milk. Is your government checking and letting you know if the whey protein products that you’re eating or drinking safe to consume? Especially since the whole Chinese baby milk scandal was because the biggest dairy companies in China where watering down there milk to make more money and using melamine to hide that since adding melamine increases the protein content in such poisoned milk products so the milk doesn’t look like it’s watered down. Melamine is a metabolite of cyromazine, a pesticide… Ingestion of melamine may lead to reproductive damage, or bladder or kidney stones, which can lead to bladder cancer In A... Adult ADD Strengths blogs http://www.medworm.com/rss/comments.php?id=1834608 Sun, 28 Sep 2008 03:36:26 +0100 1834608 http://www.medworm.com/index.php?rid=1812693&cid=t_416261_87_f&fid=34872&url=http%3A%2F%2Fwww.healthbolt.net%2F2008%2F09%2F19%2Fsexbolt-saturday-allergic-to-semen-yes-its-possible%2F Did you know that it’s possible to be allergic to the white stuff (and I’m not talking milk here, people). Yep, that very tangible sign of a guy’s pleasure can leave his partner red, itchy, blotchy and more. What causes this is a sensitivity to the proteins in a guy’s semen, a condition which actually has a name: human seminal plasma protein hypersensitivity (SPH). A person can be sensitive to the proteins in the semen of most men, or to a specific guy’s proteins in particular. Symptoms of an allergy may include localized pain, itching, redness, swelling, hives or even trouble breathing! Most symptoms usually show up within 20 -30 minutes of contact and can last for hours or days. The severity really depends on body chemistry. How to treat this very unpleasan... Healthbolt blogs http://www.medworm.com/rss/comments.php?id=1812693 Fri, 19 Sep 2008 18:12:23 +0100 1812693 http://www.medworm.com/index.php?rid=1811675&cid=t_416261_167_f&fid=37833&url=http%3A%2F%2Fnutrition.edublogs.org%2F2008%2F09%2F18%2Fprotein-synthesis-video-clips%2F Here are some good video clips that I found on Protein Synthesis that help explain the process a bit more. Part 1 & Part 2 not really discussed in class Part 3 Part 4 Part 5 Authored by drdyer. Hosted by Edublogs. (Source: Nutrition and Wellness Biology 50) Nutrition and Wellness Biology 50 blogs http://www.medworm.com/rss/comments.php?id=1811675 Fri, 19 Sep 2008 03:56:17 +0100 1811675 http://www.medworm.com/index.php?rid=1802641&cid=t_416261_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F18%2Fnot-as-many-structures-as-you-might-think%2F In the midst of preparing a talk for next Monday. It occurred to me that perhaps we don’t see more protein structure-based prediction in bioinformatics because - there aren’t enough structures.pdbstatsSure, the PDB has grown a lot in the past 5 years or so and 53 103 structures (as of now) looks impressive. However, if you’re interested in protein-protein interaction, you want at least 2 chains: which more or less halves the dataset. If you want two different protein chains, you lose almost another 75%. Let’s specify a reasonable minimum resolution for X-ray diffraction data and there go ~ 3 000 entries. We probably don’t want multiple, similar proteins so let’s remove sequence identity at a redundancy of 90%. We’re left with about 2% of the origin... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1802641 Thu, 18 Sep 2008 05:14:26 +0100 1802641 http://www.medworm.com/index.php?rid=1658166&cid=t_416261_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F347809614%2F Report concludes that a fungal genome database is of "the highest priority". This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom. The need for a comprehensive database for information about fungi, starting at least with systematic collections of genomic and transcript data, is highlighted as a major need.  Really and sort of new database effort should strive to be more comprehensive and include genetic and population data (alleles, strains) and information like protein-protein, protein-nucleic acid interactions (as Pedro mentioned). But on top of that it, it needs to be comparative so that information from systems that serve as great models can be transferred to other fungal... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1658166 Sun, 27 Jul 2008 23:01:00 +0100 1658166 http://www.medworm.com/index.php?rid=1658240&cid=t_416261_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F07%2Fquotes-from-neighbors-july-2008.html ==Receptors: Can't Live With 'Em, Can't Understand 'Em (In the pipeline)==At various points in my drug discovery career, I’ve worked on G-protein-coupled receptor (GPCR) targets. Most everyone in the drug industry has at some point – a significant fraction of the known drugs work through them, even though we have a heck of a time knowing what their structures are like.For those outside the field, GPCRs are a ubiquitous mode of signaling between the interior of a cell and what’s going on outside it, which accounts for the hundreds of different types of the things. ...==A-β Dimers- The Long-Sought Minimal Culprit in Alzheimer's Disease? (The Curious Wavefunction)==Following on the heels of the headline-making Nature publication that demonstrated that NSAIDs (Non-steroidal AntiInflamma... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1658240 Sun, 27 Jul 2008 19:27:00 +0100 1658240 http://www.medworm.com/index.php?rid=1642713&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F21%2Fthe-great-geci-shootout%2F Dierk Reiff’s lab has done another head-to-head in vivo showdown between various GECIs and a synthetic dye. Their paper, Fluorescence changes of genetic calcium indicators and OGB-1 correlated with neural activity and calcium in vivo and in vitro, is very interesting and deserves a full write-up. I will present a detailed analysis of the paper in a future update.  For now, check the abstract. Recent advance in the design of genetically encoded calcium indicators (GECIs) has further increased their potential fordirect measurements of activity in intact neural circuits. However, a quantitative analysis of their fluorescence changes (F) in vivo and the relationship to the underlying neural activity and changes in intracellular calcium concentration ([Ca2+]i) has not been given... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1642713 Mon, 21 Jul 2008 19:25:52 +0100 1642713 http://www.medworm.com/index.php?rid=1631146&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F16%2Fsensing-salty-currents-with-mermaids%2F A new genetically-encoded voltage sensor paper is out from a friend and former mentor of mine, Atsushi Miyawaki. One memorable moment when working in his lab during the RIKEN summer program of 2002 was when Atsushi took me into his office and whipped out a custom green laser pointer. These had been banned in Japan, as fans would shine their powerful light into the eyes of pitchers and batters at baseball games. Atsushi was really proud of his. He smiled and then started sweeping the light point over the rocks in his fishtank. Each ‘rock’ was actually coral his lab had collected from fluorescent protein hunting trips, and each glowed a different color when the green light hit it. He has been putting these novel discoveries to good use. In Improving membrane voltage measurements ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1631146 Thu, 17 Jul 2008 02:58:25 +0100 1631146 http://www.medworm.com/index.php?rid=1616174&cid=t_416261_133_f&fid=35096&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAutismVox%2F%7E3%2F333786046%2F Could it be something in the water? The answer might seem “yes” if all you read is the headline of an article in today’s Scotsman: Study reveals water’s role in rare autism The water in question is not the wet stuff in oceans, lakes or rivers or in pools (where we’re shortly headed to—I told you Charlie liked swimming and I meant it!). It’s water at the molecular level, and is linked to Rett Sydrome, which has been linked to a mutation in the MECP2 gene: Researchers discovered that Rett’s syndrome is caused by the Mecp2 protein interacting with water trapped around the DNA rather than reacting directly with the DNA itself. Professor Adrian Bird [of University of Edinburgh], who took part in the study, said: “We thought this process inv... Autism Vox blogs http://www.medworm.com/rss/comments.php?id=1616174 Sat, 12 Jul 2008 21:06:26 +0100 1616174 http://www.medworm.com/index.php?rid=1596486&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F08%2Fvoltage-sensitive-imaging-powering-up%2F I’m starting to come around on voltage imaging. I haven’t been a fan of it for a number of reasons. The response sizes suck.  Classic dyes and genetically encoded systems get a few percent fluorescence change at best.  The response speeds suck. Measuring continuous current injections from -100mV to +150mV is not very interesting.  Action potentials are interesting.  But they are fast. Toxicity. The dyes kill neurons, or strongly perturb their electrical properties. OK, voltage-sensitive imaging isn’t totally useless, for example see Carl Petersen’s recent paper on Spatiotemporal Dynamics of Cortical Sensorimotor Integration in Behaving Mice (2007). But if the above problems could be solved, then voltage sensitive imaging would be a strong competitor to calciu... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1596486 Tue, 08 Jul 2008 22:29:44 +0100 1596486 http://www.medworm.com/index.php?rid=1560925&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F01%2Fslick-labeling-and-new-fps%2F There is a nice writeup of the single-neuron labeling with inducible Cre-mediated knockout (SLICK) paper from Guoping Feng’s lab over at the Alzheimer’s Research forum. The method simultaneously knocks out a gene in a small number of cells, while highlighting the knocked-out cells with a cytosolic fluorescent protein. In a comment to the Schizophrenia Research Forum, Joseph Gogos points out a similar technique his lab published last year in Current Biology. Also in the writeup is coverage of the new fluorescent protein variants from the Tsien Lab.  These include mOrange2 made by Nathan Shaner, which is a much more photostable version of mOrange. This should immediately replace mOrange in most constructs.  Also of note is TagRFP-T from Michael Lin and his trusty undergraduat... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1560925 Tue, 01 Jul 2008 19:40:08 +0100 1560925 http://www.medworm.com/index.php?rid=1556392&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F06%2F30%2Fgiving-synapses-a-born-on-labelinthe%2F Memories are thought to be encoded by the patterns of synaptic connections in the brain. Learning can either delete or change the strength of existing synapses, or add new synapses. Following a learning process, how can we tell which synapses were added to encode this new memory?   One strategy is to make a timelapse movie of the synapses.  In mice, this can be accomplished by installing a cortical window on the skull, and imaging the changes in structure of GFP labelled neurons. However, this is technically demanding, only works with sparsely labeled neurons, and accesses only a small subset of the neurons which may be involved in the learning process.   Ideally, one could have a tag which can discriminate between synapses existing before learning takes place, and new ones generated ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1556392 Mon, 30 Jun 2008 17:25:43 +0100 1556392 http://www.medworm.com/index.php?rid=1543150&cid=t_416261_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2008%2F06%2F25%2Fpromising-new-alzheimers-research-published%2F Which came first, the beta-amyloid plaque or the Alzheimer’s? It’s the plaque, but only one subtype, according to a new report by Harvard researchers in the online journal Nature Medicine and profiled in this TIME article from Sunday. Physicians and researchers have long noted the presence of these plaques, made up of “sticky” beta-amyloid proteins, in the brains of Alzheimer’s patients, and wondered whether there might be some connection between the plaque and the disease. To complicate things, however, beta-amyloid plaques have also been found in patients with no sign of the disease, making scientists wonder whether the plaques could be an advance warning sign of Alzheimer’s rather than a byproduct of the disorder. So, how was this chicken-and-egg problem solved? Researcher... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=1543150 Wed, 25 Jun 2008 06:16:46 +0100 1543150 http://www.medworm.com/index.php?rid=1531156&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2008%2F06%2Foutsourced-to-death.html A while back, we posted frequently about the sudden toxicity of what used to be an apparently well understood drug. A summary of the story to date is below (in smaller type.):- We have posted several times, recently here and here, about the tragic case of suddenly allergenic heparin. Although heparin, an intravenous biologic anti-coagulant, has been in use for over 70 years, serious allergic reactions to it had heretofore been rare. Starting late last year, hundreds of such reactions, and now 21 deaths were reported in the US after intravenous heparin infusions.All the heparin related to these events in the US was made by Baxter International.- We then learned that although the heparin carried the Baxter label, it was not really made by Baxter. The company had outsourced production of the ... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=1531156 Thu, 19 Jun 2008 20:12:00 +0100 1531156 http://www.medworm.com/index.php?rid=1436793&cid=t_416261_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F05%2F12%2Fproteomics-discussion-from-the-science-streamosphere%2F We find ourselves wondering why codon adaptation index (CAI) is used as a measure of protein expression level in this article. One answer is that CAI does correlate well with protein expression in many proteomics studies; but surely these same studies contain raw data with protein expression level? On reflection, I bet the answer is that it’s too difficult and laborious to access this type of data. There are plenty of papers that describe large-scale analysis of protein expression using proteomics, but the data are locked up in the articles or as inappropriate supplementary files. Note to self: look into open-source software and standard data formats for proteomic data. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1436793 Mon, 12 May 2008 01:27:45 +0100 1436793 http://www.medworm.com/index.php?rid=1432559&cid=t_416261_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F287066761%2F Technology Review was the first place I saw it, then someone put it up on Friendfeed and now Andrew Perry has a great post on Foldit. Foldit comes out of the lab of a bbgm favorite, David Baker, right here at the University of Washington. Foldit combines gaming with protein structure prediction. It’s an interesting approach to spreading scientific problems. Folding@home built upon the success of Seti@home and the geek cred of running on gaming consoles and has built quite a following. Will Foldit, which presents a simple, fun interface to get people interested in protein structure (and the existence of Folding@home makes this somewhat familiar to geeks everywhere) be an example of how we can leverage crowdsourcing? Andrew makes some interesting points (which I agree with) on weightin... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1432559 Fri, 09 May 2008 20:17:11 +0100 1432559 http://www.medworm.com/index.php?rid=1432541&cid=t_416261_132_f&fid=35021&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2F286440409%2F David Baker’s lab and friends, have recently released a new ‘experiment’ in protein folding called FoldIt. Essentially, individuals or teams can compete online to manually fold protein structures, guided by the internal energy function within the game (it very likely uses code from the impressive ab initio folding software Rosetta under the hood). The interface is designed as a game to make it accessible to everyone, not just experts in protein folding. While it’s pretty simplified compared with your average molecular structure editing software, I think designers of scientific software (often scientists themselves) should take note; a good clean interface can really assist getting a specific job done painlessly. I haven’t played enough with it yet, but I get t... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=1432541 Thu, 08 May 2008 23:57:17 +0100 1432541 http://www.medworm.com/index.php?rid=1413423&cid=t_416261_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2008%2F05%2Fblaming-some-dude-for-contaminated.html It is time to update the story of the contaminated heparin. A summary of the story to date is below (in smaller type.):- We have posted several times, recently here and here, about the tragic case of suddenly allergenic heparin. Although heparin, an intravenous biologic anti-coagulant, has been in use for over 70 years, serious allergic reactions to it had heretofore been rare. Starting late last year, hundreds of such reactions, and now 21 deaths were reported in the US after intravenous heparin infusions.All the heparin related to these events in the US was made by Baxter International.- We then learned that although the heparin carried the Baxter label, it was not really made by Baxter. The company had outsourced production of the active ingredient to a long, and ultimately mysterious s... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=1413423 Thu, 01 May 2008 14:08:00 +0100 1413423 http://www.medworm.com/index.php?rid=1407195&cid=t_416261_111_f&fid=36048&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAHeartyLife%2F%7E3%2F280117439%2F High levels of C-reactive protein, an inflammatory marker that may warn of impending heart disease, are tied to variations in genes that control metabolism, two new studies show. Dr. Alexander Reiner of the University of Washington, Seattle states that the studies identify “new genes that are of potential importance for either the treatment of cardiovascular disease or potentially screening individuals who may be at higher risk of developing cardiovascular disease”. What they still need to discover is the exact relationship between C-reactive protein levels and heart disease. That will be the crucial piece of the puzzle. Just what was discovered here though? The teams found seven genomic regions that appeared to be strongly correlated with CRP levels. Six of those regions conta... A Hearty Life blogs http://www.medworm.com/rss/comments.php?id=1407195 Tue, 29 Apr 2008 14:19:39 +0100 1407195 http://www.medworm.com/index.php?rid=1389196&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F274806921%2F And so the new cooperation pact with the US Health and Human Services and the FDA begins with a disagreement - Chinese officials are voicing doubts that a contaminant identified in Heparin was the root cause of 62 deaths and severe allergic reactions in hundreds of Americans, the Associated Press reports. The officials suggested at an embassy news conference that the problem with the drug could have occurred in the US and plan to visit a Baxter International plant in New Jersey to get a better picture of how the finished product is manufactured. “When you see it, then you believe it,” Jin Shaohong, the deputy director general for the National Institute for the Control of Pharmaceutical and Biological Products in China, tells reporters. Heparin is derived from a mucus obtained f... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1389196 Mon, 21 Apr 2008 16:19:22 +0100 1389196 http://www.medworm.com/index.php?rid=1331519&cid=t_416261_132_f&fid=35624&url=http%3A%2F%2Fsuicyte.wordpress.com%2F2008%2F03%2F27%2Fstrange-paper-i%2F This week, I found two strange but interesting papers, one from the area of bioinformatics, the other from gene silencing. The unifying topic is that in both published works something went wrong, but the results were nevertheless as good - or even better - than intended. The first paper, published in the latest issue of Nature Biotechnology, is from Mark Styczynski et al. The title is “BLOSUM62 miscalculations improve search performance“. I must say that I was very surprised to see a paper like this. BLOSUM substitution matrices are widely used throughout bioinformatics. In particular the BLOSUM62 version is popular as it is used per default in NCBI’s protein BLAST applications. I am a heavy user of BLOSUM matrices myself; on my computer it is the BLOSUM45 matrix doing mo... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1331519 Thu, 27 Mar 2008 22:37:47 +0100 1331519 http://www.medworm.com/index.php?rid=1325144&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F03%2F25%2Fjournal-club-gfp-reconstitution-across-synaptic-partners-grasp%2F This week, I’m guest presenting a recent Neuron paper over at the Nature Network’s neuroscience journal club. The authors propose a clever new technique, Genetic Reconstitution Across Synaptic Partners, to track the locations of selected synaptic connections backed by an impressive set of in vivo proof-of-principal experiments in C. elegans. The gist of the strategy is to split a fluorescent marker into two non-functional components and then distribute each half on different sides of circuit’s connection. Only at synaptic connections would the two components be close enough to undergo trans-complementation and reconstitute a functional marker. Check out the full presentation and join the discussion. (Source: Brain Windows) Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1325144 Tue, 25 Mar 2008 16:51:14 +0100 1325144 http://www.medworm.com/index.php?rid=1298766&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F03%2F12%2Foptical-imaging-of-neuronal-glutamate-release-and-spillover-with-glusnfr%2F This post is difficult to craft. I’ve been struggling with whether to write an epic post describing the history of glutamate imaging, the major advances and players in the field and where I fit into it, or a simple post focused on my new paper. Since glutamate imaging is my field, I’ve got tons to say about it, but also there is probably no way to avoid significant personal bias in my account. So, I’ll go with the short form. For those interested in further reading, please check out these earlier reports, including our brief mention of neuronal glutamate measurements with GluSnFR prototypes, neuronal glutamate measurement with FLIPE and the optimization of FLIPE constructs from Wolf Frommer’s group, and the use of FLIPE’s in brain slice to look at broad patter... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1298766 Wed, 12 Mar 2008 22:11:05 +0100 1298766 http://www.medworm.com/index.php?rid=1280990&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F246286544%2F The disclosure was made during the latest briefing given by the agency, which is under siege for, among other things, failing to inspect a plant in China that supplied the active ingredient for Baxter’s Heparin, a blood thinner that has been linked to nearly 800 serious side effect reports and at least 19 deaths in the US. In a teleconference call this afternoon, FDA deputy commmish Janet Woodcock, who heads the agency’s drug review center, calls the contaminant a ‘Heparin-like compound’ and say that it accounted for anywhere between 5 percent and 20 percent of the active pharmaceutical ingredient and finished product tested. However, she adds that, while there is an association, there is “no direct causal link between the contaminant and the adverse events.&#... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1280990 Wed, 05 Mar 2008 18:49:07 +0100 1280990 http://www.medworm.com/index.php?rid=1243476&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F02%2F19%2F3d-and-multicolor-superresolution-imaging%2F Progress in superresolution imaging is still moving very quickly. Here are two more great papers in the field. First, Huang et al. from Xiaowei Zhuang’s group published a Science paper that moves superresolution imaging into three dimensions. Previously, STORM and PALM techniques were most useful for thin sections where the z-axis depth is well-constrained. Breaking the diffraction limit in the z-dimension was thought to possibly require recording from multiple angles, standing wave TIRF or optical lattice microscopy. Instead, the authors simply inserted a weak cylindrical mirror in between the imaging lens and the objective. This distorted the shape of the point spread function in the x- and y-dimensions, dependent on the z-axis distance from the focal plane. By examining the shape ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1243476 Tue, 19 Feb 2008 21:48:34 +0100 1243476 http://www.medworm.com/index.php?rid=1240219&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F02%2F18%2Fpulse-shaping-for-2-photon-signal-enhancement%2F Gains in signal to noise ratios of organic dyes and genetically encoded indicators often come in modest steps following screening of large numbers of compounds or clones. Improvements are usually specific to individual chromophores, leading to the pigeonholing of development efforts on a small handful of indicators that have already undergone systemic optimization (i.e. cameleons, G-CaMP and troponin-based GECIs). Indicator photobleaching imposes strict limits on the amount of information which can be extracted by optical indicators. Improvement of specific indicators and their constituents is a worthy and necessary goal, but more generalizable improvements can be made by changing the nature of the illumination source. A series of papers from a variety of groups has shown that careful mani... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1240219 Tue, 19 Feb 2008 06:11:59 +0100 1240219 http://www.medworm.com/index.php?rid=1239363&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F237123109%2F An FDA official says the failure to inspect the Chinese plant that produced the active ingredient in Baxter’s Heparin was due to a mistake in paperwork submitted to the agency. The FDA received an incorrect name on the Heparin application, which meant the agency apparently wouldn’t have known to inspect the Changzhou SPL facility that supplies the ingredient to Baxter, according to Joseph Famulare, deputy director of the Office of Compliance in the FDA’s Center for Drug Evaluation and Research. “This facility is an isolated instance right now,” Famulare says in a teleconference call with the media. “It was not the correct firm named in application…We’ve discovered that, we’re acting upon that. We’re looking at this process and not... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1239363 Mon, 18 Feb 2008 19:06:05 +0100 1239363 http://www.medworm.com/index.php?rid=1237094&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F236071661%2F A Chinese factory that supplies much of the active ingredient for Baxter’s Heparin, which has been linked to hundreds of adverse reactions and four deaths in the US, isn’t certified by China’s drug regulators to make pharmaceutical products, The New York Times reports. As a result, China’s drug agency never inspected the plant run by Changzhou SPL. Earlier this week, the FDA acknowledged it never inspected the plant either. Although Chinese drug regulators have said that all ingredient producers are required to obtain certification, some chemical companies don’t fall under the Chinese drug agency’s jurisdiction. The Changzhou plant hasn’t been accused of providing a harmful product. But in response to questions, Scientific Protein, which is a majority owne... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1237094 Sat, 16 Feb 2008 13:01:24 +0100 1237094 http://www.medworm.com/index.php?rid=1234808&cid=t_416261_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F235653651%2F The distance between Changzhou in China to Baxter International in Illinois is, symbolically, as long as a pig intestine. Baxter’s Heparin, you see, is derived from piggie innards, but the blood thinner has also been linked to some 350 adverse events, many of which were serious, and four deaths. And the episode is casting another harsh spotlight on the ability of the FDA to supervise drugmaking in China, which is fast becoming the equivalent of pharma’s Wild West. In this case, the active ingredient in Heparin was supplied by a Chinese manufacturing facility co-owned by a Wisconsin company, Scientific Protein Laboratories, which has manufacturing facility in China and a joint-venture operation called Changzhou, The Wall Street Journal reports. “There’s nothing that ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1234808 Fri, 15 Feb 2008 17:08:15 +0100 1234808 http://www.medworm.com/index.php?rid=1223724&cid=t_416261_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F233360453%2F The UniProtKB/Swiss-Prot team is curating fungal proteins in their databases and reportedly have curated more than 20,000 fungal proteins in Release 54.8 of 05-Feb-2008. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under bioinformatics, database, fungi, genome, genome annotation, genome sequencing, news. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1223724 Mon, 11 Feb 2008 22:42:37 +0100 1223724 http://www.medworm.com/index.php?rid=1455512&cid=t_416261_134_f&fid=36985&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fsugarstats%2F%7E3%2F223618060%2F You know, I’ve always liked mice. Cute and furry little guys. Now it seems some new studies out of the University of Florida research labs (http://www.ufl.edu/) show that a certain Protein (Complex Amino Acid Chain) called Pdx1 is stimulating insulin production in mice. In this article titled: *“Researchers trigger insulin production in diabetic mice”* [...] (Source: SugarStats.com - Simple, Online Blood Sugar Tracking for Diabetes Management) SugarStats.com - Simple, Online Blood Sugar Tracking for Diabetes Management blogs http://www.medworm.com/rss/comments.php?id=1455512 Sat, 26 Jan 2008 18:37:19 +0100 1455512 http://www.medworm.com/index.php?rid=1170030&cid=t_416261_111_f&fid=36048&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAHeartyLife%2F%7E3%2F220998687%2F Useful info! Broccoli is heart healthy. Well yeah… that makes me happy considering my kids love those green tree tops (I make them eat the stems as well, I am such a mean mommy). University of Connecticut researchers have associated broccoli with producing helpful proteins that aid damaged cardiac cells and tissue. The broccoli diet appears to persuade the body to produce a protein called thioredoxin, which protects against cell damage in the heart. Broccoli contains sulforaphane, which is seen as particularly effective in triggering this process. Don’t overcook or boil your beautiful green veggie though- lightly steamed broccoli helps to retain all of it’s power and benefits. When it is overcooked it loses its protective qualities. via BBC.com Share This (Source: A Hear... A Hearty Life blogs http://www.medworm.com/rss/comments.php?id=1170030 Tue, 22 Jan 2008 13:57:30 +0100 1170030 http://www.medworm.com/index.php?rid=1148265&cid=t_416261_136_f&fid=36051&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FCancerCommentary%2F%7E3%2F216189813%2F The quantity and identity of specific protein markers in the human saliva can be used as an early, non-invasive diagnostic test for breast cancer that can even be conducted by dentists. Such were the findings of a new study by researchers at The University of Texas Health Science Center at Houston. The study describes how the onset of breast cancer produces a change in the normal type and amount of proteins in glandular secretions from the salivary glands. The protein profile in a healthy person is altered by the presence of cancer. The study is being applied to a “lab-on-a-chip” technology platform developed by biochemists at The University of Texas at Austin. The ultimate goal is to bring this type of diagnostic test, which is capable of detecting the presence of cancer befor... Cancer Commentary blogs http://www.medworm.com/rss/comments.php?id=1148265 Mon, 14 Jan 2008 02:20:55 +0100 1148265 http://www.medworm.com/index.php?rid=1132679&cid=t_416261_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F01%2F07%2Fprokaryotes-not-so-simple-after-all%2F One of my research challenges for 2008 is to marry my previous work (and my “true interest”), microbial genomics, with my current project which focuses on protein kinase substrate prediction. It should prove to be fascinating and fun, provided that publications such as this one keep appearing: Schneiker, S. et al. (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nature Biotech. 25: 1281-1289 doi:10.1038/nbt1354 | Abstract | Full Text (subscription) | PubMed It’s years since I read a textbook but I imagine that many of them will tell you that cell signalling via serine/threonine/tyrosine phosphorylation is “eukaryotic”, whereas Bacteria and Archaea use two-component sensor/histidine kinase systems. Some far-sighted individuals have b... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1132679 Mon, 07 Jan 2008 04:29:26 +0100 1132679 http://www.medworm.com/index.php?rid=1091444&cid=t_416261_134_f&fid=36049&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FDiabetesNotes%2F%7E3%2F199749549%2F 5 Tips on Staying A Fit, Strong and Healthy Diabetic During the Holiday Season… and it can be tough! 1. Eat something before you go to any party or “get together”. This is a great tidbit of information. It is also good for non diabetics that are watching their weight. You will be so much less inclined to stuff your face with the fillers and high carb fluff! 2. Offer to bring a dish, especially a dessert dish, that you know all the nutritional content about. This will allow you to enjoy a small amount of sweets without gorging yourself on 101 sugar cookies and cheesecake bites. And what is even better… you know exactly what the carb count and serving size is so you can enjoy without worry. 3. Bring your own beverages. I know you think it is tacky but I do it all the... Diabetes Notes blogs http://www.medworm.com/rss/comments.php?id=1091444 Thu, 13 Dec 2007 14:21:39 +0100 1091444 http://www.medworm.com/index.php?rid=1049082&cid=t_416261_134_f&fid=36049&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FDiabetesNotes%2F%7E3%2F190390259%2F Glucose and fructose are metabolized in the liver. When there’s too much sugar in the diet, the liver converts it to lipid. Using a mouse model and human liver cell cultures, the scientists discovered that the increased production of lipid shut down a gene called SHBG (sex hormone binding globulin), reducing the amount of SHBG protein in the blood. SHBG protein plays a key role in controlling the amount of testosterone and estrogen that’s available throughout the body. This would indicate that the bodies liver metabolism is all “out of whack” before there are even disease symptoms and we could in turn use SHGB as a bio-marker for liver function. Pretty good idea, huh? Less SHGB protein means more testosterone and estrogen released in the body and an increased risk for infer... Diabetes Notes blogs http://www.medworm.com/rss/comments.php?id=1049082 Sun, 25 Nov 2007 21:30:42 +0100 1049082 http://www.medworm.com/index.php?rid=1025329&cid=t_416261_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F11%2F14%2Fthe-protein-structure-initiative-money-well-spent%2F The latest issue of the journal Structure looks at structural genomics. While the number of structures and impact has been substantive, the cost of the PSI-2 initiative is large. In the US alone, the NIH spends approximately $65 million each year on this effort. As a result, legitimate questions arise as to whether or not the money on PSI is well spent, especially at a time when funding for independent investigator-driven research appears scarce. To facilitate this debate, we will publish commentaries from both supporters and opponents of the structural genomics effort in the next few issues of Structure; we invite any additional comments from readers to be e-mailed to the Editors (structure@cell.com) We believe this debate is especially timely because of the ongoing need to shape PSI-3, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1025329 Wed, 14 Nov 2007 04:10:00 +0100 1025329 http://www.medworm.com/index.php?rid=1001041&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F11%2F02%2Fbrainbow-mice-are-out%2F Jeff Lichtman’s Brainbow mouse paper is out! Not that I really need to report that news, as it is, of course, on the cover of Nature. Jean Livet comes up with some really clever genetic strategies involving incompatible, overlapping Lox sites to generate random, combinatorial patterns of multiple fluorescent proteins inside the cell. Around 90 different shades can be discerned by spectral deconvolution. Besides making pretty covers, why is this so cool? Well, this technique provides a method for generating high resolution maps of the brain. With a single fluorescent tag, the processes of neighboring cells blur together and became impossible to trace unambiguously. With brainbow, many neighboring axons are clearly resolvable. This is the perfect genetic tool to use for a large-scale,... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1001041 Fri, 02 Nov 2007 19:46:05 +0100 1001041 http://www.medworm.com/index.php?rid=999436&cid=t_416261_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F11%2F02%2Fover-the-brainbow%2F I’m a big fan of cell imaging - pretty pictures of fluorescent cells always enhance a conference presentation. A Harvard team have taken fluorescent labelling to a new level, using combinatorial fluorescent proteins to image brain tissue in 90 distinct colours. What’s more, they’ve come up with a memorable word in “brainbow”. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system (Nature abstract) Colours light up brain structure (Nature News) Cell stains create a ‘brainbow’ (BBC Science News) Search: brainbow at del.icio.us (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=999436 Fri, 02 Nov 2007 01:05:55 +0100 999436 http://www.medworm.com/index.php?rid=1147427&cid=t_416261_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F10%2Funiprot-over-billion-protein-database.html As posted by Eric Jain (via Egon) are now more than a billion RDF available.The latest release of the UniProt protein database contains just over abillion triples*! PRESS RELEASE :-)The data is all available via the (Semantic or otherwise) Web:http://beta.uniprot.org/...or can be bulk-downloaded from:ftp://ftp.uniprot.org/* Counting some reification statements, and assuming no overlap between"named graphs".P.S. This should be the last you'll hear from me on this topic -- I'm offto new adventures...Furthermore is it notable thatThe UniProt Knowledgebase (UniProtKB) and NCBI Reference Sequence (RefSeq) in conjunction with Entrez Gene are widely used resources for protein information, including function, classification and cross-references. Prior efforts in ID mapping (iProClass ID mapping ta... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147427 Wed, 24 Oct 2007 23:39:00 +0100 1147427 http://www.medworm.com/index.php?rid=1147428&cid=t_416261_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F10%2Fsupertarget-matador-chemspider-when.html Although the first version of SuperTarget with all the search and discovery tools around drug-target relations is already an extensive resource for both large-scale research and in depth analysis, the captured knowledge is still far from complete and we would like to invite the community to help in increasing quality and quantity of the records. SuperTarget offers an option to upload and incorporate drug-target relations into a working queue. Uploaded entries will be reviewed and approved by an annotation team comprised of graduated scientists. Both SuperTarget and Matador can be used as knowledge sources, discovery tools or training sets for various applications in chemical biology and elsewhere. [DOI 10.1093/nar/gkm862]Dear community, as already highlighted earlier is it a logical step t... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147428 Tue, 23 Oct 2007 23:50:00 +0100 1147428 http://www.medworm.com/index.php?rid=961700&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F10%2F18%2Fthree-quick-paper-picks%2F Here are three papers that are worth reading over. No time for full reviews. New Single-FP GECIs The Russian fluorescent protein team has come out with some new single fluorescent protein G-CaMP/pericam-like sensors. They fiddled with the linker sites at the 145 and 148AA insertion points and found a great deal of fluorescence sensitivity to the amino acid composition at those sites. They note two new sensor constructs Case12 and Case16 that have 12-16.5x maximal changes in fluorescence upon calcium binding, a significant improvement over G-CaMP2. The tradeoff appears to be that they are dimmer. They show calcium responses in HeLa, PC-12 and cortical neuron cells, but no direct head-to-head with other sensors in cells. Multipoint multiphoton microscopy In this technical paper, an MIT gro... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=961700 Thu, 18 Oct 2007 19:55:09 +0100 961700 http://www.medworm.com/index.php?rid=958838&cid=t_416261_117_f&fid=34612&url=http%3A%2F%2Fwww.thedoctorweighsin.com%2Fjournal%2F2007%2F10%2F17%2Falzheimers-disease-is-there-daylight-at-the-end-of-the-tunne.html So let’s be honest, baby boomer, aren’t you worried about turning a geezer boomer soon? After all, the first of you just got on Social Security. And what about those memory lapses? In your heart of hearts, are’nt you scared just a little bit? If you are not—read on. Here are some sobering statistics. · More than 5 million Americans are estimated to have Alzheimer’s disease or AD today. It is projected that 14.3 million Americans will have the disease by mid-century: a 350 percent increase from 2000, when there were 4 million people with the disease. Reason for the expected explosive growth: a tidal wave of aging baby boomers turning old geezers. In the United States, AD was the 7th leading cause of death in 2004 , with 65,829 number of deaths (and risin... The Doctor Weighs In blogs http://www.medworm.com/rss/comments.php?id=958838 Wed, 17 Oct 2007 00:07:25 +0100 958838 http://www.medworm.com/index.php?rid=935304&cid=t_416261_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F10%2F08%2Fupdate-on-far-field-superresolution-optics%2F Its thesis crunch time for me, so I have had limited time to do ‘extracurricular’ reading and reporting for Brainwindows. However, there have been some very exciting developments in the field of superresolution fluorescence imaging that deserve a mention. First, let’s take a look at this excellent review of far-field superresolution imaging techniques by Stefan Hell. I was almost able to understand the basics of the current techniques after reading it. Hopefully my summary doesn’t contain too many errors ☺. Axial resolution is particularly bad in conventional superresolution techniques. Confocal imaging and 2 photon imaging provides ~450 nm resolution at best, while 4Pi microscopy with immersion lenses above and below the sample has delivered ~100nm axial resolution images of fix... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=935304 Mon, 08 Oct 2007 23:02:55 +0100 935304 http://www.medworm.com/index.php?rid=1147434&cid=t_416261_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fpathguide-light-in-pathway-and.html I found today in my del.ico.us network a bookmark from Egon to PathguidePathguide contains information about 231 biological pathway resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.This is a fantastic collection of interaction/metabolic/signaling pathways and networks!Though, I was astonished and a little bit disappointed about the low number of databases, which support open standards.14 PSI-MI (Proteomics Standards Initiative - Molecular Interactions)13 BioPAX (Biological Pathways Exchange)13 SBML (Systems Biology Markup Language)3 CellML---------43 databases use open standardsThat are only 18.6% of all databases! In other words, t... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147434 Sat, 15 Sep 2007 13:50:00 +0100 1147434 http://www.medworm.com/index.php?rid=1147440&cid=t_416261_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fprotein-foldinghome.html Folding@Home saysWhat is protein folding and how is folding linked to disease? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery. Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes. You can help by simply running a piece of software. Folding@Home is a distributed computing project -- people... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147440 Sat, 01 Sep 2007 21:43:00 +0100 1147440