Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Genetic Parameters of Body Weight Traits in Kourdi Sheep

For estimating genetic parameters for body weight traits in Kourdi sheep data were collected from 1996 to 2013 in Kourdi Breeding Station in Northern Khorasan province of Iran. Studied traits were birth weight (BW), weaning weight (WW), six-month weight (6MW), nine-month weight (9MW) and yearling weight (YW). The fixed effects in the model were lambing year, sex, type of birth and age of dam. (Co)variance components and corresponding genetic parameters were obtained with the univariate and multivariate analyses fitting animal models using the restricted maximum likelihood (REML) methods. The most appropriate model for each trait was determined based on log likelihood values. Model including maternal genetic effects as well as direct genetic effects, without considering covariance between them, was chosen as the most appropriate model for BW and WW. Model which included only direct genetic effects was the best model for other traits (6MW, 9MW and YW). Year of birth, lamb sex and type of birth were significant sources of variation on body weight traits (P<0.01). Direct heritability estimates of 0.10, 0.28, 0.32, 0.22 and 0.20 were obtained for BW, WW, 6MW, 9MW and YW, respectively. The estimate of maternal heritabilities for BW and WW were 0.27 and 0.13, respectively. Direct genetic correlation estimates between body weight traits were positive ‎and varied from 0.56 for BW-YW to 0.97 for 6MW-9MW. Estimates of maternal genetic correlations between body ‎weight traits were positive and ranged from 0.84 to 0.99. The estimates of correlations between body weight traits suggest that selection for any of these traits could result in genetic progress for the other traits. ‎
dMARCH8, a Drosophila ubiquitin E3 ligase, regulates polymodifications of tubulin in the spermiogenic pathway

Ciliary stability and function are regulated by the covalent addition of polyglutamate and polyglycine chains to axonemal tubulin subunits. The Drosophila gene CG13442 encodes a predicted ubiquitin E3 ligase involved in the regulation of tubulin glycylation and glutamylation. Homologous to mammalian MARCH8, CG13442/dMARCH8 is required for male fertility. Sperm in dMARCH8 mutant testes appear to undergo a normal individualization process but fail to be transferred to the seminal vesicle. This phenotype is very similar to that of mutants in the Ntl gene, shown here to be a glycine transporter using a [3H]glycine uptake assay. Mutations in dMARCH8 are associated with a reduction of both polyglutamylation and polyglycylation of sperm tubulin. Polyglutamylation of tubulin is significantly increased in the Ntl− background, and recovers to wild-type levels in the Ntl−-dMARCH8− double mutant background, indicating that glycine and glutamate compete for some common site(s) on tubulin molecules in this system. By analogy to the regulation of the mammalian glycine transporter GlyT2 through ubiquitin-mediated trafficking between the plasma membrane and endosome, dMARCH8 may target Ntl and glutamate transporters, or other upstream regulators of these proteins.
Effects of Dietary Tribulus terrestris Extract Supplementation on Growth, Feed Utilization, Hematological, Immunological, and Biochemical Variables of Nile Tilapia Oreochromis niloticus

The present study was conducted for 88 days to evaluate the effect of dietary Tribulus terrestris supplementation on growth performance, feed utilization, and hematological, immunological, and biochemical indices of Nile tilapia, Oreochromis niloticus. A total of 144 Nile tilapia, average body weight 2.61±0.35 g, were divided into four experimental treatments. There were three replicates of each treatment. Four isonitrogenous (40% CP) and isolipidic (10% CL) experimental diets contained T. terrestris extract at levels of 0, 200, 400 and 600 mg/kg respectively. Growth performance and feed utilization of Nile tilapia were significantly higher (p<0.05) in all treatment groups fed with T.terrestris extract supplemented diets than those fed the control diet. There were no significant differences between body composition of fish (p>0.05). Hematocrit, hemoglobin, mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and myeloperoxidase variables were not significantly affected by herb extract (p>0.05). However, mean corpuscular volume (MCV) value and lysozyme activity increased with increasing T. terrestris extract (p<0.05). Serum albumin, total protein, and triglyceride levels were not affected by T. terrestris extract. Serum globulin and glucose levels increased and cholesterol levels decreased in Nile tilapia fed with herbal supplemented diets. The results of the present study suggest that Nile tilapia fed diets containing at least 400 mg/kg T. terrestris extract enhanced growth performance, feed utilization, hematological, immunological, and biochemical indices. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.
Old before your time: Ancient carbon incorporation in contemporary aquatic foodwebs

The current paradigm in trophic dynamic theory is that organisms will gain more energy from fresh, “young” organic materials because they contain the essential elements and chemical characteristics for enhancing growth, unlike more aged and thus conceptually degraded resources. However, a growing body of recent literature is raising exceptions to this resource‐age paradigm and highlights that organisms present in diverse aquatic settings in fact incorporate old organic carbon into their biomass. This shift in resource utilization has the potential to alter foodweb stability, structure, and dynamics, but has yet to be integrated into ecological studies and conceptual frameworks. In this review, we first outline a number of recent studies providing direct evidence of the transport and incorporation of old organic carbon in aquatic food webs, and then discuss the ecological implications of this changing view in resource utilization. We ultimately highlight future research avenues that will provide new insights into the response of aquatic foodwebs to the increased mobilization and delivery of old organic carbon to aquatic settings following anthropogenic perturbations and ongoing climatic change.
Molecular Diagnosis of Lung Cancers

Recent advances in cancer diagnosis have seen a rapid and accurate diagnostic test. Initially used as research tools the molecular diagnostic tests have been applicable in the clinical scenario. Purpose: Current study focuses on the significant approach of detection of epidermal growth factor receptor (EGFR) mutations in exon 18-21 and anaplastic lymphoma kinase gene (ALK) rearrangement analysis using molecular methods such as pyrosequencing and florescence in-situ hybridization (FISH) on formalin fixed paraffin embedded (FFPE) from tissue biopsy and cell blocks of 267 lung cancer patients. Methods: In this study, FISH using a break-apart probe for the ALK gene was performed on formalin fixed paraffin-embedded tissue to determine the incidence of ALK rearrangements and hybridization patterns in 267 patients with a referred diagnosis of non-small cell lung cancer. EGFR mutations detection was performed on 267 samples by using Pyrosequencing. Results: Among the 267 patients 11 were positive for ALK-1 gene rearrangement. 260 of the 267 cases were confirmed of adenocarcinoma and 7 of the 267 cases were squamous cell carcinoma. EGFR mutations were detected in 55 patients. The most common mutations found were exon 19 (56.36%), exon 21 (27.27%), exon 20 (3.63%) and exon 18 (9.09%). The influence of gender, non-smoking, and histological type on the EGFR mutations showed increase in female group. Conclusions: Mutation detection testing is mandatory in lung carcinomas for the diagnosis and management of NSCLC.
The Effect of IKKbeta on Estrogen Receptor Positive Breast Cancer Phenotypes

S: Susan G. Komen Scholar-In-Training Award for early-career scientists, American Association of Cancer Research 106th Annual Meeting 2015, Philadelphia, PA, 2015 Endocrine Society Travel Award for abstract presentation, Great Lakes Nuclear Receptor Meeting (GLNRM), University of Wisconsin-Madison, Madison, WI, 2014 Poster competition, second place, Student Research Forum, University of Illinois at Chicago, Chicago, IL, 2014 Poster competition, first place, International Fulbright Science and Technology Awardees Capstone Meeting, US Department of State, Washington DC, 2013 International Fulbright Science and Technology Award, 2010-2013 Graduation with Honors, Institute of Graduate Studies and Research, University of Alexandria, Alexandria, Egypt, 2008 Graduation with Distinction Honors, Faculty of Pharmacy, University of Alexandria, Alexandria, Egypt, 1997 American Association of Cancer Research (AACR) Women in Cancer Research (WICR) Endocrine Society Egyptian Pharmacist Syndicate Member of College of Pharmacy Graduate Student Committee, University of Illinois at Chicago, Chicago, IL El-Shennawy L and Frasor J. Constitutively active NF-κB signaling switches estrogen receptor positive breast cancer cells from a proliferative to an invasive phenotype through luminal/basal plasticity. American Association of Cancer Research 106th Annual Meeting 2015, Philadelphia, PA, 2015. El-Shennawy L and Frasor J. Constitutively active NF-κB signaling switches estrogen receptor positive breast cancer cells from a proliferative to an invasive phenotype through luminal/basal plasticity. College of Pharmacy Research Day, University of Illinois at Chicago, Chicago, IL, 2015.
Assessment of Biochemical Parameters and Histological Study of Spleen in the Wistar Rats Exposed To Cadmium Sulfate

The pollution of the ecosystem by the industrial effluents and sewages has different consequences as air and food contamination with the toxic agents such are heavy metals. It constitutes a significant risk of public health.Six (6) batches of 5 males and females rats were made up. These rats were contaminated with various doses of cadmium sulfate (0; 4; 5; 6, 6,6; 10; 20 mg/kg of body weight) by daily during 30 days. At the end of the experiment, animals were sacrificed and their blood serum is used for the dosage of spleen biochemical parameters. Also, the spleens of these animals were extracted and weighed. After, they were placed in formalin (10%) for histopathologic study by the technique of inclusion to paraffin.Cadmium sulfate reduced significantly the concentration of total bilirubin (p<0,001) and the weight of the spleen (p<0,05) without varying the concentration of total cholesterol. At the tissue level, the cadmium sulfate induced histological transformations characterized by iron deposit, veins dilatation, structural disorganization and edema in the contaminated rats.Cadmium sulfate caused a disturbance of splenic tissue in the rats.
Interactive effects of 6-BA, GA4+7, and prohexadione-calcium on Gala apples

Abstract: Gibberellic acid (GA4+7) and the cytokinin 6-benzyladenine (6-BA) are used during bloom and fruit set to reduce russeting and improve typiness of select apple cultivars. The gibberellin synthesis inhibitor prohexadione-calcium (P-Ca) is used at the same developmental stage to reduce vegetative growth and susceptibility to fireblight. The use of GA4+7/6-BA for enhancing the typiness of Gala apples and the interaction of GA4+7/6-BA and P-Ca was investigated in a 2-yr experiment on mature Royal Gala/Bud 9 trees. Six treatments were imposed: (i) untreated control; (ii) 5.5 mg L-1 of GA4+7 and 6-BA; (iii) 11 mg L-1 of GA4+7 and 6-BA; (iv) 21 mg L-1 of GA4+7 and 6-BA; (v) 123 mg L-1 P-Ca; and (vi) a tank mixture of 21 mg L-1 GA4+7/6-BA and 123 mg L-1 P-Ca. Trees treated with P-Ca had 21%–45% less growth than the untreated trees or trees treated with GA4+7/6-BA. In one of two years, the addition of GA4+7 and 6-BA tank-mixed with P-Ca reduced the efficacy of P-Ca on shoot growth. GA4+7/6-BA decreased soluble solids and fruit firmness in 1 yr, suggesting a delay in fruit maturity. P-Ca alone reduced scarf skin by 7%–10%; however, this effect was negated when combined with GA4+7 + 6-BA in one of the two years. GA4+7 + 6-BA increased fruit typiness and length to diameter ratios.
Biophysics of Dendritic Spine Morphogenesis

Dendritic filopodia are actin-filled dynamic subcellular structures that sprout on neuronal dendrites during neurogenesis. The exploratory motion of the filopodia is crucial for synaptogenesis but the underlying mechanisms are poorly understood. To study the filopodial motility, we collected and analyzed image data on filopodia in cultured rat hippocampal neurons. We hypothesized that mechanical feedback among the actin retrograde flow, myosin activity and substrate adhesion gives rise to various filopodial behaviors. We have formulated a minimal one-dimensional partial differential equation model that reproduced the range of observed motility. To validate our model, we systematically manipulated experimental correlates of parameters in the model: substrate adhesion strength, actin polymerization rate, myosin contractility and the integrity of the putative microtubule-based barrier at the filopodium base. The model predicts the response of the system to each of these experimental perturbations, supporting the hypothesis that our actomyosin-driven mechanism controls dendritic filopodia dynamics.
The influence of diet on the development of swine dysentery upno experimental infection

The purpose of the present study was to evaluate the effect of fermented liquid food (FLF) and the addition of lactic acid to a diet based on wheat and barley on the development of swine dysentery in pigs experimentally infected with a Danish field isolate of Brachyspira hyodysenteriae. Furthermore, to confirm if low non-starch polysaccharide (NSP)-containing diets reduce swine dysentery the effect of different dietary levels of NSP and resistant starch (RS) was evaluated. These diets were based on cooked rice and animal protein, cooked rice and potato starch, cooked rice and wheat bran, or cooked rice and sugar-beet pulp. The experiment was designed as a randomized-block trial and was performed in triplicate including a total of 192 pigs. After feeding the diets for 2 weeks, six pigs in each group were challenged orally with B. hyodysenteriae and observed for another 4 weeks. After challenge, swine dysentery was observed in all feeding groups. The incidence of disease varied between 94% (rice/wheat bran) and 44% (FLF). The effect of diet on faecal shedding of B. hyodysenteriae was statistically significant (P < 0·05). Feeding a diet based on cooked rice with a low content of NSP and RS, did not prevent the development of swine dysentery upon experimental challenge, and increasing the level of NSP or RS did not result in a higher incidence of disease or faecal shedding of B. hyodysenteriae. The incidence of swine dysentery in the FLF group was significantly lower (P < 0·05) compared with all other feeding groups, except for the lactic acid group. In conclusion, a low level of NSP or RS in the diet did not prevent the development of swine dysentery. Furthermore, the lowest incidence of disease was observed in the FLF group, even though this diet has a high content of NSP. The addition of organic acids to the food was not able to reduce infection with B. hyodysenteriae.
Emergência e análise ultraestrutural de plântulas de soja inoculadas com Sclerotinia sclerotiorum sob efeito da aplicação de Trichoderma harzianum

The high susceptibility of soybean to white mold has negatively impacted its productivity. Currently, biological control methods, such as the use of Trichoderma spp. , have provided alternatives to chemical control, as they promote less environmental impact and favor the plant growth. The aim of this study was to evaluate the effects of T. harzianum on the emergence of soybean seeds inoculated with Sclerotinia sclerotiorum, besides identifying the interaction between fungi and soybeans by means of scanning electron microscopy (SEM). Soybean seeds were subjected to the following treatments: 1. Without S. sclerotiorum, in PDA+Mannitol; 2. With S. sclerotiorum, in PDA+Mannitol; 3. With Ecotrich®WP and without S. sclerotiorum, in PDA+Mannitol; 4. With S. sclerotiorum and Ecotrich® WP, in PDA+Mannitol. The emergence test was conducted on trays with sterile sand at 25 °C for 8 days. Then, the vegetative organs of emerged seedlings were sectioned to evaluate, by scanning electron microscopy (SEM), T. harzianum potential to parasitize and inhibit S. sclerotiorum. In fact, the white mold is capable of colonizing and deteriorating all soybean seeds. T. harzianum is effective in colonizing the root system of soybeans but does not contribute to emergence, compared to control. Based on the ultrastructural analysis, mycoparasitism of T. harzianum and S. Sclerotiorum was evidenced, but the control of the causal agent of white mold was not as effective as shown in other studies.
Pollen types from colonies of Melipona scutellaris Latreille, 1811 (Hymenoptera: Apidae) established in a coffee plantation

Abstract Melipona scutellaris is a eusocial bee with potential to be used as a crop pollinator. This study aimed to identify pollen types used by Melipona scutellaris through the analysis of pollen loads and honey samples in colonies established in a coffee plantation. We analysed 117 pollen loads and pollen content of 15 honey samples. In the pollen loads, we identified 40 pollen types. Poincianella pyramidalis, Coffea arabica, Commelina villosa, Mimosa tenuiflora, Myrcia, Senna macranthera, Solanum and Syagrus coronata stood out as predominant pollen. We found a negative correlation between the abundances of the pollen types Coffea arabica and Mimosa tenuiflora during coffee flowering. In the honey samples, we recorded 33 pollen types. Eucalyptus and Machaerium occurred in frequencies of between 16 and 45%. Although Melipona scutellaris gathers resources from several plant species, its diet is based on a relatively narrow subset of plants.
Genetic and environmental factors affecting the human gut microbiom in obesity

The human microbiota is defined as the collective microbes living on and in the human body. Microbes can confer many benefits to the host including pathogen protection, complex carbohydrate breakdown and essential compound biosynthesis. Imbalances in the microbiome have been linked to disease, in particular obesity. The aim of this thesis is to explore the genetic and environmental effects on the human gut microbiome in twins, and characterise the microbiome species related to obesity. The primary dataset included gut microbiome 16s profiles of 982 twins from the TwinsUK cohort with extensive phenotype data. I first explored the heritability of the gut microbiome and obesity using twin modelling. The results revealed several heritable families, including the most heritable family, Christensenellaceae, which was also associated with lean BMI and measures of adiposity, including visceral fat. In addition, I found further associations between Christensenella and immune-related phenotypes such as white blood cell count, as well as host immune genetic variants. The next major analysis focused on identifying gut bacterial species that significantly differed between obese and lean individuals. I refer to these analyses as a Microbiome-Wide Association Study (MiWAS). The majority of the significant MiWAS results in obesity were obtained for members of the Ruminococcaceae and Lachnospiraceae. A candidate gene analysis was performed which aimed to identify obesity-associated human variants linked to these microbes. The strongest association was obtained between Lachnospiraceae and a variant within the human RPTOR gene, which controls the insulin-signalling path-
Integrated genomic analysis by whole exome and transcriptome sequencing of tumor samples from EGFR-mutant non-small-cell lung cancer (NSCLC) patients (p) with acquired resistance to erlotinib.

11010 Background: NSCLC p with EGFR mutations initially respond to EGFR tyrosine kinase inhibitors (TKIs) but ultimately relapse. Sub-genomic molecular studies indicate that the EGFR T790M mutation and the activation of MET, PI3K, AXL, HER2 and MAPK can lead to acquired resistance to EGFR TKIs. To date, no integrated comprehensive genomic investigation of EGFR TKI resistance has been performed. Methods: FFPE biopsies of erlotinib-sensitive and erlotinib-resistant tumors were obtained from 11 EGFR mutant NSCLC p. DNA was extracted from all tumor and corresponding normal tissue samples and underwent whole exome sequencing using the Illumina HiSeq2500. RNA was extracted from all tumor samples and analyzed by whole transcriptome sequencing, also using the Illumina HiSeq2500. Results: Erlotinib resistant NSCLC specimens harbored upregulation of known resistance drivers including MET and AXL and novel alterations including upregulation of genes that are: 1) recurrently mutated in NSCLC, including ALK, STK11; 2).
Molecular probe, colony structure and SEM of antennal sensillae substantiate intermediate workers of Oecophylla smaragdina (Fab.) as typical worker

The polymorphic colony of arboreal weaver ant Oecophylla smaragdina Fabricius has three categories of workers designated as typical, major and minor. The colony structure fluctuated sharply with seasons but the numerical ratio of worker castes always remained as 65:25:10. Typical workers have highest number of sensillae/unit area on the terminal segment of antenna and all the above characters established their role in the colony different from major and minor workers. Microsatellite DNA analysis of worker castes indicated high degree of genetic diversity, heterozygocity and genetic polymorphism among three worker castes, reproductive males and females. Mitochondrial DNA analysis proved that all the three categories of worker castes were developed from eggs of a single queen.
Molecular Factors that Influence BCG Vaccine Properties

Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the only vaccine against tuberculosis (TB). Although in use for nearly a century, it is far from ideal, exhibiting variable protection against pulmonary TB in adulthood and can cause disseminated disease in immunocompromised individuals. Therefore, there is an urgent need to develop more effective and safer TB vaccines than BCG. Understanding molecular factors that influence BCG vaccine properties including safety, immunogenicity, and protective efficacy will help to achieve this goal. This is especially relevant since vaccine candidates designed to boost BCG efficacy have yielded disappointing results in recent clinical trials. Several hypotheses exist for the variable protection of BCG and one of which concerns BCG strain heterogeneity. While it was widely recognized that different BCG strains exhibited varying degrees of virulence and protection in animal models, it has been attributed to quality control issues during the manufacturing process. However, work from our lab suggests that this variability may reflect true biological differences among BCG strains. Notably, we discovered a correlation between the production of the cell wall lipids, phthiocerol dimycocerosates (PDIMs)