Miracle-dz/UniFAR-FTUs huggingface dataset:
Allele Specific Expression in Human – Genomic Makeup and Phenotypic Implications

The allele-specific expression phenomenon refers to unbalanced expression from the two parental alleles in a tissue of a diploid organism. AlleleDB is a high-quality resource that reports on about 30,000 ASE variants (ASE-V) from hundreds of human samples. In this study, we present the genomic characteristics and phenotypic implications of ASE. We identified tens of segments with extreme density of ASE-V, many of them are located at the major histocompatibility complex (MHC) locus. Notably, at a resolution of 100 nucleotides, the likelihood of ASE-V increases with the density of polymorphic sites. Another dominant trend of ASE is a strong bias of the expression to the major allele. This observation relies on the known allele frequencies in the healthy human population. Overlap of ASE-V and GWAS associations was calculated for 48 phenotypes from the UK-Biobank. ASE-V were significantly associated with a risk for inflammation (e.g. asthma), autoimmunity (e.g., rheumatoid arthritis, multiple sclerosis, and type 1 diabetes) and several blood cell traits (e.g., red cell distribution width). At the level of the ASE-genes, we seek association with all traits and conditions reported in the GWAS catalog. The statistical significance of ASE-genes to GWAS catalog reveals association with the susceptibility to virus infection, autoimmunity, inflammation, allergies, blood cancer and more. We postulate that ASE determines phenotype diversity between individuals and the risk for a variety of immune-related conditions.
The complete mitochondrial genome of Anthomyza sp. (Diptera: Anthomyzidae)

Abstract Anthomyza sp. belongs to family Anthomyzidae of superfamily Opomyzoidea. The mitogenome of Anthomyza sp. was sequenced as the first representative of the family. The mitogenome is 16,308 bp totally, consisting of 13 protein-coding genes, 2 rRNAs and 22 transfer RNAs and control region. Anthomyza sp. has the similar gene structures with other published species of Acalyptratae. The nucleotide composition biases toward A and T is 78.7% of the entirety. IQ-TREE analysis recovered the monophyly of Opomyzoidea, which is inferred from 12 species. It indicated that Opomyzoidea is assigned to be the sister of the clade of (Ephydroidea + (Tephritoidea + Lauxanioidea)).
Human health risks of metalloids and metals in muscle tissue of silver carp Hypophthalmichthys molitrix (Valenciennes, 1844) from Lake Flag Boshielo, South Africa

The Olifants River, a major tributary of the Limpopo River, is one of the most polluted rivers in South Africa. Consequently, concerns regarding the human health impact of long-term consumption of fish from the Olifants River have been raised in recent studies. Nevertheless, Lake Flag Boshielo situated on the main stem of the Olifants River has been proposed as a site for an inland fishery. Planktivorous silver carp Hypophthalmichthys molitrix (Valenciennes, 1844) is among the potential target species for such a fishery. Therefore, a desk-top human health risk assessment was conducted for silver carp from Lake Flag Boshielo. From January to November 2013, muscle samples from 50 specimens were collected and analysed for metals and metalloids. The hazard quotient based on a weekly meal of 150 g exceeded the acceptable level for As, Cd, Cr, Co, Pb, Hg, Se, V and Zn. Compared with previous studies from Lake Flag Boshielo, muscle tissue concentrations of As, Cr, Pb, Hg, Se, V and Zn for H. molitrix were higher. Based on the metal and metalloid concentrations reported in this study, long-term consumption of silver carp from Lake Flag Boshielo might pose a health risk to impoverished rural communities.
Perception of the Müller–Lyer illusion in guppies

Abstract The Müller–Lyer illusion is a well-known distortion illusion that occurs when the spatial arrangement of inducers (i.e., inwards- or outwards-pointing arrowheads) influences a line’s perceived relative length. To date, this illusion has been reported in several animal species but only in 1 teleost fish (i.e., redtail splitfins Xenotoca eiseni), although teleost fish represent approximately 50% of vertebrate diversity. We investigated the perception of this illusion in another teleost fish: guppies Poecilia reticulata, a species that diverged from the redtail splitfin 65 million years ago. The guppies were trained to select the longer between 2 lines; after meeting the learning criterion, illusory trials were presented. Control trials were also arranged to exclude the possibility that their choices were based on potential spatial biases that relate to the illusory pattern. The guppies’ overall performance indicated that they were susceptible to the Müller–Lyer illusion, perceiving the line with the inwards-pointing arrowheads as longer. The performance in the control trials excluded the possibility that the subjects used the physical differences between the 2 figures as the discriminative cue in the illusory trials. Our study suggests that sensibility to the Müller–Lyer illusion could be widespread across teleost fish and reinforces the idea that the perceptual mechanisms underlying size estimation might be similar across vertebrates.
Multi-epitope Peptide Vaccine Prediction for Candida albicans targeting Pyruvate Kinase Protein; an Immunoinformatics Approach

The fungus Candida albicans is an opportunistic pathogen that causes a wide range of infections. It’s the primary cause of candidiasis and the fourth most common cause of nosocomial infection. In addition, disseminated invasive candidiasis which is a major complication of the disease has an estimated mortality rate of 40%-60% even with the use of antifungal drugs. Over the last decades, several different anti-Candida vaccines have been suggested with different strategies for immunization against candidiasis such as, live-attenuated fungi, recombinant proteins, and glycoconjugates but none has been approved by the FDA, yet. This study aims to introduce a new possible vaccine for C. albicans through analyzing peptides of its pyruvate kinase (PK) protein as an immunogenic stimulant computationally. A total number of 28 C. albicans, pyruvate kinase proteins were obtained from NCBI on the 9th of February 2019 and were subjected to multiple sequence alignment using Bioedit for conservancy. The main analytical tool was IEDB, Chimera for homology modelling, and MOE for docking. Among the tested peptides, fifteen promising T-cell peptides were predicted. Five peptides were more important than the others (HMIFASFIR, YRGVYPFIY, AVAAVSAAY, LRWAVSEAV, and IFASFIRTA) They show high Binding Affinity to MHC molecules, low binding energy required indicating more stable bonds, and their ideal length of nine peptides. (PTRAEVSDV) peptide is the most promising linear B-cell peptide due to its physiochemical parameters and optimal length (nine amino acids). It’s highly recommended to have these five strong candidates in future in vivo and in vitro analysis studies.
Plant-based milks: unexplored source of emerging mycotoxins. A proposal for the control of enniatins and beauvericin using UHPLC-MS/MS

ABSTRACT Mycotoxins have become one of the most common contaminants reported worldwide. Current legislation has established maximum levels only for some well-known mycotoxins; however, there are many other “emerging mycotoxins” for which there is no regulation, as enniatins and beauvericin. An analytical method based on salting-out assisted liquid-liquid extraction followed by ultra-high performance liquid chromatography tandem mass spectrometry is proposed for determination of enniatin A, A1, B, B1, and beauvericin in different plant-based milks, as a possible source of these contaminants, is proposed. The method showed good precision and trueness (RSD <8% and recoveries between 84-97%) with a moderate matrix effect. From a total of 32 samples of plant-based milks of different compositions (including 8 rice milks, 8 oat milks and 16 soy milks), 3 samples were contaminated with the five mycotoxins, while 5 samples were contaminated with four of them, being oat milk the most susceptible for contamination.
Maintenance of embryogenic potential of calli derived from embryonic shoot of West Coast Tall cv. of coconut (Cocos nucifera L.)

Maintenance of embryogenic potential of calli is important as the totipotency is often lost in a short time in vitro. This caters to the need for year round availability of somatic embryos in a regenerable state. In the present study, 14 media combinations, with either 2,4-D or picloram as auxin source, were tested for maintaining embryogenic calli obtained from embryonic shoot explants of coconut. Irrespective of type and concentration of auxins, callusing was observed in all the media combinations. However, high dose of 2,4-D (above 74.6 μM) in the initial medium resulted in intense browning and lesser percentage of callusing. Embryogenic nature of calli could be maintained to a maximum of 21 weeks in medium supplemented with 2,4-D (74.6 μM) and subsequent culturing into higher concentration of 2,4-D (90.4 μM). Gene expression studies carried out using qRT-PCR revealed that genes such as ECP, GST, LEAFY and WUS were highly expressed in long term embryogenic calli (21 week old) and genes such as SERK, GLP, WRKY and PKL in initial embryogenic calli (21 days old). The study concludes that coconut plumular calli could be maintained for longer periods without compromising on the embryogenic potential of the calli.
In vitro model for resistance in oncogene-dependent tumors at the limit of radiological detectability

In solid tumors, the response to targeted therapy is typically short-lived, as therapy-resistant mutants can quickly expand during therapy. Here we analyze the spectrum of such resistance mutations coexisting in a large population of cancer cells. We use an iterative scheme of artificial evolution to amplify and isolate different resistance mechanisms. As a proof of concept, we apply our scheme to PC-9 cells, a human non-small cell lung cancer cell line with an activating EGFR mutation. The mechanisms we find comprise the well-known gatekeeper-mutation T790M in EGFR, a mutation in NRAS, the amplification of MET-ligand HGF, as well as induction of AKT-mTOR signaling. In this model, a combination of four drugs targeting these mechanisms prevents not only the expansion of resistant cells, but also inhibits the growth of drug-tolerant cells, which can otherwise act as a reservoir for further resistance mutations. These data suggest that a finite number of drugs specifically acting on individual resistant clones may be able to control resistance in oncogenically driven lung cancer.
Polygenic Risk Scores for Cardio-renal-metabolic Diseases in the Penn Medicine Biobank

Cardio-renal-metabolic (CaReMe) conditions are common and the leading cause of mortality around the world. Genome-wide association studies have shown that these diseases are polygenic and share many genetic risk factors. Identifying individuals at high genetic risk will allow us to target prevention and treatment strategies. Polygenic risk scores (PRS) are aggregate weighted counts that can demonstrate an individual’s genetic liability for disease. However, current PRS are often based on European ancestry individuals, limiting the implementation of precision medicine efforts in diverse populations. In this study, we develop PRS for six diseases and traits related to cardio-renal-metabolic disease in the Penn Medicine Biobank. We investigate their performance in both European and African ancestry individuals, and identify genetic and phenotypic overlap within these conditions. We find that genetic risk is associated with the primary phenotype in both ancestries, but this does not translate into a model of predictive value in African ancestry individuals. We conclude that future research should prioritize genetic studies in diverse ancestries in order to address this disparity.
NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

The set of peptides presented on a cell's surface by MHC molecules is poly-specific (it contains multiple sequence motifs matching the quantity of MHC molecules expressed). NNAlign_MA can exploit this type of data, by means of: (1) clustering peptides into individual specificities; (2) automatic annotation of clusters to an MHC molecule; and (3) training of a prediction model covering all MHCs present in the training set. NNAlign_MA expands MHC allelic coverage, thus improving T-cell epitope predictions. Graphical Abstract Highlights NNAlign_MA enables full deconvolution of single MHC specificities from MS assays. NNAlign_MA expands MHC allelic coverage, improving identification of T-cell epitopes. NNAlign_MA was benchmarked on MHC classes I and II, outperforming current methods. NNAlign_MA offers a universal solution to analyze and exploit MHC peptidomics data. The set of peptides presented on a cell's surface by MHC molecules is known as the immunopeptidome. Current mass spectrometry technologies allow for identification of large peptidomes, and studies have proven these data to be a rich source of information for learning the rules of MHC-mediated antigen presentation. Immunopeptidomes are usually poly-specific, containing multiple sequence motifs matching the MHC molecules expressed in the system under investigation. Motif deconvolution -the process of associating each ligand to its presenting MHC molecule(s)- is therefore a critical and challenging step in the analysis of MS-eluted MHC ligand data. Here, we describe NNAlign_MA, a computational method designed to address this challenge and fully benefit from large, poly-specific data sets of MS-eluted ligands. NNAlign_MA simultaneously performs the tasks of (1) clustering peptides into individual specificities; (2) automatic annotation of each cluster to an MHC molecule; and (3) training of a prediction model covering all MHCs present in the training set. NNAlign_MA was benchmarked on large and diverse data sets, covering class I and class II data. In all cases, the method was demonstrated to outperform state-of-the-art methods, effectively expanding the coverage of alleles for which accurate predictions can be made, resulting in improved identification of both eluted ligands and T-cell epitopes. Given its high flexibility and ease of use, we expect NNAlign_MA to serve as an effective tool to increase our understanding of the rules of MHC antigen presentation and guide the development of novel T-cell-based therapeutics.
Role of cAMP Homeostasis in Intra-Macrophage Survival and Infectivity of Unicellular Parasites likeLeishmania

Unicellular eukaryotic pathogen Leishmania donovani , an intra-macrophage protozoan parasite, on exposure to phagolysosome conditions (PC) of mammalian macrophages, show increased cAMP level and cAMP-dependent protein kinase A (PKA) resulting in resistance to macrophage oxidative burst. In order to have a com-prehensive understanding of cAMP signaling and their contribution to infectivity, studies were carried out on all the enzymes associated with cAMP metabolism such as adenylate cyclase, phosphodiesterase, pyrophosphatase and the regulatory and catalytic subunits of PKA. This chapter deals in detail the contribution of these components of cAMP signaling in cAMP homeostasis of the parasite as well as their role on successful host-parasite interaction leading to intracellular parasite survival and establishment of infection. Finally, a discussion is made about how these observations might be exploited for developing drug candidates targeting parasite specific features. elevation in intracellular cAMP level after PC. Moreover, there was a 10.2% decrease in cAMP level when RAC-A knocked-down PC-exposed parasites were further treated with DDA. Ldrac-B knocked-down parasites behaved as control parasites showing elevated cAMP levels on PC exposure. However, there was a significant decrease of cAMP level when RAC-B knocked-down cells were treated with DDA. The results indicate that LdRAC-A plays a conspicuous role in triggering cAMP response in the parasites during stress condition.
Bacterial diversity and its relationship to growth performance of broilers

The microbial community is known to have a key role during the rearing period of broilers. In this study, gut microbial composition and diversity were examined to evaluate the relationships between these factors and broiler growth performance. By applying 454-pyrosequencing of the V1−V3 regions of bacterial 16S rRNA genes, six fecal samples from fourand 28-day-old chickens from three broiler farms and 24 intestinal samples of broilers with heavy and light body weights were analyzed. Microbial composition assessment revealed Firmicutes to be the most prevalent phylum at farm A, while Proteobacteria were predominant at farms B and C. Fecal microbial richness and diversity indices gradually increased from four to 28 days at all three farms. Microbial diversity assessment revealed that small intestine microbial diversity was lower in heavy birds than in light birds. In light birds, the Firmicutes proportion was lower than that in heavy birds. In conclusion, each broiler farm revealed a specific microbial profile which varied with the age of the birds. The microbial communities appeared to affect growth performance; therefore, gut microbial profiles can be utilized to monitor growth performance at broiler farms.
Putatively cancer-specific alternative splicing is shared across patients and present in developmental and other non-cancer cells

We compared cancer and non-cancer RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) Project, and the Sequence Read Archive (SRA). We found that: 1) averaging across cancer types, 80.6% of exon-exon junctions thought to be cancer-specific based on comparison with tissue-matched samples are in fact present in other adult non-cancer tissues throughout the body; 2) 30.8% of junctions not present in any GTEx or TCGA normal tissues are shared by multiple samples within at least one cancer type cohort, and 87.4% of these distinguish between different cancer types; and 3) many of these junctions not found in GTEx or TCGA normal tissues (15.4% on average) are also found in embryological and other developmentally associated cells. This study probes the distribution of putatively cancer-specific junctions across a broad set of publicly available non-cancer human RNA-seq datasets. Overall, we identify a subset of shared cancer-specific junctions that could represent novel sources of cancer neoantigens. We further describe a framework for characterizing possible origins of these junctions, including potential developmental and embryological sources, as well as cell type-specific markers particularly related to cell types of cancer origin. These findings refine the meaning of RNA splicing event novelty, particularly with respect to the human neoepitope repertoire. Ultimately, cancer-specific exon-exon junctions may affect the anti-cancer immune response and may have a substantial causal relationship with the biology of disease.
Weed Interference in the Establishment of Urochloa ruziziensis

ABSTRACT: This research aimed to study weed interference relationship on morphogenesis, yield, and greenhouse gas production potential of Urochloa ruziziensis under pasture renovation conditions. The experimental design was a randomized block design with four replications. Treatments consisted of seven coexistence periods: 0, 15, 30, 45, 60, 75, and 90 days after emergence (DAE). The following morphological parameters were analyzed: number of tillers, number of leaves, photosynthetically active leaf blade biomass, fresh stem biomass, dead material biomass, and total dry biomass. In vitro analyses of methane (CH4) and carbon dioxide (CO2) production were also carried out. The results were submitted to analysis of variance by the F-test, and the test of means was carried out by the Scott-Knott test at 5%. Biomass, CH4, and CO2 production of U. ruziziensis were modified with only 15 days of weed coexistence, with an effect even higher from 45 DAE. Therefore, weeds interfere with all morphological parameters, yield, and greenhouse gas production in the pasture establishment with the forage grass U. ruziziensis.
Description of the carbon mineralization of swine manure and oat straw in the soil through nonlinear models

Agricultural management is a viable way for recycling animal residues in feedlots. Thesubstances that make up organic residues change the dynamics of the organic matter decompositionin the soil. Information on carbon mineralization curves allows seeking improvements in soil qualityand, consequently, in crop productivity. The Stanford & Smith Nonlinear Model is the most usedto describe C mineralization of organic residues in the soil. This model considers organic residuesare composed of substances that are mineralized exponentially. The Cabrera Model considers twofractions, one composed of substances that are mineralized exponentially and other composed ofmore resistant substances with constant mineralization. The objective of this work was to comparenonlinear models that describe carbon mineralization, considering residues on surface or incorporatedinto the soil. The data evaluated were from an experiment with oat straw, liquid swine manure, andswine litter bedding. The Stanford & Smith and Cabrera Models were used considering structure offirst order autoregressive errors - AR(1), when necessary. The fittings were compared using the AkaikeInformation Criterion (AIC). The Cabrera Model was more adequate to describe C mineralization infour treatments (soil + incorporated liquid swine manure; soil + oat straw on surface + liquid swinemanure on surface; soil + incorporated straw; and soil + straw on surface). The Stanford & SmithModel was better in three treatments (soil + incorporated straw + incorporated liquid swine manure;swine litter bedding on surface; and incorporated swine litter bedding). None of the models describedthe treatment soil + liquid swine manure on surface.Keywords: Decomposition. Half-life. Stanford & Smith Model. Cabrera Model.
Study on Indigestible Foreign Body in Rumen and Reticulum of Cattle Slaughtered at Bahir Dar Municipal Abattoir, Ethiopia

A cross-sectional study was conducted from October 2016 to April, 2017 at Bahirdar municipal abattoir, Amhara National Regional State, to determine the prevalence of rumen and reticulum foreign bodies and to identify types of foreign bodies and associated risk factors for the occurrences of foreign bodies. The study animals were selected by using simple random sampling method from the total slaughtered animals. From the total of 384 examined cattle, 78 (20.3%) were found positive for the occurrence of indigestible foreign bodies in rumen and reticulum. Prevalence of foreign body occurrence recorded in young ( 10 years) 34 (45.95%) respectively while the prevalence rate recorded in poor, medium and good cattle were 33 (35.48%), 29 (22.3%) and 16 (9.93%). The types of foreign bodies encountered in rumen and reticulum were plastic, nails, wires, hair ball, clothes and key. Out of 78 positive cases of foreign body, 51 (13.5%) were occurred in rumen, 21 (5.5%) in reticulum and 6 (1.5%) were encountered in both rumen and reticulum. Among the considered risk factors, age, stomach compartment and body condition score of the examined animals found highly significantly associated (p<0.05) with the occurrence of foreign bodies. The prevalence of rumen and reticulum foreign bodies was lower in local breed cattle 57 (19.38%) than that of the cross breeds 21 (23.3%). It was not stastically significant (p=0.999) between local and cross breed. In general, detection of the foreign bodies in rumen and reticulum causes loss of production and high mortality rate as well it has also impact on animal welfare. Hence, appropriate solid waste disposal system need to be implemented in the study area to prevent health risk of ruminants and environment.