Miracle-dz/UniFAR-FTUs huggingface dataset:
Syntheses and applications of small molecule inhibitors of miRNAs miR-21 and miR-122

MicroRNAs (miRNAs) are regulatory RNA molecules of 22 nucleotides that (in part) control up to 60% of all genes in humans. They act by binding to the 3' untranslated regions of target messenger RNAs, leading either to translational repression or mRNA degradation. In addition to being involved in the regulation of several fundamental cellular processes, the misregulation of miRNAs has been linked to a wide range of diseases including cancer. Particularly, miR-21 is significantly upregulated in nearly all types of human cancers, and its overexpression is often associated with poor prognosis. The downregulation of miR-122 is found in more than 70% of hepatocellular carcinoma cases and miR-122 is a required factor for the replication of the HCV virus. The modulation of miRNA function is commonly achieved using oligonucleotide agents. However, compared to oligonucleotides, small molecules have several advantages, such as fast activity, systemic delivery, and excellent cell permeability. Taking advantage of luciferase-based reporters, two separate high-throughput screens of >300,000 compounds each, were conducted to discover new small molecule inhibitors of miR-21 or miR-122. Several hit compounds were re-synthesized, their ability to inhibit miR-21 was validated, and the most promising compounds were investigated by SAR studies, which revealed two additional, structurally diverse classes of miR-21 inhibitors. Similarly, extensive SAR studies of previously discovered miR-122 inhibitors were performed in order to better understand the molecular requirements for the miR-122 inhibitory activity. The hit compounds identified in the HTS were analyzed through secondary assays that led to the identification of two new promising miR-122 inhibitors. Furthermore, the knowledge gained during the SAR studies was further used to synthesize several small molecule miR-21/miR-122 inhibitors as probes to explore their mechanisms of action. MicroRNAs represent promising, novel drug targets, and small molecule miRNA inhibitors provide tools to study the molecular mechanisms of miRNA biogenesis and have the potential to be new therapeutic agents for the treatment of cancers and viral infections.
Prevalence of human enteric viruses in coastal canal communities

Coastal canal communities provide waterway access to individual residential units and are increasingly popular along the Texas Gulf coast. A 1969 survey revealed a total of 58 canal communities along the Gulf coast, most of which are situated in Galveston County. The impact of domestic waste from resi dential communities on the water quality of these canals has not been adequately studied. In addition, there is a need for adequate evalu ation of the occurrence of pathogenic human enteric viruses in polluted marine waters, and their relationship to conventional bacteriolog ical standards for assessing water quality. Pre vious studies on the occurrence of enteric
Complete mitochondrial genome of a treefrog, Hyla sp. (Anura: Hylidae)

Abstract The complete mitochondrial genome of a treefrog (Hyla sp.) was determined. The circular mitochondrial genome is 18,288 bp long and encodes 13 proteins, 22 transfer RNAs, and 2 ribosomal RNAs. Phylogenetic analysis of its full genome sequences showed that H. sp. was closely related to H. ussuriensis and H. japonica rather than Dryophytes suweonensis, consistent with the results from each protein-coding gene and a cluster between 12S rRNA and 16S rRNA. The present study will provide essential genomic information for biogeographical distribution and evolutionary history of an endemic treefrog, H.sp.
Identification of epilepsy related pathways from methylome analysis

Epilepsy is a disorder which affects approximately 1% of the world’s population. It is possible to explain the underlying mechanisms of epilepsy by not only alterations in genetic structure and environmental factors, but also epigenetic mechanisms. As a significant epigenetic modification, DNA methylation may play a crucial role for understanding biological pathways related to epilepsy. Even though the relationship between CpG islands, DNA methylation and gene expression is quite complex, in this thesis we aimed to determine significant biological pathways related to epilepsy, using the difference of methylation levels at CpG loci in family trios. Dataset was gathered from 10 family trios (30 individuals) and it includes methylation level information for each CpG locus determined by Illumina HumanMethylation450 Bead Chip which is a microarray based analysis tool. Considering the difference of methylation levels at each CpG locus, we prepared lists of genes that we marked as significant. Applying several filters to the dataset allowed us to gather more reliable information from the dataset. We identified a number of significant pathways that may be related to epilepsy, especially immune system related pathways stand out as a significant and novel finding.
OVARIAN EXPRESSION OF SOX2 DURING MOUSE ESTROUS CYCLE

The transcriptional factor Sox2 regulates the expression of some of the developmental genes, which are essential for the maintenance of pluripotency of stem cells. Sox2 also expresses in the female gamete during folliculogenesis, but its role remains ambiguous. The aim of this study was to investigate the expression of Sox2 in the mice ovarian tissue during different stage of estrous cycle. Adult National Medical Research Institute (NMRI) mice were considered as pro-estrous, estrous, met-estrous and di-estrous based on the cell type of the vaginal smear. Immunohistochemical staining of Sox2 marker was performed in mice ovarian tissue. Immunohistochemical staining revealed the expression of Sox2 in the cytoplasm of corpus luteum cells, stromal cells and oocyte. Our results suggest that adult mice ovaries accommodate cells carrying stem cell features.
Legacy microsite effect on the survival of bitterbrush outplantings after prescribed fire: capitalizing on spatial variability to improve restoration

Restoration of shrubs in arid and semi‐arid rangelands is hampered by low success rates. Planting shrub seedlings is a method used to improve success in these rangelands; however, it is expensive and labor intensive. The efficiency of shrub restoration could be improved by identifying microsites where shrub survival is greater. Bitterbrush (Purshia tridentata Pursh DC) is an important shrub to wildlife that has declined because of conifer encroachment, excessive defoliation, wildfires, and low recruitment. We investigated planting bitterbrush seedlings in western juniper (Juniperus occidentalis ssp. occidentalis Hook) encroached shrublands after prescribed fire was used to control trees. Bitterbrush seedlings were planted in under (canopy) and between (interspace) former juniper canopies at five blocks and evaluated for three growing seasons. Bitterbrush survival was greater than 50% in the former canopy, but only 5% in the interspace microsite by the third growing season. Growth of bitterbrush was also greater in the former canopy compared with the interspace, potentially due to markedly less perennial vegetation in this microsite. Exotic annual grasses and annual forbs became prevalent in the former canopy in the second and third growing season, suggesting that soil resource availability was greater in this microsite. These results suggest that restoration success will vary by specific locations within a burned landscape and that this variability can be used to improve restoration efficiency. In this situation, bitterbrush restoration can be improved by planting seedlings in former canopy compared with interspace microsites.
The effects of male philopatry on reproductive behaviors and fitness in Columbian ground squirrels (Urocitellus columbianus)

ii Acknowledgments. iv List of Tables . vii List of Figures . viii Chapter 1: The effects of co-occurrence with close female relatives on mating behaviors of male Columbian ground squirrels . 1 Abstract .
Karyotype Diversity in Astyanax sacbripinnis (Pisces, Characiformes) from the São Francisco River Basin, Brazil

2017 Summary The Astyanax scabripinis population from the São Francisco River, analyzed in the present study, had two different diploid numbers: 2 n =50 chromosomes (cytotype I) with the karyotypic formula of 10m+20sm+8st+12a and NF=88, and 2 n =48 chromosomes (cytotype II) with the karyotypic formula of 11m +18sm+9st+10a and NF=86. Individuals with cytotype II also had a heteromorphic pair in male and female karyotype (24 pair), and in some cells, a supernumerary acrocentric chromosome, which was similar in size to the last acrocentric. C-banding and Ag-NOR staining patterns also differed between the two cytotypes, reinforcing the hypothesis that there are two different species and that A. scabripinnis is a species
Symbiotic Fungus of Marine Sponge Axinella sp. Producing Antibacterial Agent

The emerging of multidrug resistance pathogenic bacteria cause the treatment of the diseaseshave become ineffective. There for, invention of a new drug with novel mode of action is an essential for curing the disease caused by an MDR pathogen. Marine fungi is prolific source of bioactive compound that has not been well explored. This study aim to obtain the marine sponges-associated fungus that producing anti-MDR bacteria substaces. We collected the sponge from Riung water, NTT, Indonesia. The fungus was isolated with affixed method, followed with purification with streak method. The overlay and disk diffusion agar methods were applied for bioactivity test for the isolate and the extract, respectively. Molecular analysis was employed for identification of the isolate. The sponge was identified based on morphological and spicular analysis. The ovelay test showed that the isolate KN15-3 active against the MDR Staphylococcus aureus and Eschericia coli. The extract of the cultured KN15-3 was also inhibited the S. aureus and E. coli with inhibition zone 2.95 mm and 4.13 mm, respectively. Based on the molecular analysis, the fungus was identified as Aspergillus sydowii. While the sponge was identified as Axinella sp.
Predicting site productivity of the timber tree Pterocarpus angolensis§

Pterocarpus angolensis is an important timber tree of the miombo woodlands of sub-Saharan Africa. The species only grows in natural mixed forests and little is known about is productivity potential. This study aimed at investigating productivity of P. angolensis on a local scale in Namibia and Angola and on a regional scale in southern Africa. The most commonly accepted productivity indicator is stem diameter increment and this was used to study productivity at a regional scale. Indicators of productivity used at the local scale were basal area, proportional basal area and site form, which were derived from 217 forest inventory plots in Namibia and Angola. The productivity measures were modelled with abiotic site factors; biotic factors were added for the local scale. Results indicated that the most consistent site factors at local and regional scale were not related to climate but to forest cover, with the species having a competitive advantage in more open forests. Mean annual diameter increment in the open forests of Namibia was 0.51 cm after 50 years. Boosted regression tree models at a local scale showed that species presence can be modelled more successfully than species basal area, proportional basal area (correlation of 0.72 vs 0.56 and 0.45, respectively) and site form. The sites with the highest productivity of P. angolensis at the local scale had a temperature seasonality below 34.5 °C, a slope of less than 1.5°, tree cover less than 20% and stand basal area higher than 9 m2 ha−1. The results can assist in establishing a site-dependent growth model for the species and direct forest and fire management towards the most productive areas.
Escherichia coli entérohémorragiques et/ou résistantes aux antibiotiques : contamination des effluents d'origine bovine

Les bovins sont porteurs de souches d'Escherichia coli enterohemorragiques (EHEC), pathogenes pour l'homme et egalement de souches d'E. coli resistantes aux antibiotiques. Dans un premier temps, nous avons evalue la frequence de ces souches dans les effluents de station d'epuration des eaux usees de deux abattoirs, l'un de bovins adultes et l'autre de veaux de boucherie. Les pourcentages d'E. coli antibioresistantes et porteuses d'integrons de resistance de classe 1 etaient significativement plus eleves dans les effluents et boues d'abattoirs de veaux (87,5%, 56,2%) par rapport aux bovins adultes (5,0%, 0%). Ces pourcentages n'etaient pas modifies par le traitement epuratoire. Le traitement epuratoire n'a egalement eu aucun impact sur les pourcentages de souches d'E. coli productrices de shigatoxines (STEC). Une souche STEC O157:H7 hautement pathogene a ete isolee des boues destinees a l'epandage agricole dans la station d'epuration d'abattoir de bovins adultes. Ces resultats ont confirme qu'il existe des risques de dissemination environnementale d'E. coli antibioresistantes et/ou pathogenes via les effluents d'abattoir de bovins et ont mis en evidence que ce risque etait different selon la categorie de bovins abattus. Dans un deuxieme temps, nous avons evalue la resistance de souches STEC du top 5 (O26:H11, O103:H2, O111:H8, O145:H28 et O157:H7) isolees de feces de bovins adultes. Sept des 39 souches STEC testees etaient resistantes, dont 6 a au moins 3 classes d'antibiotiques. Les souches non-STEC et aEPEC du top 5 d'E. coli de la flore fecale de ces memes bovins etaient toutes sensibles, indiquant un possible lien genetique entre genes de resistance et virulence. Nous avons mis en evidence que le gene ehxA, marqueur fiable du plasmide de virulence des EHEC, et les genes de resistance blaTEM, strA-strB, tet(A), sulII etaient localises sur un meme plasmide de grande taille pour 4 souches STEC (1 O26:H11, 1 O103:H2 et 2 O111:H8). Cette association genetique souleve la problematique de la selection clonale de ces souches pathogenes lors du traitement des bovins porteurs avec des antibiotiques.
EFFECTS OF FATTY ACIDS AT DIFFERENT POSITIONS IN THE TRIGLYCERIDES ON CHOLESTEROL LEVELS

Previous studies established a series of regression equations for predicting the risk factor effects from serum cholesterol concentrations. However, the degree of saturation was solely based on total fatty acid composition in triglycerides. Our article is focused on the relationships between the published human nutrition studies and predicted values of serum cholesterol levels based on total fatty acid compositions and at sn-2 position in triglycerides. Twenty-two published human nutrition studies were chosen to assess the effects of palm olein, olive oil, cocoa butter, sunflower seed oil, corn oil, soyabean oil, grapeseed oil, groundnut oil and rice bran oil diets on serum cholesterol levels. There were no statistically significant differences between the predicted values of serum cholesterol levels based on fatty acids at sn-2 position and the published human nutrition studies as proven by the statistical analyses with p values more than 0.05. In contrast, there were statistically significant differences between the predicted values of serum cholesterol levels based on total fatty acids and the published human nutritional studies with p values less than 0.05. Fatty acids at sn-2 position appear to influence the cholesterol levels rather than total fatty acids of the triglyceride.
Divergent Patterns of Selection on Crassulacean Acid Metabolism Photosynthesis in Contrasting Environments

Premise of research. Crassulacean acid metabolism (CAM), a photosynthetic pathway that evolved in response to aridity, is beneficial for plant species in arid and semiarid environments, with positive effects on plant fitness. However, since it implies a higher metabolic cost compared with that for C3 plants, its expression under moist conditions, where it might be less necessary, could have fewer positive or even negative effects on plant fitness. Variations of the effects of CAM expression under different moisture regimes have never been addressed. Our objectives were to determine whether there are such variations and, if so, their possible ecological and evolutionary implications. Methodology. We measured CAM expression (as nocturnal acidification, ∆H+) and moisture-related morphological leaf traits, estimating their impact on reproductive effort in two populations of Puya chilensis living under contrasting moisture regimes in a natural climatic gradient in central Chile. To evaluate the effects of the measured traits on fitness, a phenotypic selection analysis was performed. Pivotal results. Phenotypic selection analysis showed that ∆H+ was the only trait significantly associated with relative fitness in both populations. There is a significant “switch” in the direction of selection between both studied populations: directional selection on CAM was positive in the dry population and negative in the moist population. Conclusions. Results suggest that under moist regimes the expression of CAM by P. chilensis could be removed by natural selection. To our knowledge, this is the first report of a negative effect of CAM on plant fitness. Since CAM is not usually studied in moist environments, we believe this pattern might be more frequent than expected. Further research on this issue is needed, especially in the context of current climate change.
Correlation of morphological diversity with molecular marker diversity in the rough periwinkle Littorina saxatilis (Olivi)

Two morphological varieties of Littorina saxatilis, widespread around the United Kingdom, are a thin-shelled, high-shore morph (L. saxatilis H) and a thick-shelled, mid-shore animal (L. saxatilis M). Mitochondrial DNA (mtDNA) analysis by PCR-RFLP was used to test whether gene flow between these morphs is restricted. At Galloway, Scotland, replicated sampling (different years and different transects over a distance of 800 m) has been undertaken. One mtDNA haplotype is predominant in H and a different haplotype common in the M animals. Repeatability in space and time suggests a real H/M differentiation. A similar pattern of mtDNA haplotype variation is seen in a single sample of the Swedish E and S morphs of Littorina saxatilis. However, this pattern is not evident everywhere. Variation in the mtDNA and four nuclear DNA loci was examined within and between L. saxatilis H and M morphs from the south coast of England. Because shape variation in this region additionally separates into three shape groupings (regions identified from multivariate morphometric analysis where shape is more homogeneous within, than between groups), generic variability was examined within and between these groupings as well as between H and M. On the south coast, an apparent association of shape and mtDNA haplotype is identified, but AMOVA analysis shows no support for the association being with shape grouping or H and M morphs. Although the nature of this shape-genotype association is unknown, a mtDNA haplotype and an allele at the nuclear CAL-2 locus are confined mainly to one shape group. Analysis of association of mtDNA haplotype with H and M morphology suggests a strong correlation can be found in some areas (Galloway, Mumbles (south Wales), and between similar morphs in Sweden) yet no association is seen at others (Ravenscar, UK, Ballynahown, Ireland, and the south coast of England). Thus, unravelling the basis of the H and M forms will require more detailed studies, with replication, as at Galloway, and also with additional molecular markers.
Probiotics Beverages of Sweet Lime and Sugarcane juices and its Physiochemical, Microbiological & Shelf-life Studies

The research was undertaken to estimate the suitability of Sugarcane and Sweet Lime juices as a sole source for growth of beneficial Lactobacillus acidophilus. Suitability of culture growth was also checked in various combinations which were prepared with herbs of Ashwagandha (Withania somnifera) and Green tea extract (Camellia sinensis), wheat grass juice, whey and oats. Juice samples were inoculated with 24-h-old lactic culture and incubated at 37 oC. Lactobacillus acidophilus grew well in all these combinations and reached nearly upto 108 CFU/ml after 24 h of fermentation at 37 oC. Sugarcane and Sweet Lime juice were also supplemented with 10 % & 5% v/v whey, with better growth of Lactobacillus acidophilus. After 3 weeks of storage at 4oC, the viable cell counts of Lactobacillus acidophilus in the juices of Sugarcane control (SOC), Sugarcane juice with Wheat grass juice and Withnia somnifera (SOF1) and Sugarcane juice with green tea and whey (SOF2) were 4.0×108, 2.0×108 and 5.5×108 CFU/ ml, respectively. Culture viability in Sweet Lime juices was lost after 2nd week of storage because of the decrease in pH and higher acidity. Glucose (0.89%), sucrose (16.28%) and fructose (1.70%) was detected in Sugarcane juice and glucose (2.61%), sucrose (0.86%), fructose (2.70%) and maltose (0.38%) was detected in fermented Sweet Lime juice by HPLC analysis. Various secondary metabolites were detected in the SOF2 and CLF2 samples by GC/MS analysis. These juice samples were found phytochemically rich because of herb extracts. Fermented Sweet Lime and Sugarcane juice can be developed to perform as a functional probiotic beverage for vegetarians and lactose-allergic consumers.
Evaluation of Some Immunostimulants on the Immune-response of Broiler Chickens Against Avian Influenza and Newcastle Diseases Vaccination

Immunostimulants get an increasing importance to enhance the immune system and allowing maximum performance in poultry production. The effects of using different immunostimulants on the immune response of broiler chickens to Newcastle disease (ND) and Avian influenza (AI) vaccination were investigated in this study. 100 day-old Ross broiler chicks were randomly divided into 4 groups, 25 birds for each group. Group A was not treated with any immunostimulants and used as a control, while groups B, C and D were supplemented with Imutrix ® (oregano oils plus β-glucan), Evit liquid ® (Vitamin E plus selenium) and inmunair ® 17.5 ( Propionibacterium acnes and E. coli lipopolysaccharides), respectively. Statistical analysis results demonstrated significant divergence ( P < 0.05) in body weight (BW) and feed conversion ratio among the applicable treatments. Birds of group B had the heaviest body weight (2.03 kg), followed by group C (1.87 Kg) and D (1.82 Kg) in comparison to the birds of group A (control, 1.79 Kg). Bursa of Fabricius weight showed non-signiﬁcant differences among groups except in group B that showed an increase in the Bursa of Fabricius weight more than other groups especially the control group (1.15 g more). Comparable immune response was recorded for both AI and ND vaccination. The highest mean antibody titers were recorded for birds in group B at 14, 28 and 35 days old, while those in group D had the lowest antibody titre values. Thus, supplementing immunostimulants especially Imutrix ® and Evit liquid ® had a significant positive effect on performance characteristics and immune response against AI and ND vaccination in broiler chickens in contrast to non-treated group, which had low levels of immune response, rapid decreasing and no persistence for keeping high HI titer for long time.