Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential expression at the proteomic level of stem-cell markers and other gene markers in high-grade serous vs. other subtypes of ovarian cancer.

Ovarian carcinoma is the most lethal neoplasm and the fifth leading cause of death in women due to gynecological malignancies. It is estimated that there are 225,000 new cases diagnosed and 140,000 deaths occurring annually worldwide. Among the different subtypes, widely heterogeneous high-grade serous ovarian cancer (HGSOC) poses a great challenge to modern chemotherapy due to its high recurrence rate and resistance to standard treatments. Both of those causes are linked to the presence of a small subpopulation of cancer stem cells (CSCs) in the tumor microenvironment. Recent studies suggest that survival timeline and disease recurrence are linked to the variable expression of both cancer CSC and other gene biomarkers in cancer cells. Therefore, using Western blot and immunohistochemistry analyses, we assessed the expression of a host of CSC and other gene products at the whole-cell level in total protein extracts and sub-cellular levels in PFA-fixed cells from three HGSOC and five non-HGSOC cell lines. We found that no CSCmarkers were expressed in monolayer two-dimensional cultures that could differentiate HGSOCs from non-HGSOCs. In fact, no CSC-biomarker proteins were detected in any of the subtypes of the cancer-cell lines in our studies. Upon assessing other gene biomarkers at the proteomic level, we observed prominent differential expression patterns among the HGSOC and non-HGSOC subtypes and even within a subtype but no definite pattern to distinguish HGSOCs from nonHGSOCs. In conclusion, determining a differential protein expression profile in subtypes of ovarian cancer requires much further attention in order to provide earlier detection methods and personalized treatment options for patients.
Defensible Inference: Questioning Global Trends in Tiger Populations

Reports claim a dramatic 22% increase in wild-tiger Panthera tigris abundance within five years (3200 to 3890 individuals; WWF 2016). Such significant population increases could potentially change the status of tigers from endangered to vulnerable on the IUCN Red List, and substantially contribute to the global target of doubling wild-tiger numbers by 2022 (GTRP 2010). While this purported increase has been attributed to improved conservation practices in India, Nepal, Bhutan and Russia, the claimed increase is questionable given unreported methodology (Russia), lack of comparable baselines (Bhutan and Russia), and failure to adjust population estimates to account for expanded survey effort and methodological changes (Nepal and India). The latter source of bias requires explanation as it accounts for a large portion of the assumed population increase. This article is protected by copyright. All rights reserved
Comparative study on resistant starch, amilose content and glycaemic index after precooked process in white rice

Rice is a staple food and regarded as a useful carbohydrate source. In general rice is high in glycaemic index (GI) and low colonic fermentation. People are aware of the alterations in blood glucose levels or glycaemic index after consuming rice. Resistant starch (RS) and amylose content play an important role in controlling GI. GI and RS content have been established as important indicators of starch digestibility. The aim of this study was to determine the precooked process with hydrothermal (boiling at 80°C, 10 minutes) and cooling process with low temperature (4°C, 1 h) to increase potential content of RS and decrease of glycaemic index of white rice. There were two stages of this research, 1) preparation of white rice with precooked process; 2) analysis of precooked white rice characteristics (resistant starch, amylose content, and estimated glycaemic index). The result of analysis on precooked white rice showed an increased RS content (1.11%) and white rice (0.99%), but the difference was not statistically significant. The amylose content increased significantly after precooked process in white rice (24.70%) compared with white rice (20.89%). Estimated glycaemic index (EGI) decreased after precooked proses (65.63%) but not significant as compared to white rice (66.47%). From the present study it was concluded that precooked process had no significant impact on increasing RS and decreasing EGI of white rice. This may be due to the relatively short cooling time (1hour) in 4°C.
The Antidiabetic Activity of Curry Leaves “Murraya Koenigii” on the Glucose Levels, Kidneys, and Islets of Langerhans of Rats with Streptozotocin Induced Diabetes

Background : The aims of this study were to explore the antihyperglycemic effect of curry leaves, Murraya koenigii "MK" aqueous extract, and to examine its possible protective effects on the islets of Langerhans and kidneys of streptozotocin (STZ) diabetic rats. Methods : Thirty healthy adult male Sprague Dawley rats were randomized into five groups (n=6); normal control, normal treated with "MK" control, diabetic control (non-treated with "MK"), diabetic treated with 200 mg/kg MK aqueous leaf extract and diabetic treated with 400 mg/kg MK aqueous leaf extract. Blood glucose levels and body weight were monitored gravimetrically. The animals were sacrificed on the 30th day; the kidney and pancreatic tissues were processed for histological studies. Results : The diabetic group showed considerable loss of body weight and increase in blood glucose levels and degeneration of the glomeruli and renal convoluted tubules and atrophied islets with disintegration of β-cells. Treatment of diabetic rats with MK extract showed significant ( p < 0.001) improvement in blood glucose levels and body weight gain. The MK extract also caused an improvement in tissue injury induced by STZ injection in the kidney and islets of Langerhans. Conclusion s : These findings highlighted the beneficial effects of MK aqueous extract against cellular oxidative damage in STZ-induced diabetic rats.
Early to rise, early to breed: a role for daily rhythms in seasonal reproduction

Lay SummaryDo daily activity rhythms underlie observed variation in seasonal reproductive timing? Laboratory studies have found a link between daily activity rhythms and activation of the reproductive system. However, this relationship remains largely unexplored in the wild. We asked if females with early onset of activity would also breed earlier in the year. We found this to be true in 2 species of songbird, on 2 different continents, thus supporting our hypothesis.
COMPLEX FORMATION EQUILIBRIA OF COPPER(II), METFORMIN AND D-(+)MANNOSE OR D-(+)GLUCOSE IN METHANOL

Diabetes Mellitus is a metabolic disorder affecting carbohydrate metabolism, metformin is a drug widely used in the treatment of this disease. However, its mechanism of action has not been know yet, although several theories have been proposed to explain its hypoglycemic activity. A recent theory suggests a relationship between metformin and mitochondrial copper. On the other hand, glucose is the most abundant carbohydrate working as energy source; this carbohydrate has an important role in Diabetes Mellitus. In the present research work is reported a UV-VIS study with the purpose of analyzing the in vitro interaction between the ionic copper, metformin and glucose or mannose. The formation constant of ternary complexes of copper with metformin and glucose or mannose and its calculated electronic spectrum of each species in methanol solution, are reported. Hopefully, this information can be used in order to predict some of the possible interactions in vivo.
Cell-Free Synthesis of Proteins with Unnatural Amino Acids: Exploring Fitness Landscapes, Engineering Membrane Proteins and Expanding the Genetic Code

Cell-Free Synthesis of Proteins with Unnatural Amino Acids: Exploring Fitness Landscapes, Engineering Membrane Proteins, and Expanding the Genetic Code Song Min Schinn Department of Chemical Engineering, BYU Doctor of Philosophy Unnatural amino acids (uAA) expand the structural and functional possibilities of proteins. Numerous previous studies have demonstrated uAA as a powerful tool for protein engineering, but challenges also remain. Three notable such challenges include: (1) the fitness of uAA-incorporated proteins are difficult to predict and time-consuming to screen with conventional methods, (2) uAA incorporation in difficult-to-express proteins (e.g. membrane proteins such as G-protein coupled receptors) remain challenging, and (3) the incorporation of multiple types of uAA are still limited. In response, we pose cell-free protein synthesis (CFPS), a rapid and versatile in vitro expression system, as a platform to explore solutions to these challenges. The “cell-free” nature of CFPS enables it to accelerate protein expression and tolerate extensive modifications to its translational environment. In this work, these advantages were utilized to address the aforementioned challenges by: (1) rapidly expressing and screening uAA-containing proteins, (2) incorporating uAA in functional G-protein coupled receptor in the presence of membranemimicking lipid additives, and (3) engineer the translational environment extensively towards multiple uAA incorporation.
Illuminating the intra-species diversity of bacterial populations from shotgun metagenomes

Author(s): Nayfach, Stephen | Advisor(s): Pollard, Katherine S | Abstract: Deep metagenomic sequencing has the potential to illuminate the intra-species genomic variation of abundant microbial species. In this thesis, I develop a new tool MIDAS (Metagenomic Intra-species Diversity Analysis System) for rapidly and automatically quantifying species abundance, single nucleotide polymorphisms (SNPs), and gene copy number variants (CNVs) from metagenomes. To illustrate the utility of this approach, I reanalyze three public datasets with MIDAS. First, I re-analyze stool metagenomes from 98 mother-infant pairs and used rare SNPs to track strain transmission. I find that early colonizers are likely transmitted from the mother whereas late colonizers are likely transmitted from the environment. Second, I re-analyze g300 stool metagenomes from healthy adults and use SNPs to identify examples of both strain co-existence and strain coexclusion. Third, I re-analyze 198 globally distributed marine metagenomes and used gene copy number variants to show that many species have population structure that correlates with geographic location. Strain level genetic variants clearly reveal extensive structure and dynamics that are obscured when metagenomes are analyzed at coarser taxonomic resolution.
Toxicity of Randia nilotica fruit extract on Schistosoma mansoni, Biomphalaria pfeifferi and Bulinus truncatus

Ebodi AYE, Ahmed MM. 2017. Toxicity of Randia nilotica fruit extract on Schistosoma mansoni, Biomphalaria pfeifferi and Bulinus truncatus . Cell Bio Dev 1 (1): 23-30. The aqueous filtered and unfiltered extract of the fruits of Randia nilotica (locally name as Shagarat El-Murfaein) were assessed as molluscicides against Biomphalaria pfeifferi and Bulinus truncatus as well as their effect on cercariae and miracidia of Schistosoma mansoni . The plant was tested on uninfected B. pfeifferi and B. truncatus , the results showed that unfiltered extracts were found relatively more potent than filtered one (i.e. 100% was attained at 90 ppm and 80 ppm) respectively. While, filtered extract tested on uninfected B. pfeifferi and B. truncatus (100% was attained at 100 ppm and 90 ppm) respectively. The effect of unfiltered extract on infected B. pfeifferi produced 100% mortality in concentration of 70 ppm. The activity of the plant on cercariae and miracidia revealed that cercariae was more resistance than miracidia (i.e.50 ppm killed all cercariae within 3 hours while killed miracidia within 2 hours. The results were statistically analyzed and discussed, and the findings were promising and could open new avenues for the
Charakterisierung von keimungsinduzierten Genen pilzlicher Phytopathogene für ein targetspezifisches Fungiziddesign

Der Entwicklung von Fungiziden mit neuen Ansatzstellen und Wirkmechanismen hat aufgrund stetiger Resistenzbildung gegen landwirtschaftlich genutzte Fungizide eine herausragende Bedeutung fur die Sicherung einer auch zukunftig hochproduktiven und -qualitativen Pflanzenproduktion. Insbesondere durch Fungizidmasnahmen wahrend fruher Infektionsstadien kann ein nachhaltiger Schutz der Nutzpflanze erreicht werden. Unter Verwendung der cDNA-AFLP-Methode sowie durch Einsatz der SSH Technik konnten insgesamt 50 bzw. 47 singulare differentiell exprimierte cDNA-Sequenzen aus keimenden Sporen von Phytophthora infestans bzw. Pyrenophora teres identifiziert werden. Zur exakten Quantifizierung der Expression wurden 14 dieser Transkripte zusatzlich uber real time RT PCR analysiert. Die Normalisierung von differentiell exprimierten Genen erfolgte mit der 18S rRNA, die sich als geeigneter endogener Standard in quantitativen Expressionsstudien mittels realtime RT PCR wahrend der Sporenkeimung von phytopathogenen Pilzen erwiesen hat. Alle Transkripte zeigten wahrend der 24-stundigen in vitro Keimung einen im Vergleich zur ungekeimten Spore signifikanten Anstieg ihrer relativen Expressionsraten, was die Wirksamkeit der angewandten differentiellen Techniken bestatigt. Die maximalen Expressionsraten variierten zwischen dem 1,5- und 29,0-fachen der Ausgangsexpression. In vegetativem Mycel wurden im Vergleich zu den Expressionsmaxima wahrend der Sporenkeimung deutlich niedrigere Expressionsniveaus festgestellt. Nach einem Datenbankabgleich der 97 differentiell exprimierten Gene konnte fur 35 Sequenzen deren mutmasliche Funktion aufgrund signifikanter Homologien zu Datenbankeintragen vorhergesagt werden. Darunter befinden sich 18 Gene, die dem nachweislich keimungsrelevanten Ca2+/Phosphoinositid-Signalsystem und cAMP/PKA-Signaltransduktionsweg sowie der fur die Keimung vermutlich essentiellen Transkription oder Proteinsynthese zugeordnet werden konnen. Des weiteren wurden Gene identifiziert, denen Bedeutung im zellularen Metabolismus und Transport, bei der Sporenadhasion und zellularen Kommunikation sowie bei der Zellteilung und Stressabwehr zu kommt. Neue target-orientierte Verfahren erlauben eine im Vergleich zu den etablierten auf Massenscreenings basierenden Methoden eine schnellere und zielgerichtetere Entwicklung von neuen fungiziden Wirkstoffen. Verschiedene im Rahmen dieser Arbeit identifizierte und charakterisierte Gene stellen aufgrund teilweise hoher Sequenzspezifitat fur pilzliche Organismen und moglicher Essentialitat bei der Sporenkeimung vielversprechende Ansatzstellen fur ein target-orientiertes Fungiziddesign dar.
Senna macranthera: constituição química e atividades biológicas

Varias especies de Senna sao bastante conhecidas por suas propriedades terapeuticas, sendo utilizadas na medicina popular para o tratamento de inflamacao na garganta e constipacao. Neste estudo, foram avaliadas algumas propriedades biologicas e farmacologicas das folhas de Senna macranthera como as atividades anti-inflamatoria, laxativa, sobre motilidade intestinal, antimicrobiana e antioxidante. A triagem fitoquimica do seu extrato metanolico e particoes permitiu a identificacao de compostos fenolicos como flavonoides, taninos e cumarinas na maioria das amostras, com excecao da particao em hexano, que apresentou antronas, triterpenos e esteroides em sua composicao. O perfil cromatofrafico obtido por CLAE mostrou a presenca da antraquinona emodina em todas as amostras. A particao em hexano reduziu significativamente o edema de pata induzido pela carragenina em ratos, de maneira similar ao diclofenaco de sodio. Atividade laxativa comparavel ao padrao bisacodil foi observada para o extrato em metanol e particao em hexano, porem somente o ultimo aumentou a motilidade intestinal. Alem disso, o extrato metanolico e particoes foram avaliados quanto a sua atividade antioxidante e a particao em acetato de etila apresentou pronunciada atividade, comparavel ao padrao rutina. Significativa atividade antibacteriana sobre Pseudomonas aeruginosa tambem foi encontrada para o extrato em metanol e particao em hexano. Nao foi observada citotoxidade para Artemia salina ou especies de Leishmania para nenhuma amostra.
Environmental correlates of breeding abundance and population change of Eurasian Curlew Numenius arquata in Britain

ABSTRACT Capsule: Across Britain, breeding Eurasian Curlew Numenius arquata are less numerous and have shown greater population declines in areas with more arable farming, woodland cover and higher generalist predator abundance. Aims: We present the first national-scale analysis of the potential drivers of Curlew population change in Britain, which is needed to guide conservation action for this globally near-threatened, declining species. Methods: Breeding Bird Survey data and environmental predictors were used to model variation in Curlew abundance in 1995–99 and 2007–11, and population change between these periods. Results: Arable farming and woodland cover were negatively associated with Curlew abundance and population declines. Curlew abundance was positively associated with extent of protected area coverage and gamebird numbers. Abundance and population change were positively associated with cooler temperatures and higher summer rainfall, but negatively associated with numbers of generalist predators. Conclusions: We found support for the negative effects of intensive agriculture, forestry, increases in generalist predator populations and climate warming on Curlew abundance and population change. Effective site protection and measures to reduce generalist predator abundance may be important conservation measures, together with improving breeding habitat quality in the wider countryside.
Purification and characterization of α-L-arabinofuranosidases from Geobacillus stearothermophilus strain 12

Abstract In order to characterize two α-L-arabinofuranosidases (α-L-AFases), Abf1Geo12 and Abf2Geo12, produced by Geobacillus stearothermophilus strain 12, the genes (abf 1 and abf 2) coding for these enzymes were cloned and sequenced. Based on the protein sequence similarities, approximately 57 kDa two α-L-AFases were assigned to the glycoside hydrolase family 51. To obtain pure enzymes, the abf 1 and abf 2 genes were cloned into pET28a+ expression vector and recombinant α-L-AFases were produced in E.coli BL21(DE3): pLysS. Characterization of recombinant α-L-AFases revealed that Abf1Geo12 and Abf2Geo12 were active in a broad temperature range from 50 to 85°C and from 40 to 80°C, respectively. Also, the Abf1Geo12 was active in a broad pH range from 5.0 to 9.0. The optimum pH and temperature for Abf1Geo12 were determined as pH 6.0 and 65°C, respectively, whereas the optimum pH and temperature for Abf2Geo12 were determined as pH 5.5 and 60°C, respectively. Based on characterization studies, it was determined that the Abf1Geo12 was more stable than Abf2Geo12 and previously identified α-L-AFases from G. stearothermophilus. Using p-nitrophenyl α-L-arabinofuranoside as a substrate, the Km and Vmax values for Abf1Geo12 and Abf2Geo12 were determined as 0.31 mM and 290 U/mg for the former enzyme and 0.19 mM and 213.2 U/mg for the latter enzyme, respectively. The activities of Abf1Geo12 and Abf2Geo12 were strongly inhibited by 1 mM Hg2+. Interestingly, Cu2+ and Co2+ stimulated the activity of Abf1Geo12, but they reduced the activity of Abf2Geo12. The recombinant enzymes released L-arabinose from sugar beet arabinan, arabinobiose, arabinotriose, arabinotetraose and arabinopentaose. Consequently, these characterized two enzymes may be used in industrial fields since they are stable at high temperatures.
Metabolomics, biomass and lignocellulosic total sugars analysis in foxtail millet (Setaria italica) inoculated with different combinations of plant growth promoting bacteria and mycorrhiza.

Authors declare no conflict of interest Foxtail millet (Setaria italica) is the second most widely produced millet with potential as a biofuel source. Employment of plant growth promoting bacteria (PGPB) and mycorrhiza could serve as environment-friendly alternatives for the use of excessive NPK fertilizers and producing biofuel. The highest increase of biomass was associated with endomycorrhiza combined with PGPB in comparison to control. Nuclear magnetic resonance (NMR) analysis detected 28 metabolites in foxtail shoot with most of them upregulated in ecto/endomycorrhiza group and combined with PGPB. The upregulation of metabolites associated with synthesis of amino acids correlated positively with biomass. The inoculation with both PGPB and endomycorrhiza gave the best results with reference to total sugar yield. Our study indicates that PGPB and endomycorrhiza combination is well suited for enhancing biomass and boosting sugar yield, which are useful attributes for utilizing foxtail millet as a biofuel source.
Effects of breeds on the formation of heterocyclic aromatic amines in smoked lamb

Summary Heterocyclic aromatic amines (HAAs) are mutagenic and carcinogenic compounds, which are commonly detectable in cooked meat products. The objective of this study was to evaluate the effect of sheep breeds on the formation of HAAs in smoking cooked lamb. The results showed that HAAs in smoked lamb meat products were generally low (2.74–5.42 ng g−1), with most being Harman and Norharman. IQ, MeIQx, 4,8-DiMeIQx, Trp-p-2, PhIP and MeAaC were not detected in smoked lamb meat products in the present study. The total content of HAAs differed between meat products of different sheep breeds, but no difference in the order of magnitude was determined. Smoking altered the content of protein, fat, moisture and free amino acids in lamb meat products, which was probably mostly contributed by the reduction in meat moisture. Free tryptophan decreased in all breeds after smoking, which was probably used to synthesise HAAs. In summary, HAAs were low in smoked lamb meat products of all sheep breeds; thus, consumption of smoked lamb meat products should contribute very limited intake of HAAs.
Effect Of Season On Haematological Profile And Erythrocyte Indices In White Leghorn Layers

A total of 36 blood samples were obtained from White Leghorn layers, comprising 18 samples each in winter and summer season with the aim of determining the effect of season on their Haematological profile viz., Haemoglobin (Hb), Packed Cell Volume (PCV), Red Blood Cell (RBC) and Erythrocyte indices viz, Mean Corpuscular Volume (MCV), Mean Corpuscular Haemoglobin (MCH), Mean Corpuscular Haemoglobin Concentration (MCHC). The highest Hb (g %), PCV (%) and RBC (x10μl) values of 10.09 ± 0.27, 29.11 ± 0.60 and 2.71 ±0.12 respectively, were obtained during winter, while the lowest Hb, PCV and RBC values of 9.22 ±0.186, 26.44 ± 0.92 and 2.33 ± 0.9 in summer respectively. Hb, PCV and RBC values were significantly (P < 0.05) higher in winter than summer season. Erythrocyte indices did not differ statistically (P > 0.05) between seasons, but numerically higher values were obtained during winter season. Erythrocyte indices viz, MCV (fL), MCH (pg), MCHC (g/dl) obtained during winter and summer were 116.05 ± 4.24, 42.41 ±1.19 and 37.19 ± 1.36; and 107.74 ± 3.29, 39.98 ± 2.01 and 35.26 ± 1.41 respectively. The results revealed a significant seasonal variation in Hb, PCV, RBC values of White Leghorn layer and it indicates that the winter season is apparently less stressful to the White Leghorn than summer season. Keyword: Haemotological profile, Erythrocyte indices, White Leghorn