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conservation biology

James Starrett, Shahan Derkarabetian, Marshal Hedin, Robert W Bryson, John E McCormack, Brant C Faircloth
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress...
October 21, 2016: Molecular Ecology Resources
Sajjad Karim, Hend Fakhri NourEldin, Heba Abusamra, Nada Salem, Elham Alhathli, Joel Dudley, Max Sanderford, Laura B Scheinfeldt, Sudhir Kumar
BACKGROUND: Genome-wide association studies (GWAS) have become a mainstay of biological research concerned with discovering genetic variation linked to phenotypic traits and diseases. Both discrete and continuous traits can be analyzed in GWAS to discover associations between single nucleotide polymorphisms (SNPs) and traits of interest. Associations are typically determined by estimating the significance of the statistical relationship between genetic loci and the given trait. However, the prioritization of bona fide, reproducible genetic associations from GWAS results remains a central challenge in identifying genomic loci underlying common complex diseases...
October 17, 2016: BMC Genomics
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. RESULTS: In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks...
October 6, 2016: BMC Bioinformatics
David J McKenzie, Michael Axelsson, Denis Chabot, Guy Claireaux, Steven J Cooke, Richard A Corner, Gudrun De Boeck, Paolo Domenici, Pedro M Guerreiro, Bojan Hamer, Christian Jørgensen, Shaun S Killen, Sjannie Lefevre, Stefano Marras, Basile Michaelidis, Göran E Nilsson, Myron A Peck, Angel Perez-Ruzafa, Adriaan D Rijnsdorp, Holly A Shiels, John F Steffensen, Jon C Svendsen, Morten B S Svendsen, Lorna R Teal, Jaap van der Meer, Tobias Wang, Jonathan M Wilson, Rod W Wilson, Julian D Metcalfe
The state of the art of research on the environmental physiology of marine fishes is reviewed from the perspective of how it can contribute to conservation of biodiversity and fishery resources. A major constraint to application of physiological knowledge for conservation of marine fishes is the limited knowledge base; international collaboration is needed to study the environmental physiology of a wider range of species. Multifactorial field and laboratory studies on biomarkers hold promise to relate ecophysiology directly to habitat quality and population status...
2016: Conservation Physiology
Natalia Lifshitz, Colleen Cassady St Clair
Growth in human populations causes habitat degradation for other species, which is usually gauged by physical changes to landscapes. Corresponding habitat degradation to air and water is also common, but its effects on individuals can be difficult to detect until they result in the decline or disappearance of populations. More proactive measures of pollution usually combine abiotic samples of soil, water or air with invasive sampling of expendable species, but this approach sometimes creates ethical dilemmas and has limited application for threatened species...
2016: Conservation Physiology
Casey T Clark, Alyson H Fleming, John Calambokidis, Nicholas M Kellar, Camryn D Allen, Krista N Catelani, Michelle Robbins, Nicole E Beaulieu, Debbie Steel, James T Harvey
Understanding reproductive rates of wild animal populations is crucially important for management and conservation. Assessing pregnancy status of free-ranging cetaceans has historically been difficult; however, recent advances in analytical techniques have allowed the diagnosis of pregnancy from small samples of blubber tissue. The primary objectives of this study were as follows: (i) to test the efficacy of blubber progesterone assays as a tool for diagnosing pregnancy in humpback whales (Megaptera novaeangliae); (ii) to estimate the pregnancy rate of humpback whales in Monterey Bay, California; and (iii) to investigate the relationship between stable isotopes and reproductive status of these whales...
2016: Conservation Physiology
Ying Qiao, Yong Mao, Jun Wang, Ruanni Chen, Yong-Quan Su, Jia Chen, Wei-Qiang Zheng
The white-spot disease caused by marine ciliate Cryptocryon irritans hindered the sustainable development of large yellow croaker Larimichthys crocea industry. Better understandings about the parasite-host interactions in the molecular level will facilitate the prevention of mass mortality of the L. crocea caused by white-spot disease. MicroRNAs (miRNAs) are a class of small RNA molecules about 20-22 nucleotides which post-transcriptionally regulated many protein-coding genes and involved in many biological processes, especially in host-pathogen responses...
October 17, 2016: Fish & Shellfish Immunology
Insa Joost, Johannes Steinfurt, Philipp T Meyer, Winfried V Kern, Siegbert Rieg
BACKGROUND: Ustekinumab (Stelara®), a human monoclonal antibody targeting the p40-subunit of interleukin (IL)-12 and IL-23, is indicated for moderate to severe plaque psoriasis and psoriatic arthritis. In large multicenter, prospective trials assessing efficacy and safety of ustekinumab increased rates of severe infections have not been observed so far. CASE PRESENTATION: Here, we report the case of a 64-year old woman presenting with chills, pain and swelling of her right foot with dark maculae at the sole, and elevated inflammatory markers...
October 20, 2016: BMC Infectious Diseases
Jana Jakubikova, Danka Cholujova, Teru Hideshima, Paulina Gronesova, Andrea Soltysova, Takeshi Harada, Jungnam Joo, Sun-Young Kong, Raphael E Szalat, Paul G Richardson, Nikhil C Munshi, David M Dorfman, Kenneth C Anderson
Specific niches within the tumor bone marrow (BM) microenvironment afford a sanctuary for multiple myeloma (MM) clones due to stromal cell-tumor cell interactions, which confer survival advantage and drug resistance. Defining the sequelae of tumor cell interactions within the MM niches on an individualized basis may provide the rationale for personalized therapies. To mimic the MM niche, we here describe a new 3D co-culture ex-vivo model in which primary MM patient BM cells are co-cultured with mesenchymal stem cells (MSC) in a hydrogel 3D system...
October 13, 2016: Oncotarget
G P Adams, M H Ratto, M E Silva, R A Carrasco
The ovulation-inducing effect of seminal plasma was first reported in Bactrian camels over 30 years ago, and the entity responsible was dubbed 'ovulation-inducing factor' (OIF). More recent studies, primarily in llamas and alpacas, characterized the biological and chemical properties of OIF and ultimately identified it as βNGF. This recent discovery has allowed a convergence of knowledge previously separated by discipline and by mechanism; that is, neurobiology and reproductive biology, and autocrine/paracrine vs endocrine...
October 2016: Reproduction in Domestic Animals, Zuchthygiene
Sieglinde Bayer, Matthias Wirth
The protein sequences of class I HDACs in mice and humans are 96-99 % identical. These highly conserved proteins have crucial roles in biological processes, such as proliferation and development, which is reflected in the lethality that occurs in conventional whole body knockout mice. Therefore, conditional knockouts are inevitable to investigate the functions of class I HDACs in mice. Here, we describe the generation of conditional class I Hdac knockout mice, using Hdac1 as an example. We explain a relatively quick procedure to generate the necessary target vectors by recombination-mediated genetic engineering and gateway techniques...
2017: Methods in Molecular Biology
Joseph F O'Grady, Laura S Hoelters, Martin T Swain, David C Wilcockson
BACKGROUND: Talitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species...
2016: PeerJ
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
Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Long intergenic non-coding RNAs (lincRNAs) are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae...
October 2016: PLoS Neglected Tropical Diseases
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
S Sun, Y Wang, H Chen, L Fang, Y Cui, X Han, D Wu, H Li, M Ye, X Zhao, J Liu
BACKGROUND: Sip1/Tuftelin Interacting Protein (STIP) is highly conserved from Caenorhabditis elegans to Homo sapiens and has essential biological functions. However, its function in leukemia remains unknown. METHODS: Clinic Samples and cell model were used in this article to investigate the expression of STIP in lymphoblastic leukemia. The functional research of STIP was performed in ARH-77 by siRNA transfection, Immunofluorescence, cell count, cell cycle analysis, quantitative real-time RT-PCR, Sub-cellular Fractionation assays, Immunoprecipitation and Western blotting...
October 18, 2016: Current Molecular Medicine
B Li, J Liu, Y Y Zhang, P Q Wang, Y N Yu, R X Kang, H L Wu, X X Zhang, Z Wang, Y Y Wang
Module-based methods have made much progress in deconstructing biological networks. However, it is a great challenge to quantitatively compare the topological structural variations of modules (allosteric modules [AMs]) under different situations. A total of 23, 42, and 15 coexpression modules were identified in baicalin (BA), jasminoidin (JA), and ursodeoxycholic acid (UA) in a global anti-ischemic mice network, respectively. Then, we integrated the methods of module-based consensus ratio (MCR) and modified Zsummary module statistic to validate 12 BA, 22 JA, and 8 UA on-modules based on comparing with vehicle...
October 19, 2016: CPT: Pharmacometrics & Systems Pharmacology
Nynke Oosterhof, Inge R Holtman, Laura E Kuil, Herma C van der Linde, Erik W G M Boddeke, Bart J L Eggen, Tjakko J van Ham
Microglia are brain resident macrophages important for brain development, connectivity, homeostasis and disease. However, it is still largely unclear how microglia functions and their identity are regulated at the molecular level. Although recent transcriptomic studies have identified genes specifically expressed in microglia, the function of most of these genes in microglia is still unknown. Here, we performed RNA sequencing on microglia acutely isolated from healthy and neurodegenerative zebrafish brains...
October 19, 2016: Glia
Nabil K El Ayoubi, Samia J Khoury
Multiple sclerosis (MS) is an autoimmune demyelinating disorder of the central nervous system. Only a few biomarkers are available in MS clinical practice, such as cerebrospinal fluid oligoclonal bands and immunoglobulin index, serum anti-aquaporin 4 antibodies, and serum anti-John Cunningham virus antibodies. Thus, there is a significant unmet need for biomarkers to assess prognosis, response to therapy, or potential treatment complications. Here we describe emerging biomarkers that are in development, focusing on those from peripheral blood...
October 18, 2016: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
Chao Tan, Jun Wang, Yifang Hu, Peng Wang, Lili Zou
Staphylococcus aureus and Staphylococcus epidermidis are two of the most significant opportunistic human pathogens, causing medical implant and nosocomial infections worldwide. These bacteria contain surface proteins that play crucial roles in multiple biological processes. It has become apparent that they have evolved a number of unique mechanisms by which they can immobilise proteins on their surface. Notably, a conserved cell membrane-anchored enzyme, sortase A (SrtA), can catalyse the covalent attachment of precursor bacterial cell wall-attached proteins to peptidoglycan...
October 18, 2016: Antonie Van Leeuwenhoek
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