Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi Epitope Peptide Vaccine Prediction against Sudan Ebola Virus UsingImmuno-Informatics Approaches

Sudan Ebola virus is single stranded negative sense RNA genome belonging to Filovirus Filoviridae family that causes hemorrhagic fever. There is no treatment or vaccine for it, thus the aim of this study is to design a peptide vaccine using immuoinformatics approaches to analyse the glycoprotein of the all strain of SUDV, to determine the conserved region which is further studied to predict all possible epitopes that can be used as a peptide vaccine. A total of 21 Sudan Ebola virus glycoprotein retrieved from NCBI database were aligned to determine the conservancy and to predict the epitopes using IEDB analysis resource. Three epitopes predicted as a peptide vaccine for B cell (PPPPDGVR, ETFLQSPP, LQSPPIRE). For T cell four epitopes showed high affinity to MHC class I (FLYDRLAST, IIIAIIALL, MHNQNALVC and RTYTILNRK) and high coverage against Sudan and the whole world population. Also in MHC class II, Four epitopes that interact with most frequent MHC class II alleles (FAEGVIAFL, FLRATTELR, FLYDRLAST and FVWVIILFQ) with high coverage against Sudan and the whole world population. We recommend in vivo and in vitro study to prove the effectiveness of these predicted epitopes as a peptide vaccine.
Nitrogen allocation in barley: Relationships between amino acid transport and storage protein synthesis during grain filling

Egle, K. , Beschow, H. and Merbach, W. 2015. Nitrogen allocation in barley: Relationships between amino acid transport and storage protein synthesis during grain filling. Can. J. Plant Sci. 95: 451-459. A better knowledge of the source-sink relationships relating to nitrogen allocation within plant and synthesis of storage protein in grains could be of particular importance contributing to better define grain sink capacity for improving nitrogen use efficiency by plant species. The objectives of this study were to assess N partitioning in barley cv ‘Barke’prior and after anthesis, and to investigate whether the synthesis of the major storage protein (hordein) is an indicator of the sink strength of the developing grain for nitrogenous compounds. Pot experiments were performed using N fertilizer, labelled N (15N fertilizer) or feeding of labelled proteinogenic and non-proteinogenic amino acids (15N-L-a-alanine: 15N-a-Ala or 15N-a-aminoisobutyric acid: 15N-a-Aib, respectively). Results showed that N filling of spike occurred from N remobilized predominantly from leaves and stem, and from current N uptake. Post-anthesis applied 15N was taken up and predominantly transported into spike. Experiment with feeding of labelled amino acids demonstrated that most of the 15N from a-Ala and a-Aib was transferred to grains, but that more (about 37% versus 24%) was retained in the fed leaf when 15N was applied in the form of a-Aib. The strongest effect was observed in partitioning between N fractions in grains: hordein acted as a main reservoir for 15N-a-Ala while 15N-a-Aib predominantly remained in NaCl-extractable fractions (non-protein nitrogen and salt-soluble proteins). The biosynthesis of hordein in grains did not seem to be exclusively the potential sink for nitrogenous compounds but could enhance the transport of amino acids into the grain by the instantaneous incorporation of imported amino acids into hordein.
Repelentes de aves aplicados a la semilla de soja: compatibilidad con el inoculante y residualidad en cotiledones

Tres especies de palomas causan significativas perdidas economicas en soja ( Glycine max [L.] Merr), por consumo total o parcial de cotiledones durante la emergencia del cultivo. Los repelentes son una alternativa no letal para disminuir esos danos, evitando que las aves se alimenten del cultivo. Este trabajo tuvo como objetivos conocer si repelentes aplicados a las semillas poseen la capacidad de ingresar y permanecer en los cotiledones. Los ensayos evaluaron sus efectos en la sobrevivencia de rizobios sobre las semillas y la capacidad de estos de nodular y fijar nitrogeno. Se evaluo Draza® (methiocarb 50 %), Avipel® (antraquinona 50 %) y Rayen® (metil antranilato 30 %). Las semillas fueron tratadas con los repelentes y posteriormente con inoculantes formulados en soporte liquido y turba. Se evaluo el numero de rizobios viables sobre semillas a los dos y siete dias luego de tratadas, y se determinaron parametros de nodulacion y peso seco de parte aerea en invernaculo. Se evaluo el contenido (ppm) de antraquinona y metil antranilato en cotiledones. La sobrevivencia de rizobios disminuyo con metiocarb y antraquinona pero no con metil antranilato. La capacidad de nodular de los rizobios y la fijacion biologica de nitrogeno (FBN) fueron afectadas negativamente por el uso de metiocarb y antraquinona, siendo esta ultima menos perjudicial. Se observo presencia del repelente en cotiledones para antraquinona aunque no para metil antranilato. Futuras investigaciones deberian estar dirigidas a incrementar la cantidad de metil antranilato presente en cotiledones, sin afectar los rizobios.
ROLE OF PIGMENTS AND TANNINS IN THE REACTION OF TAN AND RED NEAR-ISOGENIC SORGHUM LINES TO LEAF DISEASES

Sorghum ( Sorghum bicolor L. Moench) plant pigments have been associated with resistance to leaf diseases and grain deterioration. Four near-isogenic pairs of tan and non-tan (red) sorghum lines were assayed for their phenolic content and evaluated for their reaction to leaf diseases along with six other sorghum lines. Leaves, stems, sheaths, glumes and seeds of mature plants were assayed for tannins, pigments, and precursors of these pigments. No tannins were detected in the various plant tissues although other genotypes can have high levels of these compounds in seed coats. The red plants (especially the glumes and sheath) were found to accumulate 3-deoxyanthocyanidins, the major pigments in sorghum, but these were absent in the tan plants. The glumes and sheath of tan plants accumulated apigenin. Near-isogenic pairs were tested for differential reactions to anthracnose ( Colletotrichum graminicola Ces.) at Tifton, Georgia and to rust ( Puccinia purpurea Cooke) at Isabella, Puerto Rico during the 1991 growing season. Tan and red isogenic pairs, which differ significantly in phenolic composition, did not show significant differences in their disease reaction. The six other sorghum lines which showed marked differences in their reaction to leaf diseases also showed differences in their phenolic composition. However, for the phenols that were analyzed, there was no correlation with resistance or susceptibility. It is proposed that tannins, pigments, and pigment precursors are not responsible for disease resistance in these genotypes.
Screening selection and optimization of extracellular methanol and ethanol tolerant lipase from Acinetobacter sp. K5b4

An extracellular methanol and ethanol tolerant lipase producing bacterial strain K5b4 was isolated from soil samples contaminated with hydrocarbon residues, and further identified as Acinetobacter species. The immobilized lipase from Acinetobacter sp. K5b4 retained more than 98% of its residual activity after incubation with pure methanol and ethanol for 24 hours. The highest hydrolytic activity of the immobilized enzyme was obtained in the presence of 75% (v/v) methanol in the assay solution. In contrary, the enzyme was able to maintain its original activity up to only 25% (v/v) ethanol meanwhile, at elevated concentrations of 50 and 75% (v/v) the enzyme activity were reduced by 10 and 40% respectively. Maximum lipase activity of 31.5 mU/mL was achieved after 48 hr cultivation when the optimized medium (pH 7.0) that composed of 1.0% (w/v) olive oil, 0.2% (w/v) glycerol, 0.15% (w/v) yeast extract, and 0.05% (w/v) NaCl was inoculated with 0.4% (v/v) seed culture and incubated at 30°C and 150 rpm agitation speed. However, the presence of CaCl2 in the growth media did not show any inhibitory or stimulatory effect on the enzyme production as it compared to the control experiment. Meanwhile, the other mineral salts MgCl2, MnCl2, KCl and CoCl2 were negatively affected the production of lipase enzyme. The inhibition of lipase production from Acinetobacter sp. K5b4 in presence of glucose suggesting that lipase gene expression is prone to catabolic repression. * Corresponding Author:Muhamad O. Allimoun muhamadodeh@gmail.com
Best Practices for Genotyping Analysis of Plant and Animal Genomes with Affymetrix® Axiom® Arrays

SNP QC metrics generation and SNP classification Background: Large-scale multiplexed SNP genotyping has been made possible by the ongoing development of high-density DNA oligonucleotide arrays coupled with new molecular biology assays. The data analysis processing of these arrays requires automated methods and workflows and thus Axiom® genotyping best practices has been developed and applied to the human genome (http://www.affymetrix.com/support/downloads/manuals/ axiom_best_practice_supplement_user_guide.pdf). Plant and animal genomes however present additional challenges due to the complex organization of polyploid genomes, high levels of species-specific nucleotide and structural diversity, and the use of relatively novel sequencing-derived content that has The steps of post-processing genotypes (Step 8 in Figure 1) are as follows: 1. Generate probe set quality control metrics, including call rate, FLD, HetSO, HomRO, HomFLD, nMinorAllele, Nclus. 2. SNPs/probe sets are classified based on SNP QC metrics into six categories: Polymorphic high-resolution", "Monomorphic highresolution", "Off-target variant", "Call rate below threshold", "No minor homozygote", and "Other". Note: These two functions are achieved in the SNPolisherTM R package. Figure 2: Typical patterns of six SNP/probe set categories. not been previously validated with independent genotyping methods. Results: We describe the Axiom® data analysis workflow that combines the best practices for human genotyping with new steps and software that are specifically targeted to the complexities associated with plant and animal genotyping. Genotyping calls are produced for humans, plants, and animal genomes with AxiomGT1, which is an automated clustering algorithm used in Axiom® Genotyping ConsoleTM Software that features adaptive, dynamic clustering. Following genotyping, “SNPolisherTM”, a newly developed R package for Axiom® Genotyping Arrays, uses AxiomGT1 output to (1) produce SNP Quality Control (QC) metrics; (2) divide markers into six classes that are relevant to the genomic complexities of plants and animals; (3) provide cluster Monomorphic high-resolution Off-target variant Polymorphic high-resolution visualization; and (4) execute “Off-target variant (OTV) genotyping”. In summary, this workflow returns the maximum number of high-quality genotype calls along with automatic division of polymorphic, high-resolution markers from those markers that can benefit from further examination based on knowledge of the genetics of the sample under study. Best practice workflow Plant and animal genomes have long been known to be much more complex than human genomes, which pose computational challenges in the genotyping process We adapted the best practice Axiom® workflow for human genotyping Call rate below threshold Other No minor homozygote
Chemical Inhibition of Nitrification: Evaluating Methods to Detect and Characterize Inhibition and the Role of Selected Stress Responses Upon Exposure to Oxidative and Hydrophobic Toxins

This research first examined nitrification inhibition caused by different classes of industrially relevant chemicals on activated sludge and found that conventional aerobic nitrification was inhibited by single pulse inputs of every chemical tested, with 1-chloro-2,4dinitrobenzene (oxidant) having the most severe impact, followed by alkaline pH 11, cadmium (heavy metal), cyanide, octanol (hydrophobic) and 2,4-dinitrophenol (respiratory uncoupler). Of the different chemicals tested, the oxidative and hydrophobic chemicals showed severe nitrification inhibition relative to other treatment processes and therefore deserved further investigation. For oxidative chemicals, we hypothesized that the more severe inhibition was because nitrifying bacteria lack one or more of the microbial stress response mechanisms used to mediate the toxic effect of oxidative chemicals. During these experiments, we showed that a rapid (minutes) antioxidant potassium efflux mechanism does not exist in two nitrifying bacteria, Nitrosomonas europaea and Nitrospira moscoviensis. Furthermore, we showed that another important antioxidant molecule, glutathione, was not oxidized as readily as in a non-nitrifying bacterium. Furthermore, we hypothesized that hydrophobic chemical-induced nitrification inhibition recovered more quickly because of the presence of membrane modification stress response mechanisms. While testing this hypothesis, we showed that N. europaea modified its cell membrane in response to hydrophobic chemicals using a long-term (hours) membrane modification mechanism that required the synthesis of new fatty acids, but it did not contain a short-term (minutes) response mechanism involving a cis/trans isomerase. Therefore, investigating these nitrifier stress responses showed that nitrifiers lack short-term stress responses that may be used to rapidly detect inhibition, indicating that conventional methods of detecting nitrification inhibition, like differential respirometry and nitrate generation rate (NGR), are still the fastest and easiest methods to use. Because several conventional methods exist, we also investigated differences between differential respirometry and a UV method we developed to measure NGR. During these tests, we showed that the UV NGR method provided a more reliable measure of nitrification inhibition than differential respirometry, and that the time to maximum nitrification inhibition depended on the properties of the chemical toxin, which implies that longer exposure times may be needed to accurately predict nitrification inhibition.
Etude du rôle de la protéine Dlg1 dans le cycle de réplication et la transmission du VIH-1

La propagation du VIH-1 dans l’organisme est un processus dependant du bourgeonnement de particules correctement assemblees. Pour ce faire, le virus utilise une strategie de detournement de certaines proteines cellulaires, qui sont souvent des partenaires des proteines de structure virale Gag et Env. Le VIH-1 se transmet de deux facons dans un organisme : par particules libres ou par transfert de cellule a cellule via une structure appelee synapse virologique. Ce dernier moyen de propagation est considere comme le plus efficace et predominant in vitro. Nous avons precedemment identifie Dlg1, l’homologue humain de la proteine « Discs Large » de la drosophile, comme un nouveau partenaire de la proteine Gag du VIH-1. Dans ce contexte, nous avons etudie le role de Dlg1 dans les deux modes de transmission du VIH-1 dans des lymphocytes T, cellules cibles naturelles du virus, ou l’extinction stable de Dlg1 est obtenue avec un vecteur shRNA. Nous avons montre que le virus se propage plus efficacement dans les cellules n’exprimant pas Dlg1. Des observations en microscopie confocale nous ont revele que l’absence de Dlg1 n’empechait pas la formation de la synapse virologique, et des analyses quantitatives nous ont montre que l’efficacite de la transmission de cellule-a-cellule du virus n’etait egalement pas affectee. La meilleure efficacite de propagation en absence de Dlg1 resulte d’une augmentation significative de l’infectivite des particules relâchees. Ce phenotype des particules virales correspond a une augmentation de leur contenu en cholesterol qui permettrait d’augmenter l’efficacite de la fusion virus-cellule lors de l’etape d’entree du virus. Nous avons donc montre que Dlg1 est un regulateur negatif de la transmission par particules libres du VIH-1, et que la transmission cellule-a-cellule du virus parvient a contourner cette regulation.
Study of the antiepileptic drugs transport through the immature blood-brain barrier

Resistance to Antiepileptic Drugs (AEDs) has been a major concern in infantile epilepsies such as for example the Dravet Syndrome. One hypothesis concerning the pharmacoresistance in epilepsy is that a decreased delivery of these drugs to the brain may occur in relation to changes in the Blood-Brain Barrier (BBB) function. BBB exhibits ATP-binding cassette (ABC) and SoLute Carrier (SLC) transporters at the surface of endothelial cells that control the blood-brain transport. Pharmacoresistance in epilepsy may be linked to changes in the functions of these transporters since some AEDs are substrates of the P-glycoprotein (P-gP) and Breast Cancer Resistance Protein (BCRP) transporters. The increased expression of efflux transporters in epileptogenic tissue and the identification of polymorphisms in the efflux transporters genes of resistant patients further support this potential relationship. The interaction of endothelial cells with astrocytes and neurons during brain development could change the pattern of transporters in the BBB. AEDs are also known as either inducers or inhibitors of drug metabolic enzymes and membrane transporters. Taken together, these facts led us to test the following hypothesis: 1) the developing BBB in immature animals presents a different pattern of transporters that could change AEDs disposition in the brain of immature subjects; and 2) the chronic pharmacotherapy used in infantile epilepsies such as the Dravet Syndrome may change the transporters phenotype of the BBB. Our work showed that the expression of P-gP and BCRP increases during development as a function of age. We also showed the maturation of the BBB has an impact on brain disposition of the studied AEDs. We finally observed an increase in the expression of various ABC and SLC transporters induced by the pharmacotherapy of the Dravet Syndrome in immature animals. One of the drugs used, valproic acid, appeared nonetheless to reduce the efflux activity of P-gP in developing and adult animals, which was confirmed in an in-vitro model of the immature BBB. Taken together, these results demonstrated that the interaction between the developing BBB and the AEDs chronic treatment may lead to differences in brain disposition of the AEDs that may impact on the response to AEDs.
THE ROLE OF p53 AND CASPASE IN REGULATION APOPTOSIS ACTIVITY

Apoptosis, or programmed cell death, is a common property of all multicellular organism. Apoptosis occurs normally during development and aging and as a homeostatic mechanism to maintain cell populations in tissue. Apoptosis also accurs as a defense mechanism such as in immune reactions or when cells are damaged by disease or noxious agents. Dysregulation of apoptosis leads to a variety of human pathologies including cancer, autoimmune disease, and neurodegenerative disorders.
The Decomposition of Similarity-Based Diversity and its Bias Correction

Similarity-based diversity (Leinster and Cobbold 2012) encompasses classical measures of diversity, including the number of species, Shannon and Simpson diversity, and also phylogenetic and functional diversity. We derive two estimators to allow applying it to real, often under-sampled data, and its decomposition into alpha, beta and gamma diversity when an assemblage of communities is considered.
Molecular strategies in the treatment of skin cancers

Non-melanoma skin cancers (NMSC) are the most frequent malignant neoplasms in Caucasians, presenting constantly increasing frequency and morbidity. Surgical excision remains the gold standard in the treatment of NMSC. The discovery of molecular pathways of cell growth and differentiation, apoptosis and invasion enables the introduction of molecularly guided therapies of skin cancer. The most thoroughly investigated signalling pathways are the epidermal growth factor receptor (EGFR) pathway and hedgehog pathway. We present an overview of the mechanisms of both signalling pathways and their significance in the development and treatment of skin cancers. The data indicate that EGFR plays a significant role in skin carcinogenesis and its inhibitors may be potentially utilized in growth reduction of advanced tumors inappropriate for surgical treatment. Disturbance in the hedgehog pathway, attributed to UVR-dependent PATCHED gene mutations, plays an important role in the development of NMSC. SŁOWA KLUCZOWE: rak skóry, leczenie molekularnie ukierunkowane.
Selection of appropriate reference genes for qPCR in the Chinese mitten crab, Eriocheir sinensis (Decapoda, Varunidae)

The accuracy of qPCR depends on the stability of the reference gene used for data normalization. However, the stably expressed reference genes in the Chinese mitten crab, Eriocheir sinensis , have not been well identified under different experimental conditions. In this study, the stabilities of the expressions of 10 candidate reference genes were evaluated in different developmental stages, tissues, and moulting stages of E. sinensis . Our results indicated that UBE and S27 were the most stable reference genes. To validate the suitability of the reference genes, the EcR (ecdysone receptor) gene was analysed among different moulting stages. The results showed that the expression level of EcR was elevated using the least stable reference gene, GST , compared with using the three most stable reference genes. Taken together, our results indicate that reference genes should be assessed and selected in accordance with the experimental conditions, and more than one reference gene should be selected.
Investigating plasmepsin flexibility as a function of the flap region : a unique structural and dynamic feature of aspartic protease.

Aspartic proteases are hydrolytic enzymes that have been implicated in a number of diseases such as HIV, malaria, cancer and Alzheimer’s. Generally speaking, their structure is relatively conserved in which the active site (aspartic acids) is housed at the interface of the Nand C-terminal lobes. Partially covering the active site is a flexible hairpin flap, lying perpendicular to the active site. The flap region in this class of enzyme is a characteristic unique to aspartic proteases; and has a profound impact on protein function. Dynamics in the flap region substantially affects the overall dynamics and conformation of the protein. Flap dynamics play a crucial role in drug binding, regulating access to the active site. Mutations in this region has a significant impact on the conformation of the protein and on drug binding; mutations that alter flap dynamics can lead to the development of resistance. Therefore understanding the dynamics and behaviour of the flap regions is crucial in the design of potent, selective inhibitors of aspartic proteases with increased efficacy and potency, and potentially reduce the incidence of resistance. The current review focuses on the flap region of aspartic proteases and the parameters used to measure the dynamics of the active site. Clear, concise and accurate parameters will aid in a better understanding of the dynamic nature of this enzyme family.
The effect of linoleic acid on the growth and vascularity of L-1 Sarcoma in mice and on the cutaneous angiogenesis induced by tumour cells

Liczne badania epidemiologiczne i doœwiadczalne na zwierzêtach wskazuj1 na istotn1 rolê t3uszczów w rozwoju procesu nowotworowego i w zjawisku przerzutów [1, 2, 3]. Znaczenie ma zarówno iloœæ t3uszczu, jak i jego sk3ad [4, 5]. Szczególnie wa¿n1 rolê odgrywaj1 wielonienasycone kwasy t3uszczowe, zwane niezbêdnymi, które nie s1 wytwarzane w organizmie i musz1 byæ dostarczane w pokarmie. Nale¿y do nich kwas linolowy (LA), nienasycony kwas t3uszczowy z rodziny n-6, znajduj1cy siê w du¿ych iloœciach w oleju s3onecznikowym, sojowym, kukurydzianym i wiesio3kowym.