Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographic distribution pattern of low and high nucleic acid content bacteria on a river-catchment scale

Bacteria with low nucleic acid content (LNA) and high nucleic acid content (HNA) are widely distributed in aquatic environments. Most of the current understanding of these two subgroups is derived from studies in marine environments. In comparison, information on the spatial distribution of these two subgroups in freshwater environments is very limited. The present study analysed the biogeographical pattern of those two groups on a large-river scale (i.e. the Songhua River catchment, >1000km). The results showed that the concentrations of LNA and HNA bacteria were distributed over a wide range from 5.45×104 to 4.43×106cellsmL–1, and from 1.35×105 to 4.37×106cellsmL–1 respectively. The two groups have almost equal proportions in the Songhua River, with the average contribution of LNA bacteria reaching 47.0%. In comparison, the abundance of LNA bacteria in the mainstream was significantly higher than in the tributaries. The cytometric expressions (green fluorescence and side scatter) within LNA and HNA were strongly covaried, which implies that these two subgroups are intrinsically linked. Multivariate redundancy analysis indicated that both the abundance and cytometric characteristics of co-occurring LNA and HNA bacteria were regulated differently in the Songhua River. This suggests that LNA and HNA bacteria play different ecological roles in river ecosystems.
RL mechanisms of short-term plasticity of auditory cortex

The decision-making process is exposed to modulatory factors, and, according to the expected value (EV) concept the two most influential factors are magnitude of prospective behavioural outcome and probability of receiving this outcome. The discrepancy between received and predicted outcomes is reflected by the reward prediction error (RPE), which is believed to play a crucial role in learning in dynamic environment. Feedback related negativity (FRN), a frontocentral negative component registered in EEG during feedback presentation, has been suggested as a neural signature of RPE. In modern neurobiological models of decision-making the primary sensory input is assumed to be constant over the time and independent of the evaluation of the option associated to it. In this study we investigated whether the electrophysiological changes in auditory cues perception is modulated by the strengths of reinforcement signal, represented in the EEG as FRN. We quantified the changes in sensory processing through a classical passive oddball paradigm before and after performance a neuroeconomic monetary incentive delay (MID) task. Outcome magnitude and probability were encoded in the physical characteristics of auditory incentive cues. We evaluated the association between individual biomarkers of reinforcement signal (FRN) and the degree of perceptual learning, reflected by changes in auditory ERP components (mismatch negativity and P3a). We observed a significant correlation of MMN and valence - dFRN, reflecting differential processing of gains and omission of gains. Changes in P3a were correlated to probability - dFRN, including information on salience of the outcome, in addition to its valence. MID task performance evokes plastic changes associated with more fine-grained discrimination of auditory anticipatory cues and enhanced involuntary attention switch towards these cues. Observed signatures of neuro-plasticity of the auditory cortex may play an important role in learning and decision-making processes through facilitation of perceptual discrimination of valuable external stimuli. Thus, the sensory processing of options and the evaluation of options are not independent as implicitly assumed by the modern neuroeconomics models of decision-making.
Antibacterial Activity of Eel (Anguilla spp.) Mucus against Salmonella typhi

BACKGROUND: Typhoid fever has become one global health problem. Typhoid fever is caused by a Gram-negative bacterium, Salmonella typhi. Eel (Anguilla spp.) is a fish which lives in the sea or in freshwater. Several previous studies have found that Anguilla spp. mucus has the ability as antibacterial against Gram-positive and negative. Although the antibacterial activity of Anguilla spp. against various pathogens had been reported, very little is known about its activity against Salmonella typhi. The aim of this study was to investigate antibacterial activity of Anguilla spp. mucus against Salmonella typhi bacteria. METHODS: Present study was an experimental in vitro test. Antibacterial activity assays were carried out by the disc diffusion method. Antibacterial activity was determined by the clear zone formed around the paper disc and minimum inhibitory concentration was determined by observing the lowest concentration which could inhibit the growth of Salmonella typhi. RESULTS: Result of the present study showed that the Anguilla spp. mucus has inhibitory effects against Salmonella typhi. Minimum inhibitory concentration from the Anguilla spp. mucus was 12.5%. CONCLUSION: Anguilla spp. mucus has antibacterial activity against the Salmonella typhi bacteria. KEYWORDS: eel fish mucus, Anguilla spp. , antibacterial activity, Salmonella typhi
Sarcocystis neurona Protein Kinases: Computational Identification, Evolutionary Analysis and Putative Inhibitor Docking

The apicomplexan parasite, Sarcocystis neurona causes the degenerative neurological equine protozoal myeloencephalitis (EPM) disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions such as host cell invasion, cell cycle progression and host immune responses evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. Further, three-dimensional (3D) homology models for selected S. neurona putative PKs were constructed and evaluated for inhibitor docking. We identified 92 putative PKs clustering within the AGC, CAMK, CK1, CMGC, STE, TKL, aPK and OPK groups. Although containing the universally conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC, but contained the six apicomplexan conserved CDPKs (CAMK group). The OPK group was represented by ROPKs 19A, 27, 30, 33, 35 and 37, but was devoid of the virulence-associated ROPKs 5, 6, 18 and 38. Two out of the three S. neurona CK1 enzymes had high sequence similarities to T. gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Docking of four inhibitors onto homology models of putative ROP27 and PKA indicated that inhibition of S. neurona PKs is feasible, but needs to be experimentally tested. The essentiality of apicomplexan PKs makes the elucidation of S. neurona kinome a key milestone for development of novel therapeutics for EPM.
Soil quality assessment under shifting cultivation and forests in Northeastern Himalaya of India

ABSTRACT The study aimed to evaluate the impact of shifting cultivation on soil quality, in Wokha district of Nagaland, using weighted soil quality index (SQIw). Four forest sites and three sites under shifting cultivation were selected and physical (texture and bulk density) and chemical (pH, electrical conductivity, cation exchange capacity, organic carbon, available N, P, K, exchangeable cations) parameters were analyzed. The SQIw was calculated on a minimum data set selected by principal component analysis, followed by varimax rotation algorithm and through subsequent normalization of the parameters using the linear scoring function. Significant (P < 0.05) variations in SQIw were found across the depth of the soil and land use according to severity of factors associated with land use. Three different classes of soil quality were also identified: high quality (SQIw > 0.70) for two forest soils (FS1 and FS2) and land under shifting cultivation (JH1), low quality (SQIw < 0.50), only to FS3, and intermediate quality (0.50 < SQI < 0.70) in all other soils. The approach used in this study proved to be sensitive to evaluate the soil quality, however further research is required to better understand the sustainability of shifting cultivation by including more physical, biological and chemical indicators.
Convergence problems of integral modeling of 3d electrostatic fields with singularities

Numerous electrostatic fields are characterized by the presence of singularities (for example, at the corners or along the edges of electrically conductive charged bodies). Solutions to the tasks involving such elements by classic low-order differential methods often lead to inaccurate results. One of the prospective methods seems to be the integral approach starting from finding the distribution of the charge using the system of the first-kind Fredholm equations. The paper shows an application of this approach to two electrically conductive cubes in a general position in space. Discretization of their surfaces is performed in several different ways and the results are compared with respect to their convergence.
Assessment of zearalenone contamination in processed cereal-based foods in Shahrekord, Iran

Abstract Zearalenone (ZEA) is a known mycotoxin with estrogenic, immunologic, teratogenic and carcinogenic effects. The aim of this study was to evaluate the level of ZEA in 80 samples of processed cereal-based foods including chips, cheese puffs, biscuits and cakes, collected from supermarkets in Shahrekord, Iran between April and September, 2015. The samples were analyzed using enzyme-linked immunosorbent assay (ELISA). The results showed that 83.7% of the samples contained ZEA in the range of 0.25–8.02 μg/kg and the contamination average was 1.69 ± 1.46 μg/kg. None of the samples were found ZEA more than the allowed limit of the European Union. Due to the effects of ZEA in the etiology of early puberty in children, control of ZEA is recommended in cereal-based foods in Iran.
The effects of the circadian clock on wound healing in skin

Circadian rhythms are daily cycles of physiological functions which oscillate under the control of the circadian clock in order to coincide with the temporal demands of the light/dark cycle of the day. The importance of the integrity of the circadian clock in health and disease has emerged in recent years; perturbations of the circadian clock are associated with an increased risk of malignancy and metabolic syndrome. In this study, I aimed to examine whether RNAi modification of Bmal1, a core component of the circadian clock, could be used to improve wound healing. Chronic wounds are a global problem, in part caused by diabetes and ageing. Currently there is no effective pharmaceutical treatment; wound care by specialist nurses and physical methods such as compression bandages are the main course of action. Originally, the aim was to use DNA antisense to transiently knock down Bmal1. It became clear that this was having a toxic effect so several other approaches to knocking down Bmal1 expression were attempted. Ultimately, I used a lentiviral vector to transduce cells with an shRNA construct and also generated a Bmal1:luciferase reporter cell line to measure the oscillations of Bmal1 in vitro. Experiments using the reporter cells demonstrated that commonly used methods to synchronise the circadian clock in mammalian cells confirmed that these measures are unnecessary. The generation of cells with Bmal1 knockdown was only partially successful; however, an experiment using a heterogeneous population of Bmal1 knockdown cells indicates that this intervention reduces the migration rate of these cells in a scratch wound assay but further experiments are required to definitively determine the effects once a stable knockdown cell line has been established. If these preliminary results are true then the knockdown of Bmal1 is not likely to have a beneficial effect on wound healing.
Asymmetric geographic range expansion explains the latitudinal diversity gradients of four major taxa of marine plankton

Abstract. Extensive investigation of the close association between biological diversity and environmental temperature has not yet yielded a generally accepted, empirically validated mechanism to explain latitudinal gradients of species diversity, which occur in most taxa. Using the highly resolved late Cenozoic fossil records of four major taxa of marine plankton, we show that their gradients arise as a consequence of asymmetric geographic range expansion rather than latitudinal variation in diversification rate, as commonly believed. Neither per capita speciation nor extinction rates trend significantly with temperature or latitude for these marine plankton. Species of planktonic foraminifera and calcareous nannoplankton that originate in the temperate zone preferentially spread toward and arrive earlier in the tropics to produce a normal gradient with tropical diversity peaks; by contrast, temperate-zone originating species of diatoms and radiolarians preferentially spread toward and arrive earlier in polar regions to produce reversed gradients with high-latitude diversity peaks. Our results suggest that temperature affects latitudinal diversity gradients chiefly by its effect on species' range limits rather than on probabilities of speciation and extinction. We show that this mechanism also appears to operate in various multicellular taxa, thus providing a widely applicable explanation for the origin of latitudinal diversity gradients.
Role of Focal Adhesions in Lamellipodia Dynamics

Focal adhesions (FAs) are multi-protein structures containing integrin that serve as a focal point for the association between the extracellular matrix (ECM) and actin cytoskeleton. After cells adhere to the ECM, the cell membrane forms filopodia and lamellipodia. Cells deficient in FA complexes show reduced lamellipodia dynamics and this deficiency influences cell migration. Lamellipodia dynamics have distinguishable stages of lamellipodia protrusion, retraction, and persistence. Particularly, cells with decreasing or absent FA formation commonly show longer persistence time as analyzed using computer-assisted stroboscopic analysis. These results indicate that after cells adhere to the substratum, the reduced lamellipodia dynamics associated with defective FA formation influences cell motility.
Explorations In Advancing Microalgae Productivity

Microalgae have been investigated for production of biofuels and higher value bioproducts since the 1950s, but only a few species of microalgae are currently produced commercially. The great diversity of so far untapped microalgal species found in nature holds promise for future practical applications of microalgae biotechnology. Bioprospecting is required to identify novel strains with desired product profiles that could be cultivated in large-scale systems. Here, we describe such a bioprospecting effort specifically geared to biofuels but also applicable to other bioproducts.
Impact of distillers grain solids (DGS) and seasonality on the prevalence of Escherichia coli O157 at an abattoir in the U. S. Upper Midwest

ABSTRACT Enterohaemorrhagic Escherichia coli (EHEC) serotype O157:H7 is carried asymptomatically by cattle gastrointestinal tract and the inclusion of distillers grains solids (DGS) in feed is thought to be a factor in the prevalence and persistence of EHEC O157 in a herd. The present study surveys the faecal prevalence of E. coli O157 in cattle processed at an abattoir in the Upper Midwest and its association with environmental factors and feeding practices. Faecal samples were collected from pre-processing cows during a 1-year period. E. coli O157 prevalence was estimated isolation of putative positives and confirmation of isolates by immunoassay and multiplex virulence genes PCR analysis. Overall, E. coli O157 was confirmed in 11.2% of samples. Prevalence during winter was the highest at 14% followed by summer (11.6%) and declined to less than 8% the rest of the year. Winter was the only season that had a statistically significant effect on prevalence. As a category unto itself, DGS feeding before arrival had no significant influence on faecal prevalence. However, we found a significant interaction of DGS feeding and summer. This observation is extremely relevant because it corroborates a previous study and suggests possible feeding practices to abate EHEC O157 presence during harvest.
Morphological characterization of infra‐generic lineages in Deparia (Athyriaceae: Polypodiales)

Deparia, including the previously recognized genera Lunathyrium, Dryoathyrium (=Parathyrium), Athyriopsis, Triblemma, and Dictyodroma, is a fern genus comprising about 70 species in Athyriaceae. In this study, we inferred a robust Deparia phylogeny based on a comprehensive taxon sampling (~81% of species) that captures the morphological diversity displayed in the genus. All Deparia species formed a highly supported monophyletic group. Within Deparia, seven major clades were identified, and most of them were characterized by inferring synapomorphies using 14 morphological characters including leaf architecture, petiole base, rhizome type, soral characters, spore perine, and leaf indument. These results provided the morphological basis for an infra‐generic taxonomic revision of Deparia.
First palaeohistological inference of resting metabolic rate in an extinct synapsid, Moghreberia nmachouensis (Therapsida: Anomodontia)

The independent acquisition of endothermy in synapsids and diapsids are major events in vertebrate evolution since they were the driving force of a suite of correlated changes in anatomical, physiological, behavioural and ecological traits. While avian endothermy is assumed to have occurred at the archosauriform node, the acquisition of mammalian endothermy is poorly constrained both temporally and phylogenetically. Among the many unequivocal anatomical correlates of endothermy in synapsids, the presence of insulative pelage or respiratory turbinates only allows discrete inferences of presence/absence of endothermy. The analysis of bone histology allows richer palaeobiological inferences. We described the osteohistology and growth patterns of Moghreberia nmachouensis and two related taxa (Lystrosaurus and Oudenodon) for comparative purposes. Our observations suggest increasing growth rates from Moghreberia [the presence of incipient fibrolamellar bone (FLB) in humerus and femur], to Lystrosaurus (the presence of well-developed FLB in the femur but the presence of incipient FLB in the humerus), to Oudenodon (the presence of well-developed FLB in humerus and femur). However, qualitative histology does not allow reliable inferences about the occurrence of endothermy. We performed the first quantitative inferences of resting metabolic rates on fossil synapsids (M. nmachouensis as a model and Lystrosaurus and Oudenodon for comparative purposes) using quantitative histology (size, shape and density of osteocyte lacunae) combined with phylogenetic eigenvector maps. Our inferences are consistent with our qualitative histological observations: the mass-independent resting metabolic rate inferred for M. nmachouensis (2.58 mLO2 h−1 g−0.67) is lower than the value inferred for Lystrosaurus (3.80 mLO2 h−1 g−0.67), which is lower than that inferred for Oudenodon (4.58 mLO2 h−1 g−0.67). Optimization of these inferences onto a phylogenetic tree of tetrapods using the parsimony method allowed us to better constrain the temporal (more than 260 Myr ago) and phylogenetic (Neotherapsida) frames of the acquisition of mammalian endothermy.
A GENOME-SCALE CRISPR SCREEN TO IDENTIFY ESSENTIAL GENES FOR THE EFFECTOR FUNCTION OF CYTOTOXIC T LYMPHOCYTES

Somatic gene mutations and dysregulations can alter the vulnerability of a cancer cell to T cell based immune selection. To systematically identify genes that positively regulate the sensitivity of cancer cells to T cell-mediated cytolysis, we developed a two cell-type (2CT) functional screening platform by combining human T cell engineering and CRISPR (Clustered regularlyinterspaced short palindromic repeats) genome editing. Using the 2CT genome-scale perturbation screen in melanoma cells, we identified and validated multiple genes whose loss impaired the effector function of T cells. Moreover, we uncover a group of genes from these screens that correlates with cytolytic activity across the majority of the cancer types, reflecting context independence of these genes in the modulation of inherent T cell responses in multiple cancers. This study demonstrates the broad applicability of 2CT CRISPR screens to study the interaction of cancer cells with immune cells and identify novel therapeutic targets for cellular therapies.
Antioxidant activity and the most abundant phenolics in commercial dark beers

ABSTRACT The purpose of this study was to determine antioxidant activity and the most abundant phenolics of nine commercial dark beers. In order to estimate the content of both free and bound forms of beer phenolics, the beer samples were subjected to alkaline hydrolysis. The hydrolyzed beer samples exhibited the significantly higher antioxidant activity measured using 2,2'-azino-bis (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays as compared with nonhydrolyzed ones which was associated with the release of free forms of beer phenolics after hydrolysis. The predominant phenolic compounds in analyzed dark beers were hydroxycinnamic acids, especially ferulic and synapic acids, as well as gallic acid belonging to hydroxybenzoic acids. A principal component analysis (PCA) was applied in order to differentiate the investigated dark beers in terms of phenolic compounds and antioxidant activity for both hydrolyzed and nonhydrolyzed beer samples.
Characterization and activity of antimicrobial polypeptide of Bacillus spp from wastelands of Kathmandu valley

Background: Bacillus genus have been found to produce antimicrobial polypeptides that have a remarkable capability to combat the current increasing problem of antibiotic resistance. The aim of this cross sectional study was to determine the proportion and pattern of distribution of antibiotic producing and non-producing species of Bacillus in soil and also to analyse the activity of the antibiotic producers. Methods: A total of 40 soil samples were collected from the wastelands of Kathmandu Valley and 121 isolates were studied from them. They were identified according to Bergey’s Manual. The antibiotic were extracted and the activity was analysed by agar- well diffusion method against the test organisms Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853. Result: Bacillus subtilis species were found to be in highest number (17.3%) and Bacillus macerans (0.82%) in lowest number. 18.33% of Bacillus isolates were found to produce antibiotics. The highest number of antibiotic producing isolate was B. subtilis (40.09%) and the least was B. circulans (4.54%). The number of antibiotic producing bacteria were not found to be affected by moisture content of soil and pH change. Among the antibiotic producers, 63.63% produced antibiotic against Gram positive bacteria, 27.27% against Gram negative bacteria and B. alvei (9.09%) had a broad spectrum activity. Some colonies were even found to produce antibiotic with a greater potential than the conventional antibiotics. Conclusion: Based on property of soil, moist-neutral soil had the highest number of bacilli isolates and dry-acidic and moist-alkaline had least number of isolates. DOI: 10.21276/AABS.2017. 1316