Miracle-dz/UniFAR-FTUs huggingface dataset:
Discordant expression profile between RNA and protein for the genes involved in immune response network in adenovirus type 2 infected cells

Alternation of cellular genes expressions during Adenovirus type 2 (Ad2) infection in IMR-90 cells was studied using paired-end sequencing and stable isotope labeling of amino acids in cell culture mass spectrometric analysis (SILAC-MS). At transcriptional level, cellular genes involved in different pathways revealed distinct expression profiles. At early phase, the genes involved in regulation of cellular immune response, cellular signaling and cell growth control were among the most deregulated. Later follows, in an orderly fashion, genes involved in cell cycle control, DNA replication and further on genes engaged in RNA processing and protein translation. Comparison of cellular gene expression at transcriptional and posttranscriptional levels revealed low correlation. Here we highlight the genes which expose opposite expression profiles with an emphasis on key factors that play important roles in cellular immune pathways including NFκB, JAK/STAT, caspases and MAVS. Transcription of many of these genes was transiently induced early, but became down-regulated in the late phase. In contrast, their expressions at protein level were up-regulated early and so sustained until late phase of infection. Suppression at the transcriptional level and enhancement at the protein level of immune response genes most likely illustrate counteractions between Ad2 and its host cell. Importance Our paper comprises a state of the art quality transcriptomics data set unravelling the alterations in gene expression that take place during different phases of an adenovirus infection. The information allows us to draw conclusion about the cellular pathways that are perturbed by the virus. The data set also provides an important resource for scientists in general for future studies on mechanisms behind host/virus interactions in efforts to design tools for combatting virus infections. Moreover, our paper includes novel proteomics information unravelling an unexpected role of post transcriptional events in cellular gene expression, demonstrating that the current picture of the adenovirus replication cycle is simplified.
Prevalence of leishmaniosis in dogs in Istanbul,Turkey determined by using PCR

Leishmania infantum is widespread in Mediterranean countries including Turkey and can cause a serious disease in both humans and dogs. Dogs are considered to be its main reservoirs. The current epidemiological study was carried out in Istanbul for detection of leishmaniosis among dogs. A total of 246 dogs were included in the study. Twenty one (8.54%) blood samples were found to be positive based on PCR diagnosis, using primers specific for the kinetoplast DNA of Leishmania . Infection rate was 6.51% in 169 dogs living in shelters and 12.99% in 77 client-owned dogs. The rate was significantly ( p <0.001) higher in the dogs (37.93%) presenting one or more clinical symptoms which may be attributable to leishmaniosis, than in the asymptomatic dogs (4.61%). Eleven (52.4%) of 21 PCR positive dogs presented clinical symptoms whereas the rest of the dogs (47.62%) were asymptomatic. The major clinical sign in PCR positive animals was dermatological problems. Amongst PCR positive dogs, skin lesions were present in 11, weight loss in 2, lymphadenopathy in 2, epistaxis in 2 and lethargy in 2 dogs.
A Phylogenetic Overview of the Genus Vertigo O. F. Müller, 1773 (Gastropoda: Pulmonata: Pupillidae: Vertigininae)

ABSTRACT We document global phylogenetic pattern in the pupillid land snail genus Vertigo by analyses of nDNA (ITS1 and ITS2) and mtDNA (CytB and 16S) sequence from 424 individuals representing 91 putative specific and subspecific Vertigo taxa. nDNA and mtDNA data were separately subjected to neighbor-joining, minimum evolution, maximum likelihood and Bayesian reconstruction methods, with conclusions being drawn from shared topological structures. Six highly supported, reciprocally monophyletic subgeneric level clades were identified: Vertigo, Alaea, Boreovertigo new subgenus, Isthmia, Staurodon and Vertilla. 88 species or subspecies were also confirmed, nine of which are new and formally described herein: V. beringiana, V. chiricahuensis, V. chytryi, V. genesioides, V. kodamai, V. kurilensis, V. lilljeborgi vinlandica, V. pimuensis and V. pisewensis. Thirteen taxa were synonymized: V. arthuri basidens, V. arthuri hubrichti, V. arthuri paradoxa (= V. arthuri); V. allyniana (= V. modesta); V. andrusiana (= V. columbiana); V. conecuhensis (= V. alabamensis); V. dedecora tamagonari (= V. dedecora); V. elatior, V. idahoensis (= V. ventricosa); V. eogea (= V. ovata); V. modesta insculpta (= V. modesta concinnula), V. modesta microphasma, V. modesta sculptilis (= V. modesta castanea). Qualitative observations of conchological features, ecological preferences and geographic coverage were conducted for each subgenus and genetically supported species or subspecies-level taxon. These demonstrated that: (1) a suite of diagnostic shell features usually exists to demarcate each species-level taxon; (2) shell features were incapable of defining genetically validated subgenera; (3) all subgenera had transcontinental ranges; (4) ⅓ of all species possess continental or trans-continental ranges, with very few having range extents < 1,000 km; (5) all subgenera and fully ⅔ of global Vertigo species and subspecies are found in North America, more than 2.5 times the number found in central and eastern Asia, the second most diverse region. This is similar to several other molluscan groups, such as the polygyrid land snails and unionid bivalves for which North America is the global biodiversity hotspot.
Bermudagrass (Cynodon dactylon) and Johnsongrass (Sorghum halepense) Ecotype Response to Herbicides

Common bermudagrass [Cynodon dactylon (L.) Pers. #3 CYNDA] and johnsongrass [Sorghum halepense (L.) Pers. # SORHA] ecotypes were collected from seven locations in Texas. Ecotype responses to glyphosate [N-(phosphonomethyl)glycine], SC-0224 (trimethylsulfonium carboxymethylaminomethylphosphonate), sethoxydim {2-[l-(ethoxyimino)butyl]-5-[2-(ethylthio)propyl]-3-hydroxy-2-cyclohexen-1-one}, fluazifop {(+)-2-[4-[[5-(trifluoromethyl)-2-pyridinyl] oxy] phenoxy] propanoic acid}, haloxyfop {2-[4-[[3-chloro-5-(trifluoromethyl)-2-pyridinyl] oxy] phenoxy] propanoic acid}, and quizalofop {(+)-2-[4-[(6-chloro-2-quinoxalinyl)oxy] phenoxy] propanoic acid} were evaluated in 1982, 1983, and 1984. Johnsongrass ecotype-by-herbicide interactions and ecotype differences were detected in only one of three years. Differences were observed consistently among the herbicide treatments. Numerous bermudagrass ecotype-by-herbicide interactions were detected each year with greater diversity occurring with less-than-optimum herbicide rates. The interactions were herbicide-by-ecotype specific and were not predictable with respect to geographic site of collection.
A DFT study of the Al2O3 atomic layer deposition on SAMs: Effect of SAM termination

The atomistic mechanism of the initial atomic layer deposition (ALD) reaction of trimethylaluminum [Al(CH3)3, TMA] on octadecyltrichlorosilane (OTS)-based self-assembled monolayers (SAMs) with different functional termination groups was investigated using density functional theory (DFT). The adsorption of TMA on −NH2-terminated OTS involves formation of a dative bond between the amine lone pair and the Al atom of TMA and is exothermic by 0.86 eV. Conversion of the dative bond to a covalent bond through a four-centered H transfer from the NH2 to the methyl group of TMA to form methane involves a barrier that is 1.22 eV above the adsorbed complex and is exothermic by 0.94 eV. Reaction between TMA and the −OH-terminated SAM results in an adsorption energy of 0.60 eV. Although the dative bond is weaker, the barrier to converting the dative bond to a covalent bond to form methane is only 0.65 eV relative to the complex structure and the overall reaction is exothermic by 1.44 eV. The reaction of TMA with the me.
Euphausiids (Crustacea: Euphausiacea) from a hotspot of marine biodiversity, Isla del Coco, Costa Rica, Eastern Tropical Pacific

Euphausiids have been well studied in several regions of the Pacific Ocean; however, there is lessinformation regarding euphausiids in Costa Rican waters. We analyzed euphausiid specimens collected aroundIsla del Coco National Park during 2011 and 2012. A total of 130 specimens were analyzed and 13 euphausiidspecies were identified, belonging to four genera and one family. An annotated list of species is presented,with photographs and details for their identification. All species found represent new records for waters aroundIsla del Coco in the Costa Rican Pacific. The most frequent species were Euphausia diomedeae, Euphausiadistinguenda, Nematoscelis gracilis and Stylocheiron affine. Rev. Biol. Trop. 64 (Suppl. 1): S221-S230. Epub2016 Febrary 01.
Evaluation of Phyto-extracts, Biological Agents and Chemicals against the Development of Alternaria brassicae in vitro and in vivo

Alternaria leaf blight caused by Alternaria brassicae and Alternaria brassicola, is one of the most destructive diseases of mustard (Brassica campestris, B. juncea and B.napus) in West Bengal, causing considerable damages to the crop. The experiment was conducted under in vitro and in vivo conditions to see the effect of bio-agents, plant extracts and chemicals (fungicide and SAR compound) against Alternaria brassicae. Maximum inhibition in mycelial growth (95.56%) was observed with Mancozeb 75% Wp followed by Lantana camera (80%), Salicylic acid (73.33%), Allium sativum (54.44%) and Zingiber officinale (17.78%) in comparison to control. Foliar spray with fungicide (Mancozeb 75% WP @ 0.2%) was found to be most effective in reducing disease severity (81,23%) and infection rate which increased the yield (77.23%) of mustard over untreated control. Among the plant extracts, Lantana camera was found to be excellent in controlling the Original Research Article Biswas and Ghosh; EJMP, 22(3): 1-9, 2018; Article no.EJMP. 40412 2 Alternaria blight infection in the field (71.92% reduction in disease severity and 68.18% increase in yield) in comparison to salicylic acid (SAR compound) and bio-agent (Trichoderma viride) 48.33% and 36.27% reduction in disease severity respectively.
Antimicrobial Effect of Dietary Supplementation of Turmeric Powder in Intestine of Broilers

In the present era, broiler industry as a part of poultry industry has been developing at a satisfactory level. The main goal of broiler industry is to achieve optimum weight gain with efficient feed utilization keeping the survivability of the broilers as maximum as possible which could be achieved by use of specific feed additives. Feed additives increases feed conversion ratio, growth rate and survivability (Feltwell and Fox, 1979). Poultry are vulnerable to pathogenic microorganisms in the small intestine. This leads to depressed growth and increased incidences of diseases. Herbal products like turmeric control the pathogenic microorganism by creating favorable conditions in intestine. Herbs provide beneficial effect on health due to the antimicrobial activity (Lee et al., 2004). Turmeric possess anti-inflammatory (Ammon et al., 1993), antioxidative (Osawa et al., 1995), anticoccidials (Allen and Fetterer, International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 04 (2018) Journal homepage: http://www.ijcmas. com
Living Fast and Dying Young: Life History and Ecology of a Neogene Sperm Whale

ABSTRACT Physeteroidea (sperm whales) attained great diversity during the Miocene and early Pliocene, and the phosphatic sands of the U.S. Atlantic Coastal Plain have produced thousands of specimens. Although postcranial and cranial materials are rare, teeth are remarkably common and have the potential to provide valuable insight into the lives of these animals. We examine a suite of Physeteroidea indet. teeth from the Lee Creek Mine to better constrain the life history and ecology of this extinct group. Wear facets indicate that these animals, unlike modern sperm whales, had both maxillary and mandibular teeth, suggesting a raptorial feeding ecology more akin to killer whales. A relationship between tooth diameter and body size established for modern odontocetes suggests that these animals as adults were also about the size of modern killer whales. Because physeteroid teeth grow continuously over ontogeny and are not replaced, counts of accretionary growth layer groups can be used to ascertain the age of an animal at death. Tallies of growth increments from 10 teeth, including some of the largest available, reveal that life spans only rarely exceeded 20 years, significantly shorter than the 65+ years typical of modern sperm whales or orcas. Despite their large size, these odontocetes experienced a ‘fast’ life history, more like beluga whales today. We suggest that the rapid growth and short life span exhibited by the Lee Creek physeteroids are, like the modern beluga, evolutionary responses to high predation pressure imposed by large co-occurring predatory taxa, particularly including Carcharocles megalodon or other large macroraptorial physeteorids.
Adaptations in allopatric populations of Triakis megalopterus isolated by the Benguela Current: steps towards understanding evolutionary processes affecting regional biodiversity

i Acknowledgements . iv List of tables . ix List of figures . xi Chapter 1: General introduction . 1 Thesis outline . 10 Chapter 2: Site selection and general methods . 12 Study sites . 12 Southern Angola . 12 Northern/Central Namibia . 14 Western Cape, South Africa . 15 Eastern Cape, South Africa . 15 General material and methods . 16 Chapter 3: Genetic connectivity of Triakis megalopterus across its southern African distribution . 18 Introduction . 18 Material and methods . 23 Sample collection and DNA extraction . 23 Species identification . 24 mtCR sequencing and alignment . 24 mtCR sequence analysis . 25 Population demographics . 25 Microsatellite genotyping . 26 Marker validity . 28 Genetic diversity and population differentiation . 29 Demographic history . 29
Study on endogenous protease and protein degradation of dry-salted Decapterus maruadsi

ABSTRACT Extensive proteolysis and formation of flavor substances occur during the processing of dry-salted fish due to the action of endogenous proteases. This study analyzed the evolution of the endogenous proteases and the relationship between endogenous protease levels and protein degradation during processing. Cathepsin B and L activity increased significantly during the last two stages, while cathepsin H activity decreased non-significantly (residual activity was 92.27%) compared to initial activity levels in fresh fish. Dipeptidyl peptidase (DPP I, IV) activity decreased overall. The activity of three aminopeptidases (arginine aminopeptidase; alanyl aminopeptidase; leucyl aminopeptidase) initially decreased (P < 0.05) then significantly increased (P < 0.05) during the final stage. Principal component analysis indicated that cathepsins B and L had larger influences than cathepsin H on protein degradation and flavor substance formation in dry-salted fish, but the influence of dipeptidyl peptidases and aminopeptidases on protein degradation and flavor substance formation was limited.
Mapping of the spatial distribution of carbon storage of the Pinus kesiya Royle ex Gordon (Benguet pine) forest in Sagada, Mt. Province, Philippines

ABSTRACT The objective of this study is to map the spatial distribution of the aboveground biomass (AGB, tC/ha) storage of the Pinus kesiya Royle ex Gordon (Benguet pine) forest of Sagada, Mt. Province, Philippines by integrating Landsat image and the forest cover map. The data was obtained from 66 plots that were established in the different Benguet pine stands in Sagada. The AGB was estimated using the Digital Numbers (DN) and Normalized Difference Vegetation Index (NDVI) values (with filter and with no filter). The estimated aboveground biomass (AGB) density of the Benguet pine was determined to be 249.66 tonnes/ha corresponding to 112.35 tonnesC/ha.
Behaviors of microtubules depend on two critical concentrations

The concept of critical concentration is a central idea in understanding the behaviors of microtubules (MTs) and other steady-state (energy-utilizing, non-equilibrium) cytoskeletal polymers. Classically, the critical concentration (CC) is the concentration of subunits necessary to obtain polymer. However, the classical theory used to explain and predict CC is based on equilibrium polymers and fails to account for dynamic instability (DI). It has been unclear how the classical theory should be adjusted to incorporate DI or how the behavior of an individual dynamically unstable filament relates to that of its population. To address these questions, we used previously established simulations to follow at multiple scales the behavior of systems of computationally modeled dynamic microtubules. We show that polymers such as microtubules that exhibit dynamic instability have not one but at least two critical concentrations: one above which growth phases of individual filaments can occur transiently, and another above which the population’s overall polymer mass will increase persistently. We propose that whether a steady-state polymer behaves like microtubules (displays dynamic instability) or like actin (can be modeled as an equilibrium polymer) depends on how far apart these critical concentrations are. This revised framework helps to explain and unify a wide range of experimental observations. SIGNIFICANCE STATEMENT Traditionally, biological polymers are thought to have one “critical concentration” (CC) where polymer assembly commences. It has been unclear how this framework should be adjusted to account for dynamic instability (prolonged periods of growth and shortening with random transitions). Using computational models, we show that microtubules have two critical concentrations: a lower CC where individual dynamically unstable microtubules can grow transiently (CCIndGrow), and an upper CC where a population of such filaments grows persistently (CCPopGrow). Our results show that most experiments thought to measure “the CC” actually measure CCPopGrow. “Normal” dynamic instability (where individual filaments depolymerize back to the seed) happens at subunit concentrations below what is traditionally thought to be the lower lower limit for polymer appearance.
Discrimination of dwarf honey bee (Apis florea, Fabricius 1876) populations in Iran using elliptic Fourier wing cell shape analysis

We investigated cell shape differentiation among Apis florea populations distributed in four states (Hormuzgan-Bushehr-Khuzestan-Ilam states) of Iran using elliptic Fourier analysis (EFA - outline-based geometric morphometric analysis) on all forewing cells. Outline-based analysis was performed on all closed cells on the forewings of 114 A. florea colonies from 13 locations in Iran. According to the statistical analysis of each cell shape, the most efficient cells to discriminate populations were 2nd cubital, 3rd submarginal and marginal cells. Discriminant Function Analysis of Fourier coefficients (FCs) for each cell resulted in two clusters: southern A. florea populations from lower latitude (Hormuzgan state); and the rest of the populations from higher latitude (Ilam, Khuzestan, Bushehr state) with different differential discrimination values (1st submarginal cell = 75.4%, 2nd submarginal cell = 86.0%, 1st medial cell and 2nd medial cell = 86.8%, marginal cell = 88.6%, 3rd submarginal cell = 90.4%, 2nd cubital cell = 92.1%). This study showed that EFA has been functional and effective for distinguishing A. florea populations based on the wing cell shapes. The outline-based geometric morphometric applied in our study has been as successful as the other morphometric approaches such as standard morphometric and landmark-based geometric morphometric in previous studies.
Energetic stress and infection generate immunity-fecundity tradeoffs in Drosophila

Physiological responses to short-term environmental stress, such as infection, can have long-term consequences for fitness, particularly if the responses are inappropriate or nutrient resources are limited. Genetic variation affecting energy acquisition, storage, and usage can limit cellular energy availability and may influence resource-allocation tradeoffs even when environmental nutrients are plentiful. Here, we utilize well-characterized Drosophila mitochondrial-nuclear genotypes to test whether disrupted energy metabolism interferes with nutrient-sensing pathways, and whether this disruption has consequences for tradeoffs between immunity and fecundity. We find that this energetically compromised genotype is resistant to rapamycin – a drug that stimulates nutrient-sensing pathways that are activated when resources are limited. Resource limitation also compromises survival in energetically-compromised genotypes, suggesting that this genotype may have little excess energetic capacity and fewer cellular nutrients, even when environmental nutrients are not limiting. Accordingly, we find that immune function is compromised in this genotype, but only in females, and that these females experience immunity-fecundity tradeoffs that are not evident in genotypic controls with normal energy metabolism. Thus, genetic variation in energy metabolism may act to limit the resources available for allocation to life-history traits in ways that generate tradeoffs even when environmental resources are not limiting.
Availability of food resources for pollinators in three types of lowland meadows

The availability of floral resources is considered a key factor for the maintenance and conservation of pollinators. We compared the forage floral diversity of three types of lowland meadows (Molinia meadows, tall herb fringe meadows, and hay meadows) located in south eastern Poland. The total number of plant species was 125, including 84 species (67.2%) classified as plants visited by insects. The richness and diversity of forage flora differed between the types of meadow. The Molinia meadows and hay meadows were preferred by pollinators. However, different taxonomic groups of pollinators can respond to the variability and availability of floral resources in a different way. Molinia meadows are of particular importance for the abundance of Bombus spp. , solitary bees, and flies. The RDA ordination model demonstrated that the floral community composition, plant species abundance, plant species richness, and floral attributes (size, shape, phenology) were all important for the abundance of insect visitors in the mosaic of meadows. The cluster analysis showed that most plant species were visited by similar groups of insects; however, their proportion differed considerably. Our results present arguments for inclusion of semi-natural meadows into conservation plans and for efforts of protection of highly effective floral resources aimed at maintenance of pollinators.