Miracle-dz/UniFAR-FTUs huggingface dataset:
Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

The observation that plant roots skew in microgravity recently refuted the long-held conviction that skewing was a gravity-dependent phenomenon. Further, spaceflight root skewing suggests that specific root morphologies and cell wall remodeling systems may be important aspects of spaceflight physiological adaptation. However, connections between skewing, cell wall modification and spaceflight physiology are currently based on inferences rather than direct tests. Therefore, the Advanced Plant Experiments-03-2 (APEX-03-2) spaceflight study was designed to elucidate the contribution of two skewing- and cell wall-associated genes in Arabidopsis to root behavior and gene expression patterns in spaceflight, to assess whether interruptions of different skewing pathways affect the overall spaceflight-associated process. SPIRAL1 is a skewing-related protein implicated in directional cell expansion, and functions by regulating cortical microtubule dynamics. SKU5 is skewing-related glycosylphosphatidylinositol-anchored protein of the plasma membrane and cell wall implicated in stress response signaling. These two genes function in different cellular pathways that affect skewing on the Earth, and enable a test of the relevance of skewing pathways to spaceflight physiological adaptation. In this study, both sku5 and spr1 mutants showed different skewing behavior and markedly different patterns of gene expression in the spaceflight environment. The spr1 mutant showed fewer differentially expressed genes than its Col-0 wild-type, whereas sku5 showed considerably more than its WS wild-type. Developmental age played a substantial role in spaceflight acclimation in all genotypes, but particularly in sku5 plants, where spaceflight 4d seedlings had almost 10-times as many highly differentially expressed genes as the 8d seedlings. These differences demonstrated that the two skewing pathways represented by SKU5 and SPR1 have unique and opposite contributions to physiological adaptation to spaceflight. The spr1 response is less intense than wild type, suggesting that the loss of SPR1 positively impacts spaceflight adaptation. Conversely, the intensity of the sku5 responses suggests that the loss of SKU5 initiates a much more complex, deeper and more stress related response to spaceflight. This suggests that proper SKU5 function is important to spaceflight adaptation.
SEDATIVE EFFECTS OF MIDAZOLAM IN RED-EARED SLIDER TURTLES {TRACHEMYS SCRIPTA ELEGANS)

Chelonians frequently require anesthesia or sedation to permit performance of clinical procedures. Midazolam is a safe and reversible benzodiazepine used in many other species for its sedative and muscle relaxant properties. The objective of this study was first to determine an effective dose of midazolam in red-eared slider turtles {Trachemys scripta elegans) and then to examine the extent and duration of the effects of this dose on those same turtles. In the first part of the study, 12 turtles were given increasing doses of midazolam intramuscularly at 5-min intervals until a cumulative dose was reached that allowed manual extension of the head and neck and opening of the mouth without resistance. The effective dose at which 10 of the 12 turtles were thus sedated (ED80) was 1.5 mg/kg i.m. This dose was then administered as a single i.m. injection to eight of the same turtles 3 wk later in the second phase of the study. Two other turtles were injected with saline as controls. The onset time, duration of sedation, and recovery time were measured; the medians were 5.5 min (range = 4-28 min), 82 min (range = 3-114 min), and 40 min (range = 20-60 min), respectively. Neither respiratory nor heart rates were affected by sedation. Although much individual variability in response to midazolam was found, midazolam appears to be an effective and safe sedative in red-eared slider turtles.
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

Recent advances in the routine access to space along with increasing opportunities to perform plant growth experiments on board the International Space Station have led to an ever-increasing body of transcriptomic, proteomic, and epigenomic data from plants experiencing spaceflight. These datasets hold great promise to help understand how plant biology reacts to this unique environment. However, analyses that mine across such expanses of data are often complex to implement, being impeded by the sheer number of potential comparisons that are possible. Complexities in how the output of these multiple parallel analyses can be presented to the researcher in an accessible and intuitive form provides further barriers to such research. Recent developments in computational systems biology have led to rapid advances in interactive data visualization environments designed to perform just such tasks. However, to date none of these tools have been tailored to the analysis of the broad-ranging plant biology spaceflight data. We have therefore developed the Test Of Arabidopsis Space Transcriptome (TOAST) database (https://astrobiology.botany.wisc.edu/astrobotany-toast-4-5) to address this gap in our capabilities. TOAST is a relational database that uses the Qlik database management software to link plant biology, spaceflight-related omics datasets, and their associated metadata. This environment helps visualize relationships across multiple levels of experiments in an easy to use gene-centric platform. TOAST draws on data from The US National Aeronautics and Space Administration’s (NASA’s) GeneLab and other data repositories and also connects results to a suite of web-based analytical tools to facilitate further investigation of responses to spaceflight and related stresses. The TOAST graphical user interface allows for quick comparisons between plant spaceflight experiments using real-time, gene-specific queries, or by using functional gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, or other filtering systems to explore genetic networks of interest. Testing of the database shows that TOAST confirms patterns of gene expression already highlighted in the literature, such as revealing the modulation of oxidative stress-related responses across multiple plant spaceflight experiments. However, this data exploration environment can also drive new insights into patterns of spaceflight responsive gene expression. For example, TOAST analyses highlight changes to mitochondrial function as likely shared responses in many plant spaceflight experiments.
Dexamethasone Suppression Test May Predict More Severe/Violent Suicidal Behavior

Introduction Several studies demonstrated that the hypothalamic-pituitary-adrenal (HPA) axis is dysregulated in suicide attempters. Prospective studies found that people with an abnormal response at the dexamethasone suppression test (DST) are more likely to commit suicide. However, whether DST may predict suicide attempts remains less clear. A possible strategy to address this question is to consider the suicide attempt lethality. Objectives (1) To compare the pre- and post-DST cortisol levels in serious/violent suicide attempters and in non-serious/non-violent suicide attempters, and (2) to investigate whether cortisol level can predict new suicide attempts or their lethality. Methods The study included 70 recent suicide attempters (25 with a serious or violent attempt) who were followed for two years. Three saliva samples for cortisol measurement were obtained at 8a.m. , 3p.m. , and 9p.m. before the DST (pre-DST). Then, at 11 p.m. , 1 mg of dexamethasone was given orally. The following day (post-DST), three saliva samples were collected at the same hours as before. The post-DST–pre-DST salivary cortisol Δ index was calculated for each collection time. The Risk-Rescue Ratio Scale (RRRS) and the Suicidal Intent Scale (SIS) were used to characterize the suicide attempt at inclusion and those occurring during the follow-up. Results Post-DST cortisol level at 9 p.m. was higher in patients with an initial violent or serious suicide attempt than in non-violent/non-serious attempters (p < .010). Higher post-DST cortisol at 9p.m. was associated with lower RRRS rescue score and higher clinical impression of suicide severity at inclusion. Among the 66 patients who completed the follow-up, 26 attempted suicide again at least once. Higher pre-DST cortisol at 8a.m. predicted new suicide attempts during the follow-up (OR = 2.15 [1.11, 4.15]), and higher cortisol Δ index at 9p.m. was associated with higher suicide intent during the follow-up. Conclusions Our results suggest that HPA axis hyper-reactivity monitored with the DST is a marker of violent/serious suicide attempt with lower rescue possibility. Furthermore, higher changes between pre-DST and post-DST cortisol levels may predict higher suicide intent. These findings might help to characterize the biological features of nearest suicide phenotypes.
Editorial: Interactions of Plants With Bacteria and Fungi: Molecular and Epigenetic Plasticity of the Host

Interactions of Plants with Bacteria and Fungi: Molecular and Epigenetic Plasticity of the Host In both natural and agricultural environments plants live in association with a multitude of microorganisms belonging to diﬀerent microbial types, mainly bacteria and fungi. Some of these microbes regulate positively plant growth and productivity, while others can damage the host with important ecological and economic consequences. the last many studies contributed to unravel the multifaceted at the basis of plant microbe-interactions
Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
Evolutionary Perspectives on the Developing Skeleton and Implications for Lifelong Health

Osteoporosis is a significant cause of morbidity and mortality in contemporary populations. This common disease of aging results from a state of bone fragility that occurs with low bone mass and loss of bone quality. Osteoporosis is thought to have origins in childhood. During growth and development, there are rapid gains in bone dimensions, mass, and strength. Peak bone mass is attained in young adulthood, well after the cessation of linear growth, and is a major determinant of osteoporosis later in life. Here we discuss the evolutionary implications of osteoporosis as a disease with developmental origins that is shaped by the interaction among genes, behavior, health status, and the environment during the attainment of peak bone mass. Studies of contemporary populations show that growth, body composition, sexual maturation, physical activity, nutritional status, and dietary intake are determinants of childhood bone accretion, and provide context for interpreting bone strength and osteoporosis in skeletal populations. Studies of skeletal populations demonstrate the role of subsistence strategies, social context, and occupation in the development of skeletal strength. Comparisons of contemporary living populations and archeological skeletal populations suggest declines in bone density and strength that have been occurring since the Pleistocene. Aspects of western lifestyles carry implications for optimal peak bone mass attainment and lifelong skeletal health, from increased longevity to circumstances during development such as obesity and sedentism. In light of these considerations, osteoporosis is a disease of contemporary human evolution and evolutionary perspectives provide a key lens for interpreting the changing global patterns of osteoporosis in human health.
High Levels of BMP2 Promote Liver Cancer Growth via the Activation of Myeloid-Derived Suppressor Cells

Bone morphogenetic protein 2 (BMP2) signaling had significant roles in diverse pathological processes, such as cancer. Nevertheless, the interaction between BMP2 and carcinoma development remained largely unknown. In particular, the roles that BMP2 play in the development of liver cancer remained controversial, and mechanisms were unclear. BMP2 with strong osteogenic potential had been manufactured into various bone materials. However, cancer risk concerns were raised in recent years. Thus, we focused on analyzing the effects of exogenous BMP2 on the growth of liver cancer and the detailed mechanisms. We found that both intravenous injection of rhBMP2 and in vivo implantation of rhBMP2 materials could lead to the expansion of myeloid-derived suppressor cells (MDSCs) in peripheral blood and subsequently enhanced the infiltration of MDSCs into tumor in vivo. Furthermore, BMP2 signaling-activated MDSCs could secrete IL6 to enhance cell proliferation of liver cancer cells in vitro and facilitate liver cancer growth in vivo. Our study indicated that increased concentration of BMP2 within the peripheral blood could enhance liver cancer growth via the activation of MDSCs. In this study, the roles that BMP2 played in liver cancer growth were further confirmed and the detailed mechanisms about how BMP2 enhanced liver cancer growth were also elucidated.
Opossum Cathelicidins Exhibit Antimicrobial Activity Against a Broad Spectrum of Pathogens Including West Nile Virus

This study aimed to characterize cathelicidins from the gray short-tailed opossum in silico and experimentally validate their antimicrobial effects against various pathogenic bacteria and West Nile virus (WNV). Genome-wide in silico analysis against the current genome assembly of the gray short-tailed opossum yielded 56 classical antimicrobial peptides (AMPs) from eight different families, among which 19 cathelicidins, namely ModoCath1 – 19, were analyzed in silico to predict their antimicrobial domains and three of which, ModoCath1, -5, and -6, were further experimentally evaluated for their antimicrobial activity, and were found to exhibit a wide spectrum of antimicroial effects against a panel of gram-positive and gram-negative bacterial strains. In addition, these peptides displayed low-to-moderate cytotoxicity in mammalian cells as well as stability in serum and various salt and pH conditions. Circular dichroism analysis of the spectra resulting from interactions between ModoCaths and lipopolysaccharides (LPS) showed formation of a helical structure, while a dual-dye membrane disruption assay and scanning electron microscopy analysis revealed that ModoCaths exerted bactericidal effects by causing membrane damage. Furthermore, ModoCath5 displayed potent antiviral activity against WNV by inhibiting viral replication, suggesting that opossum cathelicidins may serve as potentially novel antimicrobial endogenous substances of mammalian origin, considering their large number. Moreover, analysis of publicly available RNA-seq data revealed the expression of eight ModoCaths from five different tissues, suggesting that gray short-tailed opossums may be an interesting source of cathelicidins with diverse characteristics.
Proteomic Analysis of Preoperative CSF Reveals Risk Biomarkers of Postoperative Delirium

Objective: To analyze the proteome of preoperative cerebrospinal fluid (CSF) in older orthopedic patients with or without postoperative delirium (POD) using untargeted proteomics. Methods: A prospective cohort study was conducted. Eighty hip fracture patients aged ≥65 years were recruited. After successful spinal anesthesia, CSF was collected. The patients were divided into POD and No-POD groups based on the Confusion Assessment Method, and patients with POD were graded using the Memorial Delirium Assessment Scale (MDAS). Thirty No-POD patients were matched to 10 POD patients by age (±2 years) and Mini–Mental State Examination score (±2 scores). Label-free proteomic analysis was performed using a liquid chromatography coupled to mass spectrometry (LC-MS) workflow. Validation was performed using mass-spectrometry-based parallel reaction monitoring (PRM) for the 30 No-POD and 10 POD patients, as well as for an additional 5 POD patients. Bioinformatics were used to investigate possible relevant pathological mechanisms. Results: The incidence of POD in older orthopedic patients was 18.8% in our cohort of 80 patients. Proteomics results revealed 63 dysregulated CSF proteins, and PRM analysis validated these results. The preoperative CSF levels of both V-set and transmembrane domain-containing protein 2B (VSTM2B) and coagulation factor V (FA5) were positively correlated with MDAS scores on postoperative day 1 (r > 0.8, p < 0.05). Bioinformatic analysis revealed that several nervous-system-related pathways are relevant to POD development. Conclusion: We identified and validated several novel CSF proteins that are dysregulated in POD, and revealed several pathways that are relevant to POD development. Our results not only provide risk biomarkers for POD, but also give clues for further investigations into the pathological mechanisms of delirium. Clinical trial registration: This study was registered in the Chinese Clinical Trial Registry (ChiCTR1900021533).
Impact of Inaccurate Documentation of Sampling and Infusion Time in Model-Informed Precision Dosing

Background Routine clinical TDM data is often used to develop population pharmacokinetic (PK) models, which are applied in turn for model-informed precision dosing. The impact of uncertainty in documented sampling and infusion times in population PK modeling and model-informed precision dosing have not yet been systematically evaluated. The aim of this study was to investigate uncertain documentation of (i) sampling times and (ii) infusion rate exemplified with two anti-infectives. Methods A stochastic simulation and estimation study was performed in NONMEM® using previously published population PK models of meropenem and caspofungin. Uncertainties, i.e. deviation between accurate and planned sampling and infusion times (standard deviation (SD) ± 5 min to ± 30 min) were added randomly in R before carrying out the simulation step. The estimation step was then performed with the accurate or planned times (replacing real time points by scheduled study values). Relative bias (rBias) and root mean squared error (rRMSE) were calculated to determine accuracy and precision of the primary and secondary PK parameters on the population and individual level. The accurate and the misspecified (using planned sampling times) model were used for Bayesian forecasting of meropenem to assess the impact on PK/PD target calculations relevant to dosing decisions. Results On the population level, the estimates of the proportional residual error (prop.-err.) and the interindividual variability (IIV) on the central volume of distribution (V1) were most affected by erroneous records in the sampling and infusion time (e.g. rBias of prop.-err.: 75.5% vs. 183% (meropenem) and 10.1% vs. 109% (caspofungin) for ± 5 vs. ± 30 min, respectively). On the individual level, the rBias of the planned scenario for the typical values V1, Q and V2 increased with increasing uncertainty in time, while CL, AUC and elimination half-life were least affected. Meropenem as a short half-life drug (~1 h) was more affected than caspofungin (~ 9–11 h). The misspecified model provided biased PK/PD target information (e.g. falsely overestimated time above MIC (T > MIC) when true T > MIC was <0.4 and thus patients at risk of undertreatment), while the accurate model gave precise estimates of the indices across all simulated patients. Conclusions Even 5-minute-uncertainties caused bias and significant imprecision of primary population and individual PK parameters. Thus, our results underline the importance of accurate documentation of time.
Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses

Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.