Miracle-dz/UniFAR-FTUs huggingface dataset:
Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.
Application of the Actiphage® Assay to Detect Viable Mycobacterium avium subsp. paratuberculosis Cells in Fresh Sheep and Goat Milk and Previously Frozen Milk and In-Line Milk Filters

Mycobacterium avium subsp. paratuberculosis (MAP) is a well-known causative agent of paratuberculosis, a chronic infectious granulomatous enteritis of ruminants contributing to significant economic losses worldwide. Current conventional diagnostic tools are far from being sufficient to manage and control this disease. Therefore, increased attention has been paid to alternative approaches including phage-based assays employing lytic bacteriophage D29 to detect MAP cells. The aim of the present study was to assess the applicability and efficiency of the recently developed phage-based kit termed Actiphage® combined with IS900 real-time PCR (qPCR) for rapid detection and quantification of viable MAP in milk samples. We demonstrated that Actiphage® in combination with IS900 qPCR allows for rapid and sensitive detection and identification of viable MAP in milk samples with a limit of detection of 1 MAP per 50 ml milk. Using this method, the presence of viable MAP cells was successfully determined in 30.77% of fresh goat, sheep and cow milk samples originating from paratuberculosis-affected herds. We further used Actiphage assay to define the time-lapse aspect of testing naturally contaminated milk and milk filters frozen for various lengths of time by phage-based techniques. Viable MAP was detected in 13.04% of frozen milk samples and 28.57% of frozen milk filters using Actiphage-qPCR. The results suggest the ability to detect viable MAP in these samples following freezing for more than 1 year. The obtained results support the views of the beneficial role of this technology in the control or monitoring of paratuberculosis.
Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis

Background: Spinal cord injury (SCI) is a severe neurological deficit affecting both young and older people worldwide. The potential role of key enhancer RNAs (eRNAs) in SCI remains elusive, which is a prominent challenge in the trauma repair process. This study aims to investigate the roles of key eRNAs, transcription factors (TFs), signaling pathways, and small-molecule inhibitors in SCI using multi-omics bioinformatics analysis. Methods: Microarray data of peripheral blood mononuclear cell (PBMC) samples from 27 healthy volunteers and 25 chronic-phase SCI patients were retrieved from the Gene Expression Omnibus database. Differentially expressed transcription factors (DETFs), differentially expressed enhancer RNAs (DEeRNAs), and differentially expressed target genes (DETGs) were identified using the Linear Models for Microarray Data (limma) package. Fraction of immune cells was estimated using CIBERSORT algorithm. Gene Set Variation Analysis (GSVA) was applied to identify the downstream signaling pathways. The eRNA regulatory network was constructed based on the correlation results. Connectivity Map (CMap) database was used to find potential drugs for SCI patients. The cellular communication analysis was performed to explore the molecular regulation mechanism of SCI based on single-cell RNA sequencing (scRNA-seq) data. Chromatin immunoprecipitation sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data were used to validate the key regulatory mechanisms. scRNA-seq dataset was used to validate the cell subtype localization of the key eRNAs. Results: In total, 21 DETFs, 24 DEeRNAs, and 829 DETGs were identified. A regulatory network of 13 DETFs, six DEeRNAs, seven DETGs, two hallmark pathways, two immune cells, and six immune pathways was constructed. The link of Splicing factor proline and glutamine rich (SFPQ) (TF) and vesicular overexpressed in cancer prosurvival protein 1 (VOPP1) (eRNA) (R = 0.990, p < 0.001, positive), VOPP1 (eRNA) and epidermal growth factor receptor (EGFR) (target gene) (R = 0.974, p < 0.001, positive), VOPP1, and T helper (Th) cells (R = −0.987, p < 0.001, negative), and VOPP1 and hallmark coagulation (R = 0.937, p < 0.001, positive) was selected. Trichostatin A was considered the best compound target to SCI-related eRNAs (specificity = 0.471, p < 0.001). Conclusion: VOPP1, upregulated by SFPQ, strengthened the transient expression of EGFR. Th cells and coagulation were the potential downstream pathways of VOPP1. This regulatory network and potential inhibitors provide novel diagnostic biomarkers and therapeutic targets for SCI.
Physiological and Biomechanical Responses to Cross-Country Skiing in Varying Terrain: Low- vs. High-Intensity

The purposes of our study were to investigate the physiological and biomechanical responses to low-intensity (LI) and high-intensity (HI) roller ski skating on varying terrain and compare these responses between training intensities. Nine elite male skiers performed treadmill roller skiing consisting of two 21 min sessions (7 × 3 min laps) at LI and HI with the same set inclines and intensity-dependent speeds (LI/HI: distance: 5.8/7.5 km, average speed: 16.7/21.3 km/h). Physiological and biomechanical variables were measured continuously, and each movement cycle and sub-technique employed were detected and classified with a machine learning model. Both the LI and HI sessions induced large terrain-dependent fluctuations (relative to the maximal levels) in heart rate (HR, 17.7 vs. 12.2%-points), oxygen uptake (V.O2, 33.0 vs. 31.7%-points), and muscle oxygen saturation in the triceps brachii (23.9 vs. 33.4%-points) and vastus lateralis (12.6 vs. 24.3%-points). A sub-technique dependency in relative power contribution from poles and skis exhibited a time-dependent shift from Lap 1 to Lap 7 toward gradually more ski power (6.6 vs. 7.8%-points, both p < 0.01). The terrain-dependent fluctuations did not differ between LI and HI for V.O2 (p = 0.50), whereas HR fluctuated less (p < 0.01) and displayed a time-dependent increase from Lap 2 to Lap 7 (7.8%-points, p > 0.01) during HI. Oxygen saturation shifted 2.4% points more for legs than arms from LI to HI (p > 0.05) and regarding sub-technique, 14.7% points more G3 on behalf of G2 was employed on the steepest uphill during HI (p < 0.05). Within all sub-techniques, cycle length increased two to three times more than cycle rate from LI to HI in the same terrains, while the corresponding poling time decreased more than ski contact time (all p > 0.05). In sum, both LI and HI cross-country (XC) skiing on varying terrain induce large terrain-dependent physiological and biomechanical fluctuations, similar to the patterns found during XC skiing competitions. The primary differences between training intensities were the time-dependent increase in HR, reduced relative oxygen saturation in the legs compared to the arms, and greater use of G3 on steep uphill terrain during HI training, whereas sub-technique selection, cycle rate, and pole vs. ski power distribution were similar across intensities on flat and moderately uphill terrain.
3D Printed Integrated Multi-Layer Microfluidic Chips for Ultra-High Volumetric Throughput Nanoliposome Preparation

Although microfluidic approaches for liposomes preparation have been developed, fabricating microfluidic devices remains expensive and time-consuming. Also, owing to the traditional layout of microchannels, the volumetric throughput of microfluidics has been greatly limited. Herein an ultra-high volumetric throughput nanoliposome preparation method using 3D printed microfluidic chips is presented. A high-resolution projection micro stereolithography (PμSL) 3D printer is applied to produce microfluidic chips with critical dimensions of 400 µm. The microchannels of the microfluidic chip adopt a three-layer layout, achieving the total flow rate (TFR) up to 474 ml min−1, which is remarkably higher than those in the reported literature. The liposome size can be as small as 80 nm. The state of flows in microchannels and the effect of turbulence on liposome formation are explored. The experimental results demonstrate that the 3D printed integrated microfluidic chip enables ultra-high volumetric throughput nanoliposome preparation and can control size efficiently, which has great potential in targeting drug delivery systems.
Altered Degree Centrality of Brain Networks in Parkinson's Disease With Freezing of Gait: A Resting-State Functional MRI Study

Freezing of gait (FOG) in Parkinson's disease (PD) leads to devastating consequences; however, little is known about its functional brain network. We explored the differences in degree centrality (DC) of functional networks among PD with FOG (PD FOG+), PD without FOG (PD FOG–), and healthy control (HC) groups. In all, 24 PD FOG+, 37 PD FOG–, and 22 HCs were recruited and their resting-state functional magnetic imaging images were acquired. The whole brain network was analyzed using graph theory analysis. DC was compared among groups using the two-sample t-test. The DC values of disrupted brain regions were correlated with the FOG Questionnaire (FOGQ) scores. Receiver operating characteristic curve analysis was performed. We found significant differences in DC among groups. Compared with HCs, PD FOG+ patients showed decreased DC in the middle frontal gyrus (MFG), superior temporal gyrus (STG), parahippocampal gyrus (PhG), inferior temporal gyrus (ITG), and middle temporal gyrus (MTG). Compared with HC, PD FOG– presented with decreased DC in the MFG, STG, PhG, and ITG. Compared with PD FOG–, PD FOG+ showed decreased DC in the MFG and ITG. A negative correlation existed between the DC of ITG and FOGQ scores; the DC in ITG could distinguish PD FOG+ from PD FOG– and HC. The calculated AUCs were 81.3, 89.5, and 77.7% for PD FOG+ vs. HC, PD FOG– vs. HC, and PD FOG+ vs. PD FOG–, respectively. In conclusion, decreased DC of ITG in PD FOG+ patients compared to PD FOG– patients and HCs may be a unique feature for PD FOG+ and can likely distinguish PD FOG+ from PD FOG– and HC groups.
South African Consumer Adoption of Plant-Based and Cultivated Meat: A Segmentation Study

The purpose of this study was to assess the likelihood of consumer adoption of plant-based and cultivated meat in South Africa as a pathway to a healthy, sustainable, and equitable food supply. We recruited a large sample of South Africans representative across age (18–61), gender, race, and income to participate in an online survey. Participants responded to a range of measures including adoption indicators, estimated yearly intake, motivators for purchasing, desired product characteristics, preferred species, and sociodemographics. We found a high degree of openness to both products. For plant-based meat, 67% were highly likely to try and 59% were highly likely to purchase. For cultivated meat, 60% were highly likely to try and 53% were highly likely to purchase. The highest acceptance was amongst the younger generations: 60% of born-frees, 62% of millennials, and 53% of Gen X were highly likely to purchase plant-based meat and 55% of born-frees, 55% of millennials, and 46% of Gen X were highly likely to purchase cultivated meat. For the general population, we observed that future meat intake was estimated to be split equally among the three meat categories (conventional, cultivated, and plant-based). We found early adopters (those highly likely to purchase) to be quite similar in attitudinal and sociodemographic characteristics in comparison to the general population. The study findings suggest that both plant-based and cultivated meat could be viable market-based options for improving the food system in South Africa, as consumers across all segments of society, and especially amongst the younger population, indicated broad acceptance.
Multipotential Alkaline Protease From a Novel Pyxidicoccus sp. 252: Ecofriendly Replacement to Various Chemical Processes

A newly isolated alkaline protease-producing myxobacterium was isolated from soil. The strain was identified as Pyxidicoccus sp. S252 on the basis of 16S rRNA sequence analysis. The extracellular alkaline proteases produced by isolate S252 (PyCP) was optimally active in the pH range of 11.0–12.0 and temperature range of 40–50°C The zymogram of PyCP showed six caseinolytic protease bands. The proteases were stable in the pH range of 8.0–10.0 and temperature range of 40–50°C. The activity of PyCP was enhanced in the presence of Na+, Mg2+, Cu2+, Tween-20, and hydrogen peroxide (H2O2) (hydrogen peroxide), whereas in Triton X-100, glycerol, ethylenediaminetetraacetic acid (EDTA), and Co2+, it was stable. PyCP showed a potential in various applications. The addition of PyCP in the commercial detergent enhanced the wash performance of the detergent by efficiently removing the stains of tomato ketchup and coffee. PyCP efficiently hydrolyzed the gelatin layer on X-ray film to release the embedded silver. PyCP also showed potent dehairing of goat skin and also efficiently deproteinized sea shell waste indicating its application in chitin extraction. Thus, the results of the present study indicate that Pyxidicoccus sp. S252 proteases have the potential to be used as an ecofriendly replacement of chemicals in several industrial processes.
Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.
Interactions Between the Kleptoplastidic Dinoflagellate Shimiella gracilenta and Several Common Heterotrophic Protists

The newly described dinoflagellate, Shimiella gracilenta, is known to survive for approximately 1 month on the plastids of ingested prey cells during starvation, indicating kleptoplastidy. To understand the population dynamics of this dinoflagellate in marine planktonic food webs, its growth and mortality rate due to predation should be assessed. Thus, we investigated the feeding occurrence of eight common heterotrophic protists on S. gracilenta. We also determined the growth and ingestion rates of Oxyrrhis marina and the naked ciliate, Rimostrombidium sp. on S. gracilenta as a function of the prey concentration. The common heterotrophic dinoflagellates (HTDs) Gyrodinium dominans, O. marina, and Pfiesteria piscicida and a naked ciliate Rimostrombidium sp. were able to feed on S. gracilenta; whereas the HTDs Aduncodinium glandula, Gyrodinium jinhaense, Oblea rotunda, and Polykrikos kofoidii were not. Shimiella gracilenta supported positive growth of O. marina and Rimostrombidium sp. but did not support that of G. dominans and P. piscicida. With increasing prey concentrations, the growth and ingestion rates of O. marina and Rimostrombidium sp. on S. gracilenta increased and became saturated. The maximum growth rates of O. marina and Rimostrombidium sp. on S. gracilenta were 0.645 and 0.903 day−1, respectively. Furthermore, the maximum ingestion rates of O. marina and Rimostrombidium sp. on S. gracilenta were 0.11 ng C predator day−1 (1.6 cells predator−1 day−1) and 35 ng C predator day−1 (500 cells predator−1 day−1), respectively. The maximum ingestion rate of O. marina on S. gracilenta was lower than that on any other algal prey reported to date, although its maximum growth rate was moderate. In conclusion, S. gracilenta had only a few common heterotrophic protist predators but could support moderate growth rates of the predators. Thus, S. gracilenta may not be a common prey species for diverse heterotrophic protists but may be a suitable prey for a few heterotrophic protists.
Accuracy of Otolith Oxygen Isotope Records Analyzed by SIMS as an Index of Temperature Exposure of Wild Icelandic Cod (Gadus morhua)

Global warming is increasing ocean temperatures, forcing marine organisms to respond to a suite of changing environmental conditions. The stable oxygen isotopic composition of otoliths is often used as an index of temperature exposure, but the accuracy of the resulting temperature reconstructions in wild, free-swimming Atlantic cod (Gadus morhua) has never been groundtruthed. Based on temperatures from data storage tags (DST) and corresponding salinity values, the stable oxygen isotope (δ18O) value was predicted for each month of tagging and compared with δ18Ootolith values measured in situ with secondary ion mass spectrometry (SIMS). Paired-sample Wilcoxon tests were applied to compare measured and predicted δ18O values. The difference between measured and predicted mean and maximum δ18Ootolith values was not significant, suggesting a good correspondence between SIMS-measured and DST-predicted δ18Ootolith values. However, SIMS-measured and predicted minimum δ18Ootolith values were significantly different (all samples: p < 0.01, coastal and frontal cod: p < 0.05), resulting in overestimation of maximum temperatures. Our results confirm that otoliths are well-suited as proxies for mean ambient temperature reconstructions. A possible matrix effect and the absence of a reliable aragonite standard for SIMS measurements appeared to cause a small divergence between measured and predicted δ18Ootolith values, which affected the estimation accuracy of absolute temperature. However, relative temperature changes were accurately estimated by SIMS-analyzed δ18Ootolith values.
Freshwater Composition and Connectivity of the Connecticut River Plume During Ambient Flood Tides

The Connecticut River plume interacts with the strong tidal currents of the ambient receiving waters in eastern Long Island Sound. The plume formed during ambient flood tides is studied as an example of tidal river plumes entering into energetic ambient tidal environments in estuaries or continental shelves. Conservative passive freshwater tracers within a high-resolution nested hydrodynamic model are applied to determine how source waters from different parts of the tidal cycle contribute to plume composition and interact with bounding plume fronts. The connection to source waters can be cut off only under low-discharge conditions, when tides reverse surface flow through the mouth after max ambient flood. Upstream plume extent is limited because ambient tidal currents arrest the opposing plume propagation, as the tidal internal Froude number exceeds one. The downstream extent of the tidal plume always is within 20 km from the mouth, which is less than twice the ambient tidal excursion. Freshwaters in the river during the preceding ambient ebb are the oldest found in the new flood plume. Connectivity with source waters and plume fronts exhibits a strong upstream-to-downstream asymmetry. The arrested upstream front has high connectivity, as all freshwaters exiting the mouth immediately interact with this boundary. The downstream plume front has the lowest overall connectivity, as interaction is limited to the oldest waters since younger interior waters do not overtake this front. The offshore front and inshore boundary exhibit a downstream progression from younger to older waters and decreasing overall connectivity with source waters. Plume-averaged freshwater tracer concentrations and variances both exhibit an initial growth period followed by a longer decay period for the remainder of the tidal period. The plume-averaged tracer variance is increased by mouth inputs, decreased by entrainment, and destroyed by internal mixing. Peak entrainment velocities for younger waters are higher than values for older waters, indicating stronger entrainment closer to the mouth. Entrainment and mixing time scales (1–4 h at max ambient flood) are both shorter than half a tidal period, indicating entrainment and mixing are vigorous enough to rapidly diminish tracer variance within the plume.