Miracle-dz/UniFAR-FTUs huggingface dataset:
Rhodopsin-based voltage imaging tools for use in muscles and neurons of Caenorhabditis elegans

Significance Neuronal and other excitable cell activity is characterized by alteration in membrane voltage, while intracellular Ca2+ levels and transmitter release are affected downstream of electrical activity. Thus, the most direct way of monitoring neuronal activity is by membrane voltage. Electrophysiology is demanding for multiple cells or cell ensembles and difficult to use in live animals, thus imaging methods are desirable. Yet, genetically encoded voltage indicators fell behind Ca2+ indicators until recently, when microbial rhodopsins and derivatives were introduced as genetically encoded voltage indicators. We evaluated rhodopsin tools for voltage imaging in muscles and neurons of Caenorhabditis elegans, a prime animal model in neuro- and cell biology, showing robust performance and the ability to characterize genetic mutants. Genetically encoded voltage indicators (GEVIs) based on microbial rhodopsins utilize the voltage-sensitive fluorescence of all-trans retinal (ATR), while in electrochromic FRET (eFRET) sensors, donor fluorescence drops when the rhodopsin acts as depolarization-sensitive acceptor. In recent years, such tools have become widely used in mammalian cells but are less commonly used in invertebrate systems, mostly due to low fluorescence yields. We systematically assessed Arch(D95N), Archon, QuasAr, and the eFRET sensors MacQ-mCitrine and QuasAr-mOrange, in the nematode Caenorhabditis elegans. ATR-bearing rhodopsins reported on voltage changes in body wall muscles (BWMs), in the pharynx, the feeding organ [where Arch(D95N) showed approximately 128% ΔF/F increase per 100 mV], and in neurons, integrating circuit activity. ATR fluorescence is very dim, yet, using the retinal analog dimethylaminoretinal, it was boosted 250-fold. eFRET sensors provided sensitivities of 45 to 78% ΔF/F per 100 mV, induced by BWM action potentials, and in pharyngeal muscle, measured in simultaneous optical and sharp electrode recordings, MacQ-mCitrine showed approximately 20% ΔF/F per 100 mV. All sensors reported differences in muscle depolarization induced by a voltage-gated Ca2+-channel mutant. Optogenetically evoked de- or hyperpolarization of motor neurons increased or eliminated action potential activity and caused a rise or drop in BWM sensor fluorescence. Finally, we analyzed voltage dynamics across the entire pharynx, showing uniform depolarization but compartmentalized repolarization of anterior and posterior parts. Our work establishes all-optical, noninvasive electrophysiology in live, intact C. elegans.
Genetic Mapping of Prince Rupprecht’s Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing

A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.
Using diphenyleneiodonium to induce a viable but non-culturable phenotype in Mycobacterium tuberculosis and its metabolomics analysis

Depletion of oxygen levels is a well-accepted model for induction of non-replicating, persistent states in mycobacteria. Increasing the stress levels in mycobacterium bacilli facilitates their entry into a non-cultivable, dormant state. In this study, it was shown that diphenyleneiodonium, an inhibitor of NADH oxidase, induced a viable, but non-culturable state in mycobacteria, having similar features to dormant bacilli, like loss of acid-fastness, upregulation of stress-regulated genes and decreased superoxide levels as compared to actively growing bacilli. Comprehensive, untargeted metabolic profiling also confirmed a decrease in biogenesis of amino acids, NAD, unsaturated fatty acids and nucleotides. Additionally, an increase in the level of lactate, fumarate, succinate and pentose phosphate pathways along with increased mycothiol and sulfate metabolites, similar to dormant bacilli, was observed in the granuloma. These non-cultivable bacilli were resuscitated by supplementation of fetal bovine serum, regaining their culturability in liquid as well as on agar medium. This study focused on the effect of diphenyleneiodonium treatment in causing mycobacteria to rapidly transition from an active state into a viable, but non-cultivable state, and comparing their characteristics with dormant phenotypes.
Supervisor Incivility and Employee Job Performance: The Mediating Roles of Job Insecurity and Amotivation

Abstract Despite the increasing body of research on workplace incivility, the relationship between supervisor incivility and employee job performance, as well as its intermediary mechanisms, has received relatively little attention from researchers. Drawing on the transactional model of stress and self-determination theory, we propose employees’ job insecurity and amotivation as mediating mechanisms between supervisor incivility and employee job performance. The proposed serial-mediation model was tested through a multilevel analysis of two-wave surveys collected from kindergarten teachers and their principals. Our mediation analysis revealed that incivility perpetrated by kindergarten principals exerted a negative effect on teachers’ job performance three months later by shaping job insecurity perceptions and amotivation. These findings have theoretical implications for the workplace incivility literature and managerial implications for practitioners.
Aetiology, Risk Factors, Diagnosis and Control of Foot-Related Lameness in Dairy Sheep

Simple Summary Despite improvements in modern livestock management, intensification of farming systems has led to the emergence of infectious and husbandry-related health and welfare challenges. Among them, foot pathology-associated lameness is one of the most significant, as it has been strongly associated with adverse consequences in the well-being of animals, and the productivity and the overall profitability of the farms. The objective of this article is to review the current status of knowledge regarding foot-related lameness in sheep, emphasizing on the etiology, risk factors, diagnostic capabilities and control strategies of foot problems in dairy sheep. Abstract During the last twenty years, considerable research efforts have recognized the consequences of foot-related lameness primarily in cattle, and meat and wool sheep. Despite the lack of extensive epidemiological studies, field observations and isolated research reports in dairy sheep have suggested that the problem might be more severe in semi-intensive and intensive farming systems. Footrot, contagious ovine digital dermatitis, ovine interdigital dermatitis, white line disease, and pedal joint abscess are the most common causes of foot-related lameness. Dichelobacter nodosus, Fusobacterium necrophorum, Treponema spp. , and Actinomyces pyogenes are the most significant foot-related lameness-associated pathogens. Despite a documented hereditary predisposition, environmental factors are the most important in determining the occurrence of foot-related lameness. Moist and warm environment, increased parity and milk yield, inappropriate housing conditions and infrastructures, inadequate hygiene status, imbalanced nutrition, and insufficient foot care are the most critical risk factors. Furthermore, a foot-lameness control plan should include targeted implementation of claw trimming and footbathing, evidence-based planning of hygiene measures in preventive veterinary practices (i.e., antibiotic administration, vaccinations against footrot), selective breeding to footrot resistance, and, most importantly, the continuous training of farming personnel. Controlling foot-lameness in dairy sheep is critical in determining the well-being of animals, and strongly affects the farm’s profitability and sustainability.
Regional differences in Ca2+entry along the proximal-middle-distal muscle axis during eccentric contractions in rat skeletal muscle.

Eccentric (ECC) contractions-induced muscle damage is associated with calcium ion (Ca2+) influx from the extracellular milieu through stretch-activated channels. It remains unknown whether Ca2+influx consequent to repetitive ECC contractions is non-uniform across different muscle regions. We tested the hypothesis that there are regional differences in Ca2+entry along the proximal-middle-distal muscle axis. Tibialis anterior (TA) muscles of adult male Wistar rats were exposed by reflecting the overlying skin and fasciae and ECC contractions evoked by nerve stimulation paired with ankle extension (50 times/set, 2 protocols: 1 set and 10 sets). During ECC in the proximal, middle and distal TA we determined: 1. muscle fiber extension by high speed camera (200/sec), 2. Ca2+ accumulation by in vivobioimaging. Muscle fiber(s) extension from resting was significantly different among regions (i.e., proximal, 4.0%: < middle, 11.2%: < distal, 17.0%: ECC phase length at 500th contraction). Intracellular Ca2+ accumulation after 1 set of ECC was highest in the distal than the proximal or middle regions. However, this regional Ca2+ accumulation difference disappeared by 32.5 minutes after 1 set protocol when the muscle was quiescent and by contractions set 5 for the 10 sets protocol. The initial preferential ECC-induced Ca2+ accumulation observed distally was associated spatially with the greater muscle extension compared with that of the proximal and middle regions. Disappearance of the regional Ca2+accumulation in quiescent and ECC-contracting muscle might be explained, in part, by axial Ca2+propagation and account for the uniformity of muscle damage across regions evident 3 days post-ECC.
Transcriptome analyses of cells carrying the Type II Csp231I restriction–modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor

Abstract Restriction-modification (R–M) systems represent an effective mechanism of defence against invading bacteriophages, and are widely spread among bacteria and archaea. In acquiring a Type II R–M system via horizontal gene transfer, the new hosts become more resistant to phage infection, through the action of a restriction endonuclease (REase), which recognizes and cleaves specific target DNAs. To protect the host cell's DNA, there is also a methyltransferase (MTase), which prevents DNA cleavage by the cognate REase. In some R–M systems, the host also accepts a cis-acting transcription factor (C protein), which regulates the counteracting activities of REase and MTase to avoid host self-restriction. Our study characterized the unexpected phenotype of Escherichia coli cells, which manifested as extensive cell filamentation triggered by acquiring the Csp231I R–M system from Citrobacter sp. Surprisingly, we found that the cell morphology defect was solely dependent on the C regulator. Our transcriptome analysis supported by in vivo and in vitro assays showed that C protein directly silenced the expression of the RacR repressor to affect the Rac prophage-related genes. The rac locus ydaST genes, when derepressed, exerted a toxicity indicated by cell filamentation through an unknown mechanism. These results provide an apparent example of transcription factor cross-talk, which can have significant consequences for the host, and may represent a constraint on lateral gene transfer.
Effect of Different Tannin Sources on Nutrient Intake, Digestibility, Performance, Nitrogen Utilization, and Blood Parameters in Dairy Cows

Simple Summary Improving dietary nitrogen utilization efficiency or at least changing the nitrogen excretion route in lactating dairy cows, benefits both the environment and dairy economics; and reduces competition for nitrogen resources between animal feeding and human consumption. However, the effects of tannin supplements from different sources on nitrogen use in dairy cows require further investigation. This study showed that dietary supplementation with tannins in lactating dairy cows significantly decreased the milk and blood urea nitrogen concentrations, and altered the nitrogen excretion routes from the urine to the feces, which may alleviate concerns about nitrogen excretion from dairy farms to the environment. Abstract This study investigated the effect of tannin sources on nutrient intake, digestibility, performance, nitrogen utilization, and blood parameters in lactating dairy cows. Four multiparous lactating Holstein cows were used in a balanced 4 × 4 Latin square design, with each period lasting 28 days. Cows were randomly assigned to one of four dietary treatments: Control diet (CON, a totally mixed ration without tannin supplements), control diet supplemented with 3% bayberry condensed tannins (BCT), control diet supplemented with 3% Acacia mangium condensed tannins (ACT), and control diet supplemented with 3% valonia hydrolyzed tannins (VHT). Dietary treatments did not significantly affect nutrient intake, milk yield or composition, microbial protein synthesis, nitrogen utilization efficiency, or plasma concentrations of glucose, non-esterified fatty acids, β-hydroxybutyrate, total protein, and globulin, or the albumin-to-globulin ratio. Tannin supplements decreased the apparent total tract nutrient digestibility to varying degrees and significantly decreased the milk and blood urea nitrogen contents (p < 0.05). Tannin supplements altered nitrogen excretion routes in lactating dairy cows, and BCT significantly decreased the urinary nitrogen excretion (p = 0.04). Compared with the CON, ACT, and VHT diets, BCT yielded the highest nitrogen retention and nitrogen retention-to-digestible nitrogen ratio despite having a similar nitrogen utilization efficiency (p < 0.05). Bayberry condensed tannin supplementation may be a potential way to improve nitrogen utilization and reduce concerns regarding nitrogen excretion in dairy cows.
The lipidome of primary murine white, brite, and brown adipocytes—Impact of beta-adrenergic stimulation

Lipid species patterns are conserved within cells to maintain physicochemical properties of membranes and cellular functions. We present the lipidome, including sterols, glycerolipids (GLs), glycerophospholipids (GPLs), and sphingolipids (SLs), of primary ex vivo differentiated (I) white, (II) brite, and (III) brown adipocytes derived from primary preadipocytes isolated from (I) epididymal white, (II) inguinal white, and (III) intrascapular brown adipose tissue. Quantitative lipidomics revealed significantly decreased fractions of phosphatidylcholine (PC) and phosphatidylethanolamine (PE), with longer (C > 36) and more polyunsaturated species, as well as lower levels of cardiolipin (CL) in white than in brite and brown adipocytes. Together, the brite and brown lipidome was comparable and indicates differences in membrane lipid packing density compared with white adipocytes. Changes in ceramide species profile could be related to the degree of browning. Beta-adrenergic stimulation of brown adipocytes led to generation of saturated lyso-PC (LPC) increasing uncoupling protein (UCP) 1-mediated leak respiration. Application of stable isotope labeling showed that LPC formation was balanced by an increased de novo synthesis of PC.
Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination

In this study, Steinfeld et al. investigated why the vast majority of eukaryotes have two Rad51/RecA family DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. They show that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family and propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.
Tuning the Swelling Properties of Smart Multiresponsive Core-Shell Microgels by Copolymerization

The present study focuses on the development of multiresponsive core-shell microgels and the manipulation of their swelling properties by copolymerization of different acrylamides—especially N-isopropylacrylamide (NIPAM), N-isopropylmethacrylamide (NIPMAM), and NNPAM—and acrylic acid. We use atomic force microscopy for the dry-state characterization of the microgel particles and photon correlation spectroscopy to investigate the swelling behavior at neutral (pH 7) and acidic (pH 4) conditions. A transition between an interpenetrating network structure for microgels with a pure poly-N,n-propylacrylamide (PNNPAM) shell and a distinct core-shell morphology for microgels with a pure poly-N-isopropylmethacrylamide (PNIPMAM) shell is observable. The PNIPMAM molfraction of the shell also has an important influence on the particle rigidity because of the decreasing degree of interpenetration. Furthermore, the swelling behavior of the microgels is tunable by adjustment of the pH-value between a single-step volume phase transition and a linear swelling region at temperatures corresponding to the copolymer ratios of the shell. This flexibility makes the multiresponsive copolymer microgels interesting candidates for many applications, e.g., as membrane material with tunable permeability.
Dynamic Contrast-Enhanced MRI in Patients with Brain Metastases Undergoing Laser Interstitial Thermal Therapy: A Pilot Study

BACKGROUND AND PURPOSE: Tumor recurrence is difficult to predict in patients receiving laser ablation for intracranial malignancy. We assessed the efficacy of the initial area under the time-to-signal intensity curve at 60 seconds (iAUC60) from dynamic contrast-enhanced MR imaging in predicting progression-free survival in patients with brain metastases following laser interstitial thermal therapy. MATERIALS AND METHODS: The study population was a consecutive series of patients undergoing laser interstitial thermal therapy for brain metastases. Patient demographics including age, sex, tumor histology, and Karnofsky Performance Scale were collected prospectively. Preoperative, postoperative, and 1-month follow-up dynamic contrast-enhanced MRIs were analyzed. Values of iAUC60 were computed using a trapezoidal rule applied to the time history of contrast uptake over the first 60 seconds postenhancement. The change in iAUC60 (ΔiAUC60) was calculated by taking the difference between the values of iAUC60 from 2 time points. Pearson correlation coefficients were calculated between progression-free survival, defined as the time from laser interstitial thermal therapy to tumor recurrence, and iAUC60 or ΔiAUC60 values. RESULTS: Thirty-three cases of laser interstitial thermal therapy for 32 brain metastases in a cohort of 27 patients were prospectively analyzed. A significant relationship was observed between the values of iAUC60 from postoperative dynamic contrast-enhanced MR imaging and progression-free survival with Pearson correlation (P = .03) and Cox univariate analysis (P = .01). The relationship between preoperative and 1-month follow-up dynamic contrast-enhanced MR imaging was not significantly correlated with progression-free survival. Similarly, no statistically significant relationship was observed with ΔiAUC60 and progression-free survival between any time points. CONCLUSIONS: Progression-free survival is difficult to predict in patients undergoing laser interstitial thermal therapy for brain metastases due to confounding with posttreatment change. iAUC60 extracted from postoperative dynamic contrast-enhanced MR imaging shows promise for accurately prognosticating patients following this operative therapy.
Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).