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https://www.readbyqxmd.com/read/28637190/evolution-of-the-sperm-methylome-of-primates-is-associated-with-retrotransposon-insertions-and-genome-instability
#1
Kei Fukuda, Yukihiro Inoguchi, Kenji Ichiyanagi, Tomoko Ichiyanagi, Yasuhiro Go, Masashi Nagano, Yojiro Yanagawa, Noboru Takaesu, Yasuyuki Ohkawa, Hiroo Imai, Hiroyuki Sasaki
Changes in gene expression resulting from epigenetic and/or genetic changes play an important role in the evolutionary divergence of phenotypes. To explore how epigenetic and genetic changes are linked during primate evolution, we have compared the genome-wide DNA methylation profiles (methylomes) of humans and chimpanzees, which have a 1.2% DNA sequence divergence, of sperm, the frontal cortices, B cells, and neutrophils. We revealed that species-specific differentially methylated regions (S-DMRs), ranging from several hundred bp to several kb, were frequently associated with sequence changes in transcription factor binding sites and insertions of Alu and SVA retrotransposons...
June 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28636075/molecular-cloning-mrna-expression-and-biological-activity-of-the-pheromone-biosynthesis-activating-neuropeptide-pban-from-the-european-corn-borer-ostrinia-nubilalis
#2
J Fodor, G Köblös, Á Kákai, Z Kárpáti, B P Molnár, T Dankó, G Bozsik, C Bognár, G Szőcs, A Fónagy
Pheromone biosynthesis activating neuropeptide (PBAN) is a member of the pyrokinin (FXPRLamide) insect neuropeptides. Here, we report the cloning of the gene Ostnu-PBAN from the E and Z pheromone strains of the European corn borer (ECB), Ostrinia nubilalis (Lepidoptera: Crambidae), a major pest of maize. The Ostnu-PBAN genomic sequence is > 5 kb in length and consists of six exons. The deduced amino acid sequence revealed a 200-residue precursor protein including a signal peptide, a 24-amino acid (aa) diapause hormone, a 37-aa PBAN and three other FXPRLamide neuropeptides...
June 21, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28634213/omega-3-fatty-acids-increase-the-unfolded-protein-response-and-improve-amyloid-%C3%AE-phagocytosis-by-macrophages-of-patients-with-mild-cognitive-impairment
#3
Henry M Olivera-Perez, Larry Lam, Johnny Dang, Weilan Jiang, Fabian Rodriguez, Elizabeth Rigali, Sarah Weitzman, Verna Porter, Liudmilla Rubi, Marco Morselli, Matteo Pellegrini, Milan Fiala
Mϕs of patients with Alzheimer's disease and mild cognitive impairment (MCI) are defective in amyloid-β1-42 (Aβ) phagocytosis and have low resistance to apoptosis by Aβ. ω-3 in vitro and in vivo and the ω-3 mediator, resolvin D1, in vitro increase Aβ phagocytosis by Mϕs of patients with MCI. We have investigated the unfolded protein response (UPR) to endoplasmic reticulum (ER) stress by Mϕs in a longitudinal study of fish-derived, ω-3-supplemented patients with MCI. Patients in the apolipoprotein E (ApoE)e3/e3 subgroup over time exhibited an increase of protein kinase RNA-like ER kinase (PERK) expression, Aβ phagocytosis, intermediate M1-M2 Mϕ type, and a Mini-Mental State Examination (MMSE) rate of change of +1...
June 20, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28633360/expression-properties-exhibit-correlated-patterns-with-the-fate-of-duplicated-genes-their-divergence-and-transcriptional-plasticity-in-saccharomycotina
#4
Florian Mattenberger, Beatriz Sabater-Muñoz, Christina Toft, Gaurav Sablok, Mario A Fares
Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed...
June 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28633298/protein-expression-in-tension-wood-formation-monitored-at-high-tissue-resolution-in-populus
#5
Joakim Bygdell, Vaibhav Srivastava, Ogonna Obudulu, Manoj K Srivastava, Robert Nilsson, Björn Sundberg, Johan Trygg, Ewa J Mellerowicz, Gunnar Wingsle
Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation...
June 13, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28633015/haploidy-in-humans-an-evolutionary-and-developmental-perspective
#6
REVIEW
Ido Sagi, Nissim Benvenisty
Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there is an innate capacity for an organism to regain haploidy and that haploidy may confer evolutionary benefits. Haploid embryonic stem cells have been experimentally generated from mouse, rat, monkey, and humans. Haploidy results in major differences in cell size and gene expression levels while also affecting parental imprinting, X chromosome inactivation, and mitochondrial metabolism genes...
June 19, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28632342/variation-in-gene-regulation-underlying-annual-and-perennial-flowering-in-arabideae-species
#7
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/28631168/the-function-of-osbhlh068-is-partially-redundant-with-its-homolog-atbhlh112-in-the-regulation-of-the-salt-stress-response-but-has-opposite-functions-to-control-flowering-in-arabidopsis
#8
Hung-Chi Chen, Vicki Hsieh-Feng, Pei-Chun Liao, Wan-Hsing Cheng, Li-Yu Liu, Yun-Wei Yang, Ming-Hsin Lai, Men-Chi Chang
The homologous genes OsbHLH068 and AtbHLH112 have partially redundant functions in the regulation of the salt stress response but opposite functions to control flowering in Arabidopsis. The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown...
June 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28630305/multiple-layers-of-heterogeneity-and-subset-diversity-in-human-mait-cell-responses-to-distinct-microorganisms-and-to-innate-cytokines
#9
Joana Dias, Edwin Leeansyah, Johan K Sandberg
Mucosa-associated invariant T (MAIT) cells are a large innate-like T-cell subset in humans defined by invariant TCR Vα7.2 use and expression of CD161. MAIT cells recognize microbial riboflavin metabolites of bacterial or fungal origin presented by the monomorphic MR1 molecule. The extraordinary level of evolutionary conservation of MR1 and the limited known diversity of riboflavin metabolite antigens have suggested that MAIT cells are relatively homogeneous and uniform in responses against diverse microbes carrying the riboflavin biosynthesis pathway...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28629935/a-dicre-recombinase-based-system-for-inducible-expression-in-leishmania-major
#10
Renato E R S Santos, Gabriel L A Silva, Elaine V Santos, Samuel M Duncan, Jeremy C Mottram, Jeziel D Damasceno, Luiz R O Tosi
Here we present the establishment of an inducible system based on the dimerizable Cre recombinase (DiCre) for controlled gene expression in the protozoan parasite Leishmania. Rapamycin-induced DiCre activation promoted efficient flipping and expression of gene products in a time and dose-dependent manner. The DiCre flipping activity induced the expression of target genes from both integrated and episomal contexts broadening the applicability of the system. We validated the system by inducing the expression of both full length and truncated forms of the checkpoint protein Rad9, which revealed that the highly divergent C-terminal domain of Rad9 is necessary for proper subcellular localization...
June 16, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28627686/hypoxia-and-acidosis-driven-aberrations-of-secreted-micrornas-in-endometrial-cancer-in-vitro
#11
Julia Eismann, Marc Hirschfeld, Thalia Erbes, Gerta Rücker, Markus Jäger, Andrea Ritter, Daniela Weiss, Gerald Gitsch, Sebastian Mayer
Due to their post-transcriptional regulatory impact on gene expression, microRNAs (miRNA, miRs) influence decisively cellular processes of differentiation, proliferation and apoptosis. In oncogenic pathways various miRNAs exert either oncogenic or tumor suppressor activities in a stage-specific manner. Dysregulation of miRNA expression pattern has been associated with several human cancers including endometrial cancer (EC). In the present study, expression profile alterations of EC associated secreted miRNAs were determined under the microenvironmental stress situations hypoxia and acidosis occurring in tumor progression and metastasis...
June 13, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28627438/genome-wide-identification-phylogeny-and-expression-of-bone-morphogenetic-protein-genes-in-tetraploidized-common-carp-cyprinus-carpio
#12
Lin Chen, Chuanju Dong, Shengnan Kong, Jiangfan Zhang, Xuejun Li, Peng Xu
Bone morphogenetic proteins (Bmps) are a group of signaling molecules known to play important roles during formation and maintenance of various organs, not only bone, but also muscle, blood and so on. Common carp (Cyprinus carpio) is one of the most intensively studied fish due to its economic and environmental importance. Besides, common carp had encountered an additional round of whole genome duplication (WGD) compared with many closely related diploid teleost, which make it one of the most important models for genome evolutionary studies in teleost...
June 13, 2017: Gene
https://www.readbyqxmd.com/read/28626969/different-patterns-of-expression-of-cell-cycle-control-and-local-invasion-related-proteins-in-oral-squamous-cell-carcinoma-affecting-young-patients
#13
Marisol Miranda Galvis, Alan Roger Santos-Silva, Juscelino Freitas Jardim, Felipe Paiva Fonseca, Marcio A Lopes, Oslei P Almeida, Clóvis A Lópes Pinto, Estela Kaminagakura, Iris Sawazaki-Calone, Paul M Speight, Luiz Paulo Kowalski
Oral squamous cell carcinoma (OSCC) predominantly affects males in the fifth decade of life; nevertheless, an increased incidence in young patients has been reported worldwide and the clinical and behavioral characteristics of tumors in this group are controversial and the literature shows divergent results PURPOSE: To investigate the clinicopathological features and prognostic significance of the immunoexpression of cell cycle and local invasion proteins in OSCC affecting young patients (≤ 40 years old) METHODS: A tissue microarray was performed with 132 OSCC samples (61 cases of young patients vs...
June 19, 2017: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/28626946/do-changes-in-gene-expression-contribute-to-sexual-isolation-and-reinforcement-in-the-house-mouse
#14
Etienne Loire, Sergio Tusso, Pierre Caminade, Dany Severac, Pierre Boursot, Guila Ganem, Carole M Smadja
Expression divergence, rather than sequence divergence, has been shown to be important in speciation, particularly in the early stages of divergence of traits involved in reproductive isolation. In the two European subspecies of house mice, Mus musculus musculus and M. m. domesticus, earlier studies have demonstrated olfactory-based assortative mate preference in populations close to their hybrid zone. It has been suggested that this behaviour evolved following the recent secondary contact between the two taxa (~3,000 years ago) in response to selection against hybridisation...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28625764/genome-wide-identification-and-expression-profiling-of-eil-gene-family-in-woody-plant-representative-poplar-populus-trichocarpa
#15
Ertugrul Filiz, Recep Vatansever, Ibrahim Ilker Ozyigit, Mehmet Emin Uras, Ugur Sen, Naser A Anjum, Eduarda Pereira
This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Gray). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization...
June 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28623279/divergent-regulation-of-actin-dynamics-and-megakaryoblastic-leukemia-1-and-2-mkl1-2-by-camp-in-endothelial-and-smooth-muscle-cells
#16
Madeleine C Smith, Claire A Hudson, Tomomi E Kimura, Stephen J White, Graciela B Sala-Newby, Andrew C Newby, Mark Bond
Proliferation and migration of vascular smooth muscle cells (VSMCs) or endothelial cell (ECs) promote or inhibit, respectively, restenosis after angioplasty, vein graft intimal thickening and atherogenesis. Here we investigated the effects of cAMP-induced cytoskeletal remodelling on the serum response factor (SRF) co-factors Megakaryoblastic Leukemia-1 and -2 (MKL1 and MKL2) and their role in controlling VSMC and EC proliferation and migration. Elevation of cAMP using forskolin, dibutyryl-cAMP (db-cAMP), BAY60-6583 or Cicaprost induced rapid cytoskeleton remodelling and inhibited proliferation and migration in VSMCs but not EC...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28622766/translational-contributions-to-tissue-specificity-in-rhythmic-and-constitutive-gene-expression
#17
Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich, David Gatfield
BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney and contrasted our findings with liver data available from the same mice. RESULTS: Rhythmic translation of constantly abundant messenger RNAs (mRNAs) affects largely non-overlapping transcript sets with distinct phase clustering in the two organs...
June 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28621432/regulatory-heterochronies-and-loose-temporal-scaling-between-sea-star-and-sea-urchin-regulatory-circuits
#18
Tsvia Gildor, Veronica Hinman, Smadar Ben-Tabou-De-Leon
It has long been argued that heterochrony, a change in relative timing of a developmental process, is a major source of evolutionary innovation. Heterochronic changes of regulatory gene activation could be the underlying molecular mechanism driving heterochronic changes through evolution. Here, we compare the temporal expression profiles of key regulatory circuits between sea urchin and sea star, representative of two classes of Echinoderms that shared a common ancestor about 500 million years ago. The morphologies of the sea urchin and sea star embryos are largely comparable, yet, differences in certain mesodermal cell types and ectodermal patterning result in distinct larval body plans...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/28619593/on-the-halt-of-spontaneous-capillary-flows-in-diverging-open-channels
#19
J Berthier, K A Brakke, D Gosselin, F Navarro, N Belgacem, D Chaussy, E Berthier
Due to their compactness and independence of exterior energy sources, capillary microsystems are increasingly used in many different scientific domains, from biotechnology to medicine and biology, chemistry, energy and space. Obtaining a capillary flow depends on channel geometry and contact angle. A general condition for the establishment of a spontaneous capillary flow in a uniform cross section channel has already been derived from Gibbs free energy. In this work, we consider spontaneous capillary flows (SCF) in diverging open rectangular channels and suspended channels, and we show that they do not flow indefinitely but stop at some location in the channel...
June 12, 2017: Medical Engineering & Physics
https://www.readbyqxmd.com/read/28618638/localized-dark-solitons-and-vortices-in-defocusing-media-with-spatially-inhomogeneous-nonlinearity
#20
Jianhua Zeng, Boris A Malomed
Recent studies have demonstrated that defocusing cubic nonlinearity with local strength growing from the center to the periphery faster than r^{D}, in space of dimension D with radial coordinate r, supports a vast variety of robust bright solitons. In the framework of the same model, but with a weaker spatial-growth rate ∼r^{α} with α≤D, we test here the possibility to create stable localized continuous waves (LCWs) in one-dimensional (1D) and 2D geometries, localized dark solitons (LDSs) in one dimension, and localized dark vortices (LDVs) in two dimensions, which are all realized as loosely confined states with a divergent norm...
May 2017: Physical Review. E
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