Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of fasting on hepatic and renal gluconeogenic enzyme activities in ducklings

Blood glucose concentration, liver and kidney gluconeogenic enzyme activites were investigated during a six-day fasting period in ducklings (English heavy breed Peking Duck). Food deprivation commenced when ducklings reached the age of twenty-eight days. Normally fed ducklings were used as a control group. The ducklings were sacrificed by decapitation after a fasting period of three, four, five and six days, and blood and tissue samples were collected from both groups for analysis. During the experiment the concentration of blood glucose was above 6 mmol/L in both the control and experimental groups, except on experimental day three. Significiant rises in glucose-6-phosphatase (EC 3.1.3.9) (G6Pase) activites in the liver were observed on starvation days four, five and six (P=0.0012, P=0.0109, P=0.0279), and in the kidney on starvation days five and six (P=0.0373, P=0.0206, respectively). Hepatic fructose-1.6-bis-phosphatase (EC 3.1.3.11) (FDPase) activity showed a significant difference between the fasted and control group only after a four-day fast (P=0.0491), whereas renal enzyme activity increased after four (P=0.0279) and six (P=0.0373) days of food deprivation. Phosphoenolpyruvate carboxykinase (EC 4.1.1.32) (PEPCK) activity in the liver of fasted ducklings significantly decreased on fasting day five (P=0.032) was observed in comparison with the normally fed controls. The results showed that ducklings are able to maintain blood glucose concentration during a six-day fasting period. Changes in gluconeogenic enzyme activities indicate the important role of liver and renal gluconeogenesis for the maintenance of blood glucose concentration in fasted ducklings. These findings agree with earlier data obtained on chicken, thus confirming the similarities between the two avian speciec regarding the maintenance of blood glucose level with the process of gluconeogenesis during longer fasting.
Norepinephrine induces internalization of Kv1.1 in hippocampal neurons

Norepinephrine (NE), a catecholamine produced by dopamine β-hydroxylase, is released either as a hormone from the adrenal medulla into the blood, or as a neurotransmitter in the brain. Norepinephrine signaling serves as a global regulator of the brain, but there is still some functional selectivity in release and in the expression patterns of the various adrenergic receptor subtypes in different brain regions, to permit more specific sculpting of responses in the brain (O'Donnell et al., 2012). Extensive physiological and behavioral studies have demonstrated that NE/β2-adrenergic signaling could facilitate the induction of spike-timing-dependent plasticity (STDP) at excitatory synapses (Lin et al., 2003; Seol et al., 2007; Zhou et al., 2013) and enhances memory (Ji et al., 2003; Lemon et al., 2009; Miranda et al., 2011; Tronel et al., 2004), potentially through inhibiting dendritic potassium conductance and therefore increase the propagation of dendritic action potentials (Hoffman and Johnston, 1999; Watanabe et al., 2002). However, it remains unknown which potassium channels are involved in the modulation of dendritic excitability by NE/ β2-adrenergic signaling, and how these potassium channels are mobilized in response to β2-adrenergic receptor activation. Our preliminary data showed that NE (norepinephrine) blocked the delayed onset of action potentials and induced the inactivation of D-type currents. This effect was mediated by signaling scaffolding SAP97, which belongs to the DLG-MAGUK family and has been indicated to regulate membrane expression and stabilization of PDZ-ligand-containing receptors and ion channels (Kim et al., 1995; Tiffany et al., 2000). A plausible mechanism would be the NE-induced reduction in surface expression of Kv1.1. In this study, we showed that in primary hippocampus neurons, NE signaling, through β2 adrenergic receptor activity, induced internalization of endogenous Kv1.1. Additionally, the NE-induced internalization of Kv1.1 was impaired in SAP97 knockout neurons, suggesting that NE/β2-adrenergic receptor signaling can regulate surface Kv1.1 trafficking in a SAP97 dependent manner. Furthermore, we designed a PDZ/ligand class switch model by using compensatory mutants of SAP97 and Kv1.1, and characterized that the binding activity of SAP97 PDZ12 tandem was required for its interaction with the C-terminal PDZ domain binding motif of Kv1.1 and NE-mediated Kv1.1 internalization. Moreover, we found the PKA-mediated phosphorylation of Kv1.1 was also responsible for the mobility of potassium channels in response to adrenergic signaling. Overall, this study reveals a role of SAP97 in linking adrenergic signaling to the modulation of potassium channels surface expression, and provide a mechanistic understanding how G protein-coupled receptors regulate dendritic excitability.
Diagnóstico de Leucoptera coffeella (Lepidoptera: Lyonetiidae) y sus parasitoides en el departamento de Antioquia, Colombia

Coffee Leaf Miner, Leucoptera coffeella is one of the main insect coffee pests in the Neotropics, causing yield decreases up to 80%, in countries such as Brazil. In Colombia, this insect pest has been poorly studied, since the damage it causes has been sporadic. This exploratory investigation was carried out in order to diagnose the damage caused by the coffee leaf miner and its parasitoids in the department of Antioquia. Pest infestation levels were evaluated as to incidences of natural parasitism, identifying the species of the parasitoids, through a bietapic sampling performed in more than 1,100 coffee crops between the ages of 2 and 5 years. Sixty (60) coffee trees per crop were evaluated four times through systematic sampling between 2013 and 2014. The results indicated an average of leaf miner infestation level under 2%, and parasitism levels between 58 and 89 %. In total, 787 parasitoid individuals emerged, all belonged to the Order Hymenoptera, family Eulophidae, comprising two subfamilies: Eulophinae and Entodininae. Seven parasitoid species were identified: Closterocerus coffeellae, Closterocerus lividus, Zagrammosoma multilineatum, Pnigalio sarasolai, Horismenus sp. , Horismenus n. sp. , and Apleurotropis n. sp. These last two new species for Colombia, and perhaps for science. The most abundant natural enemy of coffee leaf miner was the species C. coffeellae. The management of this insect pest by means of a conservation biological control strategy is recommended.
A bioinformatic analysis of Mycobacterium tuberculosis and host genomic data

Human tuberculosis disease (TB) is caused by bacteria within the Mycobacterium tuberculosis complex, including M. tuberculosis (Mtb). Genetic variation within the pathogen can lead to drug resistance, affect virulence and transmissibility. I have analysed Mtb whole genome sequence data to improve the understanding of global genetic variation, and the resulting insights could ultimately assist the development of TB control measures. Whole genome sequencing platforms are being used to infer drug resistance profiles, and thereby could assist clinical management. I investigated the reproducibility of sequence data from two platforms (Illumina MiSeq, Ion Torrent PGM™) and two rapid analytic pipelines (TBProfiler, Mykrobe predictor). DNA replicates from the reference strain (H37Rv) and 10 drug-resistant strains were sequenced, and inferred drug resistance genotypes were compared to drug susceptibility testing phenotypes. Genome-wide association study (GWAS) can be used to detect mutations associated with Mtb drug resistance. A first GWAS (n=127) attempted to identify mutations associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. A second GWAS was applied to a large global set (n>6400) to identify mutations associated with first- and secondline drug resistance. M. aurum is an environmental mycobacteria that has been proposed as a model for the development of anti-TB drugs. I have assembled and annotated its draft genome, and identified copy number variants in known drug resistance targets. Approximately 10% of the Mtb genome consists of two gene families (pe/ppe) that are poorly characterised, and are hypothesised to be important virulence factors. Using a de novo assembly approach, I characterised these genes and their diversity across a global collection of clinical isolates with high depth short-read sequence data (n=518). A follow-up study using a long-read sequence technology (n=18, diverse stain types) confirmed the findings. This work also generated new annotated reference genomes and characterised methylation sites, which may affect transmissibility, pathogenicity and virulence. A future direction of the TB genomics field is to identify genetic check points in host-pathogen interactions using both human and Mtb genotypes. I analysed the genomes of ~720 TB case–Mtb pairs and identified susceptibility markers, which are promising targets for future control measures.
Effects of Short-Term Intake of Wheat Bran with Different Particle Sizes on the Murine Intestinal Environment

Wheat bran has a high dietary fiber content. In this study, we investigated the effects of short-term intake of wheat bran on intestinal environment in a murine model. Mice were fed with AIN-93G for 1 week, followed by experimental diets containing wheat bran with an average particle size of 53 μm (powdered) or 350 μm (granulated) for 1 additional week. During a 4-week period (twice-repeated feeding cycles), the ratio of bacteria belonging to the families Prevotellaceae and S24-7 increased in murine feces after intake of both particle-size diets. Furthermore, the amount of short fatty acids, particularly butyric acid, and cecal immunoglobulin A were significantly increased in the powdered wheat bran group, probably by the changes in intestinal microbiota composition. These findings may potentially explain many of the health benefits through the alteration of intestinal microbiota, even after short-term intake of wheat bran.
The cyto-toxicity of some chemotherapeutic drugs on liver and kidney cell lines and the protective role of Ca2+ binding proteins

Cancer Chemotherapy treatment involves the administration of drugs to patients, these drugs mainly work by interacting with the cell cycle or inhibiting DNA synthesis. Unfortunately, the toxicity of these chemotherapy drugs is severe and can have serious side-effects on different tissues and organs of the body. In chemotherapy treatment about 85% of cancer patients exhibit some degree of liver or kidney damage. Therefore, the aim of this study was to investigate the cytotoxicity of some of the most commonly used chemotherapy drugs; Methotrexate (MTX), Etoposide, Cisplatin and Doxorubicin (DOX) on liver and kidney cell lines (HepG2, Huh7.5, COS-7 and HK2). Therefore, our focus were on studying the molecular mechanism by which these drugs cause cell death in liver and kidney cells. This study also investigated the effects of some Ca2+ binding proteins (RGN, SERCA1, SERCA2b, SPCA1a, SPCA2) to test their ability to decrease the toxicity of these chemotherapeutic drugs in liver and kidney cells. The results showed that Etoposide, Cisplatin and DOX induce cell death in both kidney and liver cell lines via several different pathways such as apoptosis, necrosis, and autophagy. The results presented here also showed that several of the drugs used induced cell death by a novel new autophagic pathway in liver and kidney cells. Our data also suggested that regucalcin (RGN) and the endoplasmic reticulum Ca2+ pumps (SERCA1 and SERCA2b), but not the secretory pathway Ca2+ pumps (SPCA1a and SPCA2) were able to protect against different types of chemotherapy-induced toxicity in liver and kidney cells. These new observations will help to build up our awareness of the diverse effect of these drugs have on liver and kidney cells and may also help to develop protective interventions and strategies in the future to reduce hepatotoxicity and nephrotoxicity caused by these drugs.
Dissociable roles for the rTPJ and dmPFC in self-other processing: a HD-tDCS study

Background Social interaction relies on the integration and distinction of self and other. The dorsomedial prefrontal cortex (dmPFC) and the right temporoparietal junction (rTPJ) are two regions consistently associated with social processes. Theories of rTPJ function in social cognition include self-other distinction, self-inhibition, or embodied mental rotation, whereas the dmPFC is associated with a wide range of social functions involving understanding and encoding information pertaining to others. However, to date, no study has provided causal evidence for dissociable roles of the rTPJ and dmPFC in social cognition. Method 52 healthy young adults were stratified into two studies and received either dmPFC or rTPJ anodal HD-tDCS in a sham-controlled, double-blinded, repeated measures design. Subjects completed a social cognitive battery measuring self-other processing across an implicit and explicit level one (line-of-sight) and level two (mental rotation) visual perspective taking tasks (VPT), as well as self and other encoding effects on episodic memory in order to test the self-reference effect (SRE). Results Stimulation of the dmPFC selectively enhanced integration of the other perspective into self as indexed by an increase in congruency effect (incongruent-congruent) across both explicit VPT tasks. It also removed the SRE in episodic memory, indexed by increasing the recognition of other-encoded words and reducing the recognition of self-encoded words. Stimulation of the rTPJ resulted in improved inhibition of the self-perspective during level two VPT only, as indexed by a reduction of the congruency effect when taking the other perspective. Conclusion Our results provide the first causal evidence for dissociable roles of the dmPFC and rTPJ in social cognition. This research supports theories suggesting that rTPJ facilitates embodied mental rotation, whereas the dmPFC integrates information relevant to the other into that of the self.
Effects of dietary supplementation of different vegetable oils varying in polyunsaturated fatty acid content on reproductive performance and ovarian follicular characteristics of Murrah buffalo heifers

To compare the effects of dietary supplementation of different vegetable oils varying in polyunsaturated fatty acid content on reproductive performance and ovarian follicular characteristics, twenty Murrah buffalo heifers randomly divided into four groups (T0 , T1 , T2 and T3 ) of five animals in each on the basis of age and body weight (BW). All the animals were given concentrate, green fodder and wheat straw in 50:40:10 ratios, respectively, as per Kearl (1982) feeding standard. In addition, mustard oil, soybean oil and rice bran oil 3.5% of concentrate mixture were supplemented in groups T1 , T2 and T3 respectively. The average age at puberty reduced in all the treatments groups as compared to control, however, BW at puberty remain uninfluenced (P>0.05) in all the groups. The number of small size follicles (<3 mm) were significantly higher (P<0.05) in T2 as compared to T1 and T0 group but at par with T3 . Number of medium size follicles (3 to 6 mm) differ significantly (P<0.05) among treatment groups and control group. Total number of ovarian follicles followed a similar trend as shown by number of small follicles. Overall, the findings of the present study concluded that dietary supplementation of vegetable oils reduced the age at puberty, increased the number of small size of follicles, diameter of the large follicle and improve the conception rate in Murrah buffalo heifers.
EVALUATION OF TERATOGENICITY OF SALVIA LERIIFOLIA BENTH. IN MICE

1 شناد راي ، مس و يمانيدوكامراف هورگ وراد مولع تاقيقحت زكرم و يزاسوراد هدكشناد ،يسانش ي يلعوب هدكشهوژپ ي ، مس تاقيقحت زكرم ،يكشزپ يسانش دهشم يكشزپ مولع هاگشناد 2 داتسا ، مس و يمانيدوكامراف هورگ ،يلعوب هدكشهوژپ ييوراد مولع تاقيقحت زكرم و يزاسوراد هدكشناد ،يسانش دهشم يكشزپ مولع هاگشناد 3 زاسوراد مس و يمانيدوكامراف هورگ ، شم يكشزپ مولع هاگشناد ،يزاسوراد هدكشناد ،يسانش ده 4 مس و يمانيدوكامراف هورگ سانشراك ،زاسوراد دهشم يكشزپ مولع هاگشناد ،يزاسوراد هدكشناد ،يسانش 5 ،رايداتسا دنجريب يكشزپ مولع هاگشناد ،يكشزپ هدكشناد ،يموتانآ هورگ * هبتاكم سردآ : ،يزاسوراد هدكشناد ،دهشم قودنص يتسپ : 1365 91775 نفلت : 8823255 ) 0511 ( ن ، ربام : 8823251 ) 0511 ( كينورتكلا تسپ : moallem@mums.ac. ir
Highly accelerated rates of heritable large-scale mutations under prolonged exposure to a metal mixture of copper and nickel

Mutation rate variation has been under intense investigation for decades. Despite these efforts, little is known about the extent to which environmental stressors accelerate mutation rates and influence the genetic load of populations. Moreover, most studies have focused on point mutations rather than large-scale deletions and duplications (copy number variations or “CNVs”). We estimated mutation rates in Daphnia pulex exposed to low levels of environmental stressors as well as the effect of selection on de novo mutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103 generations of MA propagation, we sequenced 60 genomes and found significantly accelerated rates of deletions and duplications in MA lines exposed to ecologically relevant concentrations of metals. Whereas control lines had gene deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10−6 per gene per generation), a mixture of nickel and copper increased rates fourfold. The realized mutation rate under selection was reduced to 0.4x that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous recombination associated with regions of DNA fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand breaks with higher CNV rates. Our findings suggest that environmental stress, in particular multiple stressors, can have profound effects on large-scale mutation rates and mutational load of populations.
Rational Use of Antimicrobials in Animal Production:A Prerequisite to Stem the Tide of Antimicrobial Resistance

Antimicrobial resistance (AMR) is a worldwide ‘One Health’ problem. The spread of AMR has limited the treatment options against infectious diseases. Inappropriate use of antimicrobials, is a major contributor for the development of AMR and its spread. In animal husbandry, antimicrobials are used for treating infectious diseases and in sub-therapeutic concentrations for growth promotion and disease prophylaxis. The use of antimicrobials in sub-therapeutic concentrations exerts selective pressure on bacteria and results in the emergence of bacterial strains resistant to one or more antimicrobials. The food animals raised on sub-optimal doses of antibiotics become reservoirs of resistant bacterial strains, transmitted subsequently to man and the environment. Various human, animal and environmental health agencies have decided to jointly address this problem. Establishment of integrated and harmonized AMR surveillance programmes, reduced use of antimicrobials in animal production, good governance of veterinary services, and development of new antimicrobials and their alternatives are some of the AMR management strategies in animals. Antibiotics are indispensable for human health; however, they should be totally banned in the food animals to preserve effectiveness of these drugs. In India, use of antimicrobials in food animals is limited for disease prophylaxis and growth promotion. However, absence of uniform regulations on the use of antimicrobials in animal production threatens the rationale use of these drugs in livestock.
SIĞIR PNÖMONİK AKCİĞERLERİNDEN İZOLE EDİLEN PSEUDOMONAS AERUGİNOSA SUŞLARININ ANTİBİYOTİK DUYARLILIKLARININ BELİRLENMESİ

In this study total of 66 Pseudomonas aeruginosa strains that were isolated form pneumonic lung samples collected in the Kars Municipality Slaughterhouse. Using Kirby Bauer Disc Diffusion method, isolated strains were tested against tetracycline, ampicillin, gentamicin, amoxicillin/clavulanik acid, trimethoprim-sulfamethoxazole, vancomysin and chloramphenicol antibiotic discs. The results of the antibiogram showed that P. aeruginosa strains were resistant 100% to ampicillin, gentamicin, trimethoprim-sulfamethoxazole and chloramphenicol, 64% to vancomysin, 6% to amoxicillin/clavulanik acid, and 9% to tetracycline. Susceptibility to tetracycline, amoxicillin/clavulanik acid and vancomysin were determined to be 91%, 94% and 36%, respectively. In the light of the results, tetracycline and amoxicillin/clavulanik acid were suggested to in Pseudomonas aeruginosa infections.
Cell Polarity Protein SCRIBBLE Regulates Pregnancy-induced Alveologenesis In the Mammary Gland

SCRIBBLE (SCRIB) was identified as a regulator of epithelial cell polarity and morphogenesis in Drosophila. Subsequent studies in mammalian cells demonstrated that SCRIB regulates epithelial cell polarization, cell migration, and tumourigenesis. SCRIB also plays important roles during mammalian development where loss of SCRIB resulted in embryonic lethality and tissuespecific knockout studies identified SCRIB as a tumor suppressor in the prostate, lung, and mammary gland. However, the role SCRIB plays in adult epithelial tissues during physiological remodeling remains unknown. To address this question, we generated an inducible RNAi mouse model whereby SCRIB expression can be controlled in vivo. Since the mouse mammary gland undergoes morphological changes during pregnancy, we investigated the effects of inactivating SCRIB in adult mammary epithelial cells. Downregulation of SCRIB in adult mammary glands resulted in a significant decrease in development of alveolar buds and reduced epithelial content, in conjunction with a decrease in iii cell proliferation during pregnancy. Surprisingly, loss of SCRIB did not affect the differentiation or polarization of alveolar structures. Mechanistically, SCRIB knockdown attenuated prolactininduced activation of the JAK2/STAT5 signaling pathway, a critical mediator of pregnancyinduced cell proliferation. Thus, in contrast to the previously reported role for SCRIB in the virgin gland as a negative regulator of proliferation, these studies identify SCRIB as a positive regulator of pregnancy-induced alveologenesis in the adult mammary gland. The attenuation of prolactin responsiveness in SCRIB knockdown cells was attributable to decreased cell surface accumulation of the prolactin receptor (PRLR). In SCRIB knockdown cells, PRLR partially co-localized with the Golgi apparatus and recycling endosome. Using an unbiased mass spectrometry approach, we found that SCRIB controlled levels of multiple cell surface proteins. Collectively, the studies in this dissertation identify SCRIB as a positive regulator of prolactin-initiated proliferation of mammary epithelial cells during pregnancy and steady state cell surface levels of PRLR.