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expression divergence

Kun Taek Park, Mahmoud M ElNaggar, Gaber S Abdellrazeq, John P Bannantine, Victoria Mack, Lindsay M Fry, William C Davis
Phylogenic comparisons of the mononuclear phagocyte system (MPS) of humans and mice demonstrate phenotypic divergence of dendritic cell (DC) subsets that play similar roles in innate and adaptive immunity. Although differing in phenotype, DC can be classified into four groups according to ontogeny and function: conventional DC (cDC1 and cDC2), plasmacytoid DC (pDC), and monocyte derived DC (MoDC). DC of Artiodactyla (pigs and ruminants) can also be sub-classified using this system, allowing direct functional and phenotypic comparison of MoDC and other DC subsets trafficking in blood (bDC)...
2016: PloS One
Hillary Anger Elfenbein, Daisung Jang, Sudeep Sharma, Jeffrey Sanchez-Burks
Emotional intelligence (EI) has captivated researchers and the public alike, but it has been challenging to establish its components as objective abilities. Self-report scales lack divergent validity from personality traits, and few ability tests have objectively correct answers. We adapt the Stroop task to introduce a new facet of EI called emotional attention regulation (EAR), which involves focusing emotion-related attention for the sake of information processing rather than for the sake of regulating one's own internal state...
October 20, 2016: Emotion
Adam M Session, Yoshinobu Uno, Taejoon Kwon, Jarrod A Chapman, Atsushi Toyoda, Shuji Takahashi, Akimasa Fukui, Akira Hikosaka, Atsushi Suzuki, Mariko Kondo, Simon J van Heeringen, Ian Quigley, Sven Heinz, Hajime Ogino, Haruki Ochi, Uffe Hellsten, Jessica B Lyons, Oleg Simakov, Nicholas Putnam, Jonathan Stites, Yoko Kuroki, Toshiaki Tanaka, Tatsuo Michiue, Minoru Watanabe, Ozren Bogdanovic, Ryan Lister, Georgios Georgiou, Sarita S Paranjpe, Ila van Kruijsbergen, Shengquiang Shu, Joseph Carlson, Tsutomu Kinoshita, Yuko Ohta, Shuuji Mawaribuchi, Jerry Jenkins, Jane Grimwood, Jeremy Schmutz, Therese Mitros, Sahar V Mozaffari, Yutaka Suzuki, Yoshikazu Haramoto, Takamasa S Yamamoto, Chiyo Takagi, Rebecca Heald, Kelly Miller, Christian Haudenschild, Jacob Kitzman, Takuya Nakayama, Yumi Izutsu, Jacques Robert, Joshua Fortriede, Kevin Burns, Vaneet Lotay, Kamran Karimi, Yuuri Yasuoka, Darwin S Dichmann, Martin F Flajnik, Douglas W Houston, Jay Shendure, Louis DuPasquier, Peter D Vize, Aaron M Zorn, Michihiko Ito, Edward M Marcotte, John B Wallingford, Yuzuru Ito, Makoto Asashima, Naoto Ueno, Yoichi Matsuda, Gert Jan C Veenstra, Asao Fujiyama, Richard M Harland, Masanori Taira, Daniel S Rokhsar
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma...
October 19, 2016: Nature
Laure D Sultan, Daria Mileshina, Felix Grewe, Katarzyna Rolle, Sivan Abudraham, Paweł Głodowicz, Adnan Khan Niazi, Ido Keren, Sofia Shevtsov, Liron Klipcan, Jan Barciszewski, Jeffrey P Mower, Andre Dietrich, Oren Ostersetzer
Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4...
October 19, 2016: Plant Cell
Cristina M Crava, Sukania Ramasamy, Lino Ometto, Gianfranco Anfora, Omar Rota-Stabelli
Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D...
October 19, 2016: G3: Genes—Genomes—Genetics
Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein
Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors (TFs), cellular growth factors and microRNAs. A subsystem's gene expression may be controlled by its internal regulatory factors, exclusively, or by external subsystems, or by both. It is thus useful to distinguish the degree to which a subsystem is regulated internally or externally-e.g., how non-conserved, species-specific TFs affect the expression of conserved, cross-species genes during evolution...
October 2016: PLoS Computational Biology
Sofia A V Fortunato, Michel Vervoort, Marcin Adamski, Maja Adamska
BACKGROUND: Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons...
2016: EvoDevo
D A Bangasser, H Dong, J Carroll, Z Plona, H Ding, L Rodriguez, C McKennan, J G Csernansky, S H Seeholzer, R J Valentino
Several neuropsychiatric and neurodegenerative disorders share stress as a risk factor and are more prevalent in women than in men. Corticotropin-releasing factor (CRF) orchestrates the stress response, and excessive CRF is thought to contribute to the pathophysiology of these diseases. We previously found that the CRF1 receptor (CRF1) is sex biased whereby coupling to its GTP-binding protein, Gs, is greater in females, whereas β-arrestin-2 coupling is greater in males. This study used a phosphoproteomic approach in CRF-overexpressing (CRF-OE) mice to test the proof of principle that when CRF is in excess, sex-biased CRF1 coupling translates into divergent cell signaling that is expressed as different brain phosphoprotein profiles...
October 18, 2016: Molecular Psychiatry
Hari Bhupathi Krishnan, Alaa Alaswad, Nathan Wayne Oehrle, Jason Gillman
Legumes form symbiotic association with soil-dwelling bacteria collectively called rhizobia. This association results in the formation of nodules, unique plant-derived organs, within which the rhizobia are housed. Rhizobia encoded-nitrogenase facilitates the conversation of atmospheric nitrogen into ammonia, which is utilized by the plants for its growth and development. Fatty acids have been shown to play an important role in root nodule symbiosis. In this study, we have investigated the role of Stearoyl-Acyl Carrier Protein Desaturase- isoform C (SACPD-C), a soybean enzyme that catalyzes the conversion of stearic acid into oleic acid, which is expressed in developing seeds and in nitrogen fixing nodules...
October 17, 2016: Molecular Plant-microbe Interactions: MPMI
Abdullah Alzaid, Samuel A M Martin, Daniel J Macqueen
The insulin-like growth factor (IGF) receptor (IGF-IR) is necessary for IGF signalling and has essential roles in cellular growth. In teleost fish, two distinct IGF-IR duplicates are conserved called IGF-IRa and IGF-IRb. However, while a salmonid-specific whole genome duplication (ssWGD) is known to have expanded several key genes within the IGF axis, its impact on the IGF-IR repertoire remains unresolved. Using bioinformatic and phylogenetic approaches, we establish that salmonids retain two IGF-IRa paralogues from ssWGD and a single IGF-IRb copy...
October 17, 2016: Scientific Reports
Schneider Ralf Friedrich, Axel Meyer
There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). This way multiple specialized sister-lineages can arise that share a common plastic ancestor - the 'flexible stem'...
October 16, 2016: Molecular Ecology
Qijiang Jin, Xin Hu, Xin Li, Bei Wang, Yanjie Wang, Hongwei Jiang, Neil Mattson, Yingchun Xu
Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions...
2016: Frontiers in Plant Science
Katelyn M Mika, Vincent J Lynch
Variation in female reproductive traits, such as fertility, fecundity, and fecundability, is heritable in humans, but identifying and functionally characterizing genetic variants associated with these traits has been challenging. Here, we explore the functional significance and evolutionary history of a T/C polymorphism of SNP rs2071473, which we have previously shown is an eQTL for TAP2 and significantly associated with fecundability (time to pregnancy). We replicated the association between the rs2071473 genotype and TAP2 expression by using GTEx data and demonstrated that TAP2 is expressed by decidual stromal cells at the maternal-fetal interface...
September 24, 2016: American Journal of Human Genetics
Tao Shi, Kun Wang, Pingfang Yang
microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
M J Madison-Villar, Cheng Sun, Nelson C Lau, Matthew L Settles, Rachel Lockridge Mueller
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules...
October 14, 2016: Journal of Molecular Evolution
Alexandra Jochmans-Lemoine, Manju Shahare, Jorge Soliz, Vincent Joseph
We previously reported that rats and mice that have been raised for more than 30 generations in La Paz, Bolivia (3600m), display divergent physiological responses to high altitude (HA), including improved respiratory and metabolic control in mice. In the present study we asked whether these traits would also be present in response to hypoxia at sea level (SL). To answer this question, we exposed rats (SD) and mice (FVB) to normoxia (21% O2) or hypoxia (15 and 12% O2) for 6 hours and measured ventilation and metabolic rate (whole body plethysmography), and expression of the transcription factor HIF-1α (ELISA and Mass Spectrometry) and other proteins whose expression are regulated by hypoxia (Glucose Transporter 1, Pyruvate Dehydrogenase Kinase 1, and Angiopoietin 2 - Mass Spectrometry) in the brainstem...
October 14, 2016: Journal of Experimental Biology
Nikolas M Eleftheriou, Jonas Sjölund, Matteo Bocci, Eliane Cortez, Se-Jin Lee, Sara I Cunha, Kristian Pietras
Angiogenesis occurs early in tumor development, sustains primary tumor growth and provides a route for metastatic escape. The TGF-β family receptors modulate angiogenesis via endothelial-cell specific pathways. Here we investigate the interaction of two such receptors, ALK1 and endoglin, in pancreatic neuroendocrine tumors (PanNET). Independently, ALK1 and endoglin deficiencies exhibited genetically divergent phenotypes, while both highly correlate to an endothelial metagene in human and mouse PanNETs. A concurrent deficiency of both receptors synergistically decreased tumor burden to a greater extent than either individual knockdown...
October 12, 2016: Oncotarget
Steven Atkinson, Frank H Stillinger, Salvatore Torquato
The nonequilibrium process by which hard-particle systems may be compressed into disordered, jammed states has received much attention because of its wide utility in describing a broad class of amorphous materials. While dynamical signatures are known to precede jamming, the task of identifying static structural signatures indicating the onset of jamming have proven more elusive. The observation that compressing hard-particle packings towards jamming is accompanied by an anomalous suppression of density fluctuations (termed "hyperuniformity") has paved the way for the analysis of jamming as an "inverted critical point" in which the direct correlation function c(r), rather than the total correlation function h(r), diverges...
September 2016: Physical Review. E
Linda Szabo, Julia Salzman
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases...
October 14, 2016: Nature Reviews. Genetics
G Andres Contreras, Kyan Thelen, Nadia Ayala-Lopez, Stephanie W Watts
There are sex associated differences in the risk for cardiovascular comorbidities in obesity and metabolic syndrome. A common clinical finding in these diseases is the expansion of perivascular adipose tissues (PVAT) which is associated with alterations in their role as regulators of vessel function. PVAT hyperplasia and hypertrophy are dependent on the biology of populations of adipocyte progenitor cells (APC). It is currently unclear if PVAT enlargement diverges between males and females and the mechanisms linking APC biology with sexual dimorphism remain poorly understood...
October 2016: Physiological Reports
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