Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence and Mechanisms of Ontogenetic Changes in Body Colour Lightness in Intertidal Marine Invertebrates

ABSTRACT Ontogenetic changes in body colouration are known to occur in some benthic marine invertebrates and have been associated with ecological shifts in diet and physiological tolerance. It is not known, however, whether ontogenetic colour changes are common among benthic marine invertebrate species or which mechanisms control these changes in body colour. This study therefore examines the degree of lightness in body coloration (converted to greyscale); the specific goals were to determine (1) the proportion of species that undergo a change in body colour lightness from a sample of 15 intertidal species, (2) if changes in lightness during ontogeny are associated with changes in microhabitat use, and (3) if diet or exposure to light affects the production of shell pigmentation in the snail Nucella ostrina, which are known to hatch white but later add coloured pigments to new shell growth. For each of the 15 species that I examined, 60-140 individuals of varying sizes were collected, weighed, and their body lightness index was quantified using digital imaging. Six motile species were then analyzed for a microhabitat shift during ontogeny. Of the 15 species studied, 11 underwent some degree of change in body colour lightness during ontogeny. Six of those 11 species had a change in body colour lightness of at least 10% between the 10 smallest and 10 largest individuals. The study of microhabitat use by six motile species revealed only one (a hermit crab) that substantially changed microhabitat use during ontogeny; two species partially changed microhabitat use during ontogeny, one other species showed no change, and results were inconclusive for the last two species. The last experiment revealed that N. ostrina hatchlings raised in the dark remained significantly lighter in colour than those exposed to light and that diet did not appear to impact shell colour, indicating that the production of dark shell pigmentation in this species is stimulated by exposure to bright sunlight.
Bacteriological profile and their antimicrobial susceptibility pattern in central venous catheter tip culture

Background: Bacterial colonization of central venous catheter (CVC) carries risk of developing catheter-related blood stream infections (CRBSI). The purpose of this study is to find out the frequency of colonization of CVC by different bacterial pathogens and their antibiotic sensitivity pattern. Materials and Methods: A total of 53 CVC tip were received in one-year duration for culture and antibiotic sensitivity pattern. The isolated organisms were identified by standard microbiological procedure and subjected to antimicrobial sensitivity. Results: out of 53 CVC tip sent for culture and sensitivity, 21 (39.6%) showed significant growth. Out of 21 culture positive 52.3% were gram negative bacilli, 33.3% were gram positive cocci, 4.8% were Candida spp. Acenitobacter baumannii and Staphylococcus aureus were frequent pathogens isolated. Gram negative bacteria were less sensitive to antibiotics whereas gram positive bacteria were sensitive to Vancomycin. Conclusion: Though various organisms were isolated as colonizer of CVC, Acenitobacter baumannii is the most common colonizer. Antibiotic resistance has already emerged and represents a major problem.
SSR FINGERPRINTING OF BLACK RASPBERRY CULTIVARS SHOWS DISCREPANCIES IN IDENTIFICATION

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars are noted for showing very few differences, and seedlings for a lack of segregation for important traits. Genetic fingerprinting using microsatellite, or simple sequence repeat (SSR) markers, can reliably identify unique clones and evaluate diversity in black raspberry cultivars. Twenty-one black raspberry cultivars were sampled from the USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. Black raspberry clones were also sampled from nurseries, grower’s fields, and other black raspberry breeding programs for comparison. These genotypes were compared using 18 polymorphic SSR primer pairs. The black raspberries 'Bristol,' 'Jewel,' and 'Mac Black' had consistent SSR fingerprints between sources. However, plants being sold as 'Black Hawk' and 'Cumberland' had the same fingerprint as 'Jewel'. Plants of 'Bristol', 'Cumberland', 'Munger', 'New Logan', 'Plum Farmer' and 'Shuttleworth' in the NCGR collection had identical fingerprints. Eleven unique SSR fingerprints were found among plants being grown or sold as ‘Munger’, though there was one predominant fingerprint for this cultivar. 'Allen' and 'John Robertson' were each represented by three different fingerprints from three different sources, and 'Earlysweet' and 'Jewel' had SSR alleles at multiple loci that cannot be explained by their reported pedigrees. While overall genetic diversity in black raspberry cultivars is low, discrepancies in the naming of clones appear to be widespread in commercial and research plantings. Future work in this area should focus on sampling additional independent sources of plant material and evaluating clones to determine the extent of performance differences. Further SSR development in black raspberry may be needed to fingerprint some unique clones.
High Planting Rates Improve Weed Suppression, Yield, and Profitability in Organically-Managed, No-till—Planted Soybean

High soybean populations have been shown to hasten canopy closure, which can improve both weed suppression and soybean yield. In conventional soybean production, the high cost of genetically engineered seed and seed treatments have led growers to plant at lower rates to maximize profitability. For organic farmers, market price premiums are typically double the price received for conventional soybean. Without chemical or mechanical weed management, cultural practices are particularly important for adequate weed suppression in cover crop—based organic no—till planted soybean production. In 2014, an experiment was conducted in Aurora and Hurley, New York, to assess the effects of increasing soybean planting rates on weed suppression, soybean yield, and partial economic return. Five planting rates ranging from 195,000 to 914,000 seeds ha-1 were arranged in a randomized complete block design. As soybean planting rate increased, weed biomass decreased and soybean yield increased at both sites. An asymptotic model described the relationship between increasing soybean planting rate and yield, and the estimated maximum yield was 2,504 kg ha-1 in Aurora and 3,178 kg ha-1 in Hurley. Despite high soybean populations, minimal lodging was observed. Partial returns decreased beyond the predicted economically optimal planting rate of 646,000 seeds ha-1 in Aurora and 728,000 seeds ha-1 in Hurley as higher seed costs were no longer offset by yield gains. Based on our results, planting rates that are more than double the recommended rate of 321,000 seeds ha-1 for wide row (≥76 cm) conventional soybean management in New York can enhance weed suppression, increase yield, and improve profitability in organic no-till planted soybean production. Nomenclature: Soybean, Glycine max (L.) Merr.
History of artificial insemination in poultry, its components and significance

Artificial insemination (AI) technology use in poultry production has enabled the rapid dissemination of genetic material from a small number of superior males to a high number of females. Excellent fertility in poultry can be obtained by AI compared to natural mating. Successful application of this technique needs good quality semen that should be inseminated very close to the sperm storage tubules in the female to obtain the optimum fertility in chicken. Since the 1950s, AI has been used in commercial poultry production, initially in Israel and Australia, followed by the USA. Doses of spermatozoa required for AI increases with storage time or that obtained from aged bird. The average volume of semen is between 0.05-0.50 ml in light chicken breeds and 0.1-0.9 ml in heavy males. In light turkeys, volume is 0.08-0.30 ml, whereas in heavy-weight males it is 0.1-0.33 ml. Quality evaluation of semen gives an indication of the male reproductive potential and is the major determinant of fertility and subsequently hatchability of eggs. Semen from cockerels contains between 3-7 billion sperm cells/ml. Among the several factors that influence the semen quality, sperm motility is a primary determinant of fertility in domestic fowls; however, visual examination of semen cannot be ignored for successful AI under field conditions. Dilution of low and viscous volume of avian semen is essential for handling and storage, and chicken semen typically requires a two to three-fold dilution. Collected samples should be preserved at 2-8°C for avian species, ideally with turkey sperm stored at 4-8°C, and chicken semen at 7-8°C for good fertility. Currently, the technique of AI in most of the poultry species is well developed; however, there is a need for successful development programme of this technique in non-domesticated birds to assist in creating viable, self-sustaining populations of critically endangered species.
Zebrafish as a model organism for cardiovascular studies

Cardiovascular diseases (CVD) are the leading cause of morbidity and mortality worldwide. There is a need for a model organism which is cost effective, easy to use and maintain in a lab. Zebrafish qualifies very well for all these criteria. The maintenance cost is much lower than rodents and it is a small animal and easy to use. Adult zebrafish grows to 3-4 cm and females can lay hundreds of eggs daily; providing a good supply of embryos for the experiments. The complete genome of the zebrafish is sequenced, making genetic modifications and related studies possible.
Lipid metabolism in skeletal muscle of broiler chickens after fattening period and fasting

U radu je istražen utjecaj 48-satnog gladovanja na metabolizam masnih tvari u skeletnim misicima pilica teske hibridne linije Ross. Nakon zavrsetka tova i gladovanja žrtvovano je po deset životinja kojima su uzeti uzorci grudnog i bedrenog misica. U homogenatima tkiva određene su koncentracije triglicerida, kolesterola i lipidskih peroksida te aktivnost lipoproteinske lipaze. Nakon zavrsetka tova, u bedrenom misicu pilica bila je znacajno veca koncetracija triglicerida (p<0, 05) kao i aktivnost lipoproteinske lipaze (p<0, 05) u odnosu na grudni misic pilica. Gladovanje je rezultiralo znacajnim smanjenjem koncentracija triglicerida (p<0, 05) i kolesterola (p<0, 05) te povecanjem koncentracije lipidskih peroksida (p<0, 05) u bedrenom misicu dok je u grudnom misicu koncentracija lipidskih peroksida znacajno smanjena (p<0, 05). Aktivnost lipoproteinske lipaze se nakon gladovanja znacajno povecala u grudnom (p<0, 05), a smanjila u bedrenom misicu pilica (p<0, 05) u odnosu na vrijednosti dobivene na kraju tova. Rezultati ovog istraživanja potvrđuju da sukladno razlici u građi i metabolizmu promatranih misica, bedreni misic ima vecu koncentraciju triglicerida i vecu aktivnost lipoproteinske lipaze nakon zavrsetka tova dok u gladovanju dolazi do potrosnje zaliha masnih tvari kao i povecanja osjetljivosti na oksidativna ostecenja.
Behaviour-dependent activity and synaptic organisation of septo-hippocampal GABAergic neurons

Animal behaviour is coordinated by biological rhythms over multiple timescales. In the temporal cortex, rhythmic oscillatory activity in the 5 to 12 Hz theta frequency range supports behaviour through temporal windows of changes in excitability and circuit computation. Subcortical inputs, including those from the medial septum are thought to generate the theta oscillatory activity. However, the rules of innervation of identified types of cortical cells in different cortical regions by a diverse population of septal neurons are largely unknown. During my DPhil studies, I tested the hypothesis that medial septal GABAergic neurons which exhibit distinct activity patterns would express distinct molecular marker combinations and have distinct synaptic partners. In Chapters 1 and 2, I formulate my research questions and explain the methodology used. My main findings are presented in chapters 3 to 7. In Chapter 3, I present the strategy used to identify four populations of rhythmic medial septal neurons based on their spike-train dynamics in the mouse in vivo. In Chapter 4, I present a detailed analysis of the spike-timing and molecular parameters of a specialised population of rhythmic neuron, the Teevra cells. Teevra cells are PV+, do not change their firing rate from rest to running and fire short bursts of action potentials preferentially at the trough of both CA1 theta and slow irregular activity recorded in stratum pyramidale. In Chapter 5, I show that Teevra cells selectively innervate axo-axonic cells and CCK-immunopositive interneurons in hippocampal area CA3, bypassing CA1, CA2, and the dentate gyrus. In Chapter 6, I show that Teevra cell axons terminate in restricted septo-temporal segments of CA3 according to their rhythmicity. Finally, in Chapter 7, I present the Komal cells, which fire long bursts of action potentials at the peak of theta, increase their firing rate during running, and preferentially innervate extrahippocampal cortices. I discuss the broad relevance of my observations in Chapter 8. Overall, my results show an unexpected specialisation in the organisation of medial septal GABAergic inputs to the temporal cortex. Teevra cells fire maximally at the trough and preferentially innervate the CA3 whereas Komal cells fire maximally at the peak and target extrahippocampal cortices, thereby coordinating the timing of converging glutamatergic inputs to CA1 via disinhibition. This cortical-region-specific GABAergic innervation by physiologically distinct septal neuronal types suggests a general mechanism for the coordination of network activity, both during regular theta oscillations and irregular large amplitude waves, providing windows of computation through synchronisation of neuronal activity in the cortex.
Protein Estimating in Imported Poultry Feed Mixture and Soybean Meal to Iraq

This study aimed to evaluate rate of the protein in the imported poultry feed and soybean meal to Iraq and know the effect of different rates of the protein on the poultry. Samples of used feed in poultry nutrition has collected, where (38) samples of soybean meal took and (62) samples of imported poultry feed mixture and it has been tested in the kjeldahl device. The results indicated the rate of the protein in soybean meal was (36-39) , (41-47) and (48-49) in 3 samples (8%) , 30 samples (80%) and 5 samples (13%) respectively and the rate of the protein in poultry feed was (15-16), (16-21) and (22-24) in 6 samples (6%), 56 samples (90%) and 2 samples (3%) respectively. This study concluded that it must estimate the rate of the protein for the imported soybean meal; poultry feed mixture to ensure the quality of the feed within the frame work allowed.
MECHANISTIC INSIGHTS INTO EUKARYOTIC TRANSCRIPTION USING NOVEL CRYSTALLOGRAPHIC TECHNIQUES

DNA-directed RNA Polymerase II (Pol II) is highly conserved among eukaryotic organisms and plays a fundamental role in cellular life, specifically gene transcription. This process is universal and is at the core of gene regulation; therefore, understanding its molecular details will provide essential clues that could potentially lead to pharmacological manipulation of gene expression. In this work we reveal, for the first time, the nature of interactions between Pol II and a complete nucleic acid scaffold. The upstream double helix lies over a wedge-shaped loop from Rpb2(862-874) that engages the minor groove, providing part of the structural framework for DNA tracking during elongation. Rudder and fork loop-1 residues insert in between the DNA/RNA hybrid and non-template strand at the upstream end of the bubble, suggesting a direct role in coordinating annealing of DNA strands. At the downstream end, interactions between the non-template strand, Rpb1(1103-1112) and Rpb2(501-510) support an open fork. These Rpb1 residues form a rigid domain with the trigger loop (TL), stabilizing its off, non-catalytic state, indicating that “on/off” conformational transitions, where the TL moves in close proximity to the matched nucleotide for catalysis, may be linked to interactions with the non-template strand. To further examine the role, structurally, of the trigger loop and bridge helix during translocation and catalysis, we characterized the gain of function T834P variant of Pol II. Structural studies of T834P in the presence of a matched nucleotide revealed the complete TL in the on-state, a conformation only observed previously in two low resolution datasets. Our preliminary analysis suggests that kinking of the bridge helix potentially shifts equilibrium into the post-translocation state during the nucleotide addition cycle, which would prolong interactions of the trigger loop with the matched nucleotide in the insertion site. Elucidation of these structures was achieved through the use of X-ray free electron laser sources, which extended the resolution to 3.3 A. Methodologies, like serial femtosecond crystallography and transmission electron microscopy, to aid in structural studies of highly relevant, and challenging protein targets, including multi-protein complexes of the transcriptional machinery are also discussed.
Local interactions lead to spatially correlated gene expression levels in bacterial groups

Many bacteria live in spatially structured assemblies where the microenvironment of a cell is shaped by the activities of its neighbors. Bacteria regulate their gene expression based on the inferred state of the environment. This raises the question whether the phenotypes of neighboring cells can become correlated through interactions via the shared microenvironment. Here, we addressed this question by following gene expression dynamics in Escherichia coli microcolonies. We observed strong spatial correlations in the expression dynamics for pathways involved in toxin production, SOS-stress response, and metabolism. These correlations can partly be explained by a combination of shared lineage history and spatial gradients in the colony. Interestingly, we also found evidence for cell-cell interactions in SOS-stress response, methionine biosynthesis and overall metabolic activity. Together our data suggests that intercellular feedbacks can couple the phenotypes of neighboring cells, raising the question whether gene-regulatory networks have evolved to spatially organize biological functions.
Use of sarmentine and its analogs for controlling plant pests

Viruses, fungi, bacteria, nematodes, and an effective amount of use to control the plant pathogenic infection by insects mentin and / or four mentin substantially the plant analogs of four mentin having the same activity and / or its seed and / or the plant a method for controlling the phytopathogenic infection in plants and compositions, which comprises applying to the substrate used to grow.
L'inflammation, prélude à la sclérose rénale : importance de NF-κB : La sclérose en rénale: ses mécanismes et son traitement

NF-κB forme une famille de facteurs de transcription. Ceux-ci sont consideres jouer un role central dans l'expression de genes impliques dans le recrutement, la proliferation et la differenciation cellulaires, et ainsi dans les mecanismes de l'inflammation, de la reparation et de la fibrose. En particulier, l'activation de NF-KB apparait determinante dans le developpement de maladies renales inflammatoires et leur progression vers la fibrose et l'insuffisance renale terminale. C'est pourquoi cibler NF-KB devrait permettre d'identifier de nouveaux composes pharmaceutiques susceptibles d'etre efficaces dans le traitement de ces maladies.
Fibulin-4A in zebrafish development

Fibulin-4 is an extracellular matrix protein required for the formation of the elastic fibers. Human mutations in the fibulin-4 gene cause autosomal recessive cutis laxa with widespread systemic involvement and congenital presentation. To study the developmental functions of fibulin-4, I studied one of the two fibulin-4 genes, fbln4a. The mRNA for fbln4a RNA was expressed in the adaxial cells around the notochord during somite formation, and in the myosepta, head, and heart at later stages. Fbln4a protein was localized to the notochord sheath starting from somite formation suggesting differential expression of fbln4a RNA and protein in the midline structures during development. To inactivate fbln4a in vivo, we used a retroviral mutant and an antisense morpholino oligonucleotide (MO) for transient knockdown. Embryos homozygous for the fbln4a mutation showed a complete loss of the Fbln4a protein, but presented no obvious gross abnormalities. However, fbln4a knockdown yielded cardiovascular and musculoskeletal defects at 2 days post fertilization including pooling of blood at the caudal vein plexus, vascular hemorrhage in the head, reduced circulation and heart rate, bent notochord, rounded somites and reduced embryo length. All of these features were rescued by co-injection of fbln4a mRNA with the MO. Early cardiac and vascular progenitor markers showed an expansion of the heart field and reduction of the vascular fields in knockdown embryos. Homozygous mutants were resistant, whereas heterozygotes were sensitized to the effect of fbln4a MO, protective compensatory mechanisms as a possible reason for phenotypic discrepancy between fbln4a mutant and knockdown animals. Inhibition of transforming growth factor beta (Tgfb) signaling with a small molecule rescued both the cardiovascular and connective tissue anomalies in knockdown embryos. By varying the period of treatment, I identified late gastrulation and early segmentation as the critical periods. I conclude that Fbln4a inhibits Tgfb signals emanating from the notochord and regulates cardiac and vascular progenitor pools. The public health significance of this work is the identification of Tgfb inhibition as a candidate approach for treating of fibulin-4-related cutis laxa, an orphan disease for which no treatment has been available to date.
Prevalence of carbapenemases with detection of NDM-1 gene in nonfermenters isolated from a tertiary care hospital of north India

Background: Increasing multidrug resistance in nonfermenters is of great concern to mankind because the drugs left in pipeline are only a few for the serious infections in hospital ICU settings. The present study was performed to determine the prevalence of carbapenem resistance among nonfermenters and to characterize the most prevalent MBL genes (NDM-1) by polymerase chain reaction, among phenotypically MBL positive isolates in a tertiary care centre of north India. Methods: A total of 383 clinical isolates comprising of 181 A. baumanii and 182 P. aeruginosa were included in this study. The A. baumanii and P. aeruginosa were identified by using standard bacteriological techniques. All these isolates were screened for imipenem and meropenem resistance by Kirby-Bauer disk diffusion method and Minimal Inhibitory Concentration (MIC) methods according to CLSI guidelines. Results: In the present study, the two nonfermenters ( A. baumanii and P. aeruginosa ) showed highest susceptibility to polymyxin-B (78.2%) followed by meropenem (70.5%), imipenem (66.4%), tigecyclin (57.6%) and combination of piperacillin-tazobactam (51.5%) by using disc diffusion method. Conclusion: Treatment of infections caused by nonfermerters like P. aeruginosa and A. baumanii producing different carbampenemases including NDM-1 are now posing serious challenge as these infections are resistant to almost all available antimicrobial agents.