Life Sciences Commons^™

Molecular Cloning And Sequence Characterization Of Two Genes, Dqa1 And Dqa2,From The Chinese Yakow (Bos Grunniens X Bos Taurus), Dongmei Xi, Sameeullah Memon, Guozhi Li, Xiangying Liu, Chao Su, Jing Leng, Liping Wang, Sehroon Khan, Weidong Deng

Turkish Journal of Veterinary & Animal Sciences

The major histocompatibility complex (MHC) plays a crucial role in the immune response to infectious diseases. The aim of the present study was to investigate the structural and functional characteristics and possible duplication of the MHC-DQA genes in the Chinese yakow, which is well adapted to the Qinghai?Tibetan Plateau. Two full-length cDNA sequences and partial 5'- and 3'-untranslated regions (UTRs) were retrieved and denoted as Bogr×BoLA-DQA*0101 (DQA1) and BogrxBoLA-DQA*2001 (DQA2), respectively. The percentage of nucleotide and amino acid sequences homology between BogrxBoLA-DQA1 and BogrxBoLA-DQA2 showed that these two sequences have more identity to alleles of the corresponding DQA1 and DQA2 …

Salmonella Enteritidis Predominance Determined By Serotyping Andreal-Time Pcr In Poultry-Derived Food And Avian Isolates, Zafer Ata, Seran Temelli̇, Ayşe Gül Eyi̇gör, Kami̇l Tayfun Carli

Turkish Journal of Veterinary & Animal Sciences

This study aimed to determine Salmonella enterica subspecies enterica serovar Enteritidis (SE) presence by conventional serotyping and SE-specific real-time PCR (SE-rPCR) in poultry-derived food and avian isolates in our laboratory Salmonella spp. collection. Conventional serotyping indicated that 32 (8 chicken meat, 10 egg, 14 avian) out of 56 (57%) isolates were SE, whereas 8 (3 chicken meat, 2 turkey meat, 3 avian) (14%) isolates were serogroup B, 6 (1 chicken meat, 1 egg, 4 avian) (11%) were serogroup C1, 4 (3 chicken meat, 1 turkey meat) (7%) were serogroup C2-C3, 4 (3 chicken meat, 1 turkey meat) (7%) were serogroup …

Serotypes Of Salmonella Isolated From Feces Of Cattle, Buffalo,And Camel And Sensitivities To Antibiotics In Turkey, Hasan Hüseyi̇n Hadi̇mli̇, Yasemi̇n Pinarkara, Asli Sakmanoğlu, Zafer Sayin, Osman Ergani̇ş, Ali̇ Uslu, Huda Jihad Al-Shattrawi

Turkish Journal of Veterinary & Animal Sciences

In this study, Salmonella strains from dairy cows, calves with diarrhea, and buffalo and camel feces were isolated and serotyped. There were 869 feces samples (437 calves, 287 dairy cows, 100 buffalo, and 45 camels) collected from 13 provinces and 21 farms. Preenrichment feces samples were added to Rappaport-Vassiliadis medium. Samples were then subcultured on xylose lysine tergitol-4 agar and plates. Suspected colonies of Salmonella were confirmed by latex agglutination test. The isolates of Salmonella spp. were serotyped at the Etlik Central Veterinary Control Institute. In total, 40 Salmonella spp. were isolated, including 33 from calves, 5 from dairy cows, …

Proximate Analysis Of Indian Flying Fox's (Pteropus Giganteus) Natural Food, With A Note On Its Roost Variations In Urban Areas Of Lahore, Pakistan, Arshad Javid, Tayiba Gulraiz, Muhammad Ashraf, Muhammad Nadeem, Syed Makhdoom Hussain, Muhammad Altaf, Irfan Babu

Turkish Journal of Zoology

Food habits, nutrient preferences, and roost variations of Indian flying fox Pteropus giganteus were investigated for a period of 1 year in two public parks in Lahore, Pakistan. Bolus and guano samples of P. giganteus were collected on a monthly basis, and seeds of 32 plant species belonging to 23 genera and 15 families were identified from the ejecta samples. Of these 32 food species, 8 were native and 24 were exotic; 13 were commercially important, while 19 species had no mercantile value. Proximate analysis of the food items revealed that fruits with comparatively higher moisture content were utilized during …

Human Activity Mediates Reciprocal Distribution And Niche Separationof Two Sympatric Mongoose Species On The Pothwar Plateau, Pakistan, Riaz Hussain, Tariq Mahmood, Faraz Akrim, Hira Fatima, Muhammad Sajid Nadeem

Turkish Journal of Zoology

Ecologically and morphologically similar species living in sympatry are predicted to partition their resources, although the resources themselves may vary in time and space and in relation to extrinsic factors. We studied two sympatric species of carnivores that vary in their distribution along a gradient of human activity, and one species exploits a wider range of food sources. We recorded the distribution of the small Indian mongoose (Herpestes javanicus) and the gray mongoose (Herpestes edwardsii) through reconnaissance surveys within high, medium, and low human activity areas of the Pothwar Plateau from November 2011 to June 2013. We found that the …

Macroinvertebrate Composition In The Metarhithral Zones Of The Munzur And Pülümür Rivers: A Preliminary Study, Zuhal Gülteki̇n, Rahmi̇ Aydin, Carola Winkelmann

Turkish Journal of Zoology

The aim of this work was the determination of the macroinvertebrate community in the metarhithral zones of the Munzur and Pülümür rivers. This is the first documented research on macroinvertebrates in the metarhithral zone of the Munzur and Pülümür rivers in the region of the city of Tunceli. In total, 30 taxa of 9 orders of benthic invertebrates were recorded at the four sampling sites. Larvae of Taeniopteryx caucasica (Plecoptera), Oligoneuriella baskale, and Ecdyonurus dispar (Ephemeroptera) were recorded for the first time in the province of Tunceli.

Distribution And Conservation Of Acomys Cilicicus (Mammalia: Rodentia) In Turkey, Ortaç Çeti̇ntaş, Ferhat Matur, Mustafa Sözen

Turkish Journal of Zoology

Acomys cilicicus is endemic to Turkey and known from a very restricted area. The exact distribution of the species was not known up to now and the IUCN status of the species was Data Deficient (DD). To determine the exact distribution area of the species, 39 localities within the historical distribution were surveyed by using 3243 Sherman traps between 2013 and 2016. Turkish spiny mouse samples were obtained from 14 of these 39 localities and the current distribution of the species was determined. We found that the Turkish spiny mouse has two isolated populations in the area between Silifke and …

First Results Of A Faunistic Survey On The Orthoptera Of Jadovnik Mountain, Southwestern Serbia, With Data On The Calling Songs Of Some Bush Cricket Species, Slobodan Ivkovic

Turkish Journal of Zoology

During field trips conducted in 2015 and 2016 at 22 different localities on Jadovnik Mountain, 68 species were recorded. The calling songs of 4 species were studied in detail, and a new song type of Isophya clara was described. Metrioptera brachyptera and Locusta migratoria are rerecorded for the first time in 40 years for the Serbian fauna.

Three New Truncatelloidean Gastropod Species From Turkey(Caenogastropoda: Littorinimorpha), Mustafa Emre Gürlek

Turkish Journal of Zoology

New species of Bithyniidae (Pseudobithynia adiyamanensis sp. nov.), Hydrobiidae (Pseudorientalia ceriti sp. nov.), and Bythinellidae (Bythinella yerlii sp. nov.) are described from three different locations in Turkey. Samples were collected in 2013 and 2016 and the shell and male genital tract morphology of the new species were studied. All of these new taxa were compared to congeners that live in Turkey and adjacent countries.

Galliformes Specialist Group Annual Report 2016-2017, John P. Carroll, Simon D. Dowell

Galliformes Specialist Group and Affiliated Societies: Reports and Other Materials

Annual report of the IUCN SSC Galliformes Specialist Group, 2017.

Guidelines For Successful Gamebird And Songbird Feeding, C. Sánchez García, Francis Buner

Galliformes Specialist Group and Affiliated Societies: Reports and Other Materials

The key points of this research are:

• We studied the use of 259 feeders by wildlife using camera traps during early and late winter in 2012 and 2013, taking over 160,000 photographs.
• We worked on three farms in southern England where pheasants, grey and red-legged partridges were present and feeding was part of the existing game management programme.
• We used a feeder model consisting of a spiral feed dispenser attached to the bottom of a drum, suspended within a cylindrical iron armature clad with wire sheep netting.

Assessing The Efficiency Of Different Sustainable Farming Practices In Reducing The Environmental Impacts Caused By Aquaculture, Rajee Olaganathan, Alicia Tang Kar Mun

Publications

Sustainability of aquaculture is achieved when aquaculture farming systems are capable of preserving the natural resource base and involves an institutional change to the environment by the attainment and continued satisfaction for present and future generations. Sustainable farming practices produce sufficient aquaculture output to satisfy the seafood demand while not burdening the environment more. The potentiality and efficiency of different sustainable aqua farming practices in reducing anthropogenic impacts to the environment by aquaculture are assessed in this paper. Polyculture is mostly adopted by small-scale rural farmers as it requires low entry barrier and help in income diversification. The input of …

Impact Of Aquaculture On The Livelihoods And Food Security Of Rural Communities, Rajee Olaganathan, Alicia Tang Kar Mun

Publications

Aquaculture production has prospered rapidly since the 1970s and is considered as a part of the rural development program in many countries. The impacts of aquaculture on the rural communities in terms of livelihood and food security are assessed in this paper. Aquaculture contributes to the livelihood of the poor through improved employment and income. Aquaculture creates job opportunities for rural communities, especially for illiterate women to earn side income for the household. With increased financial ability, household manage to reflect stronger purchasing power and have better access to the resources. However, there is a controversy among the researchers whether …

Technological Modernization And Its Impact On Agriculture, Fisheries And Fossil Fuel Utilization In The Asia Pacific Countries With Emphasis On Sustainability Perspective, Rajee Olaganathan, Kathleen Quigley

Publications

Modernization is a process that moves towards efficiency. This affects most of the fields such as agriculture, fisheries, forestry, urban planning, policy, fossil fuel usage, manufacturing, technology, economic growth etc. This process plays a major role in moving forward making things faster, better and basically more efficient. The effects of modernization on all these fields bring about the major changes to aspects such as social, economic and the environment. The level of operation has increased from a domestic level; small family scale business to large commercial levels. As the level of operation increased, the utilization of natural resources increased gradually …

The Progression Of Lyme Disease In The State Of Virginia, Margaret Michel

Honors Theses

Lyme disease has spread in the United States from the northeast to more southern and western parts of the country. It has been shown that the tick which most often carries the Lyme disease pathogen (Borrelia burgdorferi) in North America, Ixodes scapularis, has also spread to these new areas of concern. In Virginia, the disease has progressed from the eastern shore to the western, more mountainous regions. Through obtaining historical museum specimens of mice from 11 locations in Virginia, we seek to determine whether the Lyme disease causing pathogen, B. burgdorferi, has always been present in …

Development Of An Age-Frequency Distribution For Ocean Quahogs Arctica Islandica On Georges Bank, Sara M. Pace, Eric N. Powell, Roger Mann, M. Chase Long, John M. Klinck

CCPO Publications

Ocean quahogs [Arctica islandica (Linnaeus, 1769)] are the longest-lived, noncolonial animal known today, with a maximum life span exceeding 500 y. Ocean quahogs are a commercially important bivalve, inhabiting the continental shelf of the North Atlantic Basin. Although considerable information exists on the growth and physiology of A. islandica, limited information is available regarding recruitment; accordingly, sustainably managing the fishery is a challenge. To investigate long-term recruitment trends, the age of ocean quahogs from Georges Bank which were fully recruited to the commercial fishery (>80 mm shell length) was determined by analysis of annual growth lines in …

Anti-Proliferative Role Of Recombinant Lethal Toxin Of Bacillus Anthracis On Primary Mammary Ductal Carcinoma Cells Revealing Its Therapeutic Potential, Rekha Khandia, Bramhadev Pattnaik, Katherikamem Rajukumar, Atul Pateriya, Sandeep Bhatia, Harshad Murugkar, Anil Prakash, Hare Krishna Pradhan, Kildeep Dhama, Ashol Munjal, Sunil K. Joshi

Bioelectrics Publications

Bacillus anthracis secretes three secretary proteins; lethal factor (LF), protective antigen (PA) and edema factor (EF). The LF has ability to check proliferation of mammary tumors, chiefly depending on mitogen activated protein kinase (MAPK) signaling pathway. Evaluation of therapeutic potential of recombinant LF (rLF), recombinant PA (rPA) and lethal toxin (rLF + rPA = LeTx) on the primary mammary ductal carcinoma cells revealed significant (p < 0.01) reduction in proliferation of tumor cells with mean inhibition indices of 28.0 ±1.37% and 19.6 ± 1.47% respectively. However, treatment with rPA alone had no significant anti-proliferative effect as evident by low mean inhibition index of 3.4 ± 3.87%. The higher inhibition index observed for rLF alone as compared to LeTx is contrary to the existing knowledge on LF, which explains the requirement of PA dependent endocytosis for its enzymatic activity. Therefore, the plausible existence of PA independent mode of action of LF including direct receptor mediated endocytosis or modulation of signal transduction cascade via unknown means is hypothesized. In silico protein docking analysis of other cellular receptors for any plausibility to play the role of receptor for LF revealed c-Met receptor showing strongest affinity for LF (H bond = 19; Free energy = …

Improving Syntactic Parsing Of Clinical Text Using Domain Knowledge, Min Jiang

Dissertations and Theses (Open Access)

Syntactic parsing is one of the fundamental tasks of Natural Language Processing (NLP). However, few studies have explored syntactic parsing in the medical domain. This dissertation systematically investigated different methods to improve the performance of syntactic parsing of clinical text, including (1) Constructing two clinical treebanks of discharge summaries and progress notes by developing annotation guidelines that handle missing elements in clinical sentences; (2) Retraining four state-of-the-art parsers, including the Stanford parser, Berkeley parser, Charniak parser, and Bikel parser, using clinical treebanks, and comparing their performance to identify better parsing approaches; and (3) Developing new methods to reduce syntactic ambiguity …

Insulin-Like Growth Factor Signaling Regulates Developmental Trajectory Associated With Diapause In Embryos Of The Annual Killifish Austrofundulus Limnaeus, S. Cody Woll, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Annual killifishes exhibit a number of unique life history characters including the occurrence of embryonic diapause, unique cell movements associated with dispersion and subsequent reaggregation of the embryonic blastomeres, and a short postembryonic life span. Insulin-like growth factor (IGF) signaling is known to play a role in the regulation of metabolic dormancy in a number of animals but has not been explored in annual killifishes. The abundance of IGF proteins during development and the developmental effects of blocking IGF signaling by pharmacological inhibition of the insulin-like growth factor I receptor (IGF1R) were explored in embryos of the annual killifish Austrofundulus …

Plant–Insect Interactions In A Changing World, S. Pincebourde, J. Van Baaren, S. Rasmann, P. Rasmont, G. Rodet, B. Martinet, P. A. Calatayud

All Peer-Reviewed Publications

Global change is resetting the spatial and ecological equilibrium of complex co-evolutionary relationships between plants and their insect herbivores. We review the mechanisms at play in the responses of plant–insect interactions to global changes, including increased temperature and atmospheric CO2 concentrations, modification of land use and pollution. We distinguish between the direct effects of global changes on each partner from the indirect impacts on insects via the responses of plants. The indirect effects include a change in the nutritional quality of the plant tissues for herbivore insects, as well as a change in the microclimatic conditions at the leaf surface. …

Pseudomonas Aeruginosa And Its 4 Arsenal Of Proteases: Weapons 5 To Battle The Host, A.C.M. Galdino, M.H.B Branquinha, A.L.S. Santos, L. Viganor

Books/Book chapters

Pseudomonas aeruginosa is a ubiquitous and opportunistic human pathogen that 12 represents a critical problem to the clinician due to the increased number of 13 resistant strains isolated from hospital settings. In addition, there is a great 14 variety of pathologies associated with this versatile Gram-negative bacterium. 15 P. aeruginosa cells are able to produce an incredible arsenal of virulence factors, 16 especially secreted molecules that act singly or together to ensure the 17 establishment, maintenance, and persistence of a successful infection in 18 susceptible hosts. In this context, pseudomonal proteases roles are highlighted 19 due to their ability to …

From Disposable Culture To Disposable People: Teaching About The Unintended Consequences Of Plastics, Sasha Adkins

Antioch University Dissertations & Theses

Plastics, the epitome of disposable culture, pose both a toxicological and a spiritual problem. This dissertation examines plastics at a molecular level using the discourse of endocrine disruption, and at a sociological level using the discourses of eco-theology and environmental justice. Adding to the literature on the adsorption of toxicants to plastic marine debris, I demonstrate that certain types of plastic -- those containing mercaptans, such as styrene butadiene block copolymer -- efficiently concentrate methyl mercury from seawater. Further, samples of polycarbonate contributed mercury to seawater. I propose the term plastic-mediated magnification to describe the phenomenon that plastics, along with …

The Database Of The Predicts (Projecting Responses Of Ecological Diversity In Changing Terrestrial Systems) Project, Lawrence N. Hudson, Tim Newbold, Sara Contu, Samantha L.L. Hill, Igor Lysenko, Adriana De Palma, David J. Flaspohler, Et. Al.

Michigan Tech Publications, Part 1

The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in …

Elevated Trace Metal Content Of Prokaryotic Communities Associated With Marine Oxygen Deficient Zones, Daniel C. Ohnemus, Sara Rauschenberg, Gregory A. Cutter, Jessica N. Fitzsimmons, Robert M. Sherrell, Benjamin S. Twining

OES Faculty Publications

Little is known about the trace metal content of marine prokaryotes, in part due to their co-occurrence with more abundant particulate phases in the upper ocean, such as phytoplankton and biogenic detritus, lithogenic minerals, and authigenic Mn and Fe oxyhydroxides. We attempt to isolate these biomass signals in particulate data from the US GEOTRACES Eastern Pacific Zonal Transect (cruise GP16) in the Eastern Tropical South Pacific (ETSP), which exhibited consistent maxima in P and other bioactive trace metals, and minima in particulate Mn, in the oxygen deficient zones (ODZs) of 13 stations. Nitrite maxima and nitrate deficits indicated the presence …

Twenty-First Century Climate Change And Submerged Aquatic Vegetation In A Temperate Estuary: The Case Of Chesapeake Bay, Thomas M. Arnold, Richard C. Zimmerman, Katharina A.M. Engelhardt, J. Court Stevenson

OES Faculty Publications

Introduction: The Chesapeake Bay was once renowned for expansive meadows of submerged aquatic vegetation (SAV). However, only 10% of the original meadows survive. Future restoration effortswill be complicated by accelerating climate change, including physiological stressors such as a predicted mean temperature increase of 2-6°C and a 50-160% increase in CO2 concentrations.

Outcomes: As the Chesapeake Bay begins to exhibit characteristics of a subtropical estuary, summer heat waves will become more frequent and severe. Warming alone would eventually eliminate eelgrass (Zostera marina) from the region. It will favor native heat-tolerant species such as widgeon grass (Ruppia maritima) while facilitating colonization by …

Metagomics: A Web-Based Tool For Peptide-Centric Functional And Taxonomic Analysis Of Metaproteomics Data, Michael Riffle, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, Daniel Jaschob, William S. Noble, Brook L. Nunn

OES Faculty Publications

Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the …

Eukaryotic Microbes, Principally Fungi And Labyrinthulomycetes, Dominate Biomass On Bathypelagic Marine Snow, Alexander B. Bochdansky, Melissa A. Clouse, Gerhard J. Herndl

OES Faculty Publications

In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto μm filters from similar to 1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant …

Frontiers In Otolith Chemistry: Insights, Advances And Applications, B. D. Walther, K. E. Limburg, C. M. Jones, J. J. Schaffler

OES Faculty Publications

The rapid proliferation of publications employing chemical assays of fish hard parts, and otoliths in particular, has led to many novel insights into the migration patterns, life history strategies and mixed stock dynamics of fishes across the globe (Campana et al., 2000; Elsdon et al., 2008; Walther & Limburg, 2012). These insights include uncovering diverse migratory strategies within species and populations (Kerr et al., 2009; Hogan et al., 2014; Schoen et al., 2016), quantifying rates of mixing among stocks across management boundaries (Rooker et al., 2008; Walther & Thorrold, 2010) and estimating the relative …

Beyond Zar: The Use And Abuse Of Classification Statistics For Otolith Chemistry, C. M. Jones, M. Palmers, J. J. Schaffler

OES Faculty Publications

Classification method performance was evaluated using otolith chemistry of juvenile Atlantic menhaden Brevoortia tyrannus when assumptions of data normality were met and were violated. Four methods were tested [linear discriminant function analysis (LDFA), quadratic discriminant function analysis (QDFA), random forest (RF) and artificial neural networks (ANN)] using computer simulation to determine their performance when variable-group means ranged from small to large and their performance under conditions of typical skewness to double the amount of skewness typically observed. Using the kappa index, the parametric methods performed best after applying appropriate data transformation, gaining 2% better performance with LDFA performing slightly better …

Phytoplankton Plastid Proteomics: Cracking Open Diatoms To Understand Plastid Biochemistry Under Iron Limitation, Skyler J. Nunn, Phoebe Dreux Chappell, Kristofer Gomes, Anasthasia Bonderenko, Bethany D. Jenkins, Brook L. Nunn

OES Faculty Publications

Diatoms, such as Thalassiosira pseudonana, are important oceanic primary producers, as they sequester carbon dioxide (CO₂) out of the atmosphere, die, and precipitate to the ocean floor. In many areas of the world’s oceans, phytoplankton, such as diatoms, are limited in growth by the availability of iron (Fe). Fe is an essential nutrient for phytoplankton, as it is central in the electron transport chain component of photosynthesis. Through this study, we examined if Fe-limitation makes a significant difference in the proteins expressed within the chloroplast, the power source for diatoms. Here, we utilized a new plastid isolation technique specific …