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conservation biology

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https://www.readbyqxmd.com/read/29036608/insights-into-rna-polymerase-catalysis-and-adaptive-evolution-gained-from-mutational-analysis-of-a-locus-conferring-rifampicin-resistance
#1
Olga Yurieva, Vadim Nikiforov, Vadim Nikiforov, Michael O'Donnell, Arkady Mustaev
S531 of Escherichia coli RNA polymerase (RNAP) β subunit is a part of RNA binding domain in transcription complex. While highly conserved, S531 is not involved in interactions within the transcription complex as suggested by X-ray analysis. To understand the basis for S531 conservation we performed systematic mutagenesis of this residue. We find that the most of the mutations significantly decreased initiation-to-elongation transition by RNAP. Surprisingly, some changes enhanced the production of full-size transcripts by suppressing abortive loss of short RNAs...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29035258/neodymium-in-the-oceans-a-global-database-a-regional-comparison-and-implications-for-palaeoceanographic-research
#2
Tina van de Flierdt, Alexander M Griffiths, Myriam Lambelet, Susan H Little, Torben Stichel, David J Wilson
The neodymium (Nd) isotopic composition of seawater has been used extensively to reconstruct ocean circulation on a variety of time scales. However, dissolved neodymium concentrations and isotopes do not always behave conservatively, and quantitative deconvolution of this non-conservative component can be used to detect trace metal inputs and isotopic exchange at ocean-sediment interfaces. In order to facilitate such comparisons for historical datasets, we here provide an extended global database for Nd isotopes and concentrations in the context of hydrography and nutrients...
November 28, 2016: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29034845/predicting-mirna-association-with-corresponding-target-genes-and-single-nucleotide-polymorphisms-in-altered-renal-pathophysiology
#3
Pradeep Jaswani, Swayam Prakash, Narayan Prasad, Suraksha Agrawal, Raj Kumar Sharma
BACKGROUND: Translational research on miRNAs develops reliable biomarkers for diagnosis and prognosis of renal diseases. Bioinformatic analyses and systems biology could drive the research for knowing new informative miRNA targets. OBJECTIVES: This study proposes an approach to identify miRNA specific significant target genes, and single nucleotide polymorphisms (SNPs) associated with renal pathophysiology. METHODS: miRNAs were selected after removing duplicity, on the basis of techniques used, and disease spectrum width score...
October 16, 2017: MicroRNA
https://www.readbyqxmd.com/read/29032806/multidetector-computed-tomography-evaluation-of-candidates-for-transcatheter-aortic-valve-implantation
#4
M E Guillén Subirán, L H Mendoza, E Ángulo Hervías, D Yagüe Romeo, M E Núñez Motilva
In transcatheter aortic valve implantation (TAVI), a biologic valve mounted in a stent is implanted without removing the native valve. This procedure was first done in humans by Alain Cribier in 2002 and was included in clinical guidelines after the multicenter PARTNER (Placement of AoRtic TraNscathetER) randomized clinical trial, which showed that TAVI obtained better outcomes than conservative medical treatment and is an alternative to surgery in patients with high surgical risk. Candidates for TAVI must be assessed to determine whether the procedure is feasible, because TAVI is not ideal for all patients who are considered inoperable...
October 9, 2017: Radiología
https://www.readbyqxmd.com/read/29031235/homeobox-genes-and-tooth-development-understanding-the-biological-pathways-and-applications-in-regenerative-dental-science
#5
REVIEW
Anand Ramanathan, Thekkeparambil Chandrabose Srijaya, Prema Sukumaran, Rosnah Binti Zain, Noor Hayaty Abu Kasim
OBJECTIVES: Homeobox genes are a group of conserved class of transcription factors that function as key regulators during the embryonic developmental processes. They act as master regulator for developmental genes, which involves coordinated actions of various auto and cross-regulatory mechanisms. In this review, we summarize the expression pattern of homeobox genes in relation to the tooth development and various signaling pathways or molecules contributing to the specific actions of these genes in the regulation of odontogenesis...
October 4, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/29031011/a-framework-for-the-identification-of-hotspots-of-climate-change-risk-for-mammals
#6
Michela Pacifici, Piero Visconti, Carlo Rondinini
As rates of global warming increase rapidly, identifying species at risk of decline due to climate impacts and the factors affecting this risk have become key challenges in ecology and conservation biology. Here we present a framework for assessing three components of climate-related risk for species: vulnerability, exposure and hazard. We used the relationship between the observed response of species to climate change and a set of intrinsic traits (e.g., weaning age) and extrinsic factors (e.g., precipitation seasonality within a species geographic range) to predict, respectively, the vulnerability and exposure of all data-sufficient terrestrial non-volant mammals (3953 species)...
October 14, 2017: Global Change Biology
https://www.readbyqxmd.com/read/29030957/mollusc-shells-as-metagenomic-archives-the-true-treasure-is-the-chest-itself
#7
Marie-Agnès Coutellec
Mollusc shells, beyond the treasure of information inherently conveyed through their morphology and chemical composition also have the capacity to preserve DNA sequences over the long term in their inner structure. This has been clearly demonstrated for the first time in the study published in this issue of Molecular Ecology Resources by Der Sarkissian et al. (). With a methodology specifically dedicated to ancient DNA and solid matrices, the authors were able to successfully extract and amplify DNA from marine shells spanning the last 7,000 years...
September 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29030723/eric-davidson-and-deep-time
#8
Douglas H Erwin
Eric Davidson had a deep and abiding interest in the role developmental mechanisms played in generating evolutionary patterns documented in deep time, from the origin of the euechinoids to the processes responsible for the morphological architectures of major animal clades. Although not an evolutionary biologist, Davidson's interests long preceded the current excitement over comparative evolutionary developmental biology. Here I discuss three aspects at the intersection between his research and evolutionary patterns in deep time: First, understanding the mechanisms of body plan formation, particularly those associated with the early diversification of major metazoan clades...
October 13, 2017: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/29030567/plasmodium-falciparum-specific-helicase-3-is-nucleocytoplasmic-protein-and-unwinds-dna-duplex-in-3-to-5-direction
#9
Manish Chauhan, Mohammed Tarique, Renu Tuteja
Plasmodium falciparum is responsible for most dangerous and prevalent form of malaria. The emergence of multi drug resistant parasite hindered the prevention of malaria burden worldwide. Helicases are omnipresent enzymes, which play important role in nucleic acid metabolism and can be used as potential targets for development of novel therapeutics. The genome wide analysis of P. falciparum 3D7 strain revealed some novel parasite specific helicases, which are not present in human host. Here we report the detailed biochemical characterization of P...
October 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29030426/molecular-insights-into-the-m-aaa-protease-mediated-dislocation-of-transmembrane-helices-in-the-mitochondrial-inner-membrane
#10
Seoeun Lee, Hunsang Lee, Suji Yoo, Hyun Kim
In the mitochondrial inner membrane, many protein complexes involved in respiration, ATP synthesis, and protein import reside, thus proper regulation of these proteins is essential for cell viability. The mAAA protease, a conserved heterohexameric AAA (ATPases associated with diverse cellular activities) protease composed of the Yta10 and Yta12 proteins, regulates mitochondrial proteostasis by mediating protein maturation and degradation. It also recognizes and mediates dislocation of membrane embedded substrates, including foreign transmembrane (TM) segments, yet the molecular mechanism involved in these processes remains elusive...
October 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29030425/quantitative-time-course-metabolomics-in-human-red-blood-cells-reveal-the-temperature-dependence-of-human-metabolic-networks
#11
James T Yurkovich, Daniel C Zielinski, Laurence Yang, Giuseppe Paglia, Ottar Rolfsson, Ólafur E Sigurjónsson, Jared T Broddrick, Aarash Bordbar, Kristine Wichuk, Sigurður Brynjólfsson, Sirus Palsson, Sveinn Gudmundsson, Bernhard O Palsson
The temperature dependence of biological processes has been studied at the levels of individual biochemical reactions and organism physiology (e.g., basal metabolic rates) but has not been examined at the metabolic network level. Here, we used a systems biology approach to characterize the temperature dependency of the human red blood cell (RBC) metabolic network between 4C and 37C through absolutely quantified exo- and endo-metabolomics data. We used an Arrhenius-type model (Q10) to describe how the rate of a biochemical process changes with every 10C change in temperature...
October 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29030023/on-universal-coding-events-in-protein-biogenesis
#12
REVIEW
Vladimir Kubyshkin, Carlos G Acevedo-Rocha, Nediljko Budisa
The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by cellular matching with the acceptor units of their cognitive tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code")...
October 10, 2017: Bio Systems
https://www.readbyqxmd.com/read/29029611/identification-of-15-candidate-structured-noncoding-rna-motifs-in-fungi-by-comparative-genomics
#13
Sanshu Li, Ronald R Breaker
BACKGROUND: With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies...
October 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29029602/erp-arrangement-a-strategy-for-assembled-genomic-contig-rearrangement-based-on-replication-profiling-in-bacteria
#14
Nobuaki Kono, Masaru Tomita, Kazuharu Arakawa
BACKGROUND: The reduced cost of sequencing has made de novo sequencing and the assembly of draft microbial genomes feasible in any ordinary biology lab. However, the process of finishing and completing the genome remains labor-intensive and computationally challenging in some cases, such as in the study of complete genome sequences, genomic rearrangements, long-range syntenic relationships, and structural variations. METHODS: Here, we show a contig reordering strategy based on experimental replication profiling (eRP) to recapitulate the bacterial genome structure within draft genomes...
October 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29026099/subcortical-facilitation-of-behavioral-responses-to-threat
#15
Mark D Vida, Marlene Behrmann
Behavioral responses to threat are critical to survival. Several cortical and subcortical brain regions respond selectively to threat. However, the relation of these neural responses and their underlying representations to behavior is unclear. We examined the contribution of lower-order subcortical representations to behavioral responses to threat in adult humans. In Experiments 1 and 2, participants viewed pairs of images presented to the same eye or to different eyes. We observed a monocular advantage, which indicates subcortical facilitation, for ancestral threats (snakes, spiders), but not for modern threats, positive images, or neutral images...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025975/recognition-of-hyperacetylated-n-terminus-of-h2az-by-tbbdf2-from-trypanosoma-brucei
#16
Xiao Yang, Xuelei Wu, Jiahai Zhang, Xuecheng Zhang, Chao Xu, Shanhui Liao, Xiaoming Tu
Histone modification plays an important role in various biological processes, including gene expression regulation. Bromodomain, as one of histone readers, recognizes specifically the ε-N-lysine acetylation (KAc) of histone. Although the bromodomains and histone acetylation sites of Trypanosoma brucei ( T. brucei ), a lethal parasite responsible for sleeping sickness in human and nagana in cattle, have been identified, how acetylated histones are recognized by bromodomains is still unknown. Here, the bromodomain factor 2 (TbBDF2) from T...
October 12, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29025973/dynamic-multi-site-phosphorylation-by-fyn-and-abl-drives-the-interaction-between-crkl-and-the-novel-scaffolding-receptors-dcbld1-and-dcbld2
#17
Anna M Schmoker, Jaye L Weinert, Kyle J Kellett, Hannah E Johnson, Ryan M Joy, Marion E Weir, Alicia M Ebert, Bryan A Ballif
Discoidin, CUB, and LCCL Domain-containing (DCBLD) 2 is a neuropilin-like transmembrane scaffolding receptor with known and anticipated roles in vascular remodeling and neuronal positioning. DCBLD2 is also upregulated in several cancers and can drive glioblastomas downstream of activated Epidermal Growth Factor Receptor. While a few studies have shown either a positive or negative role for DCBLD2 in regulating growth factor receptor signaling, little is known about the conserved signaling features of DCBLD family members that drive their molecular activities...
October 12, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29024770/biochemical-biological-and-molecular-characterization-of-an-l-amino-acid-oxidase-laao-purified-from-bothrops-pictus-peruvian-snake-venom
#18
Fanny Lazo, Dan E Vivas-Ruiz, Gustavo A Sandoval, Edith F Rodríguez, Edgar E G Kozlova, F Costal-Oliveira, Carlos Chávez-Olórtegui, Ruperto Severino, Armando Yarlequé, Eladio F Sanchez
An L-amino acid oxidase from Peruvian Bothrops pictus (Bpic-LAAO) snake venom was purified using a combination of size-exclusion and ion-exchange chromatography. Bpic-LAAO is an homodimeric glycosylated flavoprotein with molecular mass of ∼65 kDa under reducing conditions and ∼132 kDa in its native form as analyzed by SDS-PAGE and gel filtration chromatography, respectively. N-terminal amino acid sequencing showed highly conserved residues in a glutamine-rich motif related to binding substrate. The enzyme exhibited optimal activity towards L-Leu at pH 8...
October 9, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29024510/discovery-of-a-potentially-new-subfamily-of-elfv-dehydrogenases-effective-for-l-arginine-deamination-by-enzyme-mining
#19
Wenjun Wu, Ye Zhang, Jinhai Huang, Yao Wu, Dehua Liu, Zhen Chen
Discovery of enzymes with new functions is very important for de novo pathway design in synthetic biology. Amino acid dehydrogenases catalyze the oxidative deamination of an amino acid to its keto acid, which have been widely used for the production of various valuable chemicals. To discover amino acid dehydrogenases with new functions, we reevaluated the sequence variability and substrate diversity of ELFV dehydrogenases superfamily in this study. With insights gained from structural and sequential studies, we developed an in silico strategy and discovered a new category of proteins which are originally annotated as glutamate dehydrogenase but show altered conservation pattern of specificity determined motifs and completely different substrate spectrum...
October 12, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29024140/do-genetic-drift-and-accumulation-of-deleterious-mutations-preclude-adaptation-empirical-investigation-using-radseq-in-a-northern-lacustrine-fish
#20
Charles Perrier, Anne-Laure Ferchaud, Pascal Sirois, Isabel Thibault, Louis Bernatchez
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation...
October 12, 2017: Molecular Ecology
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