Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential gene expression induced by Toll-like receptor ligands in equine monocytes

Toll–like receptors (TLRs) recognize conserved molecular motifs of microbes and elicit inflammatory and immune responses through specific intracellular adaptor molecules, particularly MyD88 and TRIF. Initiation of inflammatory responses is an important component of the host response to microbial pathogens and for the development of immunity. The first two studies reporting this dissertation project established the basis for the subsequent three studies. Firstly, an optimal source of lipopolysaccharide-binding protein (LBP) for eliciting responses by equine monocytes to lipopolysaccharide (LPS) was identified. Secondly, twenty-nine equine primer pairs to measure gene expression by real-time quantitative RT-PCR in equine monocytes were optimized and validated. The remaining three studies investigated the response of equine monocytes to different TLR agonists and a specific TLR4 antagonist. Based on the results of the initial study, pooled commercial and autologous equine sera are optimal sources of LBP activity for studies elucidating the effects of LPS on equine monocytes. A reliable set of equine primer pairs were used to determine that similar gene expression profiles were induced by the TLR4 (E. coli LPS) and TLR2 (Pam3CSK4) ligands that signal via MyD88. In contrast, the TLR3 (Poly I:C) ligand that signals through TRIF induced significantly higher expression of interferon-ß, IFN-γ inducible protein 10 and CCL5 than either the TLR2 or TLR4 ligands. Natural and synthetic lipid A compounds derived from E. coli strongly induced signaling through the MyD88-dependent pathway. Furthermore, the presence of the KDO moiety, resulted in significantly greater expression of inflammatory cytokines than did lipid A compounds lacking KDO. Differences in the length of the fatty acid chains attached to the lipid A backbone induced different levels of biological responses from equine monocytes. Finally, the second-generation synthetic lipid A analagoue, E5564, induced minimal proinflammatory effects in equine whole blood or monocytes. Most importantly, E5564 inhibited LPS-induced expression of procoagulant activity and tumor necrosis factor- (TNF-) production and mRNA expression of TNF-, interleukin-1ß (IL-1ß) and IL-10. INDEX WORDS: Equine, Monocytes, Toll-like receptors, Lypopolysaccharide, Lipid A, Gene expression, Procoagulant activity, TNF-α, TLR4 antagonist DIFFERENTIAL GENE EXPRESSION INDUCED BY TOLL-LIKE RECEPTOR LIGANDS IN EQUINE MONOCYTES
A new method to isolate algal species from mix algal culture

To meet the issues of energy and environment, algae cultivation for biofuel and CO2 sequestration is getting popular at the global level. Specific algal strains have been identified for production of biofuel, biomolecules and biomass. To start algae cultivation at lab or industrial scale, it is requirement to have isolated and identified algal culture for targeted products. Water sample for algae from aquatic system is usually consist of mix culture of algae and need to be processed for targeted isolated algal strains using reported techniques like streaking, spraying, serial dilution, and single-cell isolations. But none of these techniques is considered as efficient or popular except streaking on agar plate which involves a set of microbial techniques and may take months to make isolation properly. Here, a new method is proposed to make alginic acid solution using aquatic sample followed by pouring it in calcium chloride solution drop by drop which makes the beads with single or more algal species trapped in each bead. The trapped algal species in the beads are grown in 96 wells plate having single bead in each well with standard medium leading to microscopic verification of the isolated algal species to process further. A mix culture from a lake was subjected to isolation using proposed method and excellent results were obtained in one week duration.
Giraffe Mother-Calf Relationships in the Miombo Woodland of Katavi National Park, Tanzania

Abstract. Both predator pressure and habitat type influence mother-offspring relationship. Giraffe's herd size and herd composition can be influenced by these two environmental factors. We sought to uncover whether predator pressure and habitat type also have an impact on giraffe mother-calf proximity and time spent together. We studied giraffe mother-calf relationships to compare mother-calf dyadic relationships in dense woodland with those reported in open woodlands. We collected data from three calves (within the first six months after birth) and their mothers at the miombo woodland of Katavi National Park, Tanzania. We observed the mother giraffe leaving or staying with her calf and recorded the initiation and termination of each of these behaviors. We found that the duration of both states was rarely more than 1 h. We never observed a mother leaving her calf for more than 1.5 h, as has been reported in open woodlands. We found that in calf-calf dyads, giraffe were more likely to maintain closer proximity to one another than in female-calf dyads. Our results suggest that the flexibility recorded in mother-calf social relationships is influenced by both social and ecological factors, differing to some extent in tree density, food preference during nursing, and predators' prey preference.
INHIBITION OF THE EXPRESSION OF PHYSIOLOGICAL PRIONS WITH ANTISENS-OLIGONUCLEOTIDES

43 Prion infections are caused by a particular pathological form of prion protein, which is present in all mammals. Today, there are no effective methods and means for treating and preventing prion infections [1]. The pathogenesis of prion infections is associated with the synthesis of cellular prion (PrPC), so that removing this protein from the body may prevent their development [2]. There is a whole arsenal of drugs that can effectively inhibit the biosynthesis of the necessary proteins. Among them are — antisense technology, which results in the use of specific single-stranded oligonucleotides (asODN), which block the mRNA areas and mediate its hydrolysis [3, 4 ]. The success of using the antisense technology largely depends on the availability of polymer carriers, which is especially important in modern biology, medicine and veterinary medicine. Cationic synthetic and natural polymers are a convenient tool for delivering genetic material to cells, because through electrostatic interactions they effectively bind negatively charged DNA molecules. Thus, polymers screen DNA from the action of hydrolytic ferments, so they continue to stay in the body of genetic constructs and facilitate their penetration into the middle of the cell. In these studies polymers based on dimethylaminomethylmethacrylate (DMAEM) were used as carriers. They contain tertiary amino groups and significantly increase the efficiency of mammalian transfection of plasmid DNA, however, the molecular mechanisms of this process have not been fully established [5]. The aim of our work was to investigate the ability of new polymer DMAEM based carriers to form conjugates with asODN, to study the efficiency of data transport systems, to analyze their effect on the organism of laboratory rats and to determine the ability to suppress the expression of the physiological prion.
Restoring habitat for coastal California Gnatcatchers (Polioptila californica californica)

ABSTRACT One goal of Habitat Conservation Plans is to protect viable populations of animal species. Management actions included in such plans often focus on vegetation restoration to benefit the target animal species. Yet, such restoration activities are often uninformed by fine-scale animal survey data. Using the California Gnatcatcher (Polioptila californica californica), we demonstrate how survey data can guide restoration toward the goal of improving gnatcatcher viability by identifying habitat conditions most favorable for gnatcatcher occupancy. We found that gnatcatcher presence and colonization probabilities tripled as the coverage of coastal sagebrush (Artemisia californica) increased from 10% to 40%. Coastal sagebrush was more likely to be present at low elevations, and was most closely associated with soil texture of 5%–20% clay, 40%–70% sand, and 20%–40% silt. Higher gnatcatcher extinction probabilities were associated with closed, dense habitat; optimal conditions were between 30% and 40% openness, creating a slightly closed canopy. Open habitat was associated with southern aspects, shallow slopes, and inland areas. An understanding of the soil types and physical parameters of the environment that affect vegetation, especially the amount of coastal sagebrush needed for high gnatcatcher occupancy and colonization rates, will help to define restoration target conditions. Using multiseason, occupancy-based surveys in conjunction with detailed habitat measurements will allow ornithologists and land managers to design powerful restoration prescriptions, even within narrowly defined ecosystems.
Towards building an automated bioinformatician: more accurate transcript assembly via parameter advising

Computational tools used for genomic analyses are becoming increasingly sophisticated and complex. While these applications often provide more accurate results than their predecessors, a new problem is emerging in that these pieces of software have a large number of tunable parameters. Choosing the wrong parameter values for an application may lead to significant results being overlooked or false results being reported. We take some first steps towards generating a truly automated genomic analysis pipeline by developing a method for automatically choosing input-specific parameter values for reference-based transcript assembly. We extend the parameter advising framework, first developed for multiple sequence alignment, to optimize parameter choices for the Scallop transcript assembler. In doing so, we provide the first method for finding advisor sets for applications with large numbers of tunable parameters. By choosing parameter values for each input, the area under the curve (AUC) when comparing assembled transcripts to a reference transcriptome is increased by 28.9% over using only the default parameter choices on 1595 RNA-Seq samples in the Sequence Read Archive. This approach is general, and when applied to StringTie it increases AUC by 13.1% on a set of 65 RNA-Seq experiments from ENCODE. Parameter advisors for both Scallop and StringTie are available on Github1.
A Non-Pathogenic Environmental Isolate of Pseudomonas aeruginosa MCCB 123 with Biotechnological Potential

Pseudomonas aeruginosa is bacterium that is ubiquitously distributed in aquatic habitats and soil and is a normal bacterial flora of intestine, mouth and skin. The colonization is normally harmless and infection occurs only when general or local defence mechanism is reduced (Kiewitz and Tummler, 2000). i.e., it is an opportunistic human pathogen (Lyczak, 2000 and Ortiz-Herrera, 2004). It is frequently isolated from hospital environments, clinical specimens and soil and water environments (Palleroni, 1992). As several members of P. aeruginosa are known human pathogens, it is pertinent to differentiate between pathogenic and non-pathogenic strains.
Genomics of microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae)

Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees - whose large and undisturbed populations often span a variety of environmental conditions and local habitats - are particularly good models to study this process. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a nested sampling design, to evaluate microgeographic adaptation in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae). A high-coverage genomic resource of ∼250 Mb was assembled de novo and annotated, leading to 32,789 predicted genes. 97,062 bi-allelic SNPs were detected over 25,803 contigs, and a custom Bayesian model was implemented to uncover candidate genomic targets of divergent selection. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. These genes potentially underlie ecologically important phenotypes and indicate that adaptation to microgeographic habitat patchiness would affect genomic regions involved in a variety of physiological processes, among which plant response to stress (for e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Identification of genomic targets of microgeographic adaptation in the Neotropics is consistent with the hypothesis that local adaptation is a key driver of ecological diversification, operating across multiple spatial scales, from large- (i.e. regional) to microgeographic- (i.e. landscape) scales.
Molecular Characterization of Escherichia Coli Isolated from Poultry Meat and its Products

This study was conducted on chicken breast, chicken thigh, Shish Taouk, chicken shawarma, chicken nuggets and chicken luncheon (35 of each) collected from different supermarkets at Menoufia Governorates for isolation and identification of E. coli and using PCR for detection of virulence gene. The obtained results indicated that the incidence of E. coli was 14.3%, 20%, 14.3%, 17.1%, 14.3% and 20% of examined samples of chicken breast, chicken thigh, Shish Taouk, chicken shawarma, chicken nuggets and chicken luncheon, respectively. Moreover, the incidence of serologically identified E. coli O78, O26: H11, O2: H6, O91:H21, O44:H18, O128:H2, O1:H7, O103:H2, O127:H4, O114:H4 and O158. PCR results showed shiga toxin 2 gene(stx2) detected in (O1), (O2), (O114) & (O128), while shiga toxin 1 gene(stx1) detected in (O44), (O127) & (O158), also (O78) & (O91) Positive E. coli strains for stx1 and stx2 genes, and(O26) & (O103) Positive E. coli strains for stx1, stx2 and eaeA genes.
Growth and Calculation of Age for Red-Winged Blackbird Nestlings

We undertook this study (1) to determine mean growth and relative growth rate of several different body parts of nestlings, including feathers, (2) to develop a method of determining their ages with a reasonable degree of accuracy, and (3) to find if any differences exist between the growth of nestling redwings raised in a marsh and those in upland habitat. Redwing eggs hatch asynchronously, with as much as 48 hours between hatching of the first and last eggs in a clutch. Consequently we also wanted to learn whether the growth rate of the nestlings depends on the hatching sequence, on the number of birds in the nest, or whether it is independent of these factors. Mean growth in weight of Red-winged Blackbird nestlings in marshes has been reported by Williams (1940) and Brenner (1964). Williams gave mean tarsal growth; both he and Nero (1961) showed methods of sexing redwing nestlings of known age. No one has given methods of determining age of nestling redwings.
Aspect and slope influence plant community composition more than elevation across forest–tundra ecotones in subarctic Canada

Questions How does treeline community composition vary between elevations, aspects and slope angles in the alpine subarctic and what are the specific abiotic factors governing this variability? How do species richness and rates of community turnover vary from low to high elevation across the forest-tundra ecotone? What do the results indicate about future vegetation change? Location: Kluane Region, southwest Yukon, Canada. Methods We surveyed plant communities and measured key abiotic variables across forest-tundra ecotones in six alpine valleys, each with a north and a south-facing slope, in two mountain ranges of southwest Yukon. We used non-metric multidimensional scaling to identify patterns in plant community composition and infer which abiotic variables drive these patterns. We calculated species richness and community dissimilarity at regular elevational intervals to assess trends in richness and rates of community turnover within the ecotone. Results Plant communities varied more with aspect and slope angle than they did with elevation. Aspect-related differences were driven by warmer soil temperatures and deeper active layers on south compared to north-facing slopes, while differences related to slope angle occurred only on north-facing slopes and were driven by soil moisture. Species richness increased with elevation on north-facing slopes and showed no trend with elevation on south-facing slopes. Rates of community turnover were higher on south-facing than north-facing slopes. Conclusions Plant community composition within the forest-tundra ecotone is driven primarily by soil temperature and, to a lesser extent, soil moisture, both of which vary more in relation to aspect and slope angle than they do between forest and tundra elevations. We recommend that models of vegetation change in subarctic alpine regions address the possibility of change occurring at different rates and in different directions depending on the topographic characteristics of each slope. This article is protected by copyright. All rights reserved.
Modeling of a negative feedback mechanism explains age-dependent genetic architecture in reproduction in domesticated C. elegans strains

Most biological traits and common diseases have a strong but complex genetic basis, controlled by large numbers of genetic variants with small contributions to a trait or disease risk. The effect-size of most genetic variants is not absolute, but can depend on a number of factors including the age and genetic background of an organism. In order to understand the mechanisms that cause these changes, we are studying heritable trait differences between two domesticated strains of C. elegans. We previously identified a major effect locus, caused by a mutation in a component of the NURF chromatin remodeling complex, that regulated reproductive output in an age-dependent manner. The effect-size of this locus changes from positive to negative over the course of an animal’s reproductive lifespan. Using a previously published macroscale model of egg-laying rate in C. elegans, we show how time-dependent effect-size can be explained by an unequal use of sperm combined with negative feedback between sperm and ovulation rate. We validate a number of key predictions of this model using controlled mating experiments and quantification of oogenesis and sperm use. By incorporating this model into QTL mapping, we identify and partition new QTLs into specific aspects of the egg-laying process. Finally, we show how epistasis between two genetic variants is predicted by this modeling as a consequence of unequal use of sperm. This work demonstrates how modeling of multicellular communication systems can improve our ability to predict and understand the role of genetic variation on a complex phenotype. Negative autoregulatory feedback loops, common in transcriptional regulation, could play an important role in modifying genetic architecture in other traits. AUTHOR SUMMARY Complex traits are influenced not only by the individual effects of genetic variants, but also how these variants interact with the environment, age, and each other. While complex genetic architectures seem to be ubiquitous in natural traits, little is known about the mechanisms that cause them. Here we identify an example of age-dependent genetic architecture controlling the rate and timing of reproduction in the hermaphroditic nematode C. elegans. Using computational modeling, we demonstrate how this age-dependent genetic architecture can arise as a consequence of two factors: hormonal feedback on oocytes mediated by major sperm protein (MSP) released by sperm stored in the spermatheca and life history differences in sperm use caused by genetic variants. Our work also suggests how age-dependent epistasis can emerge from multicellular feedback systems.
Molecular phylogeny of Malenchus and Filenchus (Nematoda: Tylenchidae)

The family Tylenchidae is phylogenetically important to understanding early‐branching Tylenchomorpha and to assess soil ecosystems. In this study, we focus on Malenchus and Filenchus as representatives of the Tylenchidae. Samples collected worldwide result in 58 new sequences, and light microscopy and transmission electron microscopy provide details on morphological features. For the first time, comprehensive morphological data are evaluated in the context of a molecular framework, thus highlighting the phylogenetic and evolutionary complexity of this structurally minimalistic group. Results show that the genus Filenchus is polyphyletic in both the 18S and 28S rDNA phylogeny, while Malenchus is polyphyletic and monophyletic in the 28S rDNA and the 18S rDNA, respectively. Ultrastructural study demonstrates specific aspects of lateral cuticular incisures, cuticular layering and the amphideal fovea are surprisingly congruent with the obtained molecular phylogenies, while classical characteristics such as cuticle annulations are evolutionary highly plastic and mosaic in distribution. The study also reveals the shortage of D2/D3 domain in 28S rDNA as a phylogenetic marker for early‐branching Tylenchomorpha.
Crop coefficient of a popular potato variety in Bangladesh

Crop evapotranspiration (ET c ) and crop coefficient (K c ) values of potato (variety: BARI Alu -7, Diamant) at different growth stages were determined through lysimeter method at Irrigation and Water Management Division of Bangladesh Agricultural Research Institute (BARI), Gazipur during 2008 - 2009. The study was conducted by applying irrigation at 25 and 40 days after planting (DAP) allowing drainage (AD) (T 1 ), at 25, 40, and 55 DAP AD (T 2 ), at 25, 40, and 60 DAP AD (T 3 ), and at 25, 40, 55, and 60 DAP AD (T 4 ) within and adjacent of four lysimeter tanks. Irrigation at 25, 40, and 55 DAP produced the highest tuber yield and was considered to be suitable for estimating seasonal ET c , and K c values. The seasonal highest ET c was found to be 162 mm. The K c values of 0.25, 0.62, 0.70 and 0.18 were determined at initial, development, midseason and late season stages of potato. These values differed slightly from the FAO recommended values. As the lysimeter provides control environment, the K c values determined by this method are most dependable and recommended for estimating ET c of potato in semi-arid climatic conditions of Bangladesh. Bangladesh J. Agril. Res. 42(1): 67-76, March 2017