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https://www.readbyqxmd.com/read/28645144/increased-alignment-sensitivity-improves-the-usage-of-genome-alignments-for-comparative-gene-annotation
#1
Virag Sharma, Michael Hiller
Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28643450/scpp-genes-and-their-relatives-in-gar-rapid-expansion-of-mineralization-genes-in-osteichthyans
#2
Kazuhiko Kawasaki, Masato Mikami, Mitsushiro Nakatomi, Ingo Braasch, Peter Batzel, John H Postlethwait, Akie Sato, Ichiro Sasagawa, Mikio Ishiyama
Gar is an actinopterygian that has bone, dentin, enameloid, and ganoin (enamel) in teeth and/or scales. Mineralization of these tissues involves genes encoding various secretory calcium-binding phosphoproteins (SCPPs) in osteichthyans, but no SCPP genes have been identified in chondrichthyans to date. In the gar genome, we identified 38 SCPP genes, seven of which encode "acidic-residue-rich" proteins and 31 encode "Pro/Gln (P/Q) rich" proteins. These gar SCPP genes constitute the largest known repertoire, including many newly identified P/Q-rich genes expressed in teeth and/or scales...
June 22, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28642634/analysis-of-map-kinase-mpk4-mekk1-mkk-genes-of-carica-papaya-l-comparative-to-other-plant-homologues
#3
Muhammad Hanam Hamid, Lina Rozano, Wee Chien Yeong, Janna Ong Abdullah, Noor Baity Saidi
Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species...
2017: Bioinformation
https://www.readbyqxmd.com/read/28642229/evolutionary-dynamics-of-the-kinetochore-network-in-eukaryotes-as-revealed-by-comparative-genomics
#4
Jolien Je van Hooff, Eelco Tromer, Leny M van Wijk, Berend Snel, Geert Jpl Kops
During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule-mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes...
June 22, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28641136/age-exacerbates-abnormal-protein-expression-in-a-mouse-model-of-down-syndrome
#5
Md Mahiuddin Ahmed, Aaron Block, Suhong Tong, Muriel T Davisson, Katheleen J Gardiner
The Ts65Dn is a popular mouse model of Down syndrome (DS). It displays DS-relevant features of learning/memory deficits and age-related loss of functional markers in basal forebrain cholinergic neurons. Here we describe protein expression abnormalities in brain regions of 12-month-old male Ts65Dn mice. We show that the magnitudes of abnormalities of human chromosome 21 and non-human chromosome 21 orthologous proteins are greater at 12 months than at ∼6 months. Age-related exacerbations involve the number of components affected in the mechanistic target of rapamycin pathway, the levels of components of the mitogen-activated protein kinase pathway, and proteins associated with Alzheimer's disease...
May 10, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28640975/nac-transcription-factor-jungbrunnen1-enhances-drought-tolerance-in-tomato
#6
Venkatesh P Thirumalaikumar, Vikas Devkar, Nikolay Mehterov, Shawkat Ali, Rengin Ozgur, Ismail Turkan, Bernd Mueller-Roeber, Salma Balazadeh
Water deficit (drought stress) massively restricts plant growth and the yield of crops; reducing the deleterious effects of drought is therefore of high agricultural relevance. Drought triggers diverse cellular processes including the inhibition of photosynthesis, the accumulation of cell-damaging reactive oxygen species, and gene expression reprogramming, besides others. Transcription factors (TF) are central regulators of transcriptional reprogramming and expression of many TF genes is affected by drought, including members of the NAC family...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28639397/ovarian-polarity-and-cell-shape-determination-by-btk29a-in-drosophila
#7
Noriko Hamada-Kawaguchi, Daisuke Yamamoto
Drosophila Btk29A is a Tec family nonreceptor tyrosine kinase, the ortholog of which causes X-linked agammagluburinemia in humans when mutant. In Btk29A(ficP) mutant ovaries, multiple defects are observed: extra polar cells form ectopically; osk mRNA fails to accumulate posteriorly in mature oocytes; the shape and alignment of follicle cells are grossly distorted. All these phenotypes are rescued by selectively overexpressing the type 2 isoform of wild-type Btk29A in follicle cells. Expression of certain proteins enriched in adherens junctions is markedly affected in Btk29A(ficP) mutants; the anterior-posterior gradient normally observed in the expression of DE-Cadherin and Armadillo are lost and Canoe is sequestered from adherens junctions...
June 22, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28638976/lilrb-receptor-mediated-regulation-of-myeloid-cell-maturation-and-function
#8
REVIEW
William van der Touw, Hui-Ming Chen, Ping-Ying Pan, Shu-Hsia Chen
The leukocyte immunoglobulin-like receptor (LILR) family comprises a set of paired immunomodulatory receptors expressed among human myeloid and lymphocyte cell populations. While six members of LILR subfamily A (LILRA) associate with membrane adaptors to signal via immunoreceptor tyrosine-based activating motifs (ITAM), LILR subfamily B (LILRB) members signal via multiple cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIM). Ligand specificity of some LILR family members has been studied in detail, but new perspective into the immunoregulatory aspects of this receptor family in human myeloid cells has been limited...
June 21, 2017: Cancer Immunology, Immunotherapy: CII
https://www.readbyqxmd.com/read/28637321/amino-acid-substrates-impose-polyamine-eif5a-or-hypusine-requirement-for-peptide-synthesis
#9
Byung-Sik Shin, Takayuki Katoh, Erik Gutierrez, Joo-Ran Kim, Hiroaki Suga, Thomas E Dever
Whereas ribosomes efficiently catalyze peptide bond synthesis by most amino acids, the imino acid proline is a poor substrate for protein synthesis. Previous studies have shown that the translation factor eIF5A and its bacterial ortholog EF-P bind in the E site of the ribosome where they contact the peptidyl-tRNA in the P site and play a critical role in promoting the synthesis of polyproline peptides. Using misacylated Pro-tRNAPhe and Phe-tRNAPro, we show that the imino acid proline and not tRNAPro imposes the primary eIF5A requirement for polyproline synthesis...
June 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28634826/tai-vacuolar-invertase-orthologs-the-interspecific-variability-in-tomato-plants-solanum-section-lycopersicon
#10
M A Slugina, A V Shchennikova, E Z Kochieva
Understanding the genetic mechanisms underlying carbohydrate metabolism can promote the development of biotechnological advances in fruit plants. The flesh tomato fruit represents an ideal system for examining the role of sucrose cleavage enzymes in fruit development, and wild tomato species differing in storage sugars serve as an excellent research material for this purpose. Plant vacuolar invertase is a key enzyme of sucrose metabolism in the sink organs. In the present study, we identified complete gene sequences encoding the TAI vacuolar invertase in 11 wild and one cultivated tomato accessions of the Solanum section Lycopersicon...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28634384/alternative-splicing-regulates-distinct-subcellular-localization-of-epithelial-splicing-regulatory-protein-1-esrp1-isoforms
#11
Yueqin Yang, Russ P Carstens
Epithelial-Splicing-Regulatory-Protein 1 (Esrp1) is a cell-type specific RNA-binding protein (RBP) that is essential for mammalian development through maintenance of epithelial cell properties including barrier function. Esrp1 also regulates splicing during the epithelial to mesenchymal transition (EMT). It contains three highly conserved RNA recognition motifs (RRMs) in the absence of other clearly defined protein domains. Esrp1 itself is also alternatively spliced to produce multiple protein isoforms. Here we determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differential nucleocytoplasmic localization...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634239/the-dual-activity-responsible-for-the-elongation-and-branching-of-%C3%AE-1-3-glucan-in-the-fungal-cell-wall
#12
Vishukumar Aimanianda, Catherine Simenel, Cecile Garnaud, Cecile Clavaud, Rui Tada, Lise Barbin, Isabelle Mouyna, Christoph Heddergott, Laura Popolo, Yoshikazu Ohya, Muriel Delepierre, Jean-Paul Latge
β-(1,3)-Glucan, the major fungal cell wall component, ramifies through β-(1,6)-glycosidic linkages, which facilitates its binding with other cell wall components contributing to proper cell wall assembly. Using Saccharomyces cerevisiae as a model, we developed a protocol to quantify β-(1,6)-branching on β-(1,3)-glucan. Permeabilized S. cerevisiae and radiolabeled substrate UDP-((14)C)glucose allowed us to determine branching kinetics. A screening aimed at identifying deletion mutants with reduced branching among them revealed only two, the bgl2Δ and gas1Δ mutants, showing 15% and 70% reductions in the branching, respectively, compared to the wild-type strain...
June 20, 2017: MBio
https://www.readbyqxmd.com/read/28634080/nong-a-constituent-of-the-nonactin-biosynthetic-gene-cluster-regulates-nocardamine-synthesis-in-streptomyces-albus-j1074
#13
Wanki Park, Jung-Kyun Woo, Jongheon Shin, Ki-Bong Oh
Many factors regulate the expression of specialised secondary metabolite biosynthetic gene clusters, which have been recognised as important for the discovery of novel microbial natural products. A cosmid library based on genomic DNA of the marine-derived Streptomyces puniceus Act1085 was constructed and screened to identify a short gene cluster similar to the nonactin biosynthetic cluster. The ORFs of the gene cluster isolated had high amino acid sequence identity, from 82% to 96%, with corresponding ORFs of the nonactin biosynthetic gene cluster from S...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28633662/orthored-a-rapid-and-accurate-orthology-prediction-tool-with-low-computational-requirement
#14
Kai Battenberg, Ernest K Lee, Joanna C Chiu, Alison M Berry, Daniel Potter
BACKGROUND: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28632342/variation-in-gene-regulation-underlying-annual-and-perennial-flowering-in-arabideae-species
#15
Jannice Friedman
The diversity of life history strategies within the angiosperms illustrates the evolutionary flexibility of reproductive characteristics. The number of times an individual reproduces is a key life history trait, and transitions from iteroparous perennials to semelparous annuals have occurred frequently in the flowering plants. Despite the frequency of this evolutionary transition, and the importance of annuality versus perenniality to both agriculture and ecology, understanding the molecular and genetic mechanisms involved in perennial flowering is in their infancy...
July 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28630801/characterization-of-the-transcriptome-and-est-ssr-development-in-boea-clarkeana-a-desiccation-tolerant-plant-endemic-to-china
#16
Ying Wang, Kun Liu, De Bi, Shoubiao Zhou, Jianwen Shao
BACKGROUND: Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown...
2017: PeerJ
https://www.readbyqxmd.com/read/28630437/phylogenetic-analysis-of-f-bzip-transcription-factors-indicates-conservation-of-the-zinc-deficiency-response-across-land-plants
#17
Pedro Humberto Castro, Grmay H Lilay, Antonio Muñoz-Mérida, Jan K Schjoerring, Herlânder Azevedo, Ana G L Assunção
Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing AtbZIP24, is more prone to gene loss and expansion events...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630114/towards-universal-forward-genetics-using-a-draft-genome-sequence-of-the-nematode-oscheius-tipulae-to-identify-mutations-affecting-vulva-development
#18
Fabrice Besnard, Georgios Koutsovoulos, Sana Dieudonné, Mark Blaxter, Marie-Anne Félix
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in non-model species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28629814/abcb1a-p-glycoprotein-limits-brain-exposure-of-the-anticancer-drug-candidate-seliciclib-in-vivo-in-adult-mice
#19
Franciska Erdő, Ildikó Nagy, Beáta Tóth, Annamária Bui, Éva Molnár, Zoltán Tímár, Rémi Magnan, Peter Krajcsi
Seliciclib displayed limited brain exposure in vivo in adult rats with mature blood-brain barrier (BBB). Selicilib was shown to be a specific substrate of human ABCB1 in vitro. To demonstrate that ABCB1/Abcb1 can limit brain exposure in vivo in mice we are showing that seliciclib is a substrate of mouse Abcb1a, the murine ABCB1 ortholog expressed in the BBB as LLC-PK-Abcb1a cells displayed an efflux ratio (ER) of 15.31±3.54 versus an ER of 1.44±0.10 in LLC-PK1-mock cells. Additionally, in the presence of LY335979, an ABCB1/Abcb1a specific inhibitor, the observed ER for seliciclib in the LLC-PK1-mMdr1a cells decreased to 1...
June 16, 2017: Brain Research Bulletin
https://www.readbyqxmd.com/read/28628829/ectromelia-virus-accumulates-less-double-stranded-rna-compared-to-vaccinia-virus-in-bs-c-1-cells
#20
Tiffany R Frey, Michael H Lehmann, Colton M Ryan, Marie C Pizzorno, Gerd Sutter, Adam R Hersperger
Most orthopoxviruses, including vaccinia virus (VACV), contain genes in the E3L and K3L families. The protein products of these genes have been shown to combat PKR, a host defense pathway. Interestingly, ectromelia virus (ECTV) contains an E3L ortholog but does not possess an intact K3L gene. Here, we gained insight into how ECTV can still efficiently evade PKR despite lacking K3L. Relative to VACV, we found that ECTV-infected BS-C-1 cells accumulated considerably less double-stranded (ds) RNA, which was due to lower mRNA levels and less transcriptional read-through of some genes by ECTV...
June 16, 2017: Virology
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