MedWorm: Genetics & Stem Cells

Cytogenetic analysis in western atlantic snappers (perciformes, lutjanidae)

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

The Lutjanidae or snappers are a family of perciform fishes, mainly marine but with some members living in estuaries and entering fresh water to feed. Some are important food fish. Cytogenetic data for Lutjanidae are scarce. In the present work, we cytogenetically characterized through conventional Giemsa staining techniques, Ag-NOR and C-banding the species Ocyurus chrysurus, Lutjanus analis, L. alexandrei, L. cyanopterus, L. jocu and L. synagris, all found along the Brazilian coast. Karyotype analysis of all six species showed a modal value of 2n = 48 acrocentric chromosomes. Single NORs were found at pericentromeric position on the long arms of the 2nd pair in O. chrysurus, L. alexandrei and L. cyanopterus, on the 5th pair in L. analis and on the 23rd pair in L. synagris. The species L. jocu presented multiple NORs located on the 2nd pair at a pericentromeric region and on the 5th pair at a telomeric region. Heterochromatic blocks were identified at the centromeric region of all chromosomes of the studied species. These results indicate that, despite of the chromosomal stability of this family, a relative structural diversification seems to have occurred in the chromosome evolution of the group. Such diversification was evidenced by divergent number and location of ribosomal sites among species. The NOR-bearing pairs represented an efficient cytotaxonomic marker for most of the analyzed species. The data suggest that the presence of interstitially located single NORs on a large acrocentric pair should represent a basal condition for lutjanids. (Source: Genetics and Molecular Biology)

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The mitochondrial genome of the stingless bee melipona bicolor (hymenoptera, apidae, meliponini): sequence, gene organization and a unique trna translocation event conserved across the tribe meliponini

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees) has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini). The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced). We also report the genome organization (gene content and order), gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe. (Source: Genetics and Molecular Biology)

Differentiation of melipona quadrifasciata l. (hymenoptera, apidae, meliponini) subspecies using cytochrome b pcr-rflp patterns

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

Melipona quadrifasciata quadrifasciata and M. quadrifasciata anthidioides are subspecies of M. quadrifasciata, a stingless bee species common in coastal Brazil. These subspecies are discriminated by the yellow stripe pattern of the abdominal tergites. We found Vsp I restriction patterns in the cytochrome b region closely associated to each subspecies in 155 M. quadrifasciata colonies of different geographical origin. This mitochondrial DNA molecular marker facilitates diagnosis of M. quadrifasciata subspecies matrilines and can be used to establish their natural distribution and identify hybrid colonies. (Source: Genetics and Molecular Biology)

Spermatogenesis and nucleolar activity in triatoma klugi (triatomine, heteroptera)

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

Triatoma klugi is a Chagas disease vector in the Rio Grande do Sul State. Triatominae chromosomes are holocentric and sex chromosomes segregation is post-reductional. In this paper we describe the karyotype of male T. klugi and a meiotic analysis including the nucleolar behavior during spermatogenesis. Testis cells were analyzed after lacto-acetic orcein and silver nitrate staining. Two autosomes and the heterochromosomes presented nucleolar activity (Ag-NORs) during diplotene-diakinesis. The analysis of metaphase I and II revealed a karyotype with 2n = 20+XY. In metaphase I a prominent nucleolar mass was observed in the cell periphery and small silver grains were detected in metaphase II. During anaphase, the chromosomes segregated in parallel and a typical holocentric late migration behavior was observed. The restoration of the nucleolus was an important feature in this phase. During telophase nucleolar masses persisted and in early spermiogenesis the spermatids presented a small peripheral mass until elongation. The present study is a contribution to the study of chromatin behavior and nucleolar persistence in meiosis. (Source: Genetics and Molecular Biology)

High levels of chromosomal differentiation in euchroma gigantea l. 1735 (coleoptera, buprestidae)

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

Euchroma gigantea was karyotypically studied using conventional staining, C-banding, silver nitrate staining and ribosomal fluorescent in situ hybridization (rDNA FISH). Broad wide autosomal polymorphism and a complex sex determination system were found in this beetle. Karyotype complements ranging from 2n = 32, X1X2X3Y1Y2Y3 to 2n = 36,X1X2X3Y1Y2Y3 were detected in the sample analyzed. Punctiform supernumerary chromosomes were present in the different karyotypes. The karyotypic evolution of Brazilian E. gigantea may have taken two directions, reduction in the diploid number of 2n = 36 to 24 through centric fusions or 2n = 24 to 36 due to chromosomal fissions. In addition, pericentric inversions were also involved. The complex multiple sex mechanism of this species seems to be old and well established since it is found in specimens from different populations. Small pericentromeric blocks of constitutive heterochromatin were located on the autosomes and terminal blocks were also found on some small pairs. The sex chromosomes showed larger constitutive heterochromatin blocks. Silver nitrate staining during prophase I of meiosis showed labeling of the sex chromosome chain. However, the rDNA sites could only be precisely determined by FISH, which permitted the identification of these ribosomal sites on chromosomes X1 and X2 of this species. (Source: Genetics and Molecular Biology)

Infrequent v617f mutation of the jak2 gene in myeloid leukemia and its absence in lymphoid malignancies in japan

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

A unique mutation of the JAK2 gene, V617F, has recently been identified in polycythemia vera, essential thrombocythemia and myeloid metaplasia with myelofibrosis. To determine the relevance of this mutation in other types of hematological neoplasms in Japan, we performed allele-specific polymerase chain reaction analysis on the JAK2 gene. The V617F mutation was detected in one out of 130 myeloid neoplasms, but in none of 114 lymphoid malignancies and four biphenotypic acute leukemias. Although a favorable chromosomal alteration t(8;21)(q22;q22) was observed in one acute myeloid leukemia (AML) patient with the mutation, two courses of chemotherapy resulted in induction failure and short survival. Sequencing of JAK2 cDNA revealed expression of the mutant allele in the patient. The V617F mutation might play a role in the pathogenesis of certain AML cases. (Source: Genetics and Molecular Biology)

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Prevalence of the serpin peptidase inhibitor (alpha-1-antitrypsin) pis and piz alleles in brazilian children with liver disease

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 (SERPINA1) deficiency is one of the main genetic causes related to liver disease in children. In SERPINA1 deficiency the most frequent SERPINA1 alleles found are the PI*S and PI*Z alleles. We used the polymerase chain reaction and the amplification created restriction site (ACRS) technique to investigate the prevalence of the PI*S and PI*Z alleles in a group of Brazilian children (n = 200) with liver disease and established the general frequency of the PI*S allele in our population. We found a significant association of the PI*Z allele and liver disease, but no such relationship was found for the PI*S allele. Our results show that SERPINA1 deficiency due to the PI*Z allele, even when heterozygous, is a frequent cause of liver disease in our group of Brazilian children but that the PI*S allele does not confer an increased risk of hepatic disorders in our group of Brazilian children. (Source: Genetics and Molecular Biology)

Array-cgh testing in spontaneous abortions with normal karyotypes

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

In about 50% of first trimester spontaneous abortion the cause remains undetermined after standard cytogenetic investigation. We evaluated the usefulness of array-CGH in diagnosing chromosome abnormalities in products of conception from first trimester spontaneous abortions. Cell culture was carried out in short- and long-term cultures of 54 specimens and cytogenetic analysis was successful in 49 of them. Cytogenetic abnormalities (numerical and structural) were detected in 22 (44.89%) specimens. Subsequent, array-CGH based on large insert clones spaced at ~1 Mb intervals over the whole genome was used in 17 cases with normal G-banding karyotype. This revealed chromosome aneuplodies in three additional cases, giving a final total of 51% cases in which an abnormal karyotype was detected. In keeping with other recently published works, this study shows that array-CGH detects abnormalities in a further ~10% of spontaneous abortion specimens considered to be normal using standard cytogenetic methods. As such, array-CGH technique may present a suitable complementary test to cytogenetic analysis in cases with a normal karyotype. (Source: Genetics and Molecular Biology)

Modulation of thyroid hormone receptor transactivation by the early region 1a (e1a)-like inhibitor of differentiation 1 (eid1)

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

Transcriptional activation (TA) mediated by the effect of thyroid hormones on target genes requires co-activator proteins such as the early region 1A (E1A) associated 300 kDa binding protein (p300) and the cAMP response element binding protein (CREB) binding protein (CBP), known as the p300/CBP complex, which acetylate histones 3 and 4 to allow transcriptional machinery access to the target gene promoter. Little is known on the role of p300 in thyroid hormone receptor (TR) mediated TA but the E1A-like inhibitor of differentiation 1 (EID1), an inhibitor of p300 histone acetyltransferase (HAT), is a functional homolog of E1A and may inhibit myogenic differentiation factor D (MyoD) transcriptional activity and reduces muscle cell differentiation. We evaluated the influence of EID1 on TR-mediated transcriptional activity using transfection and mammalian two-hybrid studies to show that EID1 may partially reduces TA activity of the TR receptor, probably due to p300 blockage since EID1 mutants cannot reduce TR-mediated TA. The EID1 does not affect the function of p160 co-activator proteins (160 kDa proteins of steroid receptor co-activators) and is functionally independent of co-repressor proteins or TR binding. Summarizing, EID1 reduces TR-mediated transcriptional activity by blocking p300 and may play an important role in thyroid receptor activity in muscle and other tissues. (Source: Genetics and Molecular Biology)

Adaptive response: some underlying mechanisms and open questions

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

Organisms are affected by different DNA damaging agents naturally present in the environment or released as a result of human activity. Many defense mechanisms have evolved in organisms to minimize genotoxic damage. One of them is induced radioresistance or adaptive response. The adaptive response could be considered as a nonspecific phenomenon in which exposure to minimal stress could result in increased resistance to higher levels of the same or to other types of stress some hours later. A better understanding of the molecular mechanism underlying the adaptive response may lead to an improvement of cancer treatment, risk assessment and risk management strategies, radiation protection, e.g. of astronauts during long-term space flights. In this mini-review we discuss some open questions and the probable underlying mechanisms involved in adaptive response: the transcription of many genes and the activation of numerous signaling pathways that trigger cell defenses - DNA repair systems, induction of proteins synthesis, enhanced detoxification of free radicals and antioxidant production. (Source: Genetics and Molecular Biology)

Soft inheritance: challenging the modern synthesis

Genetics and Molecular Biology — Sat, 05 Jul 2008 15:35:03 +0100

This paper presents some of the recent challenges to the Modern Synthesis of evolutionary theory, which has dominated evolutionary thinking for the last sixty years. The focus of the paper is the challenge of soft inheritance - the idea that variations that arise during development can be inherited. There is ample evidence showing that phenotypic variations that are independent of variations in DNA sequence, and targeted DNA changes that are guided by epigenetic control systems, are important sources of hereditary variation, and hence can contribute to evolutionary changes. Furthermore, under certain conditions, the mechanisms underlying epigenetic inheritance can also lead to saltational changes that reorganize the epigenome. These discoveries are clearly incompatible with the tenets of the Modern Synthesis, which denied any significant role for Lamarckian and saltational processes. In view of the data that support soft inheritance, as well as other challenges to the Modern Synthesis, it is concluded that that synthesis no longer offers a satisfactory theoretical framework for evolutionary biology. (Source: Genetics and Molecular Biology)

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To silence a gene, join the quantum dots

New Scientist - Genetics — Sat, 05 Jul 2008 06:13:37 +0100

Quantum dots tiny pieces of semiconductor turn out to be extremely good at making deliveries inside living cells (full text available to subscribers) (Source: New Scientist - Genetics)

Relaxation response can influence expression of stress-related genes

Genetics News From Medical News Today — Fri, 04 Jul 2008 08:00:00 +0100

How could a single, nonpharmacological intervention help patients deal with disorders ranging from high blood pressure, to pain syndromes, to infertility, to rheumatoid arthritis? That question may have been answered by a study finding that eliciting the relaxation response - a physiologic state of deep rest - influences the activation patterns of genes associated with the body's response to stress. (Source: Genetics News From Medical News Today)

The mechanistic imperative for pharmacogenomics

Future Medicine: Pharmacogenomics — Fri, 04 Jul 2008 03:01:17 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 801-803. (Source: Future Medicine: Pharmacogenomics)

Interview: it's a dog's life... again

New Scientist - Genetics — Thu, 03 Jul 2008 12:38:00 +0100

Will you miss your dog when it's gone? Willing to fork out on a clone? Then biotech entrepreneur Lou Hawthorne (Source: New Scientist - Genetics)

Potential new ways to treat metastatic cancer following discovery of gene mechanism

Genetics News From Medical News Today — Thu, 03 Jul 2008 11:00:00 +0100

Virginia Commonwealth University and VCU Massey Cancer Center researchers have uncovered how a gene, melanoma differentiation associated gene-7/interleukin-24 (mda-7/IL-24), induces a bystander effect that kills cancer cells not directly receiving mda-7/IL-24 without harming healthy ones, a discovery that could lead to new therapeutic strategies to fight metastatic disease. (Source: Genetics News From Medical News Today)

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Discovery explains how cold sore virus hides during inactive phase

Genetics News From Medical News Today — Thu, 03 Jul 2008 10:00:00 +0100

Now that Duke University Medical Center scientists have figured out how the virus that causes cold sores hides out, they may have a way to wake it up and kill it. Cold sores, painful, unsightly blemishes around the mouth, have so far evaded a cure or even prevention. They're known to be caused by the herpes simplex virus 1 (HSV1), which lies dormant in the trigeminal nerve of the face until triggered to reawaken by excessive sunlight, fever, or other stresses. (Source: Genetics News From Medical News Today)

Study finds possible link between genetic variant and earlier onset of alzheimer’s symptoms

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:44 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 809-811. (Source: Future Medicine: Pharmacogenomics)

Focus on erbb2

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:43 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 825-828. The ERBB2 (HER2) gene codes for a tyrosine kinase receptor that activates pathways involved in cell division, differentiation and apoptosis. Gene amplification, and as a result protein overexpression, are commonly seen in breast tumors and correlate with ... (Source: Future Medicine: Pharmacogenomics)

Genetic variants in fkbp5 affecting response to antidepressant drug treatment

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:42 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 841-846. Introduction: Hyperactivity of the hypothalamic–pituitary–adrenal (HPA) axis is a pathogenic mechanism of depression, and genetic polymorphisms in HPA axis genes have been described to influence response to antidepressant drugs. In particular, two ... (Source: Future Medicine: Pharmacogenomics)

Global pharmacogenetics: genetic substructure of eurasian populations and its effect on variants of drug-metabolizing enzymes

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:41 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 847-868. Aims: To study the frequency distribution of cytochrome P450 (CYP) functional genetic variants in five Eurasian populations from the territory of Siberia in Russia. Materials & Methods: Unrelated healthy Tuvinians, Buryats, Altaians, Yakuts and Russians ... (Source: Future Medicine: Pharmacogenomics)

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Pharmacokinetics of mycophenolate mofetil and its glucuronide metabolites in healthy volunteers

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:40 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 869-879. We previously reported that polymorphisms in the UGT2B7 and UGT1A9 genes are associated with significant alteration in the disposition of mycophenolic acid (MPA) in healthy volunteers. Aim: This study further evaluates the impact of genetic polymorphisms ... (Source: Future Medicine: Pharmacogenomics)

Acknowledgements

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:37 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 985-985. (Source: Future Medicine: Pharmacogenomics)

Pharmacogenomics with antidepressants in the star*d study

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:37 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 935-946. Major depressive disorder is one of the most common psychiatric disorders worldwide. No single antidepressant has been shown to be more effective than any other in lifting depression, and the effectiveness of any particular antidepressant in an ... (Source: Future Medicine: Pharmacogenomics)

Genetic variation in fcer2: implications for children with asthma

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:36 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 805-807. (Source: Future Medicine: Pharmacogenomics)

Pharmacogenetics of analgesics: toward the individualization of prescription

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:32 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 905-933. The use of analgesics is based on the empiric administration of a given drug with clinical monitoring for efficacy and toxicity. However, individual responses to drugs are influenced by a combination of pharmacokinetic and pharmacodynamic factors that ... (Source: Future Medicine: Pharmacogenomics)

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Prediction of paclitaxel resistance in breast cancer: is cyp1b1*3 a new factor of influence?

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:31 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 969-974. This article focuses on the recent findings by Marsh and colleagues, and also discusses recent findings with regards to breast cancer. Taxanes are amongst the most active agents in the treatment of breast cancer. However, many tumors are intrinsically ... (Source: Future Medicine: Pharmacogenomics)

Towards a raav-based gene therapy for ada-scid: from ada deficiency to current and future treatment strategies

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:30 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 947-968. Adenosine deaminase deficiency fosters a rare, devastating pediatric immune deficiency with concomitant opportunistic infections, metabolic anomalies and multiple organ system pathology. The standard of care for adenosine deaminase deficient severe ... (Source: Future Medicine: Pharmacogenomics)

Mthfd1 gene: role in disease susceptibility and pharmacogenetics

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:28 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 829-832. 5,10-methylene-tetrahydrofolate and its derivates are essential cofactors for thymidylate and purine synthesis. Their formation is influenced among other factors by the action of the trifunctional enzyme, 5,10-methylenetetrahydrofolate dehydrogenase/5,10-... (Source: Future Medicine: Pharmacogenomics)

Interview

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:28 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 813-817. George Uhl founded and heads the Molecular Neurobiology Research Branch in the NIH intramural Research Program (NIDA), and also holds adjunct appointments in Neurology and Neuroscience at the Johns Hopkins School of Medicine. His laboratory pioneered ... (Source: Future Medicine: Pharmacogenomics)

Relation between cyp2d6 phenotype and genotype and personality in healthy volunteers

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:27 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 833-840. Objectives: Our group has previously show that interindividual variability in CYP2D6 hydroxylation capacity was related to personality differences in cognitive social anxiety. Thus, we aimed to analyze whether this relationship between personality and ... (Source: Future Medicine: Pharmacogenomics)

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Pharmacogenetics of crohn’s disease

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:21 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 881-893. The considerable interindividual differences in efficacy and side effects of commonly used medications in Crohn’s disease are partly owing to genetic polymorphisms. Many genetic variants have been studied in genes possibly involved in the metabolism or ... (Source: Future Medicine: Pharmacogenomics)

Pharmacogenomics and treatment for dementia induced by alzheimer’s disease

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:18 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 895-903. Pharmacogenomics is the study of interindividual genetic variability, which plays a significant role in defining drug response and toxicity. As research has graduated from studying single candidate genes to whole-genome scans, pharmacogenomics is ... (Source: Future Medicine: Pharmacogenomics)

Warfarin and prime time

Future Medicine: Pharmacogenomics — Thu, 03 Jul 2008 09:44:17 +0100

Pharmacogenomics , July 2008, Vol. 9, No. 7, Pages 819-823. (Source: Future Medicine: Pharmacogenomics)

10,000 people in world-first cerebral palsy study

Genetics News From Medical News Today — Thu, 03 Jul 2008 09:00:00 +0100

Researchers from the University of Adelaide, Australia, have launched the largest study of its kind in the world in a bid to better understand the possible genetic causes of cerebral palsy. The study requiring cheek swabs of mothers and their children aims to gather genetic samples from 10,000 people right across Australia. (Source: Genetics News From Medical News Today)

Three-dimensional positioning of genes in mouse cell nuclei

Chromosoma — Thu, 03 Jul 2008 08:17:12 +0100

Abstract To understand the regulation of the genome, it is necessary to understand its three-dimensional organization in the nucleus. We investigated the positioning of eight gene loci on four different chromosomes, including the β-globin gene, in mouse embryonic stem cells and in in vitro differentiated macrophages by fluorescence in situ hybridization on structurally preserved nuclei, confocal microscopy, and 3D quantitative image analysis. We found that gene loci on the same chromosome can significantly differ from each other and from their chromosome territory in their average radial nuclear position. Radial distribution of a given gene locus can change significantly between cell types, excluding the possibility that positioning is determined solely by the DNA sequence. For the set of investigated gene loci, we found no relationship between radial distribution and local gene density, as it was described for human cell nuclei. We did find, however, correlation with other genomic properties such as GC content and certain repetitive elements such as long terminal repeats or long interspersed nuclear elements. Our results suggest that gene density itself is not a driving force in nuclear positioning. Instead, we propose that other genomic properties play a role in determining nuclear chromatin distribution. Content Type Journal ArticleCategory Research ArticleDOI 10.1007/s00412-008-0168-2Authors Claudia Hepperger, Ludwig-Maximilians-Universität München Department Biologie II Großhaderner Staße 2 82152 Planegg-Martinsried GermanyAlexander Mannes, Ludwig-Maximilians-Universität München Department Biologie II Großhaderner Staße 2 82152 Planegg-Martinsried GermanyJulia Merz, Ludwig-Maximilians-Universität München Department Biologie II Großhaderner Staße 2 82152 Planegg-Martinsried GermanyJürgen Peters, Ludwig-Maximilians-Universität München Walter-Brendel-Zentrum für experimentelle Medizin Marchioninistr. 27 81377 Munich GermanySteffen Dietzel, Ludwig-Maximilians-Universität München Department Biologie II Großhaderner Staße 2 82152 Planegg-Martinsried Germany Journal ChromosomaOnline ISSN 1432-0886Print ISSN 0009-5915 (Source: Chromosoma)

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Just out - the future of health and nutrition thru dna testing...

Genetics News From Medical News Today — Thu, 03 Jul 2008 08:00:00 +0100

Discover the amazing future of health and nutrition through genetic and DNA testing - just out. This exciting new scientific breakthrough will make you look better, feel better, live longer and healthier lives. Learn the secrets and details about this health revolution, visit http://www.GeneWise4U.com which is completing their pre-launch campaign. (Source: Genetics News From Medical News Today)

Database similarity searches.

Genomics Proteomics ... — Thu, 03 Jul 2008 07:03:05 +0100

Database similarity searches.

Methods Mol Biol. 2008;484:361-78

Authors: Plewniak F

With genome sequencing projects producing huge amounts of sequence data, database sequence similarity search has become a central tool in bioinformatics to identify potentially homologous sequences. It is thus widely used as an initial step for sequence characterization and annotation, phylogeny, genomics, transcriptomics, and proteomics studies. Database similarity search is based upon sequence alignment methods also used in pairwise sequence comparison. Sequence alignment can be global (whole sequence alignment) or local (partial sequence alignment) and there are algorithms to find the optimal alignment given particular comparison criteria. However, as database searches require the comparison of the query sequence with every single sequence in the database, heuristic algorithms have been designed to reduce the time required to build an alignment that has a reasonable chance to be the best one. Such algorithms have been implemented as fast and efficient programs (Blast, FastA) available in different types to address different kinds of problems. After searching the appropriate database, similarity search programs produce a list of similar sequences and local alignments. These results should be carefully examined before coming to any conclusion, as many traps await the similarity seeker: paralogues, multidomain proteins, pseudogenes, etc. This chapter presents points that should always be kept in mind when performing database similarity searches for various goals. It ends with a practical example of sequence characterization from a single protein database search using Blast.

PMID: 18592192 [PubMed - in process]

(Source: Genomics Proteomics ...)

Discovery of a novel cytoplasmic male-sterility and its restorer lines in radish (raphanus sativus l.).

TAG. Theoretical and Applied Genetics — Thu, 03 Jul 2008 04:00:00 +0100

Discovery of a novel cytoplasmic male-sterility and its restorer lines in radish (Raphanus sativus L.).

Theor Appl Genet. 2008 Jul 3;

Authors: Lee YP, Park S, Lim C, Kim H, Lim H, Ahn Y, Sung SK, Yoon MK, Kim S

A male-sterile (MS) radish (Raphanus sativus L.) was found in an accession collected from Uzbekistan. Unlike Ogura MS radishes in which no pollen grain is typically visible during anthesis, a small number of pollen grains stuck together in the dehiscing anthers was observed in the newly identified MS radish. Fluorescein diacetate tests and scanning electron micrographs showed that pollen grains in the new MS radish were severely deformed and non-viable. Cytological examination of pollen development stages showed a clear difference in the defective stage from that seen in Ogura male-sterility. Reciprocal cross-pollination with diverse male-fertile lines indicated that pollen grains of the new MS radish were completely sterile, and the female organs were fully fertile. When the new MS radish and Ogura MS lines were cross-pollinated with a set of eight breeding lines, all F(1) progeny originating from crosses with the new MS radish were male-sterile. In contrast, most of the F(1) progeny resulting from crosses with Ogura MS lines were male-fertile. These results demonstrated that factors associated with induction of the newly identified male-sterility are different from those of Ogura male-sterility. The lack of restorer lines for the newly identified male-sterility led us to predict that it might be a complete cytoplasmic male-sterility without restorer-of-fertility genes in nuclear genomes. However, cross-pollination with more diverse radish germplasm identified one accession introduced from Russia that could completely restore fertility, proving the existence of restorer-of-fertility gene(s) for the new male-sterility. Meanwhile, the PCR amplification profile of molecular markers for the classification of radish mitochondrial genome types revealed that the new MS radish contained a novel mitotype.

PMID: 18597066 [PubMed - as supplied by publisher]

(Source: TAG. Theoretical and Applied Genetics)

Analysis of introgression of aegilops ventricosa tausch. genetic material in a common wheat background using c-banding.

TAG. Theoretical and Applied Genetics — Thu, 03 Jul 2008 04:00:00 +0100

Analysis of introgression of Aegilops ventricosa Tausch. genetic material in a common wheat background using C-banding.

Theor Appl Genet. 2008 Jul 3;

Authors: Badaeva ED, Dedkova OS, Koenig J, Bernard S, Bernard M

Seven Triticum aestivum (cv. Moisson)-Aegilops ventricosa addition lines and four VPM-1 lines were studied by C-banding, and compared with the parental common wheat cultivars Marne-Desprez (hereafter Marne), Moisson, and A. ventricosa lines 10 and 11. All of the VPM-1 lines had similar C-banding patterns and carried the same major 5B:7B translocation as the parental Marne cultivar. According to the C-banding analysis, the VPM-1 lines carry a complete 7D(7D(v)) chromosome substitution and a translocation involving the 5D and 5D(v) chromosomes. However, the translocation of the 2N(v)/6N(v) chromosome of A. ventricosa to the short arm of the 2A chromosome of wheat that had been identified in an earlier study using molecular analysis (Bonhomme A, Gale MD, Koebner RMD, Nicolas P, Jahier J, Bernard M in Theor Appl Genet 90:1042-1048, 1995; Jahier J, Abelard P, Tanguy AM, Dedryver F, Rivoal R, Khatkar S, Bariana HS Plant Breed 120:125-128, 2001) was not detected in our study. However, the appearance of a small pAs1 site at the tip of the chromosome 2A short arm in VPM-1 could be indicative of a minor translocation of the A. ventricosa chromosome. The 5B:7B translocation was also found in all seven T. aestivum-A. ventricosa addition lines, although it was not present in the parental common wheat cultivar Moisson. These lines showed different introgression patterns; besides the addition of the five N(v)-genome chromosomes, they also possessed different D(D(v)) genome substitutions or translocations. A whole arm translocation between chromosome 1N(v) and 3D(v) was identified in lines v86 and v137, and also in the A. ventricosa line 10. This observation lends further support to the idea that A. ventricosa line 10, rather than line 11, was used to develop a set of wheat A. ventricosa addition lines.

PMID: 18597067 [PubMed - as supplied by publisher]

(Source: TAG. Theoretical and Applied Genetics)

Asymmetric histone modifications between the original and derived loci of human segmental duplications

Genome Biology — Thu, 03 Jul 2008 04:00:00 +0100

Background: Sequencing and annotation of several mammalian genomes have revealed that segmental duplications are a common architectural feature of primate genomes; in fact, about 5% of the human genome is comprised of large blocks of interspersed segmental duplications. These segmental duplications have been implicated in genomic copy-number variation, gene novelty, and various genomic disorders. However, the molecular processes involved in the evolution and regulation of duplicated sequences remain largely unexplored. Results: In this study, the profile of about 20 histone modifications within human segmental duplications was characterized using high-resolution, genome-wide data derived from a ChIP-Seq study. The analysis demonstrated that derivative loci of segmental duplications often differ significantly from the original with respect to many histone methylations. Further investigation showed that genes are present 3x more frequently in the original than in the derivative, whereas pseudogenes exhibit the opposite trend. These asymmetries tend to increase with the age of segmental duplications. The uneven distribution of genes and pseudogenes did not, however, fully account for the asymmetry in the profile of histone modifications. Conclusions: The first systematic analysis of histone modifications between segmental duplications demonstrates that two seemingly "identical" genomic copies are distinct in their epigenomic properties. Results here suggest that local chromatin environments may be implicated in the discrimination of derived copies of segmental duplications from their originals, leading to a biased pseudogenization of the new duplicates. The data also indicate that further exploration of the interactions between histone modification and sequence degeneration is necessary in order to understand the divergence of duplicated sequences. (Source: Genome Biology)

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Taxonomic distribution of large dna viruses in the sea

Genome Biology — Thu, 03 Jul 2008 04:00:00 +0100

Background: Viruses are ubiquitous and the most abundant biological entities in marine environments. Metagenomics studies are increasingly revealing the huge genetic diversity of marine viruses. In this study, we used a new approach - "phylogenetic mapping" - to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set. Results: Using DNA polymerase genes as a taxonomic marker, we identified 811 homologous sequences of likely viral origins. As expected, most of these sequences corresponded to phages. Interestingly, the second largest viral group corresponded to the one containing mimivirus and three related algal viruses. We also identified several DNA polymerase homologs closely related to Asfarviridae, a viral family poorly represented among isolated viruses and until now limited to terrestrial animal hosts. Finally, our approach allowed the identification of a new combination of genes in "viral-like" sequences. Conclusions: Albeit only recently discovered, giant viruses of the Mimiviridae family appear to constitute a diverse, quantitatively important and ubiquitous component of the population of large eukaryotic DNA viruses in the sea. (Source: Genome Biology)

[research] very small mobile repeated elements in cyanobacterial genomes

Genome Research — Thu, 03 Jul 2008 04:00:00 +0100

Mobile DNA elements play a major role in genome plasticity and other evolutionary processes, an insight gained primarily through the study of transposons and retrotransposons (generally about 1000 nt or longer). These elements spawn smaller parasitic versions (generally greater than 100 nt) that propagate through proteins encoded by the full elements. Highly repeated sequences smaller than 100 nt have been described, but they are either nonmobile or their origins are not known. We have surveyed the genome of the multicellular cyanobacterium, Nostoc punctiforme, and its relatives for small highly repeated sequences and have identified eight families in the range of 21 to 27 nucleotides. Three of the families (SDR4, SDR5, and SDR6), despite little sequence similarity, share a common predicted secondary structure, a conclusion supported by patterns of compensatory mutations. The SDR elements are found in a diverse set of contexts, often embedded within tandemly repeated heptameric sequences or within minitransposons. One element (SDR5) is found exclusively within instances of an octamer, HIP1, that is highly overrepresented in the genomes of many cyanobacteria. Two elements (SDR1 and SDR4) often are found within copies of themselves, producing complex nested insertions. An analysis of SDR elements within cyanobacterial genomes indicate that they are essentially confined to a coherent subgroup. The evidence indicates that some of the SDR elements work through RNA intermediates and have been mobile in recent evolutionary time, making them perhaps the smallest known mobile elements. (Source: Genome Research)

Cancer gene therapy using mesenchymal stem cells expressing interferon-β in a mouse prostate cancer lung metastasis model

Gene Therapy — Thu, 03 Jul 2008 04:00:00 +0100

Cancer gene therapy using mesenchymal stem cells expressing interferon-β in a mouse prostate cancer lung metastasis model Gene Therapy advance online publication, July 3, 2008. doi:10.1038/gt.2008.101 Authors: C Ren, S Kumar, D Chanda, L Kallman, J Chen, J D Mountz & S Ponnazhagan (Source: Gene Therapy)

Mesp1 at the heart of mesoderm lineage specification.

Cell Stem Cell — Thu, 03 Jul 2008 04:00:00 +0100

Mesp1 at the heart of mesoderm lineage specification.

Cell Stem Cell. 2008 Jul 3;3(1):1-2

Authors: Wu SM

Stem cell-based cardiac regeneration requires a detailed understanding of the factors that induce cardiac lineage commitment. In this issue of Cell Stem Cell, Lindsley et al. (2008) and Bondue et al. (2008) use embryonic stem cells to identify a key role for Mesp1 in this process.

PMID: 18593549 [PubMed - in process]

(Source: Cell Stem Cell)

Hair follicle epithelial stem cells get their sox on.

Cell Stem Cell — Thu, 03 Jul 2008 04:00:00 +0100

Hair follicle epithelial stem cells get their sox on.

Cell Stem Cell. 2008 Jul 3;3(1):3-4

Authors: Christiano AM

Sox family transcription factors have emerged as key regulators of multiple developmental processes, including fate determination and differentiation in multiple tissues. In this issue of Cell Stem Cell, Nowak et al. (2008) implicate Sox9 in the specification of early hair follicle stem cells and subsequent epithelial lineages.

PMID: 18593550 [PubMed - in process]

(Source: Cell Stem Cell)

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Base behavior behind budding breasts: integrins and mammary stem cell activity.

Cell Stem Cell — Thu, 03 Jul 2008 04:00:00 +0100

Base Behavior behind Budding Breasts: Integrins and Mammary Stem Cell Activity.

Cell Stem Cell. 2008 Jul 3;3(1):5-6

Authors: Alexander CM

In a recent Nature Cell Biology paper, Taddei et al. (2008) reveal that deletion of beta1 integrin from K5-expressing mammary epithelial basal cells specifically attenuates ductal stem cell activity, without dramatically altering the basal cell layer, or morphogenesis overall.

PMID: 18593551 [PubMed - in process]

(Source: Cell Stem Cell)

Self-renewal made simple.

Cell Stem Cell — Thu, 03 Jul 2008 04:00:00 +0100

Self-renewal made simple.

Cell Stem Cell. 2008 Jul 3;3(1):7-8

Authors: Dunn NR

Embryonic stem cells (ESCs) are prone to differentiation in culture, suggesting that maintenance of the pluripotent state must be actively induced. In a recent issue of Nature, Ying et al. (2008) use soluble small molecules to inhibit pro-differentiation signals and reveal ESC self-renewal as a default cell fate.

PMID: 18593552 [PubMed - in process]

(Source: Cell Stem Cell)

The origins of blood: induction of hematopoietic stem cells from different sources.

Cell Stem Cell — Thu, 03 Jul 2008 04:00:00 +0100

The origins of blood: induction of hematopoietic stem cells from different sources.

Cell Stem Cell. 2008 Jul 3;3(1):8-10

Authors: Saito Y, Ishikawa F

Ex vivo hematopoiesis from embryonic sources offers exciting promises in basic research and medicine. In this issue of Cell Stem Cell, Ledran et al. (2008) describe human embryonic stem cell (hESC)-derived hematopoiesis, while Taoudi et al. (2008) define the origin of definitive hematopoietic stem cells (HSCs) from the mouse aorta-gonad-mesonephros (AGM) region.

PMID: 18593553 [PubMed - in process]

(Source: Cell Stem Cell)

Harnessing stem cells for health needs in india.

Cell Stem Cell — Thu, 03 Jul 2008 04:00:00 +0100

Harnessing stem cells for health needs in India.

Cell Stem Cell. 2008 Jul 3;3(1):11-5

Authors: Lander B, Thorsteinsdóttir H, Singer PA, Daar AS

While industrialized countries' stem cell research will be transferable to the developing world, research conducted by developing countries offers the potential to target innovation to local context, make treatments more affordable, and aid in economic development. India demonstrates that stem cell research and development (R&D) is not confined to industrialized countries and has begun to harness stem cells to address its own health needs.

PMID: 18593554 [PubMed - in process]

(Source: Cell Stem Cell)

MedWorm: Genetics & Stem Cells

Cytogenetic analysis in western atlantic snappers (perciformes, lutjanidae)

The mitochondrial genome of the stingless bee melipona bicolor (hymenoptera, apidae, meliponini): sequence, gene organization and a unique trna translocation event conserved across the tribe meliponini

Differentiation of melipona quadrifasciata l. (hymenoptera, apidae, meliponini) subspecies using cytochrome b pcr-rflp patterns

Spermatogenesis and nucleolar activity in triatoma klugi (triatomine, heteroptera)

High levels of chromosomal differentiation in euchroma gigantea l. 1735 (coleoptera, buprestidae)

Infrequent v617f mutation of the jak2 gene in myeloid leukemia and its absence in lymphoid malignancies in japan

Prevalence of the serpin peptidase inhibitor (alpha-1-antitrypsin) pi*s and pi*z alleles in brazilian children with liver disease

Array-cgh testing in spontaneous abortions with normal karyotypes

Modulation of thyroid hormone receptor transactivation by the early region 1a (e1a)-like inhibitor of differentiation 1 (eid1)

Adaptive response: some underlying mechanisms and open questions

Soft inheritance: challenging the modern synthesis

To silence a gene, join the quantum dots

Relaxation response can influence expression of stress-related genes

The mechanistic imperative for pharmacogenomics

Interview: it's a dog's life... again

Potential new ways to treat metastatic cancer following discovery of gene mechanism

Discovery explains how cold sore virus hides during inactive phase

Study finds possible link between genetic variant and earlier onset of alzheimer’s symptoms

Focus on erbb2

Genetic variants in fkbp5 affecting response to antidepressant drug treatment

Global pharmacogenetics: genetic substructure of eurasian populations and its effect on variants of drug-metabolizing enzymes

Pharmacokinetics of mycophenolate mofetil and its glucuronide metabolites in healthy volunteers

Acknowledgements

Pharmacogenomics with antidepressants in the star*d study

Genetic variation in fcer2: implications for children with asthma

Pharmacogenetics of analgesics: toward the individualization of prescription

Prediction of paclitaxel resistance in breast cancer: is cyp1b1*3 a new factor of influence?

Towards a raav-based gene therapy for ada-scid: from ada deficiency to current and future treatment strategies

Mthfd1 gene: role in disease susceptibility and pharmacogenetics

Interview

Relation between cyp2d6 phenotype and genotype and personality in healthy volunteers

Pharmacogenetics of crohn’s disease

Pharmacogenomics and treatment for dementia induced by alzheimer’s disease

Warfarin and prime time

10,000 people in world-first cerebral palsy study

Three-dimensional positioning of genes in mouse cell nuclei

Just out - the future of health and nutrition thru dna testing...

Database similarity searches.

Discovery of a novel cytoplasmic male-sterility and its restorer lines in radish (raphanus sativus l.).

Analysis of introgression of aegilops ventricosa tausch. genetic material in a common wheat background using c-banding.

Asymmetric histone modifications between the original and derived loci of human segmental duplications

Taxonomic distribution of large dna viruses in the sea

[research] very small mobile repeated elements in cyanobacterial genomes

Cancer gene therapy using mesenchymal stem cells expressing interferon-β in a mouse prostate cancer lung metastasis model

Mesp1 at the heart of mesoderm lineage specification.

Hair follicle epithelial stem cells get their sox on.

Base behavior behind budding breasts: integrins and mammary stem cell activity.

Self-renewal made simple.

The origins of blood: induction of hematopoietic stem cells from different sources.

Harnessing stem cells for health needs in india.

Prevalence of the serpin peptidase inhibitor (alpha-1-antitrypsin) pis and piz alleles in brazilian children with liver disease