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https://www.readbyqxmd.com/read/28343306/the-ins-and-outs-of-molecular-pathology-reporting
#1
REVIEW
Véronique Tack, Kelly Dufraing, Zandra C Deans, Han J van Krieken, Elisabeth M C Dequeker
The raid evolution in molecular pathology resulting in an increasing complexity requires careful reporting. The need for standardisation is clearer than ever. While synoptic reporting was first used for reporting hereditary genetic diseases, it is becoming more frequent in pathology, especially molecular pathology reports too. The narrative approach is no longer feasible with the growing amount of essential data present on the report, although narrative components are still necessary for interpretation in molecular pathology...
March 26, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28343090/developmental-systems-of-plasticity-and-trans-generational-epigenetic-inheritance-in-nematodes
#2
REVIEW
Vahan Serobyan, Ralf J Sommer
Several decades of research provided detailed insight into how genes control development and evolution, whereas recent studies have expanded this purely genetic perspective by presenting strong evidence for environmental and epigenetic influences. We summarize examples of phenotypic plasticity and trans-generational epigenetic inheritance in the nematode model organisms Pristionchus pacificus and Caenorhabditis elegans, which indicate that the response of developmental systems to environmental influences is hardwired into the organismś genome...
March 23, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28340408/ongoing-evolution-of-pseudomonas-aeruginosa-pao1-sublines-complicates-studies-of-dna-damage-repair-and-tolerance
#3
Julia Sidorenko, Tatjana Jatsenko, Maia Kivisaar
Sublines of the major P. aeruginosa reference strain PAO1 are derivatives of the original PAO1 isolate, which are maintained in laboratories worldwide. These sublines display substantial genomic and phenotypic variation due to ongoing microevolution. Here, we examined four sublines, MPAO1, PAO1-L, PAO1-DSM and PAO1-UT, originated from different laboratories, and six DNA polymerase-deficient mutants from the P. aeruginosa MPAO1 transposon library for their employment in elucidation of DNA damage repair and tolerance mechanisms in P...
March 16, 2017: Mutation Research
https://www.readbyqxmd.com/read/28339862/a-new-insight-into-the-evolution-and-functional-divergence-of-sweet-transporters-in-chinese-white-pear-pyrus-bretschneideri
#4
Jiaming Li, Mengfan Qin, Xin Qiao, Yinsheng Cheng, Xiaolong Li, Huping Zhang, Jun Wu
SWEET genes are a recently identified plant gene family that play an indispensable role in sugar efflux. However, no systematic study has been performed in pear. In this research, 18 SWEET transporters identified in pear, almost twice the number found in woodland strawberry and Japanese apricot, were divided into four clades. Conserved motifs and six exons of the SWEET transporters were found in six species. SWEET transporters contained seven transmembrane segments (TMSs) that evolved from an internal duplication of an ancestral three-TMSs unit, connected by TMS4...
March 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28338988/phylogenetics-of-lophotrochozoan-bhlh-genes-and-the-evolution-of-lineage-specific-gene-duplicates
#5
Yongbo Bao, Fei Xu, Sebastian M Shimeld
The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix-loop-helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly-studied Phyla. 56 to 88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define...
March 11, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338950/non-replicative-rna-recombination-of-an-animal-plus-strand-rna-virus-in-the-absence-of-efficient-translation-of-viral-proteins
#6
Maximiliane Kleine Büning, Denise Meyer, Sophia Austermann-Busch, Gleyder Roman-Sosa, Tillmann Rümenapf, Paul Becher
RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a non-replicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region...
March 11, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338893/site-directed-mutant-libraries-for-isolating-minimal-mutations-yielding-functional-changes
#7
Dong Hee Chung, Sarah C Potter, Ammon C Tanomrat, Krishnakumar M Ravikumar, Michael D Toney
Powerful, facile new ways to create libraries of site-directed mutants are demonstrated. These include: (1) one-pot-PCR, (2) multi-pot-PCR, and (3) split-mix-PCR. One-pot-PCR uses mutant oligonucleotides to generate megaprimers in situ, and it was used to randomly incorporate 28 mutations in a gabT gene in a single reaction. In more difficult cases, multi-pot-PCR can be employed: mutant megaprimers are synthesized individually, then combined in a single mutagenesis PCR. This method was used to incorporate 14 out of 15 mutations in a pabB gene...
March 9, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28338832/evidence-of-translation-efficiency-adaptation-of-the-coding-regions-of-the-bacteriophage-lambda
#8
Eli Goz, Oriah Mioduser, Alon Diament, Tamir Tuller
Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages...
February 28, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338826/the-evolutionary-fate-of-the-chloroplast-and-nuclear-rps16-genes-as-revealed-through-the-sequencing-and-comparative-analyses-of-four-novel-legume-chloroplast-genomes-from-lupinus
#9
J Keller, M Rousseau-Gueutin, G E Martin, J Morice, J Boutte, E Coissac, M Ourari, M Aïnouche, A Salmon, F Cabello-Hurtado, A Aïnouche
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins...
February 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338820/evolutionary-dynamics-of-regulatory-changes-underlying-gene-expression-divergence-among-saccharomyces-species
#10
Brian P H Metzger, Patricia J Wittkopp, Joseph D Coolon
Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. While previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from Saccharomyces species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338816/conserved-patterns-of-sex-chromosome-dosage-compensation-in-the-lepidoptera-wz-zz-insights-from-a-moth-neo-z-chromosome
#11
Liuqi Gu, James R Walters, Douglas C Knipple
Where previously described, patterns of sex chromosome dosage compensation in the Lepidoptera (moths and butterflies) have several unusual characteristics. Other female-heterogametic (ZW/ZZ) species exhibit female Z-linked expression that is reduced compared to autosomal expression and male Z expression. In the Lepidoptera, however, Z expression typically appears balanced between sexes but overall reduced relative to autosomal expression, i.e. Z ≈ ZZ < AA. This pattern is not easily reconciled with theoretical expectations for the evolution of sex chromosome dosage compensation...
March 2, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338804/duplications-and-positive-selection-drive-the-evolution-of-parasitism-associated-gene-families-in-the-nematode-strongyloides-papillosus
#12
Praveen Baskaran, Tegegn G Jaleta, Adrian Streit, Christian Rödelsperger
Gene duplication is one major mechanism playing a role in the evolution of phenotypic complexity and in the generation of novel traits. By comparing parasitic and nonparasitic nematodes, a recent study found that the evolution of parasitism in Strongyloididae is associated with a large expansion in the Astacin and CAP gene families.To gain novel insights into the developmental processes in the sheep parasite Strongyloides papillosus, we sequenced transcriptomes of different developmental stages and sexes. Overall, we found that the majority of genes are developmentally regulated and have one-to-one orthologs in the diverged S...
March 2, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338722/dissecting-the-transcriptional-patterns-of-social-dominance-across-teleosts
#13
Suzy C P Renn, Cynthia F O'Rourke, Nadia Aubin-Horth, Eleanor J Fraser, Hans A Hofmann
In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms...
December 16, 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28338018/isolation-and-characterization-of-the-e-coli-membrane-protein-production-strain-mutant56-de3
#14
Thomas Baumgarten, Susan Schlegel, Samuel Wagner, Mirjam Löw, Jonas Eriksson, Ida Bonde, Markus J Herrgård, Hermann J Heipieper, Morten H H Nørholm, Dirk Jan Slotboom, Jan-Willem de Gier
Membrane protein production is usually toxic to E. coli. However, using genetic screens strains can be isolated in which the toxicity of membrane protein production is reduced, thereby improving production yields. Best known examples are the C41(DE3) and C43(DE3) strains, which are both derived from the T7 RNA polymerase (P)-based BL21(DE3) protein production strain. In C41(DE3) and C43(DE3) mutations lowering t7rnap expression levels result in strongly reduced T7 RNAP accumulation levels. As a consequence membrane protein production stress is alleviated in the C41(DE3) and C43(DE3) strains, thereby increasing membrane protein yields...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337178/glucose-uptake-in-prochlorococcus-diversity-of-kinetics-and-effects-on-the-metabolism
#15
María Del Carmen Muñoz-Marín, Guadalupe Gómez-Baena, Jesús Díez, Robert J Beynon, David González-Ballester, Mikhail V Zubkov, José M García-Fernández
We have previously shown that Prochlorococcus sp. SS120 strain takes up glucose by using a multiphasic transporter encoded by the Pro1404 gene. Here, we studied the glucose uptake kinetics in multiple Prochlorococcus strains from different ecotypes, observing diverse values for the Ks constants (15-126.60 nM) and the uptake rates (0.48-6.36 pmol min(-1) mg prot(-1)). Multiphasic kinetics was observed in all studied strains, except for TAK9803-2. Pro1404 gene expression studies during the 21st Atlantic Meridional Transect cruise showed positive correlation with glucose concentrations in the ocean...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28336464/new-insights-into-the-codon-usage-patterns-of-the-bactericidal-permeability-increasing-bpi-gene-across-nine-species
#16
Wei-Yun Qin, Li-Na Gan, Ri-Wei Xia, Shou-Yong Sun, Guo-Qiang Zhu, Sheng-Long Wu, Wen-Bin Bao
Bactericidal/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. Non-uniform usage of synonymous codons for a specific amino acid during translation of a protein is known as codon usage bias (CUB). Analysis of CUB and compositional dynamics of coding sequences could contribute to a better understanding of the molecular mechanism and the evolution of a particular gene. In this study, we performed CUB analysis of the complete coding sequences of the BPI gene from nine different species...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28336271/helminth-secretomes-reflect-different-lifestyles-and-parasitized-hosts
#17
Yesid Cuesta-Astroz, Francislon Silva de Oliveira, Laila Alves Nahum, Guilherme Oliveira
Helminths cause a number of medical and agricultural problems and are a major cause of parasitic infections in humans, animals and plants. Comparative analysis of helminth genes and genomes are important to understand the genomic biodiversity and evolution of parasites and their hosts in terms of different selective pressures in their habitats. The interactions between the infective organisms and their hosts are mediated in large part by secreted proteins, known collectively as the "secretome". Proteins secreted by parasites are able to modify a host's environment and modulate their immune system...
March 20, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28335712/exploring-the-evolutionary-origin-of-floral-organs-of-erycina-pusilla-an-emerging-orchid-model-system
#18
Anita Dirks-Mulder, Roland Butôt, Peter van Schaik, Jan Willem P M Wijnands, Roel van den Berg, Louie Krol, Sadhana Doebar, Kelly van Kooperen, Hugo de Boer, Elena M Kramer, Erik F Smets, Rutger A Vos, Alexander Vrijdaghs, Barbara Gravendeel
BACKGROUND: Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands...
March 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28335073/clinical-characteristics-and-whole-exome-transcriptome-sequencing-of-coexisting-chronic-myeloid-leukemia-and-myelofibrosis
#19
Malathi Kandarpa, Yi-Mi Wu, Dan Robinson, Patrick William Burke, Arul M Chinnaiyan, Moshe Talpaz
Myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell (HSC) disorders that can be classified on the basis of genetic, clinical, phenotypic features. Genetic lesions such as JAK2 mutations and BCR-ABL translocation are often mutually exclusive in MPN patients and lead to essential thrombocythemia, polycythemia vera or myelofibrosis (ET/PV/MF) or chronic myeloid leukemia, respectively. Nevertheless, coexistence of these genetic aberrations in the same patient has been reported. Whether these aberrations occur in the same stem cell or a different cell is unclear, but an unstable genome in the HSCs seems to be the common antecedent...
March 23, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28334892/inhibition-of-homologous-phosphorolytic-ribonucleases-by-citrate-may-represent-an-evolutionarily-conserved-communicative-link-between-rna-degradation-and-central-metabolism
#20
Carlanne M Stone, Louise E Butt, Joshua C Bufton, Daniel C Lourenco, Darren M Gowers, Andrew R Pickford, Paul A Cox, Helen A Vincent, Anastasia J Callaghan
Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli...
March 3, 2017: Nucleic Acids Research
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