Miracle-dz/UniFAR-FTUs huggingface dataset:
Contemporary and Future Strategies for Immunome Research

Immunome research journal enormously contributed to understand the molecular immunology. Extensive research lead by immunologist on this direction invoked the need and a common platform for discussion dealing with immunology as a whole. Present issue Volume 12, Issue 1, could bring the existing theories and discoveries in the field of immunome from across the world.
A computational pipeline for identifying copy number variation from single nucleotide polymorphism data and applications to congenital heart disease

A computational pipeline for identifying copy number variation from single nucleotide polymorphism data and applications to congenital heart disease Daniel Seung Kim Chair of the Supervisory Committee: Professor and Chair, Patrick J. Heagerty Department of Biostatistics Copy number variants (CNVs) are duplications or deletions of regions of the genome. CNVs, similar to single nucleotide variants (SNVs), range in frequency and severity in their effects on human disease. Despite the likely importance of CNVs in pathophysiology, comparatively fewer studies have examined the effect of CNVs on human disease as compared to SNVs. In this work, I first review the methods used for determination of CNVs from widely available SNV chip data and present data from a cohort of children with congenital heart disease (CHD) that finds that increased positive predictive value can be derived from looking at the overlap in CNVs called by two divergent methodologies (94.6%, 35/37). I then compare the prevalence of these validated CNVs and find that children with nonsyndromic CHD have a higher burden of large, geneoverlapping CNVs compared to controls (12.1% vs. 5.0%, P=0.00016). Moreover, through use of Cox proportional hazards regression, I present data that the presence of a CNV is associated with significantly decreased transplant-free survival after surgery (HR=3.42, 95% CI: 1.66-7.09, P=0.00090) with confounder adjustment. These data suggest CNVs can be determined with high accuracy and that CNV burden is an important modifier of survival after surgery for CHD.
Microfluidics: a boon for biological research

Microfluidics is an emerging new interdisciplinary field that deals with the manipulation of fluids at the microscale and nanoscale. Having its origins in other areas of science and technology, microfluidics is slowly beginning to make radical changes in various fields of biological sciences. The exclusivity of fluid behaviour at the microscale offers a large number of advantages in biological research such as miniaturization of assays, faster sample processing and rapid detection. This article provides a concise overview of the applications of microfluidics technology in some of the major disciplines of biological research. Furthermore, it also mentions the hurdles that microfluidics is facing and the solutions that are envisaged for the future to make it a widely available, reliable and cost-effective technology.
Dll3 and Notch1 genetic interactions model axial segmental and craniofacial malformations of human birth defects

In the original published version of this article, the abstract contained a textual error. The sentence originally reading, “Unexpectedly, double heterozygous mice also displayed statistically significant reduction of mandibular height and elongation of maxillary hard palate. ” was incorrect. The correct sentence should read, “Unexpectedly, double heterozygous mice also displayed statistically significant reduction of mandibular height and decreased length of the maxillary hard palate. ” The authors regret this error.
Prediction of protein-protein interactions from primary structure using a Random Forest classifier

The interaction between proteins is fundamental to a broad spectrum of biological functions, including regulation of metabolic pathways, immunological recognition, DNA replication, progression through the cell cycle, and protein synthesis. Due to the growing disparity between the amount of sequenced genomic content and functional data, there exist a pressing need for tools and methods that will enable prediction of phenotypic traits, on the molecular or organism level, based on the sequence alone. In this work we have constructed a high quality dataset of protein structures that has enabled us to use the Random Forest non-linear classificator to develop a method for prediction of interacting residues from the protein primary structure. Our results have shown that, although the Random Forest algorithm has a unique capability of accurately classifying highly dimensional data, we still have an incomplete knowledge of structural factors that determine the specificity of protein-protein interactions, thus putting an upper limit the on the usefulness of the machine learning approach in predicting protein interactions on the level of single amino-acids.
International Journal of Current Research in

Article Info This research was conducted to study the spread of an important unicellular protozoan Trichomonas gallinae isolated from the mouth and esophagus of three groups of domestic pigeon Colomba livia domestica by wet mount preparation. A total of 609 domestic pigeons were tested in Kirkuk city, Iraq from August 2015 to April 2016, the total infectious rate of the prevalence were 49.26%, distributed to 64.92%, 50.98% and 30.41% in Alzajel, pakistani and zubaeri pigeon respectively. The present study compared three different stains to characterize the shape of T. gallinae namely Giemz, Gram and for first time Field’s stain, the Giemza stain showed efficient to stain T. gallinae more than other two stains, although Field’s stain requires less time for staining compared to Giemza and Gram’s stain. The parasites are cultivated in three prepared culture media (In-tube culture system), which are modified Diamond media (TYM), Cysteine Peptone Maltose media (CPLM) and Trichomonas CM0161 media (CM 161) with the initial inoculation of 2X105 cell/ml, the fourth media was In-pouch culture system that is commercially available with the initial inoculation of 105 cell/ml. In-pouch TV culture media is used for the first time to diagnose and to grow T. gallinae which is a special media for diagnosis of the vaginal trichomoniasis caused by Trichomonas vaginalis. The result showed the best growth of T. gallinae in In-pouch media compared with In-tube culture system, modified diamond media and CM 161 gave the high growth to 48 hours while CPLM gave the high growth from 24 hours, the CM 161 media showed acute decrease in the number of T. gallinae after 48 hour. Accepted:25 January 2017 Available Online:20 February 2017
Mangrove outwelling is a significant source of oceanic exchangeable organic carbon

Exchangeable dissolved organic carbon (EDOC) makes up a significant proportion of the oceanic dissolved organic carbon (DOC) pool, yet EDOC sources to the coastal ocean are poorly constrained. We measured the exchange of EDOC and concentrations of EDOC and DOC in mangrove waters over a 26° latitudinal gradient. A clear latitudinal trend was observed, with the highest EDOC concentrations in the tropics. EDOC exports to the coastal ocean were 4.7 ± 1.9 mmol m−2 d−1, equivalent to 11% of DOC exports (42.1 ± 6.7 mmol m−2 d−1). Pore‐water and groundwater exchange were minor sources of EDOC. EDOC concentrations were equal to 13% ± 4% of DOC concentrations. Based on previous global DOC export estimates, and our EDOC : DOC ratios, mangroves outwell 3.1 Tg C yr−1 as EDOC, equivalent to ∼ 60% of the global EDOC flux from the ocean to the atmosphere. However, seasonality of mangrove EDOC cycling requires further research.
Lack of Evidence for the Drought Tolerance Hypothesis of Hyperaccumulation in Astragalus Species

Premise of research. Despite a lack of experimental support, enhanced drought tolerance is one of the recurring hypotheses suggested to explain trace element hyperaccumulation. Trace elements may have osmolytic and/or antioxidative properties that help hyperaccumulating plants reduce water loss or its resultant damage. Selenium in particular seems like a promising candidate because of its known antioxidative and drought protectant properties in nonaccumulators, but it has not been tested in hyperaccumulators. Methodology. Here we investigate the drought tolerance hypothesis in a controlled greenhouse setting using a full-factorial design with seedlings of a selenium hyperaccumulator in the genus Astragalus and a nonaccumulating congener. Pivotal results. While selenium increased plant survivorship and longevity and drought reduced them, we found no evidence that selenium improved the drought tolerance of either species. Conclusions. Drought tolerance appears to not be a mechanism that would explain the evolution of hyperaccumulation in Astragalus, although it may still operate in some as-yet untested circumstances.
Synthesis of haptens and production of antibodies to bisphenol A

Three immunizing haptens of bisphenol A (BPA), including two new haptens, were used to produce highly sensitive and specific polyclonal antibodies. The spacer arms of haptens for coupling to the protein carrier were located at different positions in BPA, and different length spacer arms were tested. Highly sensitive polyclonal antibodies were obtained and characterized using indirect competitive enzyme-linked immunosorbent assay (icELISA). Under optimized conditions, the half maximal inhibitory concentration (IC50) value of the best polyclonal antibody was 2.1 mg$L, based on coating heterogeneous antigens, and this optimal polyclonal antibody was highly sensitive toward BPA and displayed negligible crossreactivity with bisphenol B and bisphenol E. A sensitive icELISA method utilizing the polyclonal antibody was developed for the determination of BPA in milk. In spiked samples (5, 10 and 20 mg$L), the recovery ranged from 80% to 102% with a coefficient of variation (CV) value below 15.8%. The limit of detection of icELISA was 1.95 mg$L. These results indicate that the icELISA method is suitable for the detection of BPA in milk.
Volatile Compound Profiles of Malus baccata and Malus prunifolia Wild Apple Fruit

A BSTRACT . Volatile compounds have a tremendous impact on fruit quality. We evaluated the volatile compound proﬁles of ripening wild apple fruit (10 Malus baccata accessions and three Malus prunifolia accessions) in the National Field Genebank for Hardy Fruits at Gongzhuling, China. Alcohols, esters, aldehydes, terpenes, hydrocarbons, ethers, heterocycles, carboxylic acids, and ketones were detected in the M. baccata and M. prunifolia fruit, with the ﬁrst four being the main volatile compounds present. Of the 92 volatiles detected, esters were the most diverse (49 compounds). This wide range of abundant volatile compounds suggests that M. prunifolia is a good resource for breeding apple cultivars with novel and interesting ﬂavors. The M. baccata accession ‘Zhaai Shandingzi’ and the M. prunifolia accession ‘Bai Haitang’ had the widest range of volatile compounds and the highest volatile compound contents of the accessions examined, and will therefore be good breeding materials for developing commercial lines with enhanced ﬂavor and for widening the genetic diversity. The number of different ester compounds present was signiﬁcantly positively correlated ( r = 0.877) with the cube root of the weight of an individual ripe fruit. Principal component analysis (PCA) showed that the contents of ester compounds could be used to distinguish between M. baccata and
Chemical and Ultrastructural Characterization of Trichophyton Mentagrophytes Arthrospore Walls and Septa

s: Hashimoto, T. , J. H. Pollack, and H. J. Blumenthal. Carotenogenesis associated with arthrosporulation of Trichoiii phyton mentagrophytes. Abstr. Annu. Meet. Am. Soc. Microbiol. 1978, J21, p. 80. Hashimoto, T. , J. H. Pollack, and H. J. Blumenthal. Ultrastructure and chemical composition of Trichophyton mentagrophytes arthrospore walls and septa. Abstr. Annu. Meet. Am. Soc. Microbiol. 1979, J23, p. 92. Pollack, J. H. , C. F. Lange, and T. Hashimoto. Characterization of fibrillar and non-fibrillar chitin associated with arthrospore wall of the dermatophyte Trichophyton mentagrophytes. 1982, Jl9, p. 94.
Visual context modulates action perception in 10-month-old infants

Research on early action perception has documented infants’ astounding abilities in tracking, predicting, and understanding other people’s actions. Common interpretations of previous findings tend to generalize across a wide range of action stimuli and contexts. In this study, ten-month-old infants repeatedly watched a video of a same-aged crawling baby that was transiently occluded. The video was presented in alternation with videos displaying visually either dissimilar movements (i.e., distorted human, continuous object, and distorted object movements) or similar movements (i.e., delayed or forwarded versions of the crawling video). Eye-tracking behavior and rhythmic neural activity, reflecting attention (posterior alpha), memory (frontal theta), and sensorimotor simulation (central alpha), were concurrently assessed. Results indicate that, when the very same movement was presented in a dissimilar context, it was tracked at more rear parts of the target and posterior alpha activity was elevated, suggesting higher demands on attention-controlled information processing. We conclude that early action perception is not immutable but shaped by the immediate visual context in which it appears, presumably reflecting infants’ ability to flexibly adjust stimulus processing to situational affordances.
Habitat fragmentation causes coevolutionary burning spots

Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the underlying eco-evolutionary processes in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community network experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community network comprises a parasitic butterfly of conservation concern, and its two obligatory host species, a plant and an ant. We show that fragmentation of butterfly habitat has the potential to impair the balance between dispersal and coevolution. This process can cause coevolutionary burning spots of decreased genetic diversity and therefore of increased extinction risk. We stress that ignoring such eco-evolutionary feed-backs inherent to the very functioning of natural communities can strongly impact their persistence. One Sentence Summary: Communities under threat of habitat fragmentation suffer increased extinction risk through coevolutionary overheating.
Survival and growth of hatchery and wild brown trout (Salmo trutta) parr in three Austrian headwater streams

Brown trout populations of three headwater streams in the Northern Limestone Alps of Austria were supplemented by three-month-old hatchery-reared parr from a wild and locally adapted strain and a nonresident domesticated hatchery strain. Growth and survival were monitored with three surveys over a period of 16 months after stocking. Fish descending from the wild reared origin strain demonstrated higher survival rates than the hatchery strain. Differences in growth were found among the investigated streams but not among the investigated strains. The differing temperature regimes of the streams were considered as the primary factor causing those disparities. We conclude that stocking measures had little or no additive effect on successful natural reproduction, as the resident wild brown trout performed significantly better than the stocked fish.
Molecular characterization and pathogenicity of Erwinia spp. associated with pineapple [Ananas comosus (L.) Merr.] and papaya (Carica papaya L.)

: The Erwinia species are well-known pathogens of economic importance in Malaysia causing serious damage to high-value fruit crops that include pineapple [ Ananas comosus (L.) Merr. ] and papaya ( Carica papaya L.). The 16S rRNA sequence using eubacteria fD1 and rP2 primers, identified two bacteria species; Dickeya zeae from pineapple heart rot, and Erwinia mallotivora from papaya dieback. Phylogenetic analysis based on the neighbor-joining method indicated that all the bacterial isolates clustered in their own taxa and formed monophyletic clades. From the pathogenicity test, all isolates of D. zeae and E. mallotivora showed pathogenic reactions on their respective host plants. Genetic variability of these isolates was assessed using repetitive sequence-based PCR (rep-PCR) fingerprinting. The results indicated interspecies, and intraspecies variation in both species’ isolates. There were more polymorphic bands shown by rep-PCR fingerprints than enterobacterial repetitive intergenic consensus (ERIC) and BOX- PCRs, however both species’ isolates produced distinguishable banding patterns. Unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis indicated that all Dickeya and Erwinia isolates from the same species were grouped in the same main cluster. Similarity among the isolates ranged from 77 to 99%. Sequencing of 16S rRNA using eubacteria fD1 and rP2 primers, and rep-PCR fingerprinting revealed diversity among Dickeya and Erwinia isolates. But this method appears to be reliable for discriminating isolates from pineapple heart rot and papaya dieback.
The Ecology of Soil Carbon: Pools, Vulnerabilities, and Biotic and Abiotic Controls

Soil organic matter (SOM) anchors global terrestrial productivity and food and fiber supply. SOM retains water and soil nutrients and stores more global carbon than do plants and the atmosphere combined. SOM is also decomposed by microbes, returning CO2, a greenhouse gas, to the atmosphere. Unfortunately, soil carbon stocks have been widely lost or degraded through land use changes and unsustainable forest and agricultural practices. To understand its structure and function and to maintain and restore SOM, we need a better appreciation of soil organic carbon (SOC) saturation capacity and the retention of above- and belowground inputs in SOM. Our analysis suggests root inputs are approximately five times more likely than an equivalent mass of aboveground litter to be stabilized as SOM. Microbes, particularly fungi and bacteria, and soil faunal food webs strongly influence SOM decomposition at shallower depths, whereas mineral associations drive stabilization at depths greater than ∼30 cm. Global uncertaint.
Molecular Mechanisms of Assembly and Long-term Maintenance of Neuronal Architecture: A Dissertation

Nervous system function is closely tied to its structure, which ensures proper connectivity and neural activity. Neuronal architecture is assembled by a series of morphogenetic events, including the coordinated migrations of neurons and axons during development. Subsequently, the neuronal architecture established earlier must persist in the face of further growth, maturation of the nervous system, and the mechanical stress of body movements. In this work, we have shed light on the molecular mechanisms governing both the initial assembly of the nervous system and the long-term maintenance of neural circuits. In particular, we identified heparan sulfate proteoglycans (HSPGs) as regulators of neuronal migrations. Our discovery and analysis of viable mutations in the two subunits of the heparan sulfate co-polymerase reveals the importance of the coordinated and dynamic action of HSPGs in neuronal and axon guidance during development. Furthermore, we uncovered that the HSPG LON-2/glypican functions as a modulator of UNC-6/netrin signaling through interactions with the UNC-40/DCC receptor. During larval and adult life, molecules such as the protein SAX-7, homologous to mammalian L1CAM, function to protect the integrity of nervous system architecture. Indeed, loss of sax-7 leads to progressive disorganization of neuronal architecture. Through a forward genetic screen, we identified LON-1 as a novel maintenance molecule that functions postembryonically with SAX-7 to maintain the architecture of the nervous system. Together, our work highlights the importance of extracellular interactions to
Prevalence of Inhibitor Resistant Beta Lactamase Producing E. coli in Human and Poultry Origin of Bangladesh

Human clinical specimens (n=48) and poultry fecal specimens (n=40) were collected from a sub district (Savar) of Bangladesh. Total 25 E. coli were isolated from these specimens. These E. coli were tested for their antibiotic sensitivity against commonly used antibiotics. In addition, to detect the ESBL (extended spectrum beta lactamases) producers, double disk synergy (DDS) test and PCR method were used. Twenty three E. coli were multidrug resistant, i.e. resistant against at least three different groups of antibiotics. DDS method showed all E. coli from poultry specimens and 78% of E. coli from clinical specimens were resistant to amoxicillin-clavulanic acid combination. Thus they are phenotypically confirmed as inhibitor resistant beta lactamase producers. PCR result showed only blaTEMgene in E. coli from poultry specimens. Thus inhibitor resistant type β-lactamase was found to be dominant in E. coli from both types of specimens.
Metabolomics analysis reveals aminoquinazolin derivative 9d-induced oxidative stress and cell cycle arrest in A549 cells

A novel aminoquinazolin derivative (named 9d), synthesized in our lab shows potential antitumor activity against A549 lung cancer cell lines. However, previous studies on the pharmacological mechanism of 9d mostly focused on cell and gene levels; the metabolic mechanism remains unknown. In this paper, an ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) based metabolomics approach was established to study the probable antitumor mechanism. Q-TOF MS and MS/MS were used to identify significantly different metabolites. 22 significantly different metabolites were observed between the 9d-treated A549 lung cells group and control group. They were involved in glycerophospholipid metabolism, glutathione metabolism, phenylalanine metabolism, cysteine and methionine metabolism, and aminoacyl-tRNA biosynthesis. The results showed that glutathione level and cell-membrane components phosphatidylcholines were decreased in 9d-treated cells, while their oxidative products, oxidized glutathione and lysophosphatidylcholines, were significantly increased. Further biological investigation showed an apparent accumulation of reactive oxygen species and a decrease in mitochondrial membrane potential. The results indicated that the aminoquinazolin derivative induced oxidative stress-mediated apoptosis. Moreover, phenylalanine metabolism suggested the up-regulation of L-phenylalanine might act as an endogenous drug carrier of 9d to improve cellular antiproliferation ability. The inhibition of aminoacyl-transfer RNA and flow cytometry results indicated that cell cycle progression was blocked in the G1 phase, which was in accordance with the results obtained from some marketed aminoquinazolin derivatives. The above results proposed that 9d could induce oxidative stress and cell cycle arrest, which finally led to cell apoptosis in A549 cells. The study supplies a rapidly and highly active strategy to investigate the antitumor mechanism of drugs, which benefits its further improvement and development.