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https://www.readbyqxmd.com/read/28335026/melting-temperature-highlights-functionally-important-rna-structure-and-sequence-elements-in-yeast-mrna-coding-regions
#1
Fei Qi, Dmitrij Frishman
Secondary structure elements in the coding regions of mRNAs play an important role in gene expression and regulation, but distinguishing functional from non-functional structures remains challenging. Here we investigate the dependence of sequence-structure relationships in the coding regions on temperature based on the recent PARTE data by Wan et al. Our main finding is that the regions with high and low thermostability (high Tm and low Tm regions) are under evolutionary pressure to preserve RNA secondary structure and primary sequence, respectively...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28333336/comparative-sperm-proteomics-in-mouse-species-with-divergent-mating-systems
#2
Alberto Vicens, Kirill Borziak, Timothy L Karr, Eduardo R S Roldan, Steve Dorus
Sexual selection is the pervasive force underlying the dramatic divergence of sperm form and function. Although it has been demonstrated that testis gene expression evolves rapidly, exploration of the proteomic basis of sperm diversity is in its infancy. We have employed a whole-cell proteomics approach to characterize sperm divergence among closely related Mus species that experience different sperm competition regimes and exhibit pronounced variation in sperm energetics, motility and fertilization capacity...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333240/structure-of-the-transcriptional-regulatory-network-correlates-with-regulatory-divergence-in-drosophila
#3
Bing Yang, Patricia J Wittkopp
Transcriptional control of gene expression is regulated by biochemical interactions between cis-regulatory DNA sequences and trans-acting factors that form complex regulatory networks. Genetic changes affecting both cis- and trans-acting sequences in these networks have been shown to alter patterns of gene expression as well as higher-order organismal phenotypes. Here, we investigate how the structure of these regulatory networks relates to patterns of polymorphism and divergence in gene expression. To do this, we compared a transcriptional regulatory network inferred for Drosophila melanogaster to differences in gene regulation observed between two strains of D...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333212/structural-history-of-human-srgap2-proteins
#4
Michael Sporny, Julia Guez-Haddad, Annett Kreusch, Sivan Shakartzi, Avi Neznansky, Alice Cross, Michail N Isupov, Britta Qualmann, Michael M Kessels, Yarden Opatowsky
In the development of the human brain, human-specific genes are considered to play key roles, conferring its unique advantages and vulnerabilities. At the time of Homo lineage divergence from Australopithecus, SRGAP2C gradually emerged through a process of serial duplications and mutagenesis from ancestral SRGAP2A (3.4-2.4 Ma). Remarkably, ectopic expression of SRGAP2C endows cultured mouse brain cells, with human-like characteristics, specifically, increased dendritic spine length and density. To understand the molecular mechanisms underlying this change in neuronal morphology, we determined the structure of SRGAP2A and studied the interplay between SRGAP2A and SRGAP2C...
February 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333083/divergent-expression-patterns-and-function-implications-of-four-nanos-genes-in-a-hermaphroditic-fish-epinephelus-coioides
#5
Zhi-Hui Sun, Yang Wang, Wei-Jia Lu, Zhi Li, Xiao-Chun Liu, Shui-Sheng Li, Li Zhou, Jian-Fang Gui
Multiple nanos genes have been characterized in several fishes, but the functional implications of their various expression patterns remain unclear. In this study, we identified and characterized four nanos genes from a hermaphroditic fish orange-spotted grouper, Epinephelus coioides. Ecnanos1a and Ecnanos1b show divergent expression patterns, and the dynamic expression change of Ecnanos1a in pituitaries during sex change is associated with testis differentiation and spermatogenesis. Ecnanos2 and Ecnanos3 might be germline stem cells (GSCs) and primordial germ cells (PGCs)-specific markers, respectively...
March 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28331095/divergent-requirement-of-fc-fc%C3%AE-r-interactions-for-in-vivo-protection-against-influenza-viruses-by-two-pan-h5-hemagglutinin-antibodies
#6
Shuangshuang Wang, Huanhuan Ren, Wenbo Jiang, Honglin Chen, Hongxing Hu, Zhiwei Chen, Paul Zhou
Recent studies have shown that Fc-FcγR interactions are required for in vivo protection against influenza viruses by broadly reactive anti-HA stem, but not virus strain-specific, anti-receptor binding site (RBS), antibodies (Abs). Since only a few Abs recognizing epitopes in the head region but outside the RBS have been tested against single challenge virus strains, it remains unknown whether Fc-FcγR interactions are required for in vivo protection by Abs recognizing epitopes outside the RBS, and whether the requirement is virus strain-specific or epitope-specific...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28330839/evolutionary-insights-into-t-type-ca-2-channel-structure-function-and-ion-selectivity-from-the-trichoplax-adhaerens-homologue
#7
Carolyn L Smith, Salsabil Abdallah, Yuen Yan Wong, Phuong Le, Alicia N Harracksingh, Liana Artinian, Arianna N Tamvacakis, Vincent Rehder, Thomas S Reese, Adriano Senatore
Four-domain voltage-gated Ca(2+) (Cav) channels play fundamental roles in the nervous system, but little is known about when or how their unique properties and cellular roles evolved. Of the three types of metazoan Cav channels, Cav1 (L-type), Cav2 (P/Q-, N- and R-type) and Cav3 (T-type), Cav3 channels are optimized for regulating cellular excitability because of their fast kinetics and low activation voltages. These same properties permit Cav3 channels to drive low-threshold exocytosis in select neurons and neurosecretory cells...
March 22, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/28328982/highlighting-of-quorum-sensing-lux-genes-and-their-expression-in-the-hydrothermal-vent-shrimp-rimicaris-exoculata-ectosymbiontic-community-possible-use-as-biogeographic-markers
#8
Simon Le Bloa, Lucile Durand, Valérie Cueff-Gauchard, Josiane Le Bars, Laure Taupin, Charlotte Marteau, Alexis Bazire, Marie-Anne Cambon-Bonavita
Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS) were then studied...
2017: PloS One
https://www.readbyqxmd.com/read/28328177/maternal-vernalization-and-vernalization-pathway-genes-influence-progeny-seed-germination
#9
Gabriela A Auge, Logan K Blair, Hannah Neville, Kathleen Donohue
Different life stages frequently respond to the same environmental cue to regulate development so that each life stage is matched to its appropriate season. We investigated how independently each life stage can respond to shared environmental cues, focusing on vernalization, in Arabidopsis thaliana plants. We first tested whether effects of rosette vernalization persisted to influence seed germination. To test whether genes in the vernalization flowering pathway also influence germination, we assessed germination of functional and nonfunctional alleles of these genes and measured their level of expression at different life stages in response to rosette vernalization...
March 22, 2017: New Phytologist
https://www.readbyqxmd.com/read/28327435/network-approaches-for-plant-phylogenomic-synteny-analysis
#10
REVIEW
Tao Zhao, M Eric Schranz
Network analysis approaches have been widely applied across disciplines. In biology, network analysis is now frequently adopted to organize protein-protein interactions, organize pathways and/or to interpret gene co-expression patterns. However, comparative genomic analyses still largely rely on pairwise comparisons and linear visualizations between genomes. In this article, we discuss the challenges and prospects for establishing a generalized plant phylogenomic synteny network approach needed to interpret the wealth of new and emerging genomic data...
March 16, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28327084/a-transcriptome-multi-tissue-analysis-identifies-biological-pathways-and-genes-associated-with-variations-in-feed-efficiency-of-growing-pigs
#11
Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, David Causeur, Hélène Gilbert, Isabelle Louveau
BACKGROUND: Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). RESULTS: Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age...
March 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28322827/structural-divergence-of-essential-triad-ribbon-synapse-proteins-among-placental-mammals-implications-for-preclinical-trials-in-photoreceptor-transplantation-therapy
#12
Christopher R J Laver, Joanne A Matsubara
As photoreceptor transplantation rapidly moves closer to the clinic, verifying graft efficacy in animal models may have unforeseen xenogeneic barriers. Although photoreceptor transplants have most convincingly exhibited functional synaptogenesis in conspecific studies, such evidence (while ruling out false-positives due to: viral graft labeling, fusion/cytosolic transfer, or neuroprotection) has not yet been shown for discordant xenografts. From this, a fundamental question should be raised: is useful xenosynaptogenesis likely between human photoreceptors and mouse retina? The triad ribbon synapse (TRS) that would normally form is unique and contains trans-synaptic proteins essential to its formation and function...
March 18, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28322764/cloning-expression-and-functional-characterization-on-vitellogenesis-of-estrogen-receptors-in-scatophagus-argus
#13
Xue-Fan Cui, Yuan Zhao, Hua-Pu Chen, Si-Ping Deng, Dong-Neng Jiang, Tian-Li Wu, Chun-Hua Zhu, Guang-Li Li
Estrogen receptors (Er) play a critical role in vitellogenesis. Three ers (erα, erβ1 and erβ2) and vitellogenins (vtg-A, vtg-B and vtg-C) subtypes were isolated in various fish species, while the contribution of each Er to the regulation of vtgs expression was not analyzed in detail. Here, erα, erβ1 and erβ2 were cloned and all were found to be expressed in female liver in Scatophagus argus. During proteic vitellogenesis stage, erα was simultaneously up-regulated, while erβ1 and erβ2 were not, with three vtgs in female liver...
March 18, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28321979/effect-of-the-early-social-environment-on-behavioural-and-genomic-responses-to-a-social-challenge-in-a-cooperatively-breeding-vertebrate
#14
Cecilia Nyman, Stefan Fischer, Nadia Aubin-Horth, Barbara Taborsky
The early social environment can have substantial, lifelong effects on vertebrate social behaviour, which can be mediated by developmental plasticity of brain gene expression. Early life effects can influence immediate behavioural responses towards later-life social challenges and can activate different gene expression responses. However, while genomic responses to social challenges have been reported frequently, how developmental experience influences the shape of these genomic reaction norms remains largely unexplored...
March 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28320954/cerberus-nodal-lefty-pitx-signaling-cascade-controls-left-right-asymmetry-in-amphioxus
#15
Guang Li, Xian Liu, Chaofan Xing, Huayang Zhang, Sebastian M Shimeld, Yiquan Wang
Many bilaterally symmetrical animals develop genetically programmed left-right asymmetries. In vertebrates, this process is under the control of Nodal signaling, which is restricted to the left side by Nodal antagonists Cerberus and Lefty. Amphioxus, the earliest diverging chordate lineage, has profound left-right asymmetry as a larva. We show that Cerberus, Nodal, Lefty, and their target transcription factor Pitx are sequentially activated in amphioxus embryos. We then address their function by transcription activator-like effector nucleases (TALEN)-based knockout and heat-shock promoter (HSP)-driven overexpression...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320947/experimental-evidence-that-parasites-drive-eco-evolutionary-feedbacks
#16
Franziska S Brunner, Jaime M Anaya-Rojas, Blake Matthews, Christophe Eizaguirre
Host resistance to parasites is a rapidly evolving trait that can influence how hosts modify ecosystems. Eco-evolutionary feedbacks may develop if the ecosystem effects of host resistance influence selection on subsequent host generations. In a mesocosm experiment, using a recently diverged (<100 generations) pair of lake and stream three-spined sticklebacks, we tested how experimental exposure to a common fish parasite (Gyrodactylus spp.) affects interactions between hosts and their ecosystems in two environmental conditions (low and high nutrients)...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320945/three-dimensional-culture-system-identifies-a-new-mode-of-cetuximab-resistance-and-disease-relevant-genes-in-colorectal-cancer
#17
Cunxi Li, Bhuminder Singh, Ramona Graves-Deal, Haiting Ma, Alina Starchenko, William H Fry, Yuanyuan Lu, Yang Wang, Galina Bogatcheva, Mohseen P Khan, Ginger L Milne, Shilin Zhao, Gregory Daniel Ayers, Nenggan Li, Huaying Hu, Mary Kay Washington, Timothy J Yeatman, Oliver G McDonald, Qi Liu, Robert J Coffey
We previously reported that single cells from a human colorectal cancer (CRC) cell line (HCA-7) formed either hollow single-layered polarized cysts or solid spiky masses when plated in 3D in type-I collagen. To begin in-depth analyses into whether clonal cysts and spiky masses possessed divergent properties, individual colonies of each morphology were isolated and expanded. The lines thus derived faithfully retained their parental cystic and spiky morphologies and were termed CC (cystic) and SC (spiky), respectively...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320862/differential-involvement-of-the-microtubule-cytoskeleton-in-insulin-receptor-substrate-1-irs-1-and-irs-2-signaling-to-akt-determines-response-to-microtubule-disruption-in-breast-carcinoma-cells
#18
Jose Mercado-Matos, Jennifer L Clark, Andrew J Piper, Jenny Janusis, Leslie M Shaw
The insulin receptor substrate (IRS) proteins serve as essential signaling intermediates for the activation of PI3K by both the insulin-like growth factor-1 receptor (IGF-1R) and its close family member the insulin receptor (IR). Although IRS-1 and IRS-2 share significant homology, they regulate distinct cellular responses downstream of these receptors and play divergent roles in breast cancer. To investigate the mechanism by which signaling through IRS-1 and IRS-2 results in differential outcomes, we assessed the involvement of the microtubule cytoskeleton in IRS-dependent signaling...
March 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28320313/retention-of-duplicated-long-wavelength-opsins-in-mosquito-lineages-by-positive-selection-and-differential-expression
#19
Gloria I Giraldo-Calderón, Michael J Zanis, Catherine A Hill
BACKGROUND: Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive opsins predicted in the yellow fever mosquito, Aedes aegypti and malaria mosquito, Anopheles gambiae, and eight in the southern house mosquito, Culex quinquefasciatus, suggest gene expansion in the Family Culicidae (mosquitoes) relative to other insects. Here we report the first detailed molecular and evolutionary analyses of LW opsins in three mosquito vectors, with a goal to understanding the molecular basis of opsin-mediated visual processes that could be exploited for mosquito control...
March 21, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28320287/subcellular-localization-and-detection-of-tobacco-mosaic-virus-orf6-protein-by-immunoelectron-microscopy
#20
T N Erokhina, E A Lazareva, K R Richert-Pöggeler, E V Sheval, A G Solovyev, S Y Morozov
Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated...
January 2017: Biochemistry. Biokhimii︠a︡
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