Miracle-dz/UniFAR-FTUs huggingface dataset:
Steroidogenic factor 1 expressing neurons in the ventromedial hypothalamus regulate feeding, metabolism and risk-associated decision making

The ventromedial hypothalamus (VMH) has long been implicated as one of the centres in the central nervous system (CNS) involved with the control of energy metabolism, feeding, fear, reproductive and aggressive behaviours. Historically, electrical stimulation and lesioning studies pointed to the VMH being a major regulator of feeding and energy metabolism, leading to it being termed the satiety centre. More recently, however, many of these functions have been attributed to the nearby arcuate nucleus (Arc) instead and the focus of the research on the VMH has been on its control of the hypoglycemic response, aggression and fear. The aim of this PhD was to employ cell-type specific optogenetic and DREADD (Designer Receptors Exclusively Activated by Designer Drugs) approaches to disentangle the role of the VMH in energy homeostasis in C57BL/6N mice. I used steroidogenic factor 1 (SF1) Cre recombinase mouse line to limit manipulations to the VMH and hypothesised that activity of SF1-expressing neurons would negatively correlate with feeding behaviour and body weight gain. Indeed, here I show that acute DREADD-mediated modulation of SF1 expressing neurons had rapid, bidirectional effects on feeding and metabolic parameters but also anxiety state. Furthermore, chronic DREADD treatment significantly altered bodyweight, nutrient partitioning and susceptibility to high fat diet (HFD) with limited effects on feeding or other behaviours. Optogenetic modulation of SF1 expressing neuron activity revealed differential prioritising of behaviours depending on the firing frequency of the SF1 neurons which is at least partially due to intrinsic synaptic properties of the SF1 neurons. In summary, I conclude that SF1 neurons have complex functions in integrating internal energy state with risk decision making, appropriate metabolic regulation and feeding behaviour.
Host-specific subtelomere: Genomic architecture of pathogen emergence in asexual filamentous fungi

Several asexual species of filamentous fungal pathogens contain supernumerary chromosomes carrying secondary metabolite (SM) or pathogenicity genes. Supernumerary chromosomes have been shown in in vitro experiments to transfer from pathogenic isolates to non-pathogenic ones and between isolates whose fusion can result in vegetative or heterokaryon incompatibility (HET). However, much is still unknown about the acquisition and maintenance of SM/pathogenicity gene clusters in the adaptation of these asexual pathogens to their hosts. We investigated several asexual fungal pathogens for genomic elements involved in maintaining telomeres for supernumerary and core chromosomes during vegetative reproduction. We found that in vegetative species or lineages with a nearly complete telomere-to-telomere genome assembly (e.g. Fusarium equiseti and five formae speciales of the F. oxysporum species complex), core and super-numerary chromosomes were flanked by highly similar subtelomeric sequences on the 3’ side and by their reverse complements on the 5’ side. This subtelomere sequence structure was preserved in isolates from the same species or from polyphyletic lineages in the same forma specialis (f.sp.) of the F. oxysporum species complex. Moreover, between some isolates within F. oxysporum f.sp. lycopersici, the mean rate of single nucleotide polymorphisms (SNPs) in a supernumerary chromosome was at least 300 times lower than those in core chromosomes. And a large number of HET domain genes were located in SM/pathogenicity gene clusters, with a potential role in maintaining these gene clusters during vegetative reproduction.
CHARACTERIZATION OF OKRA GENOTYPES BY MOLECULAR MARKERS AGAINST YELLOW VEIN MOSAIC VIRUS

Molecular characterization against yellow vein mosaic virus resistance has been observed in 18 genotypes okra genotypes. The virus associated with yellow vein mosaic virus were detected by PCR amplification of specific Primer Pair 1 and Primer Pair 3 were used for characterizing different genotypes with yellow vein mosaic virus which is linked with detection of presence or absence of okra yellow vein mosaic virus. PCR analysis revealed that all 18 genotypes screened for presence of okra yellow vein mosaic virus, were linked to susceptibility by Primer Pair 1 and Primer Pair 3 yielding band size 750bp except Phule Vimukta shows resistance and absence band in PCR analysis.
Differential Uptake and Utilization of Two Forms of Nitrogen in Japonica Rice Cultivars From North-Eastern China

Japonica rice is widely planted in north-eastern China because of its superior food quality and stable grain yields. Nitrogen (N) is an essential element for rice growth, and development and its availability directly impacts on rice yields. The knowledge of N uptake and its utilization characteristics in japonica are thus important areas of research. Three japonica rice cultivars, SN265, SN1401, and SN9816, which are planted across large areas of north-eastern China, were used here to evaluate the uptake and utilization along the life cycle of both ammonium (NH4+) and nitrate (NO3−) in hydroponically grown plants. The plants were grown in one of three different solutions with varying NH4+:NO3− ratios: 1:0, 0:1, and 1:1 (The total N content was 40 mg L−1 for each treatment). At the tillering stage, when only NO3− was provided, lower rates of N uptake and enzyme activities of three rice plants resulted in reduced tiller numbers. During the reproductive stage, the NH4+ and (NH4+) uptake rates in SN1401 were consistently maintained at high levels, whereas the rates in SN265 and SN9816 were significantly lower, across all three treatments. At the booting stage, when only NO3− was provided, SN1401 plants had significantly higher expression levels of OsNRT2.1 and OsNRT2.2, higher activity of nitrate reductase in the roots, and higher activity levels of glutamine synthetase and glutamate synthase in the leaves, compared with the SN265 and SN9816 plants. The higher enzyme activity was beneficial to the secondary assimilation of N, which ultimately promoted panicle development in SN1401. Consequently, the grain yield per plant of SN1401 was the highest with solutions of both NH4+ and NO3−. These results indicate that selecting a rice cultivar with higher utilization of NO3− is beneficial for increasing the number of grains per panicle, grain yield, and N use efficiency.
Cloning and characterization of O-xylosyltransferase gene from Pinctada fucata martensii

ABSTRACT Glycosaminoglycan (GAG), an important component of proteoglycan (PG), was biosynthesized with the initiation by peptide O-xylosyltransferase. O-xylosyltransferase activity was presented as a marker for increased PG synthesis. In the present study, a novel O-xylosyltransferase (OXT) gene was identified from Pinctada fucata martensii (PmOXT). The PmOXT-deduced protein sequence carried a typical water-soluble carbohydrate domain, branch domain, and xylosyltransferase domain. Homologous analysis of PmOXT presented the conserved DXD motif and catalytic structure characteristics. Phylogenetic tree analysis showed the traditional taxonomy and PmOXT clustered with Crassostrea gigas. PmOXT was expressed in all the detected tissues and developmental stages. PmOXT had a significantly higher expression level in the shell formation associated tissues and developmental stages. PmOXT expressed significantly decreased in the central zone of the mantle and marginal zone of the mantle after RNA interference; additionally, OXT activity and GAG content in the extrapallial fluid were significantly reduced compared with the control. Furthermore, the crystal tablets of prismatic layer displayed obvious holes and disordered crystals with obviously rough surface and irregular crystal tablets were observed in the nacre after RNAi. Results suggested that PmOXT affected the shell formation by influencing the formation of GAGs in the process of addition to the core proteins.
Current State of Modern Biotechnological-Based Aeromonas hydrophila Vaccines for Aquaculture: A Systematic Review

This systematic review describes what “the cutting edge vaccines for Aeromonas hydrophila are”. The focus is on types of high tech biotechnological based vaccines, target gene or antigen in developing these vaccines, and challenge model fish species used in vaccines efficacy testing. Vaccines delivery methods, immune response, and their efficacy, adjuvant or carrier systems used, and the overall experimental setup or design of the vaccines under investigation are also described. The search for the original papers published between 2009 and 2018 was conducted in June of 2018, using the PubMed and Google scholar electronic database. Twenty-three (23/4386) studies were included in the final assembly using PRISMA guidelines (Protocol not registered). Recombinant protein vaccines were the highly experimented type of the modern biotechnological based vaccines identified in the selected studies (16/23; 70%). Outer membrane proteins (OMPs) of different β-barrels were shown to be a potential antigenic entity for A. hydrophila vaccines (57%). Intraperitoneal route with conventional carries or adjuvants was the highly applied delivery system while very few studies used herbal based vaccine adjuvants and nanomaterial as a vaccine carrier. Variation was observed in terms of protection levels in the selected studies. The experimental designs partly contributed to the observed variation. Therefore, recombinant vaccines that use new carrier system technologies and delivered through oral route in feeds would have been of great value for use in the prevention and control of A. hydrophila infections in fish. Despite the usefulness as academic tools to identify what is important in pathogenicity of the etiological agent to the host fish, these vaccines are only economically viable in very high-value animals. Therefore, if vaccination is a good option for A. hydrophila group, then simple autogenous vaccines based on accurate typing and evidence-based definition of the epidemiological unit for their use would be the most viable approach in terms of both efficacy and economic feasibility especially in low and middle-income countries (LMIC).
Heating cell immobilization of Streptomyces griseus and its variant for economical fructose production

Aims: This study determined the optimum temperature for cell immobilization, the optimum time of fructose production by immobilized cell, and immobilized cell stability against repeated use in fructose production. Methodology and results: Research on cell immobilization of Streptomyces griseus and the variant have been done. The S. griseus variant was resulted from UV mutation. The variant was able to produce fructose as hydrolysis product 3 times as much after 30 min. Heating was done at 50, 60, 70, 80 and 90 °C. The fructose production was performed at intervals of 4 h for 32 h. The results showed that the optimum cell immobillization temperature of S. griseus and its variant was 80 °C. The optimum time of fructose production by immobilizing cell of S. griseus was 28 h and its variant cells was 24 h. Immobilized cells of S. griseus can be reused for 6 × 28 h to produce fructose compared to variants cells was 5 × 24 h, respectively. Conclusion, significance and impact of study: This study reported that immobilized cells of S. griseus can be reused and its variant were highly advantageous in the production of fructose. The amount of fructose production was increased as compared to the conventional method and the cost of production could be reduced as well.
Insulin effect during a Heatsynch protocol in dairy cows

ABSTRACT: The objective of this study was to evaluate the effect of exogenous insulin administration on follicular growth, estrus presentation and conception rate during a protocol of ovulation synchronization. Dairy cows were subjected to the Heatsynch protocol, with the insertion of an intravaginal device containing 1.9 g of progesterone (CIDR) and an intramuscular injection containing 2.5 mg of GnRH on day 0. On day 7, the CIDR was removed and subjects were given 12.5 mg of dinoprost. Also on day 7, Insulin Group (IG, n = 21) animals received a subcutaneous injection containing 0.25 IU / kg of recombinant human insulin and the control group (CG, n = 25) received a 0.9% NaCl injection. On day 8, an injection of 0.5 mg of estradiol cypionate was administered to all cows. Animals were inseminated 12 hours after estrus presentation or at day 10 at fixed time. Follicular development was evaluated on days 7, 9, and 10 using transrectal ultrasonography, estrus presentation was observed between days 8 and 10, and conception rate was evaluated 30 days after AI. There were no differences in growth rate, follicular diameter, estrus presentation, and conception rate. Therefore, application of a single dose of insulin does not promoted an increase in follicular size, estrus presentation and conception rate in dairy cows.
In vivo Anti-diarrheal and CNS Depressant Activities of Hemigraphis hirta (Vahl) T. Anders.

Hemigraphis hirta has been used by folk practitioners to alleviate symptoms of several diseases, although the pharmacological activities of this plant have not been thoroughly explored. The current study was designed to assess the anti-diarrheal and CNS depressant activities of H. hirta in mice model. For both assays, the experimental mice received the methanolic crude extract and its petroleum ether soluble fraction at dose of 200 and 400 mg/kg body weight which are denoted as CME 200, CME 400, PESF 200 and PESF 400, respectively. Both fractions remarkably attenuated castor oil-induced diarrheal effect in a dose-dependent manner and the results were comparable to standard loperamide (89.47%). Among all, PESF 400 exhibited statistically significant (p < 0.01) anti-diarrheal activity as demonstrated by 78.95% inhibition of defacetion. Compared to reference drug diazepam, all the tested samples considerably shortened the time for onset of sleep and prolonged the duration of phenobarbitoneinduced sleep in mice. The results of our present study, being reported for the first time, demonstrate that the methanol extract of leaves of H. hirta and its organic soluble partionates possesses significant anti-diarrheal and CNS depressant properties. However, this preliminary screening requires further detailed investigation to confirm these findings as well as to isolate and characterize the bioactive compounds. Bangladesh Pharmaceutical Journal 22(2): 176-180, 2019
Highly Efficient Genome Engineering in Bacillus anthracis and Bacillus cereus Using the CRISPR/Cas9 System

Genome editing is an effective tool for the functional examination of bacterial genes and for live attenuated vaccine construction. Here, we report a method to edit the genomic DNA of Bacillus anthracis and Bacillus cereus using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)9 system. Using two prophages in B. anthracis as targets, large-fragment deletion mutants were achieved with rates of 100 or 20%. In B. cereus, we successfully introduced precise point mutations into plcR, with phenotypic assays showing that the resulting mutants lost hemolytic and phospholipase enzyme activities similar to B. anthracis, which is a natural plcR mutant. Our study indicates that CRISPR/Cas9 is a powerful genetic tool for genome editing in the Bacillus cereus group, and can efficiently modify target genes without the need for residual foreign DNA such as antibiotic selection markers. This system could be developed for use in the generation of marker-free live anthrax vaccines or for safer construction of microbiological candidate-based recombinant B. cereus.
Sonographic Determination of Residual Bladder Volume after Application of Different Cystotomy Closure Techniques in Dogs

Received: Revised: Accepted: Published online: April 01, 2015 May 22, 2016 July 18, 2016 September 05, 2016 Residual urine volume is measured to diagnose various neurogenic and obstructive disorders of the urinary bladder. However, it is hypothesized that cystotomy closure using inverting patterns decreases intraluminal diameter of urinary bladder which consequently reduce residual bladder volume. This study aimed to investigate the ideal suturing style for cystotomy incision closure which would exert the least effect on residual bladder volume. The effect of various suturing styles on residual bladder volume was studied sonographically. Residual Bladder Volume (RBV) was calculated by the formula, i.e. RBV=L×W× (DL+DT)/2×0.625, where L=longitudinal diameter, W=transverse diameter, DL= depth at longitudinal diameter, DT=depth at transverse diameter. 24 healthy mongrel dogs were selected and randomly divided into four equal groups A, B, C and D (n=6). In groups A, B and C, the cystotomy incision was subsequently closed by two-layered appositional suturing pattern, two-layered inverting pattern and three layers (using a combination of appositional and inverting styles), respectively. Group-D remained as sham-operated Control. The results clearly showed that the three-layered closure technique using a combination of appositional and inverting patterns (Group-C), significantly reduced the bladder volume (P<0.01). Two-layered inverting patterns (Group B), also reduced the bladder volume but not up to a significant level, whereas, the appositional suturing technique (group-A) exerted the least effect on residual bladder volume. Conclusively, it was inferred that a two-layered appositional suturing pattern should be preferred for closure of cystotomy incision to avoid significant changes in residual bladder volume. ©2016 PVJ. All rights reserved
Small mammal distributions relative to corridor edges within intensively managed southern pine plantations.

: We characterized small mammal communities in three loblolly pine ( Pinus taeda ) stands in the Lower Coastal Plain of South Carolina during June 1998–Aug. 2000 to investigate influence of corridor edges on small mammal distribution. We live-trapped small mammals in three regenerating stands following clearcutting. Harvested stands were bisected by 100-m-wide, 20–23-year-old pine corridors. During 47,040 trap nights, we recorded 907 captures of 661 individual small mammals. Species captured included southern short-tailed shrews ( Blarina carolinensis ), cotton mice ( Peromyscus gossypinus ), cotton rats ( Sigmodon hispidus ), eastern harvest mice ( Reithrodontomys humulis ), marsh rice rats ( Oryzomys palustris ), and golden mice ( Ochrotomys nuttalli ). We did not observe an edge effect (i.e., preference or avoidance) in small mammal captures at the corridor edge. Rodent captures were greatest in harvested stands, declined near the edge of mature pine corridors, and were lowest within corridors. Shrew captures were generally greatest in mature pine corridors and least in the interior of harvested stands. Retention of mature pine corridors of only 100 m may maintain some small mammals (i.e., shrews) that would not occur if stands were completely harvested. South. J. Appl. For. 29(3):148–151.
Antitermitic Activities of Shisham (Dalbergia Sissoo Roxb.) Heartwood Extractives against two Termite Species

Shisham (Dalbergia sissoo) heartwood extractives were investigated for antitermitic activities against Heterotermes indicola and Reticulitermes flavipes. Heartwood extractives were removed from wood shavings by soxhlet extraction using (2:1) ethanol: toluene as the solvent system. Filter paper bioassays were conducted against both species to observe concentration dependent feeding response and mortality of termites. Results indicated that the highest termite mortality occurred at 10 mg/ml with a LC50 at 5.54 and 3.89 mg/ml against H. indicola and R. flavipes, respectively. Shisham extractives showed more repellency and antifeedant activity against H. indicola compared to R. flavipes. In choice and no-choice feeding bioassays with extracted and un-extracted Shisham wood blocks, increased wood loss due to termite feeding was observed on extracted blocks compared to un-extracted blocks. Higher termite mortality was also observed after feeding on un-extracted blocks compared to extracted blocks. Results also showed that extractives from Shisham imparted resistance to vacuum-pressure treated Southern pine (SYP, Pinus taeda L.) and Cottonwood (CW, Populus deltoides) against both species. These results suggest that Shisham extractives have antitermitic properties and may be potentially useful in the development of environment friendly termiticides.
Strategic Development of a Next-Generation Multi-Epitope Vaccine To Prevent Nipah Virus Zoonotic Infection

Nipah virus (NiV) is an emerging zoonotic pathogen, reported for the recent severe outbreaks of encephalitis and respiratory illness in humans and animals, respectively. Many antiviral drugs have been discovered to inhibit this pathogen, but none of them were that much efficient. To overcome the complications associated with this severe pathogenic virus, we have designed a multi-epitope subunit vaccine using computational immunology strategies. Identification of structural and nonstructural proteins of Nipah virus assisted in the vaccine designing. The selected proteins are known to be involved in the survival of the virus. The antigenic binders (B-cell, HTL, and CTL) from the selected proteins were prognosticated. These antigenic binders will be able to generate the humoral as well as cell-mediated immunity. All the epitopes were united with the help of suitable linkers and with an adjuvant at the N-terminal of the vaccine, for the enhancement of immunogenicity. The physiological characterization, along with antigenicity and allergenicity of the designed vaccine candidates, was estimated. The 3D structure prediction and its validation were performed. The validated vaccine model was then docked and simulated with the TLR-3 receptor to check the stability of the docked complex. This next-generation approach will provide a new vision for the development of a high immunogenic vaccine against the NiV.
Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence

S-adenosylmethionine (SAM) is the methyl-donor substrate for DNA and histone methyltransferases that regulate cellular epigenetic states. This metabolism-epigenome link enables the sensitization of chromatin methylation to altered SAM abundance. However, a chromatin-wide understanding of the adaptive/responsive mechanisms that allow cells to actively protect epigenetic information during life-experienced fluctuations in SAM availability are unknown. We identified a robust response to SAM depletion that is highlighted by preferential cytoplasmic and nuclear de novo mono-methylation of H3 Lys 9 (H3K9) at the expense of global losses in histone di- and tri-methylation. Under SAM-depleted conditions, de novo H3K9 mono-methylation preserves heterochromatin stability and supports global epigenetic persistence upon metabolic recovery. This unique chromatin response was robust across the mouse lifespan and correlated with improved metabolic health, supporting a significant role for epigenetic adaptation to SAM depletion in vivo. Together, these studies provide the first evidence for active epigenetic adaptation and persistence to metabolic stress.
Factors affecting the survival and implantation of human blastocysts following vitrification

i DECLARATION . ii ACKNOWLEDGEMENTS . iii TABLE OF CONTENTS. iv LIST OF TABLES . ix LIST OF FIGURES . x ABBREVIATIONS . xi PUBLICATIONS AND PRESENTATIONS. xiv Publication . xiv Oral presentations . xiv Poster presentations . xiv