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protein evolution

Mark van der Giezen
Mitochondria in the protist Brevimastigomonas motovehiculus are in the process of dismantling their mitochondrial electron transport chain complexes as they adapt to anaerobic environments. Novel protein interactions suggest a highly complicated process rather than the simple removal of unnecessary genes.
October 24, 2016: Current Biology: CB
Jie Li, He Huang, Yingguang Li, Li Li, Wenhui Hou, Zeshan You
Long non-coding RNA growth arrest-specific 5 (GAS5) was reported to be aberrantly expressed in various types of cancers. However, the role of GAS5 in the evolution and progression of ovarian cancer remains elusive. In the present study, we aimed to investigate the cellular function and clinical significance of GAS5 in ovarian cancer. GAS5 expression levels in 63 ovarian cancer tissues were detected by quantitative real-time PCR. Cell Counting Kit-8 (CCK-8) assay was performed to analyze the effect of GAS5 on cell proliferation...
October 24, 2016: Oncology Reports
Katrien H P Van Petegem, David Renault, Robby Stoks, Dries Bonte
Despite an increasing number of studies documenting life-history evolution during range expansions or shifts, we lack a mechanistic understanding of the underlying physiological processes. In this explorative study, we used a metabolomics approach to study physiological changes associated with the recent range expansion of the two-spotted spider mite (Tetranychus urticae). Mite populations were sampled along a latitudinal gradient from range core to edge and reared under benign common garden conditions for two generations...
September 2016: Ecology and Evolution
José A L Fernandes, Tâmara H R Prandini, Maria da Conceiçao A Castro, Thales D Arantes, Juliana Giacobino, Eduardo Bagagli, Raquel C Theodoro
Inteins are invasive intervening sequences that perform an autocatalytic splicing from their host proteins. Among eukaryotes, these elements are present in many fungal species, including those considered opportunistic or primary pathogens, such as Candida spp. Here we reviewed and updated the list of Candida species containing inteins in the genes VMA, THRRS and GLT1 and pointed out the importance of these elements as molecular markers for molecular epidemiological researches and species-specific diagnosis, since the presence, as well as the size of these inteins, is polymorphic among the different species...
2016: Frontiers in Microbiology
John E Pool, Dylan T Braun, Justin B Lack
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude...
October 24, 2016: Molecular Biology and Evolution
Matthew J Endsin, Ola Michalec, Lori A Manzon, David A Lovejoy, Richard G Manzon
The corticotropin releasing hormone (CRH) system, which includes the CRH family of peptides, their receptors (CRHRs) and a binding protein (CRHBP), has been strongly conserved throughout vertebrate evolution. The identification of invertebrate homologues suggests this system evolved over 500 million years ago. However, the early vertebrate evolution of the CRH system is not understood. Current theory indicates that Agnathans (hagfishes and lampreys) are monophyletic with a conservative evolution over the past 500 million years and occupy a position at the root of vertebrate phylogeny...
October 21, 2016: General and Comparative Endocrinology
Alexander Rebl, Henrike Rebl, Judith M Köbis, Tom Goldammer, Hans-Martin Seyfert
The mammalian interleukin 1 receptor-like 1 receptor (IL1RL1), commonly known as ST2, is thought to downregulate TLR signalling by sequestering the signalling adapter MYD88 (myeloid differentiation primary response protein 88). ST2 sequences are known in several fish species, but none of them have functionally been examined. We characterised ST2 from rainbow trout (Oncorhynchus mykiss) and the structure of its encoding gene. The primary sequence of ST2 is only weakly conserved from fish to human. However, the amino acid sequences forming the interfaces for ST2 and MYD88 interaction are well conserved throughout evolution...
October 21, 2016: Developmental and Comparative Immunology
Shintaro Maeno, Yasuhiro Tanizawa, Yu Kanesaki, Eri Kubota, Himanshu Kumar, Leon Dicks, Seppo Salminen, Junichi Nakagawa, Masanori Arita, Akihito Endo
Lactobacillus kunkeei is classified as a sole obligate fructophilic lactic acid bacterium that is found in fructose-rich niches, including the guts of honeybees. The species is differentiated from other lactobacilli based on its poor growth with glucose, enhanced growth in the presence of oxygen and other electron acceptors, and production of high concentrations of acetate from the metabolism of glucose. These characteristics are similar to phylogenetically distant Fructobacillus spp. In the present study, the genomic structure of L...
October 13, 2016: Systematic and Applied Microbiology
Hiroshi Hisano, Mai Tsujimura, Hideya Yoshida, Toru Terachi, Kazuhiro Sato
BACKGROUND: Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. vulgare ssp. vulgare) have cross compatibility and closely related genomes, although a significant number of nucleotide polymorphisms have been reported between their genomes...
October 24, 2016: BMC Genomics
Shun Wang, Zhe Dong, Shen Li, Haotian Yin, Zhifu Zhao, Dongmei Gao, Guimin Ren, Xuexiang Bao
Tryptophan hydroxylase (TPH) was stained in the central nervous system of the Neanthes japonica (Polychaeta, Annelida), using sheep anti-tryptophan hydroxylase antibody by the Streptavidin-Peroxidase immunohistochemical method and Colophony-Paraffin embedded section technique. The immunohistochemistry results revealed that the TPH is distributed in the brain and ventral nerve cord, which is consistent with that of serotonin (5-hydroxytryptamine, 5-HT) that labeled by anti-serotonin antibody. Using the rapid amplification of cDNA ends (RACE) technique, TPH cDNA cloned from Neanthes japonica's central nervous system was 1778bp, which encodes predicted protein of 463 amino acid residues...
October 24, 2016: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
Søren B van Witteloostuijn, Søren L Pedersen, Knud J Jensen
Peptides and proteins constitute a vast pool of excellent drug candidates. Evolution has equipped these molecules with superior drug-like properties such as high specificity and potency. However, native peptides and proteins suffer from an inadequate pharmacokinetic profile, and their outstanding pharmacological potential can only be realized if this issue is addressed during drug development. To overcome this challenge, a variety of half-life extension techniques relying on covalent chemical modification have been developed...
October 24, 2016: ChemMedChem
Joanna Melonek, James D Stone, Ian Small
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes...
October 24, 2016: Scientific Reports
Lize Cuypers, Guangdi Li, Christoph Neumann-Haefelin, Supinya Piampongsant, Pieter Libin, Kristel Van Laethem, Anne-Mieke Vandamme, Kristof Theys
Despite significant progress in hepatitis C (HCV) treatment, global viral eradication remains a challenge. An in-depth map of its genome diversity within the context of structural and immunological constraints could contribute to the design of pan-genotypic antivirals and preventive vaccines. For such analyses, extensive information is only available for the highly prevalent HCV genotypes (GT) 1a and 1b. Using 647 GT1a and 408 GT1b full-genome sequences obtained from the Los Alamos database, we found that respectively 3 per cent and 82 per cent of all codon positions are under positive and negative selective pressure, suggesting variation mainly accumulates due to random genetic drift...
July 2016: Virus Evolution
Marta Canuti, Kimberly E O'Leary, Bruce D Hunter, Grant Spearman, Davor Ojkic, Hugh G Whitney, Andrew S Lang
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography...
January 2016: Virus Evolution
Christina Kratsch, Thorsten R Klingen, Linda Mümken, Lars Steinbrück, Alice C McHardy
Human influenza viruses are rapidly evolving RNA viruses that cause short-term respiratory infections with substantial morbidity and mortality in annual epidemics. Uncovering the general principles of viral coevolution with human hosts is important for pathogen surveillance and vaccine design. Protein regions are an appropriate model for the interactions between two macromolecules, but the currently used epitope definition for the major antigen of influenza viruses, namely hemagglutinin, is very broad. Here, we combined genetic, evolutionary, antigenic, and structural information to determine the most relevant regions of the hemagglutinin of human influenza A/H3N2 viruses for interaction with human immunoglobulins...
January 2016: Virus Evolution
Shin-Ichi Yokobori, Yoshiki Nakajima, Satoshi Akanuma, Akihiko Yamagishi
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis...
2016: Archaea: An International Microbiological Journal
Stefan M Ivanov, Roland G Huber, Jim Warwicker, Peter J Bond
Critical regulatory pathways are replete with instances of intra- and interfamily protein-protein interactions due to the pervasiveness of gene duplication throughout evolution. Discerning the specificity determinants within these systems has proven a challenging task. Here, we present an energetic analysis of the specificity determinants within the Bcl-2 family of proteins (key regulators of the intrinsic apoptotic pathway) via a total of ∼20 μs of simulation of 60 distinct protein-protein complexes. We demonstrate where affinity and specificity of protein-protein interactions arise across the family, and corroborate our conclusions with extensive experimental evidence...
October 17, 2016: Structure
Jing Wei, Linyan Liu, Zhenhua Fan, Yunhan Hong, Yang Zhao, Linyan Zhou, Deshou Wang
The origin and evolution of molecular mechanisms underlying the self-renewal and differentiation of spermatogonial stem cells (SSC) are fundamental questions in stem cell biology as well as reproduction medicine. In mammals, glial cell line-derived neurotrophic factor (GDNF) is crucial for SSC self-renewal and maintenance. However, in non-mammals, the role of Gdnf in SSC still remains unknown. Here we report that the two GDNF homologs from medaka fish (Oryzias latipes), namely OlGdnfa and OlGdnfb, can promote the proliferation activity and retain the spermatogonial property of SG3, a spermatogonial cell line derived from adult medaka showing the intrinsic property of SSC by self-renewal and differentiation potential during 2 years of culture...
October 22, 2016: Stem Cells and Development
Bo Lönnerdal, Peter Erdmann, Sagar K Thakkar, Julien Sauser, Frédéric Destaillats
The protein content of breast milk provides a foundation for estimating protein requirements of infants. Because it serves as a guideline for regulatory agencies issuing regulations for infant formula composition, it is critical that information on the protein content of breast milk is reliable. We have therefore carried out a meta-analysis of the protein and amino acid contents of breast milk and how they evolve during lactation. As several bioactive proteins are not completely digested in the infant and therefore represent "non-utilizable" protein, we evaluated the quantity, mechanism of action and digestive fate of several major breast milk proteins...
June 21, 2016: Journal of Nutritional Biochemistry
Jianhe Peng, Jing Cao, Fui Mee Ng, Jeffrey Hill
: Pseudomonas aeruginosa infection is difficult to treat because of its drug resistance, but how it develops drug resistance remains largely unknown. In this study we investigated Ciprofloxacin resistance development in P. aeruginosa. Different Ciprofloxacin concentrations selected different low level resistant mutants, and high level resistant mutants emerged from low level resistant mutants if stressed further by Ciprofloxacin. A deep quantitative proteomic study of the Ciprofloxacin resistant mutants uncovered the cellular pathways that supported such resistances...
October 19, 2016: Journal of Proteomics
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