keyword
MENU ▼
Read by QxMD icon Read
search

orthology

keyword
https://www.readbyqxmd.com/read/28544607/spotted-gar-and-the-evolution-of-innate-immune-receptors
#1
Dustin J Wcisel, Tatsuya Ota, Gary W Litman, Jeffrey A Yoder
The resolution of the gar genome affords an opportunity to examine the diversification and functional specialization of immune effector molecules at a distant and potentially informative point in phylogenetic development. Although innate immunity is effected by a particularly large number of different families of molecules, the focus here is to provide detailed characterization of several families of innate receptors that are encoded in large multigene families, for which orthologous forms can be identified in other species of bony fish but not in other vertebrate groups as well as those for which orthologs are present in other vertebrate species...
May 24, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28544438/genome-wide-identification-characterization-and-evolution-of-cuticular-protein-genes-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#2
Bai-Qi Liu, Liang Qiao, Qi-Yi He, Yong Zhou, Shuang Ren, Bin Chen
Thirteen cuticular proteins (CPs) families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on motifs and phylogenetic analyses. In 11 other insect species, 9 had CP numbers > 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of 8 species occupied > 1.4% of the total genomic gene number whereas in 3 species the CPs occupied < 1%...
May 24, 2017: Insect Science
https://www.readbyqxmd.com/read/28544213/bac-recombineering-of-the-agouti-loci-from-spotted-gar-and-zebrafish-reveals-the-evolutionary-ancestry-of-dorsal-ventral-pigment-asymmetry-in-fish
#3
Laura Cal, Manuel MegÍas, José Miguel Cerdá-Reverter, John H Postlethwait, Ingo Braasch, Josep Rotllant
Dorsoventral pigment patterning, characterized by a light ventrum and a dark dorsum, is one of the most widespread chromatic adaptations in vertebrate body coloration. In mammals, this countershading depends on differential expression of agouti-signaling protein (ASIP), which drives a switch of synthesis of one type of melanin to another within melanocytes. Teleost fish share countershading, but the pattern results from a differential distribution of multiple types of chromatophores, with black-brown melanophores most abundant in the dorsal body and reflective iridophores most abundant in the ventral body...
May 24, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28543362/commd1-a-multifunctional-regulatory-protein
#4
Mario Riera Romo
The COMMD Protein Family is highly conserved among multicellular eukaryotic organisms and many orthologs of human COMMD genes have been found in different species of plants, invertebrates, lower vertebrates and mammals. COMMD1 is the best characterized member of the family and is conserved among vertebrates. This protein represents a pleiotropic factor involved in the regulation of many cellular and physiological processes that include copper and cholesterol homeostasis, ionic transport, oxidative stress, protein aggregation, protein trafficking, NF-κB-mediated transcription, hypoxia induced transcription, DNA damage response and oncogenesis...
May 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28542908/an-appraisal-of-the-enzyme-stability-activity-trade-off
#5
Scott R Miller
A longstanding idea in evolutionary physiology is that an enzyme cannot jointly optimize performance at both high and low temperatures due to a trade-off between stability and activity. Although a stability-activity trade-off has been observed for well-characterized examples, such a trade-off is not imposed by any physical chemical constraint. To better understand the pervasiveness of this trade-off, I investigated the stability-activity relationship for comparative biochemical studies of purified orthologous enzymes identified by a literature search...
May 24, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28542589/validating-regulatory-predictions-from-diverse-bacteria-with-mutant-fitness-data
#6
Shiori Sagawa, Morgan N Price, Adam M Deutschbauer, Adam P Arkin
Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium's growth across many conditions, to test regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions...
2017: PloS One
https://www.readbyqxmd.com/read/28542433/beneficial-effect-of-combined-treatment-with-octreotide-and-pasireotide-in-pck-rats-an-orthologous-model-of-human-autosomal-recessive-polycystic-kidney-disease
#7
Masanori Kugita, Kazuhiro Nishii, Tamio Yamaguchi, Atsushi Suzuki, Yukio Yuzawa, Shigeo Horie, Eiji Higashihara, Shizuko Nagao
Increased intracellular cyclic AMP (cAMP) in renal tubular epithelia accelerates the progression of polycystic kidney disease (PKD). Thus, decreasing cAMP levels by an adenylyl cyclase inhibitory G protein activator is considered to be an effective approach in ameliorating PKD. In fact, pasireotide (PAS) was effective in reducing disease progression in animal models of PKD. However, hyperglycemia caused by the administration of PAS is an adverse effect in its clinical use. Whereas, co-administration of octreotide (OCT) with PAS did not increase serum glucose in normal rats...
2017: PloS One
https://www.readbyqxmd.com/read/28542158/identifying-pathogenicity-of-human-variants-via-paralog-based-yeast-complementation
#8
Fan Yang, Song Sun, Guihong Tan, Michael Costanzo, David E Hill, Marc Vidal, Brenda J Andrews, Charles Boone, Frederick P Roth
To better understand the health implications of personal genomes, we now face a largely unmet challenge to identify functional variants within disease-associated genes. Functional variants can be identified by trans-species complementation, e.g., by failure to rescue a yeast strain bearing a mutation in an orthologous human gene. Although orthologous complementation assays are powerful predictors of pathogenic variation, they are available for only a few percent of human disease genes. Here we systematically examine the question of whether complementation assays based on paralogy relationships can expand the number of human disease genes with functional variant detection assays...
May 25, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28541415/transcriptome-wide-identification-and-expression-analysis-of-divaricata-and-radialis-like-genes-of-the-mediterranean-orchid-orchis-italica
#9
Maria Carmen Valoroso, Sofia De Paolo, Giovanni Iazzetti, Serena Aceto
Bilateral symmetry of flowers is a relevant novelty that has occurred many times throughout the evolution of flowering plants. In Antirrhinum majus, establishment of flower dorso-ventral asymmetry is mainly due to interaction of TCP (CYC and DICH) and MYB (DIV, RAD and DRIF) transcription factors. In the present study, we characterized 8 DIV-, 4 RAD- and 2 DRIF-like genes from the transcriptome of Orchis italica, an orchid species with bilaterally symmetric and resupinate flowers. We found a similar number of DIV- and RAD-like genes within the genomes of Phalaenopsis equestris and Dendrobium catenatum orchids...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28540700/strategies-to-improve-efficiency-and-specificity-of-degenerate-primers-in-pcr
#10
Maria Jorge Campos, Alberto Quesada
PCR with degenerate primers can be used to identify the coding sequence of an unknown protein or to detect a genetic variant within a gene family. These primers, which are complex mixtures of slightly different oligonucleotide sequences, can be optimized to increase the efficiency and/or specificity of PCR in the amplification of a sequence of interest by the introduction of mismatches with the target sequence and balancing their position toward the primers 5'- or 3'-ends. In this work, we explain in detail examples of rational design of primers in two different applications, including the use of specific determinants at the 3'-end, to: (1) improve PCR efficiency with coding sequences for members of a protein family by fully degeneration at a core box of conserved genetic information, with the reduction of degeneration at the 5'-end, and (2) optimize specificity of allelic discrimination of closely related orthologous by 5'-end degenerate primers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540421/yeast-env9-encodes-a-conserved-lipid-droplet-ld-short-chain-dehydrogenase-involved-in-ld-morphology
#11
Ikha M Siddiqah, Surya P Manandhar, Stephanie M Cocca, Teli Hsueh, Vanessa Cervantes, Editte Gharakhanian
Lipid droplets (LDs) have emerged as dynamic and interactive organelles with important roles in lipid metabolism and membrane biogenesis. Here, we report that Saccharomyces cerevisiae Env9 is a novel conserved oxidoreductase involved in LD morphology. Microscopic and biochemical studies confirm localization of tagged Env9 to LDs and implicate its C-terminal hydrophobic domain (aa241-265) in its membrane association and stability. Confocal studies reveal a role for Env9 in LD morphology. Env9 positively affects both formation of large LDs upon overexpression and LD proliferation under poor carbon source...
May 24, 2017: Current Genetics
https://www.readbyqxmd.com/read/28539927/a-comprehensive-analysis-of-alternative-splicing-in-paleopolyploid-maize
#12
Wenbin Mei, Sanzhen Liu, James C Schnable, Cheng-Ting Yeh, Nathan M Springer, Patrick S Schnable, William B Barbazuk
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28539651/an-orthologous-non-mhc-locus-in-rats-and-mice-is-linked-to-cd4-and-cd8-t-cell-proportion
#13
D Franckaert, R Collin, J Dooley, R H Wallis, P Poussier, A Liston, E E Hillhouse, S Lesage
CD4(+) and CD8(+) T cells have a central role in the immune system due to their ability to protect against infection and cancer development without targeting self. Consequently, changes in CD4(+) and CD8(+) T-cell homeostasis can be indicative of an array of serious illnesses, ranging from viral infections to autoimmune diseases. In addition to environmental influences, there is evidence for a genetic component regulating the proportion of CD4(+) and CD8(+) T cells in lymphoid organs. Indeed, identifying the genetic determinants defining the frequency of the T-cell subsets is critical as it may reveal a targetable genetic pathway to modulate CD4(+) and CD8(+) T-cell numbers, which could be of clinical relevance for multiple disease settings...
May 25, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28536883/identification-of-genes-related-to-skin-development-in-potato
#14
Vijaya K R Vulavala, Edna Fogelman, Lior Rozental, Adi Faigenboim, Zachariah Tanami, Oded Shoseyov, Idit Ginzberg
Newly identified genes that are preferentially expressed in potato skin include genes that are associated with the secondary cell wall and stress-related activities and contribute to the skin's protective function. Microarrays were used to compare the skin and tuber-flesh transcriptomes of potato, to identify genes that contribute to the unique characteristics of the skin as a protective tissue. Functional gene analysis indicated that genes involved in developmental processes such as cell division, cell differentiation, morphogenesis and secondary cell wall formation (lignification and suberization), and stress-related activities, are more highly expressed in the skin than in the tuber flesh...
May 23, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28536265/structural-and-enzymatic-insights-into-species-specific-resistance-to-schistosome-parasite-drug-therapy
#15
Alexander B Taylor, Kenneth M Roberts, Xiaohang Cao, Nathaniel E Clark, Stephen P Holloway, Enrica Donati, Chiara M Polcaro, Livia Pica-Mattoccia, Reid S Tarpley, Stanton F McHardy, Donato Cioli, Philip T LoVerde, Paul F Fitzpatrick, P John Hart
The antischistosomal pro-drug oxamniquine is activated by a sulfotransferase (SULT) in the human parasite Schistosoma mansoni Of the three main human blood fluke species, only S. mansoni is sensitive to oxamniquine therapy despite the presence of SULT orthologs in S. haematobium and S. japonicum The reason for this species-specific drug action has remained a mystery for decades. Here we present the crystal structures of S. haematobium and S. japonicum SULTs, including S. haematobium SULT in complex with oxamniquine...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28536259/differential-functional-regulation-of-pkc-orthologs-in-fission-yeast
#16
Marisa Madrid, Beatriz Vázquez-Marín, Teresa Soto, Alejandro Franco, Elisa Gómez-Gil, Jero Vicente-Soler, Mariano Gacto, Pilar Pérez, José Cansado
The two PKC orthologs Pck1 and Pck2 in the fission yeast Schizosaccharomyces pombe operate in a redundant fashion to control essential functions, including morphogenesis and cell wall biosynthesis, as well as the activity of the cell integrity pathway (CIP) and its core element the MAPK Pmk1. We show here that despite the strong structural similarity and functional redundancy of these two enzymes, the mechanisms regulating their maturation, activation, and stabilization have a remarkably distinct biological impact on both kinases...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28536080/a-genome-wide-identification-and-analysis-of-basic-helix-loop-helix-transcription-factors-in-cattle
#17
Debao Zhang, Guanying Li, Yong Wang
Basic helix-loop-helix (BHLH) transcription factors comprise a large family of regulatory proteins and play critical roles in the developmental processes of higher organisms. Complete lists of BHLH family members have been identified in about 50 organisms, including fruit fly, zebrafish, mouse, giant panda, worm, yeast, rice and apple. Cattle, Bos taurus, is important for agriculture and animal nutrition, and is also a good model organism for health research. In the present study, 116 putative BHLHs were identified in the cattle genome...
May 20, 2017: Gene
https://www.readbyqxmd.com/read/28535374/discovery-of-stromal-regulatory-networks-that-suppress-ras-sensitized-epithelial-cell-proliferation
#18
Huayang Liu, James A Dowdle, Safiya Khurshid, Nicholas J Sullivan, Nicholas Bertos, Komal Rambani, Markus Mair, Piotr Daniel, Esther Wheeler, Xing Tang, Kyle Toth, Michael Lause, Markus E Harrigan, Karl Eiring, Connor Sullivan, Matthew J Sullivan, Serena W Chang, Siddhant Srivastava, Joseph S Conway, Raleigh Kladney, Joseph McElroy, Sooin Bae, Yuanzhi Lu, Ali Tofigh, Sadiq M I Saleh, Soledad A Fernandez, Jeffrey D Parvin, Vincenzo Coppola, Erin R Macrae, Sarmila Majumder, Charles L Shapiro, Lisa D Yee, Bhuvaneswari Ramaswamy, Michael Hallett, Michael C Ostrowski, Morag Park, Helen M Chamberlin, Gustavo Leone
Mesodermal cells signal to neighboring epithelial cells to modulate their proliferation in both normal and disease states. We adapted a Caenorhabditis elegans organogenesis model to enable a genome-wide mesodermal-specific RNAi screen and discovered 39 factors in mesodermal cells that suppress the proliferation of adjacent Ras pathway-sensitized epithelial cells. These candidates encode components of protein complexes and signaling pathways that converge on the control of chromatin dynamics, cytoplasmic polyadenylation, and translation...
May 22, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28535078/complementation-of-ctb7-in-the-maize-pathogen-cercospora-zeina-overcomes-the-lack-of-in-vitro-cercosporin-production
#19
Velushka Swart, Bridget Genevieve Crampton, John Ridenour, Burton Bluhm, Nicholas Olivier, Marion Meyer, Dave Kenneth Berger
Gray leaf spot (GLS), caused by the sibling species Cercospora zeina or Cercospora zeae-maydis, is cited as one of the most important diseases threatening global maize production. C. zeina fails to produce cercosporin in vitro, and in most cases causes large coalescing lesions during maize infection; a symptom generally absent from cercosporin-deficient mutants in other Cercospora spp. Here we describe the C. zeina cercosporin toxin biosynthetic gene cluster. The oxidoreductase gene CTB7 contained several insertions and deletions as compared to the C...
May 23, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28532419/a-survey-of-the-complex-transcriptome-from-the-highly-polyploid-sugarcane-genome-using-full-length-isoform-sequencing-and-de-novo-assembly-from-short-read-sequencing
#20
Nam V Hoang, Agnelo Furtado, Patrick J Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P Thirugnanasambandam, Frederik C Botha, Robert J Henry
BACKGROUND: Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS: The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms...
May 22, 2017: BMC Genomics
keyword
keyword
39083
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"