HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses.

Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation, disease occurrence and progression. The recent development of single-cell RNA-seq (scRNA-seq) technologies significantly boosted the characterization of cell type heterogeneities in different human tissues. However, the huge number of datasets in the public domain also posed challenges in data integration and reuse. We present Human Universal Single Cell Hub (HUSCH, http://husch.comp-genomics.org), an atlas-scale curated database that integrates single-cell transcriptomic profiles of nearly 3 million cells from 185 high-quality human scRNA-seq datasets from 45 different tissues. All the data in HUSCH were uniformly processed and annotated with a standard workflow. In the single dataset module, HUSCH provides interactive gene expression visualization, differentially expressed genes, functional analyses, transcription regulators and cell-cell interaction analyses for each cell type cluster. Besides, HUSCH integrated different datasets in the single tissue module and performs data integration, batch correction, and cell type harmonization. This allows a comprehensive visualization and analysis of gene expression within each tissue based on single-cell datasets from multiple sources and platforms. HUSCH is a flexible and comprehensive data portal that enables searching, visualizing, analyzing, and downloading single-cell gene expression for the human tissue atlas.

The osteogenic effects of sappanchalcone in vitro and in vivo.

BACKGROUND AND OBJECTIVES: The utilization of natural products to enhance the function of periodontal ligament cells (PDLCs) has emerged as a popular area of research. Recent investigations have demonstrated that sappanchalcone (SC) possesses pharmacological properties such as anti-inflammatory and osteoprotective effects. This study aims to explore the impact of SC on the in vivo and in vitro osteogenic differentiation ability of PDLCs. MATERIALS: Cell proliferation was quantified using the CCK-8 assay, while gene expression levels were assessed through qRT-PCR analysis. Osteoblast differentiation capacity was evaluated by employing Alizarin red staining (ARS), alkaline phosphatase (ALP) staining and western blot (WB) analysis. A rat model of periodontitis was established utilizing the tether-wire method. Micro-CT imaging and hematoxylin and eosin (HE) staining were employed to evaluate alveolar bone resorption. Masson's trichrome staining was utilized to observe fiber alignment, whereas immunohistochemistry (IHC) techniques were applied for detecting osteogenic and inflammatory factors. RESULTS: The results from the CCK-8 assay indicate no observed cytotoxicity for concentrations of 1, 5, or 10 nM for SC treatment (p < .05), while qRT-PCR analysis demonstrates a significant decrease in inflammatory factors such as MMP-1 and IL-6 with treatment by SC (p < .05). Additionally, western blotting reveals an increase in protein expression levels of Runx2 and OPN within PDLCs treated with SC compared to control groups (p < .05), which is further supported by ARS and ALP staining indicating an increase in mineralized nodules formation along with elevated ALP content within these cells following treatment with this compound (p < .05). Finally, both HE staining as well as micro-CT imaging suggest potential benefits associated with using this compound including slowing alveolar bone resorption while simultaneously promoting junctional epithelium proliferation. CONCLUSIONS: Our in vitro and in vivo findings suggest that SC can effectively enhance the inflammatory response of PDLCs and promote their osteogenic differentiation ability under inflammatory conditions, indicating its potential as a promising therapeutic agent for improving periodontal inflammation and bone formation.

Incidence and risk factors of venous thromboembolism in kidney transplantation patients: a prospective cohort study.

To investigate the incidence and explore the risk factors of venous thromboembolism (VTE) within 6 months after kidney transplantation. Total of 331 kidney transplant recipients were assessed by venous ultrasonography for VTE at 14 days, 1 month, 3 months, and 6 months post-transplantation. Cox forward regression were used to identify the independent risk factors of VTE. This study registration number is ChiCTR1900020567 and the date of registration was 2019/01/08. The cumulative incidence of VTE was 2.72% (9/331) within 6 months after transplant. 77.8% (7/9) of VTEs occurred in the first 3 months post-transplantation. 88.9% (1/9) of VTEs were asymptomatic, 66.7% (6/9) of VTEs were mural thromboses and in the right lower extremity. Central vena catheterization (HR = 6.94) and severe pulmonary disease (including pneumonia) (HR = 57.35) were the risk factors for VTE in kidney transplantation recipients. KT patients are the high risk population of VTE. Future interventions should be strengthen for KT patients to receive a minimum of 3-month of precautionary measures for VTE, including infection prevention, and strengthening thromboprophylaxis on the CVC or transplanted side of lower extremity.

Serum Levels and Clinical Significance of NSE, BDNF and CNTF in Patients with Cancer-associated Ischemic Stroke Complicated with Post-stroke Depression.

BACKGROUND: The incidence of post-stroke depression (PSD) may be higher in patients with cancer-associated ischemic stroke (CAIS). The pathogenesis of PSD is mainly related to the emotional injury of stroke and the inability of neurons to effectively repair. This study aims to explore the clinical significance of serum neuron-specific enolase (NSE), brain-derived neurotrophic factor (BDNF) and ciliary neurotrophic factor (CNTF) expression levels in CAIS patients. METHODS: Clinical data of 106 patients with CAIS admitted to Jinhua Guangfu Oncology Hospital from January 2012 to December 2022 were retrospectively analyzed. Serum levels of NSE, BDNF and CNTF were measured in all patients after admission. Depression screening was performed by Hamilton Depression Scale-17 (HAMD-17) three months after intravenous thrombolysis. Patients with HAMD-17 score >7 were included in the PSD group (n = 44), and patients with HAMD-17 score ≤7 were included in the non-PSD group (n = 62). The general data and serum levels of NSE, BDNF and CNTF were compared between the two groups. According to HAMD-17 scores, patients in PSD group were further divided into mild depression group (8-16 points), moderate depression group (17-23 points) and severe depression group (≥24 points), and the serum levels of NSE, BDNF and CNTF were compared among the three groups. Pearson's correlation test was used to analyze the correlation between HAMD-17 scores and serum NSE, BDNF and CNTF levels in PSD patients. Logistic regression model was used to determine the influencing factors of PSD in CAIS patients. Receiver operating characteristic (ROC) curve was plotted to analyze the predictive efficacy of serum NSE, BDNF, CNTF and their combination on PSD. RESULTS: Among 106 CAIS patients, the incidence of PSD was 41.51% (44 cases), including 19 patients with mild PSD (43.18%), 14 patients with moderate PSD (31.82%), and 11 patients with severe PSD (25.00%). There were statistically significant differences in negative life events and complications after thrombolytic therapy between PSD and non-PSD patients (p < 0.05). The serum NSE level in PSD group was significantly higher than that in non-PSD group, and the serum BDNF and CNTF levels were notably lower than those in non-PSD group (all p < 0.001). The serum levels of NSE, BDNF and CNTF in patients with different severity of PSD were statistically significant (all p < 0.001). HAMD-17 scores in PSD patients were positively correlated with serum NSE levels (r = 0.676, p < 0.001) and negatively correlated with serum BDNF and CNTF levels (r = -0.661, p < 0.001; r = -0.401, p = 0.007, respectively). By binary logistic regression analysis, the levels of serum NSE, BDNF and CNTF were independent influencing factors for PSD in CAIS patients, among which NSE was a risk factor (odds ratio (OR) >1, p < 0.05), BDNF and CNTF were protective factors (OR <1, p < 0.05). CONCLUSION: This study reveals for the first time that the levels of serum NSE, BDNF and CNTF are closely related to the occurrence and development of PSD in CAIS patients. In clinical CAIS patients with abnormal changes in the above indicators, in addition to anti-tumor treatment and improvement of neurological deficit symptoms, attention should also be paid to the symptoms of psychological disorders.

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment.

Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy. Here, we present Tumor Immune Single Cell Hub (TISCH, http://tisch.comp-genomics.org), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.

Urban warming advances spring phenology but reduces the response of phenology to temperature in the conterminous United States.

Urbanization has caused environmental changes, such as urban heat islands (UHIs), that affect terrestrial ecosystems. However, how and to what extent urbanization affects plant phenology remains relatively unexplored. Here, we investigated the changes in the satellite-derived start of season (SOS) and the covariation between SOS and temperature (RT ) in 85 large cities across the conterminous United States for the period 2001-2014. We found that 1) the SOS came significantly earlier (6.1 ± 6.3 d) in 74 cities and RT was significantly weaker (0.03 ± 0.07) in 43 cities when compared with their surrounding rural areas (P < 0.05); 2) the decreased magnitude in RT mainly occurred in cities in relatively cold regions with an annual mean temperature <17.3 °C (e.g., Minnesota, Michigan, and Pennsylvania); and 3) the magnitude of urban-rural difference in both SOS and RT was primarily correlated with the intensity of UHI. Simulations of two phenology models further suggested that more and faster heat accumulation contributed to the earlier SOS, while a decrease in required chilling led to a decline in RT magnitude in urban areas. These findings provide observational evidence of a reduced covariation between temperature and SOS in major US cities, implying the response of spring phenology to warming conditions in nonurban environments may decline in the warming future.

Anthropogenically driven climate and landscape change effects on inland water carbon dynamics: What have we learned and where are we going?

Inland waters serve as important hydrological connections between the terrestrial landscape and oceans but are often overlooked in global carbon (C) budgets and Earth System Models. Terrestrially derived C entering inland waters from the watershed can be transported to oceans but over 83% is either buried in sediments or emitted to the atmosphere before reaching oceans. Anthropogenic pressures such as climate and landscape changes are altering the magnitude of these C fluxes in inland waters. Here, we synthesize the most recent estimates of C fluxes and the differential contributions across inland waterbody types (rivers, streams, lakes, reservoirs, and ponds), including recent measurements that incorporate improved sampling methods, small waterbodies, and dried areas. Across all inland waters, we report a global C emission estimate of 4.40 Pg C/year (95% confidence interval: 3.95-4.85 Pg C/year), representing a 13% increase from the most recent estimate. We also review the mechanisms by which the most globally widespread anthropogenically driven climate and landscape changes influence inland water C fluxes. The majority of these drivers are expected to influence terrestrial C inputs to inland waters due to alterations in terrestrial C quality and quantity, hydrological pathways, and biogeochemical processing. We recommend four research priorities for the future study of anthropogenic alterations to inland water C fluxes: (1) before-and-after measurements of C fluxes associated with climate change events and landscape changes, (2) better quantification of C input from land, (3) improved assessment of spatial coverage and contributions of small inland waterbodies to C fluxes, and (4) integration of dried and drawdown areas to global C flux estimates. Improved measurements of inland water C fluxes and quantification of uncertainty in these estimates will be vital to understanding both terrestrial C losses and the "moving target" of inland water C emissions in response to rapid and complex anthropogenic pressures.

Unusual characteristics of the carbon cycle during the 2015-2016 El Niño.

The 2015-2016 El Niño was one of the strongest on record, but its influence on the carbon balance is less clear. Using Northern Hemisphere atmospheric CO2 observations, we found both detrended atmospheric CO2 growth rate (CGR) and CO2 seasonal-cycle amplitude (SCA) of 2015-2016 were much higher than that of other El Niño events. The simultaneous high CGR and SCA were unusual, because our analysis of long-term CO2 observations at Mauna Loa revealed a significantly negative correlation between CGR and SCA. Atmospheric inversions and terrestrial ecosystem models indicate strong northern land carbon uptake during spring but substantially reduced carbon uptake (or high emissions) during early autumn, which amplified SCA but also resulted in a small anomaly in annual carbon uptake of northern ecosystems in 2015-2016. This negative ecosystem carbon uptake anomaly in early autumn was primarily due to soil water deficits and more litter decomposition caused by enhanced spring productivity. Our study demonstrates a decoupling between seasonality and annual carbon cycle balance in northern ecosystems over 2015-2016, which is unprecedented in the past five decades of El Niño events.

Low serum vitamin D concentrations are associated with obese but not lean NAFLD: a cross-sectional study.

BACKGROUND: A low serum vitamin D concentration has been reported to be associated with an increased risk of non-alcoholic fatty liver disease (NAFLD); however, whether lean or obese individuals show a similar association between vitamin D and NAFLD remains speculative. This study aimed to explore the relationship between serum vitamin D concentration and NAFLD in lean and obese Chinese adults. METHODS: This cross-sectional study included 2538 participants (1360 men and 1178 women) who underwent health checkups at the First Affiliated Hospital, Zhejiang University School of Medicine in 2019. NAFLD was diagnosed by liver ultrasound excluding other causes. The association of serum vitamin D concentration with NAFLD was analyzed in lean and obese participants. RESULTS: The overall prevalence of NAFLD was 33.61% (13.10% in lean and 53.32% in obese) in this study population. The serum vitamin D levels of obese NAFLD patients were lower than those of obese NAFLD-free controls. However, the serum vitamin D levels of lean NAFLD patients were comparable to those of lean NAFLD-free controls. Serum vitamin D level was negatively correlated with the prevalence of NAFLD in obese but not lean participants. Serum vitamin D level was independently associated with the risk of NAFLD in obese participants, with an adjusted odds ratio (95% CI) of 0.987 (0.981-0.993). However, serum vitamin D level was not related to the risk of NAFLD in lean participants. CONCLUSIONS: A low serum vitamin D level is associated with NAFLD in obese but not lean participants.

Association between Monocyte to High-Density Lipoprotein Cholesterol Ratio and Nonalcoholic Fatty Liver Disease: A Cross-Sectional Study.

BACKGROUND: The aim of the present study was to investigate the association between monocyte to high-density lipoprotein cholesterol ratio (MHR) and nonalcoholic fatty liver disease (NAFLD) in Chinese population. METHODS: We enrolled 14189 individuals who attended their annual health examinations in the study. We performed the anthropometric and laboratory measurements and diagnosed NAFLD by hepatic ultrasonography without evidence of other etiologies of chronic liver disease. Student's t-test, Mann-Whitney U test, and chi-squared (χ 2) test was used to compare the differences of clinical characteristics between participants with or without NAFLD. Pearson's and Spearman's analyses were performed to assess the correlation of MHR and NAFLD risk factors. Univariate and multivariate logistic regression analyses were conducted to explore whether MHR associated with NAFLD. RESULTS: Thirty-five percent of the participants enrolled were diagnosed with NAFLD. Compared with healthy controls, NAFLD patients were male predominant, older, and had higher body mass index, waist circumference, and systolic and diastolic blood pressure, as well as higher levels of alanine aminotransferase, aspartate aminotransferase, γ-glutamyl transferase, triglyceride, total cholesterol, low-density lipoprotein cholesterol, fasting plasma glucose, glycated hemoglobin A1c, and serum uric acid, but lower levels of serum high-density lipoprotein cholesterol. Besides, MHR was significantly higher in NAFLD patients than healthy controls [5.35 (4.18-6.84) versus 4.53 (3.48-5.93), P < 0.001]. MHR quartiles were positively related to the prevalence of NAFLD (P < 0.001 for trend). In multivariate logistic regression analysis, MHR was positively associated with the risk of NAFLD after adjusting age, gender, body mass index, waist circumference, diastolic blood pressure, alanine aminotransferase, triglyceride, total cholesterol, fasting plasma glucose, and serum uric acid (OR: 1.026, 95% CI: 1.002-1.052; P = 0.037). CONCLUSIONS: MHR is significantly and positively associated with the risk of NAFLD.

Global vegetation biomass production efficiency constrained by models and observations.

Plants use only a fraction of their photosynthetically derived carbon for biomass production (BP). The biomass production efficiency (BPE), defined as the ratio of BP to photosynthesis, and its variation across and within vegetation types is poorly understood, which hinders our capacity to accurately estimate carbon turnover times and carbon sinks. Here, we present a new global estimation of BPE obtained by combining field measurements from 113 sites with 14 carbon cycle models. Our best estimate of global BPE is 0.41 ± 0.05, excluding cropland. The largest BPE is found in boreal forests (0.48 ± 0.06) and the lowest in tropical forests (0.40 ± 0.04). Carbon cycle models overestimate BPE, although models with carbon-nitrogen interactions tend to be more realistic. Using observation-based estimates of global photosynthesis, we quantify the global BP of non-cropland ecosystems of 41 ± 6 Pg C/year. This flux is less than net primary production as it does not contain carbon allocated to symbionts, used for exudates or volatile carbon compound emissions to the atmosphere. Our study reveals a positive bias of 24 ± 11% in the model-estimated BP (10 of 14 models). When correcting models for this bias while leaving modeled carbon turnover times unchanged, we found that the global ecosystem carbon storage change during the last century is decreased by 67% (or 58 Pg C).

Determinants of anxiety and depression in patients with cubital tunnel syndrome.

BACKGROUND: The aim of this cross-sectional study to assess the proportions of anxiety and depression in patients with CuTS, and to explore the associated demographic and clinical features. METHODS: From May 2011 to January 2017, 246 patients diagnosed with CuTS were recruited. The Hospital Anxiety and Depression Scale was used to assess the proportions of depression and anxiety. Patient demographic and clinical data were collected. Univariate analysis and multivariate regression were carried out to identify the variables that were independently associated with anxiety and depression. RESULTS: The proportions of depression and anxiety were 17.9% (n = 44) and 14.2% (n = 35), respectively. Five patients had both possible/probable anxiety and depression. Logistic regression analysis revealed that diabetes mellitus was independently associated with depression; and the modified McGowan grade was independently associated with anxiety. CONCLUSIONS: In patients with CuTS, the proportions of depression and anxiety were 17.9% and 14.2%, respectively. Early screening for anxiety and depression is beneficial for patients with CuTS.

Human cytomegalovirus protein UL136 activates the IL-6/STAT3 signal through MiR-138 and MiR-34c in gastric cancer cells.

BACKGROUND: Accumulating evidences have indicated that human cytomegalovirus (HCMV) may link to multiple human malignancies, including gastric cancer. However, the mechanistic role of HCMV in GC remains largely unknown. METHODS: In this study, we have successfully established HCMV latent gene UL-136-expressing gastric cancer cells. We measured cell proliferation of GC cells, MNK-45 and SGC-7901, with stable UL136 expression or paired control cells by using CCK-8 assay. We have showed that GC cells with stable UL136 expression had a rapid cell growth. Furthermore, our data from matrigel-coated transwell assay have demonstrated that UL136 expressing GC cells showed an enhanced invasion capacity compared to control cells. Furthermore, ectopic expression of UL136 inhibits tumorigenicity in an animal model. RESULTS: We observed that IL-6/STAT3 was stimulated by UL136 overexpression. Also, miR-138 is consistently up-regulated, while miR-34 down-regulated by UL136 in either MNK-45 or SGC-7901 cells. Our mechanistic study showed that treatment of miR-138 mimics in MNK-45 cells indeed inhibited SIRT1 expression to increase phosphorylation level of STAT3. MiR-34c suppressed expression of IL6R through direct binding with the putative 3'UTR binding sites of this gene. UL136 regulate IL6/STAT3 pathway, at least in part, through down-regulation of miR-34c in GC cells. CONCLUSION: In conclusion, HCMV-induced miR-34c or miR-138 involves in the activation of IL6/STAT3 signaling. Targeting the IL6-STAT3 axis or miRNAs represent a promising strategy for HCMV-related tumor formation.

Cryptic phenology in plants: Case studies, implications, and recommendations.

Plant phenology-the timing of cyclic or recurrent biological events in plants-offers insight into the ecology, evolution, and seasonality of plant-mediated ecosystem processes. Traditionally studied phenologies are readily apparent, such as flowering events, germination timing, and season-initiating budbreak. However, a broad range of phenologies that are fundamental to the ecology and evolution of plants, and to global biogeochemical cycles and climate change predictions, have been neglected because they are "cryptic"-that is, hidden from view (e.g., root production) or difficult to distinguish and interpret based on common measurements at typical scales of examination (e.g., leaf turnover in evergreen forests). We illustrate how capturing cryptic phenology can advance scientific understanding with two case studies: wood phenology in a deciduous forest of the northeastern USA and leaf phenology in tropical evergreen forests of Amazonia. Drawing on these case studies and other literature, we argue that conceptualizing and characterizing cryptic plant phenology is needed for understanding and accurate prediction at many scales from organisms to ecosystems. We recommend avenues of empirical and modeling research to accelerate discovery of cryptic phenological patterns, to understand their causes and consequences, and to represent these processes in terrestrial biosphere models.

MiR-425 expression profiling in acute myeloid leukemia might guide the treatment choice between allogeneic transplantation and chemotherapy.

BACKGROUND: Acute myeloid leukemia (AML) is a highly heterogeneous disease. MicroRNAs function as important biomarkers in the clinical prognosis of AML. METHODS: This study identified miR-425 as a prognostic factor in AML by screening the TCGA dataset. A total of 162 patients with AML were enrolled for the study and divided into chemotherapy and allogeneic hematopoietic stem cell transplantation (allo-HSCT) groups. RESULTS: In the chemotherapy group, patients with high miR-425 expression had significantly longer overall survival (OS) and event-free survival (EFS) compared with patients with low miR-425 expression. In multivariate analyses, high miR-425 expression remained independently predictive of a better OS (HR = 0.502, P = 0.005) and EFS (HR = 0.432, P = 0.001) compared with patients with low miR-425 expression. Then, all patients were divided into two groups based on the median expression levels of miR-425. Notably, the patients undergoing allo-HSCT had significantly better OS (HR = 0.302, P < 0.0001) and EFS (HR = 0.379, P < 0.0001) compared with patients treated with chemotherapy in the low-miR-425-expression group. Mechanistically, high miR-425 expression levels were associated with a profile significantly involved in regulating cellular metabolism. Among these genes, MAP3K5, SMAD2, and SMAD5 were predicted targets of miR-425. CONCLUSIONS: The expression of miR-425 may be useful in identifying patients in need of strategies to select the optimal therapy between chemotherapy and allo-HSCT treatment regimens. Patients with low miR-425 expression may consider early allo-HSCT.

Ocean oxygenation in the wake of the Marinoan glaciation.

Metazoans are likely to have their roots in the Cryogenian period, but there is a marked increase in the appearance of novel animal and algae fossils shortly after the termination of the late Cryogenian (Marinoan) glaciation about 635 million years ago. It has been suggested that an oxygenation event in the wake of the severe Marinoan glaciation was the driving factor behind this early diversification of metazoans and the shift in ecosystem complexity. But there is little evidence for an increase in oceanic or atmospheric oxygen following the Marinoan glaciation, or for a direct link between early animal evolution and redox conditions in general. Models linking trends in early biological evolution to shifts in Earth system processes thus remain controversial. Here we report geochemical data from early Ediacaran organic-rich black shales (∼635-630 million years old) of the basal Doushantuo Formation in South China. High enrichments of molybdenum and vanadium and low pyrite sulphur isotope values (Δ(34)S values ≥65 per mil) in these shales record expansion of the oceanic inventory of redox-sensitive metals and the growth of the marine sulphate reservoir in response to a widely oxygenated ocean. The data provide evidence for an early Ediacaran oxygenation event, which pre-dates the previous estimates for post-Marinoan oxygenation by more than 50 million years. Our findings seem to support a link between the most severe glaciations in Earth's history, the oxygenation of the Earth's surface environments, and the earliest diversification of animals.

Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles.

Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R0mm and R15mm radicles (i.e., before radicle emergence and 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%). The heat-stable proteome of soybean radicles that contain many IDPs could protect lactate dehydrogenase (LDH) during freeze-thaw cycles. Comparison of the 795 heat-stable proteins in the R0mm and R15mm soybean radicles revealed that many of these proteins changed abundance during seedling growth with 170 and 89 proteins being more abundant in R0mm and R15mm, respectively. KEGG analysis identified 18 proteins from the cysteine and methionine metabolism pathways and nine proteins from the phenylpropanoid biosynthesis pathway. As an important type of IDP related to stress, 30 late embryogenesis abundant proteins were also found. Ten selected proteins with high levels of predicted intrinsic disorder were able to efficiently protect LDH from the freeze-thaw-induced inactivation, but the protective ability was not correlated with the disorder content of these proteins. These observations suggest that protection of the enzymes and other proteins in a stressed cell can be one of the biological functions of plant IDPs.

Informing climate models with rapid chamber measurements of forest carbon uptake.

Models predicting ecosystem carbon dioxide (CO2 ) exchange under future climate change rely on relatively few real-world tests of their assumptions and outputs. Here, we demonstrate a rapid and cost-effective method to estimate CO2 exchange from intact vegetation patches under varying atmospheric CO2 concentrations. We find that net ecosystem CO2 uptake (NEE) in a boreal forest rose linearly by 4.7 ± 0.2% of the current ambient rate for every 10 ppm CO2 increase, with no detectable influence of foliar biomass, season, or nitrogen (N) fertilization. The lack of any clear short-term NEE response to fertilization in such an N-limited system is inconsistent with the instantaneous downregulation of photosynthesis formalized in many global models. Incorporating an alternative mechanism with considerable empirical support - diversion of excess carbon to storage compounds - into an existing earth system model brings the model output into closer agreement with our field measurements. A global simulation incorporating this modified model reduces a long-standing mismatch between the modeled and observed seasonal amplitude of atmospheric CO2 . Wider application of this chamber approach would provide critical data needed to further improve modeled projections of biosphere-atmosphere CO2 exchange in a changing climate.

SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice.

Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of motor neuron-1 (SMN1) gene, represents the most common genetic cause of pediatric mortality. A duplicate copy (SMN2) is inefficiently spliced, producing a truncated and unstable protein. We describe herein a potent, orally active, small-molecule enhancer of SMN2 splicing that elevates full-length SMN protein and extends survival in a severe SMA mouse model. We demonstrate that the molecular mechanism of action is via stabilization of the transient double-strand RNA structure formed by the SMN2 pre-mRNA and U1 small nuclear ribonucleic protein (snRNP) complex. The binding affinity of U1 snRNP to the 5' splice site is increased in a sequence-selective manner, discrete from constitutive recognition. This new mechanism demonstrates the feasibility of small molecule-mediated, sequence-selective splice modulation and the potential for leveraging this strategy in other splicing diseases.

Human rotavirus strain Wa downregulates NHE1 and NHE6 expressions in rotavirus-infected Caco-2 cells.

Rotavirus (RV) is the most common cause of severe gastroenteritis and fatal dehydration in human infants and neonates of different species. However, the pathogenesis of rotavirus-induced diarrhea is poorly understood. Secretory diarrhea caused by rotavirus may lead to a combination of excessive secretion of fluid and electrolytes into the intestinal lumen. Fluid absorption in the small intestine is driven by Na+-coupled transport mechanisms at the luminal membrane, including Na+/H+ exchanger (NHE). Here, we performed qRT-PCR to detect the transcription of NHEs. Western blotting was employed for protein detection. Furthermore, immunocytochemistry was used to validate the NHE's protein expression. Finally, intracellular Ca2+ concentration was detected by confocal laser scanning microscopy. The results demonstrated that the NHE6 mRNA and protein expressed in the human colon adenocarcinoma cell line (Caco-2). Furthermore, RV-Wa induced decreased expression of the NHE1 and NHE6 in Caco-2 cell in a time-dependent manner. In addition, intracellular Ca2+ concentration in RV-Wa-infected Caco-2 cells was higher than that in the mock-infected cells. Furthermore, RV-Wa also can downregulate the expression of calmodulin (CaM) and calmodulin kinase II (CaMKII) in Caco-2 cells. These findings provides important insights into the mechanisms of rotavirus-induced diarrhea. Further studies on the underlying pathophysiological mechanisms that downregulate NHEs in RV-induced diarrhea are required.