Genome-wide identification and expression pattern analysis of the Aux/IAA (auxin/indole-3-acetic acid) gene family in alfalfa (Medicago sativa) and the potential functions under drought stress.

BACKGROUND: Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families of auxin, playing a crucial role in response to drought stress. However, the characteristics of the Aux/IAA gene family in alfalfa and its potential function in response to drought stress are still unknown. RESULT: A total of 41 Aux/IAA gene members were identified in alfalfa genome. The physicochemical, peptide structure, secondary and tertiary structure analysis of proteins encoded by these genes revealed functional diversity of the MsIAA gene. A phylogenetic analysis classified the MsIAA genes into I-X classes in two subgroups. And according to the gene domain structure, these genes were classified into typical MsIAA and atypical MsIAA. Gene structure analysis showed that the MsIAA genes contained 1-4 related motifs, and except for the third chromosome without MsIAAs, they were all located on 7 chromosomes. The gene duplication analysis revealed that segmental duplication and tandem duplication greatly affected the amplification of the MsIAA genes. Analysis of the Ka/Ks ratio of duplicated MsAux/IAA genes suggested purification selection pressure was high and functional differences were limited. In addition, identification and classification of promoter cis-elements elucidated that MsIAA genes contained numerous elements associated to phytohormone response and abiotic stress response. The prediction protein-protein interaction network showed that there was a complex interaction between the MsAux/IAA genes. Gene expression profiles were tissue-specific, and MsAux/IAA had a broad response to both common abiotic stress (ABA, salt, drought and cold) and heavy metal stress (Al and Pb). Furthermore, the expression patterns analysis of 41 Aux/IAA genes by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Aux/IAA genes can act as positive or negative factors to regulate the drought resistance in alfalfa. CONCLUSION: This study provides useful information for the alfalfa auxin signaling gene families and candidate evidence for further investigation on the role of Aux/IAA under drought stress. Future studies could further elucidate the functional mechanism of the MsIAA genes response to drought stress.

Genome-wide identification of B-box zinc finger (BBX) gene family in Medicago sativa and their roles in abiotic stress responses.

BACKGROUND: B-box (BBX) family is a class of zinc finger transcription factors (TFs) that play essential roles in regulating plant growth, development, as well as abiotic stress. However, no systematic analysis of BBX genes has yet been conducted in alfalfa (Medica go sativa L.), and their functions have not been elucidated up to now. RESULTS: In this study, 28 MsBBX genes were identified from the alfalfa genome, which were clustered into 4 subfamilies according to an evolutionary tree of BBX proteins. Exon-intron structure and conserved motif analysis reflected the evolutionary conservation of MsBBXs in alfalfa. Collinearity analysis showed that segmental duplication promoted the expansion of the MsBBX family. Analysis of cis-regulatory elements suggested that the MsBBX genes possessed many growth/development-, light-, phytohormone-, and abiotic stress-related elements. MsBBX genes were differentially expressed in leaves, flowers, pre-elongated stems, elongated stems, roots and nodules, and most MsBBXs were remarkably induced by drought, salt and various plant growth regulators (ABA, JA, and SA). Further functional verification demonstrated that overexpressing of the MsBBX11 gene clearly promoted salt tolerance in transgenic Arabidopsis by regulating growth and physiological processes of seedlings. CONCLUSIONS: This research provides insights into further functional research and regulatory mechanisms of MsBBX family genes under abiotic stress of alfalfa.

Integrated analysis of DNA methylome and transcriptome revealing epigenetic regulation of CRIR1-promoted cold tolerance.

BACKGROUND: DNA methylation contributes to the epigenetic regulation of nuclear gene expression, and is associated with plant growth, development, and stress responses. Compelling evidence has emerged that long non-coding RNA (lncRNA) regulates DNA methylation. Previous genetic and physiological evidence indicates that lncRNA-CRIR1 plays a positive role in the responses of cassava plants to cold stress. However, it is unclear whether global DNA methylation changes with CRIR1-promoted cold tolerance. RESULTS: In this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance. CONCLUSIONS: In summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.

Three-Month Symptom Profiles Among Symptomatic Adults With Positive and Negative Severe Acute Respiratory Syndrome Coronavirus 2 Tests: A Prospective Cohort Study From the INSPIRE Group.

BACKGROUND: Long-term symptoms following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are a major concern, yet their prevalence is poorly understood. METHODS: We conducted a prospective cohort study comparing adults with SARS-CoV-2 infection (coronavirus disease-positive [COVID+]) with adults who tested negative (COVID-), enrolled within 28 days of a Food and Drug Administration (FDA)-approved SARS-CoV-2 test result for active symptoms. Sociodemographic characteristics, symptoms of SARS-CoV-2 infection (assessed with the Centers for Disease Control and Prevention [CDC] Person Under Investigation Symptom List), and symptoms of post-infectious syndromes (ie, fatigue, sleep quality, muscle/joint pains, unrefreshing sleep, and dizziness/fainting, assessed with CDC Short Symptom Screener for myalgic encephalomyelitis/chronic fatigue syndrome) were assessed at baseline and 3 months via electronic surveys sent via text or email. RESULTS: Among the first 1000 participants, 722 were COVID+ and 278 were COVID-. Mean age was 41.5 (SD 15.2); 66.3% were female, 13.4% were Black, and 15.3% were Hispanic. At baseline, SARS-CoV-2 symptoms were more common in the COVID+ group than the COVID- group. At 3 months, SARS-CoV-2 symptoms declined in both groups, although were more prevalent in the COVID+ group: upper respiratory symptoms/head/eyes/ears/nose/throat (HEENT; 37.3% vs 20.9%), constitutional (28.8% vs 19.4%), musculoskeletal (19.5% vs 14.7%), pulmonary (17.6% vs 12.2%), cardiovascular (10.0% vs 7.2%), and gastrointestinal (8.7% vs 8.3%); only 50.2% and 73.3% reported no symptoms at all. Symptoms of post-infectious syndromes were similarly prevalent among the COVID+ and COVID- groups at 3 months. CONCLUSIONS: Approximately half of COVID+ participants, as compared with one-quarter of COVID- participants, had at least 1 SARS-CoV-2 symptom at 3 months, highlighting the need for future work to distinguish long COVID. CLINICAL TRIALS REGISTRATION: NCT04610515.

Biological function research of Fusarium oxysporum f. sp. cubense inducible banana long noncoding RNA Malnc2310 in Arabidopsis.

Long noncoding RNAs (lncRNAs) participate in plant biological processes under biotic and abiotic stresses. However, little is known about the function and regulation mechanism of lncRNAs related to the pathogen at a molecular level. A banana lncRNA, Malnc2310, is a Fusarium oxysporum f. sp. cubense inducible lncRNA in roots. In this study, we demonstrate the nuclear localization of Malnc2310 by fluorescence in situ hybridization and it can bind to several proteins that are related to flavonoid pathway, pathogen response and programmed cell death. Overexpression of Malnc2310 increases susceptibility to Fusarium crude extract (Fu), salinity, and cold in transgenic Arabidopsis. In addition, Malnc2310 transgenic Arabidopsis accumulated more anthocyanins under Fusarium crude extract and cold treatments that are related to upregulation of these genes involved in anthocyanin biosynthesis. Based on our findings, we propose that Malnc2310 may participate in flavonoid metabolism in plants under stress. Furthermore, phenylalanine ammonia lyase (PAL) protein expression was enhanced in Malnc2310 overexpressed transgenic Arabidopsis, and Malnc2310 may participate in PAL regulation by binding to it. This study provides new insights into the role of Malnc2310 in mediating plant stress adaptation.

Genome-Wide Survey of the RWP-RK Gene Family in Cassava (Manihot esculenta Crantz) and Functional Analysis.

The plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tropical crop. Herein, 13 RWP-RK proteins identified in cassava were unevenly distributed across 9 of the 18 chromosomes (Chr), and these proteins were divided into two clusters based on their phylogenetic distance. The NLP subfamily contained seven cassava proteins including GAF, RWP-RK, and PB1 domains; the RKD subfamily contained six cassava proteins including the RWP-RK domain. Genes of the NLP subfamily had a longer sequence and more introns than the RKD subfamily. A large number of hormone- and stress-related cis-acting elements were found in the analysis of RWP-RK promoters. Real-time quantitative PCR revealed that all MeNLP1-7 and MeRKD1/3/5 genes responded to different abiotic stressors (water deficit, cold temperature, mannitol, polyethylene glycol, NaCl, and H2O2), hormonal treatments (abscisic acid and methyl jasmonate), and nitrogen starvation. MeNLP3/4/5/6/7 and MeRKD3/5, which can quickly and efficiently respond to different stresses, were found to be important candidate genes for further functional assays in cassava. The MeRKD5 and MeNLP6 proteins were localized to the cell nucleus in tobacco leaf. Five and one candidate proteins interacting with MeRKD5 and MeNLP6, respectively, were screened from the cassava nitrogen starvation library, including agamous-like mads-box protein AGL14, metallothionein 2, Zine finger FYVE domain containing protein, glyceraldehyde-3-phosphate dehydrogenase, E3 Ubiquitin-protein ligase HUWE1, and PPR repeat family protein. These results provided a solid basis to understand abiotic stress responses and signal transduction mediated by RWP-RK genes in cassava.

Global identification of full-length cassava lncRNAs unveils the role of cold-responsive intergenic lncRNA 1 in cold stress response.

Long noncoding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified a total of 3004 lncRNAs in cassava under normal or cold-treated conditions from Iso-seq data. We further characterized a cold-responsive intergenic lncRNA 1 (CRIR1) as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Ectopic expression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulated a range of cold stress-related genes in a CBF-independent pathway. We further found that CRIR1 RNA can interact with cassava cold shock protein 5 (MeCSP5), which acts as an RNA chaperone, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of messenger RNA. In summary, our study extends the repertoire of lncRNAs in plants as well as their role in cold stress responses. Moreover, it reveals a mechanism by which CRIR1 affected cold stress response by modulating the expression of stress-responsive genes and increasing their translational yield.

MeSPL9 attenuates drought resistance by regulating JA signaling and protectant metabolite contents in cassava.

KEY MESSAGE: Analysis of drought-related genes in cassava shows the involvement of MeSPL9 in drought stress tolerance and overexpression of a dominant-negative form of this gene demonstrates its negative roles in drought stress resistance. Drought stress severely impairs crop yield and is considered a primary threat to food security worldwide. Although the SQUAMOSA promoter binding protein-like 9 (SPL9) gene participates extensively in numerous developmental processes and in plant response to abiotic stimuli, its role and regulatory pathway in cassava (Manihot esculenta) response to the drought condition remain elusive. In the current study, we show that cassava SPL9 (MeSPL9) plays negative roles in drought stress resistance. MeSPL9 expression was strongly repressed by drought treatment. Overexpression of a dominant-negative form of miR156-resistant MeSPL9, rMeSPL9-SRDX, in which a 12-amino acid repressor sequence was fused to rMeSPL9 at the C terminus, conferred drought tolerance without penalizing overall growth. rMeSPL9-SRDX-overexpressing lines not only exhibited increased osmoprotectant metabolites including proline and anthocyanin, but also accumulated more endogenous jasmonic acid (JA) and soluble sugars. Transcriptomic and real-time PCR analysis suggested that differentially expressed genes were involved in sugar or JA biosynthesis, signaling, and metabolism in transgenic cassava under drought conditions. Exogenous application of JA further confirmed that JA conferred improved drought resistance and promoted stomatal closure in cassava leaves. Taken together, our findings suggest that MeSPL9 affects drought resistance by modulating protectant metabolite levels and JA signaling, which have substantial implications for engineering drought tolerant crops.

pH-responsive nonwoven fabric with reversibly wettability for controllable oil-water separation and heavy metal removal.

Removal of organic solvents and heavy metals in effluents is of great significance to environmental pollution control and ecological civilization construction. pH-responsive materials have unique advantages in treating complicated oily wastewater. In this work, an intelligent pH-responsive nonwoven fabric with excellent reversible wettability was prepared. The pH-sensitive polymer was synthesized by free radical polymerization (FRP) technique, then dipped with SiO2 on PP fabric. The particular molecular structure of poly (dimethylaminoethyl methacrylate) (PDMAEMA) enabled the fabric surface to switch wettability rapidly between hydrophilic/underwater oleophobic and oleophobic/hydrophobic under pH stimulus and exhibit controllable selective separation of various oil/water mixtures. Furthermore, the fabric removed Pb2+ efficiently under a wide pH range. The experimetal results showed that the separation flux reached 19,229 ± 1656.43 L-h-1-m-2 for water and 19,342 ± 1796.77 L-m-2-h-1 for n-hexane. Besides, the obtained fabric effectively realized the separation and collection process of complex ternary mixtures. The fabric removed Pb2+ in solutions with efficiency up to 90.83%. After immersing in acid and alkali solutions for 24 h, no significant damage to the surface wettability. This economical and intelligent fabric is able to meet the different separation purposes of industrial wastewaters with complex compositions.

Natural variation MeMYB108 associated with tolerance to stress-induced leaf abscission linked to enhanced protection against reactive oxygen species in cassava.

KEY MESSAGE: Natural variation of the MeMYB108 exon was associated with reactive oxygen scavengers led to alleviate leaf abscission under drought in cassava. The reactive oxygen scavengers play important roles in regulating the cassava (Manihot esculenta Crantz) leaf abscission induced by stresses. To date, the relationship between natural variations of MYB genes and reactive oxygen scavengers under drought in cassava genotypes remains unclear. Here, we reported the transcription factor MeMYB108 played an important role in regulating leaf abscission exposed to drought in cassava. The expression levels of MeMYB108 in abscission zones of cassava leaf pulvinus were higher in cassava genotype SC124, which were less easy to shed leaves under stress than cassava genotype SC8 when the leaf abscission induced by the same drought condition. Compared with wild type and interference expression plants, overexpression of MeMYB108 significantly reduced the drought-induced leaf abscission rate under drought. The consecutively 2-year analysis of reactive oxygen scavengers showed significant differences among different cassava genotypes under drought-induced leaf abscission, indicating the relevance between reactive oxygen scavengers and leaf abscission. Correlation analysis revealed the natural variation of the MeMYB108 exon was associated with reactive oxygen scavengers during drought-induced leaf abscission. Association analysis between pairwise LD of DNA polymorphism indicated the MeMYB108 allele enhanced the tolerance of cassava to drought-induced leaf abscission. Complementation transgenic lines containing the elite allele of MeMYB108 SC124 decreased the leaf abscission rate induced by drought conditions, demonstrating natural variation in MeMYB108 contributed to leaf abscission tolerance induced by drought in cassava. Further studies showed MeMYB108 played an active role in the tolerance of cassava to drought-induced leaf abscission by inducing scavenging of reactive oxygen species.

Analysis of genetic and environmental correlation between leisure activities and cognitive function in aging Chinese twins.

OBJECTIVE: Leisure activity has been shown to be beneficial to mental health and cognitive aging. The biological basis of the correlation is, however, poorly understood. This study aimed at exploring the genetic and environmental impacts on correlation between leisure activities and cognitive function in the Chinese middle- and old-aged twins. METHODS: Cognition measured using a screening test (Montreal Cognitive Assessment, MoCA) and leisure activities including intellectual and social activity were investigated on 379 complete twin pairs of middle- and old-aged twins. Univariate and bivariate twin models were fitted to estimate the genetic and environmental components in their variance and covariance. RESULTS: Moderate heritability was estimated for leisure activities and cognition (0.44-0.53) but insignificant for social activity. Common environmental factors accounted for about 0.36 of the total variance to social activity with no significant contribution to leisure activity, intellectual activity and cognition. Unique environmental factors displayed moderate contributions (0.47-0.64) to leisure activities and cognition. Bivariate analysis showed highly and positively genetic correlations between leisure activities and cognition (rG=0.80-0.96). Besides, intellectual activity and cognition presented low but significant unique environmental correlation (rE=0.12). CONCLUSIONS: Genetic factor had the moderate contribution to leisure activities and cognition. Cognitive function was highly genetically related to leisure activities. Intellectual activity and cognitive function may share some unique environmental basis.

Differential regulation of the DNA methylome in adults born during the Great Chinese Famine in 1959-1961.

BACKGROUND: Extensive epidemiological studies have established the association between exposure to early-life adversity and health status and diseases in adults. Epigenetic regulation is considered as a key mediator for this phenomenon but analysis on humans is sparse. The Great Chinese Famine lasting from 1958 to 1961 is a natural string of disasters offering a precious opportunity for elucidating the underlying epigenetic mechanism of the long-term effect of early adversity. METHODS: Using a high-throughput array platform for DNA methylome profiling, we conducted a case-control epigenome-wide association study on early-life exposure to Chinese famine in 79 adults born during 1959-1961 and compared to 105 unexposed subjects born 1963-1964. RESULTS: The single CpG site analysis of whole epigenome revealed a predominant pattern of decreased DNA methylation levels associated with fetal exposure to famine. Four CpG sites were detected with p < 1e-06 (linked to EHMT1, CNR1, UBXN7 and ESM1 genes), 16 CpGs detected with 1e-06 < p < 1e-05 and 157 CpGs with 1e-05 < p < 1e-04, with a predominant pattern of hypomethylation. Functional annotation to genes and their enriched biological pathways mainly involved neurodevelopment, neuropsychological disorders and metabolism. Multiple sites analysis detected two top-rank differentially methylated regions harboring RNF39 on chromosome 6 and PTPRN2 on chromosome 7, both showing epigenetic association with stress-related conditions. CONCLUSION: Early-life exposure to famine could mediate DNA methylation regulations that persist into adulthood with broad impacts in the activities of genes and biological pathways. Results from this study provide new clues to the epigenetic embedding of early-life adversity and its impacts on adult health.

EWASex: an efficient R-package to predict sex in epigenome-wide association studies.

SUMMARY: Epigenome-Wide Association Study (EWAS) has become a powerful approach to identify epigenetic variations associated with diseases or health traits. Sex is an important variable to include in EWAS to ensure unbiased data processing and statistical analysis. We introduce the R-package EWASex, which allows for fast and highly accurate sex-estimation using DNA methylation data on a small set of CpG sites located on the X-chromosome under stable X-chromosome inactivation in females. RESULTS: We demonstrate that EWASex outperforms the current state of the art tools by using different EWAS datasets. With EWASex, we offer an efficient way to predict and to verify sex that can be easily implemented in any EWAS using blood samples or even other tissue types. It comes with pre-trained weights to work without prior sex labels and without requiring access to RAW data, which is a necessity for all currently available methods. AVAILABILITY AND IMPLEMENTATION: The EWASex R-package along with tutorials, documentation and source code are available at https://github.com/Silver-Hawk/EWASex. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Disparities in Excess Mortality Associated with COVID-19 - United States, 2020.

The COVID-19 pandemic has disproportionately affected Hispanic or Latino, non-Hispanic Black (Black), non-Hispanic American Indian or Alaska Native (AI/AN), and non-Hispanic Native Hawaiian or Other Pacific Islander (NH/PI) populations in the United States. These populations have experienced higher rates of infection and mortality compared with the non-Hispanic White (White) population (1-5) and greater excess mortality (i.e., the percentage increase in the number of persons who have died relative to the expected number of deaths for a given place and time) (6). A limitation of existing research on excess mortality among racial/ethnic minority groups has been the lack of adjustment for age and population change over time. This study assessed excess mortality incidence rates (IRs) (e.g., the number of excess deaths per 100,000 person-years) in the United States during December 29, 2019-January 2, 2021, by race/ethnicity and age group using data from the National Vital Statistics System. Among all assessed racial/ethnic groups (non-Hispanic Asian [Asian], AI/AN, Black, Hispanic, NH/PI, and White populations), excess mortality IRs were higher among persons aged ≥65 years (426.4 to 1033.5 excess deaths per 100,000 person-years) than among those aged 25-64 years (30.2 to 221.1) and those aged <25 years (-2.9 to 14.1). Among persons aged <65 years, Black and AI/AN populations had the highest excess mortality IRs. Among adults aged ≥65 years, Black and Hispanic persons experienced the highest excess mortality IRs of >1,000 excess deaths per 100,000 person-years. These findings could help guide more tailored public health messaging and mitigation efforts to reduce disparities in mortality associated with the COVID-19 pandemic in the United States,* by identifying the racial/ethnic groups and age groups with the highest excess mortality rates.

Delays in antibiotic redosing: Association with inpatient mortality and risk factors for delay.

OBJECTIVE: Although timely administration of antibiotics has an established benefit in serious bacterial infection, the majority of studies evaluating antibiotic delay focus only on the first dose. Recent evidence suggests that delays in redosing may also be associated with worse clinical outcome. In light of the increasing burden of boarding in Emergency Departments (ED) and subsequent need to redose antibiotic in the ED, we examined the association between delayed second antibiotic dose administration and mortality among patients admitted from the ED with a broad array of infections and characterized risk factors associated with delayed second dose administration. METHODS: We performed a retrospective cohort study of patients admitted through five EDs in a single healthcare system from 1/2018 through 12/2018. Our study included all patients, aged 18 years or older, who received two intravenous antibiotic doses within a 30-h period, with the first dose administered in the ED. Patients with end stage renal disease, cirrhosis and extremes of weight were excluded due to a lack of consensus on antibiotic dosing intervals for these populations. Delay was defined as administration of the second dose at a time-point greater than 125% of the recommended interval. The primary outcome was in-hospital mortality. RESULTS: A total of 5605 second antibiotic doses, occurring during 4904 visits, met study criteria. Delayed administration of the second dose occurred during 21.1% of visits. After adjustment for patient characteristics, delayed second dose administration was associated with increased odds of in-hospital mortality (OR 1.50, 95%CI 1.05-2.13). Regarding risk factors for delay, every one-hour increase in allowable compliance time was associated with a 18% decrease in odds of delay (OR 0.82 95%CI 0.75-0.88). Other risk factors for delay included ED boarding more than 4 h (OR 1.47, 95%CI 1.27-1.71) or a high acuity presentation as defined by emergency severity index (ESI) (OR 1.54, 95%CI 1.30-1.81 for ESI 1-2 versus 3-5). CONCLUSIONS: Delays in second antibiotic dose administration were frequent in the ED and early hospital course, and were associated with increased odds of in-hospital mortality. Several risk factors associated with delays in second dose administration, including ED boarding, were identified.

Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing.

Alternative splicing is an essential post-transcriptional regulatory mechanism that can impact mRNA stability and protein diversity of eukaryotic genomes. Although numerous forms of stress-responsive alternative splicing have been identified in model plants, a large-scale study of alternative splicing dynamics under abiotic stress conditions in cassava has not been conducted. Here, we report the parallel employment of isoform-Seq, ssRNA-Seq, and Degradome-Seq to investigate the diversity, abundance, and fate of alternatively spliced isoforms in response to cold and drought stress. We identified 38 164 alternative splicing events, among which 3292 and 1025 events were significantly regulated by cold and drought stress, respectively. Intron retention was the most abundant subtype of alternative splicing. Global analysis of splicing regulators revealed that the number of their alternatively spliced isoforms and the corresponding abundance were specifically modulated by cold stress. We found that 58.5% of cold-regulated alternative splicing events introduced a premature termination codon into the transcripts, and 77.6% of differential alternative splicing events were detected by Degradome-Seq. Our data reveal that cold intensely affects both quantitative and qualitative aspects of gene expression via alternative splicing pathways, and advances our understanding of the high complexity and specificity of gene regulation in response to abiotic stresses. Alternative splicing is responsible for reprogramming of the transcriptome and the sensitivity of cassava plants to cold.

Timely estimation of National Admission, readmission, and observation-stay rates in medicare patients with acute myocardial infarction, heart failure, or pneumonia using near real-time claims data.

BACKGROUND: To estimate, prior to finalization of claims, the national monthly numbers of admissions and rates of 30-day readmissions and post-discharge observation-stays for Medicare fee-for-service beneficiaries hospitalized with acute myocardial infarction (AMI), heart failure (HF), or pneumonia. METHODS: The centers for Medicare & Medicaid Services (CMS) Integrated Data Repository, including the Medicare beneficiary enrollment database, was accessed in June 2015, February 2017, and February 2018. We evaluated patterns of delay in Medicare claims accrual, and used incomplete, non-final claims data to develop and validate models for real-time estimation of admissions, readmissions, and observation stays. RESULTS: These real-time reporting models accurately estimate, within 2 months from admission, the monthly numbers of admissions, 30-day readmission and observation-stay rates for patients with AMI, HF, or pneumonia. CONCLUSIONS: This work will allow CMS to track the impact of policy decisions in real time and enable hospitals to better monitor their performance nationally.

Variation of the Vaginal Lactobacillus Microbiome in Cytolytic Vaginosis.

OBJECTIVE: This pilot study aimed to evaluate whether different microbial compositions cause symptoms in patients with Lactobacillus overgrowth and to investigate the variation in Lactobacillus microbiome in cytolytic vaginosis (CV). MATERIALS AND METHODS: Lactobacillus species were identified from the vaginal fluid of 70 healthy women and 79 patients with CV using molecular analysis of the 16S rRNA gene. χ and Fisher exact tests were used to compare the isolated rates of Lactobacillus species between the 2 groups. The capabilities of dominant Lactobacillus strain to produce acid in the 2 groups were analyzed by repeated measures analysis of variance. RESULTS: The isolation of 2 or more Lactobacillus species per vaginal sampling was significantly less common in the CV group (1.3%) compared with the healthy control (HC) group 12.2% (p = .013). Significant differences in Lactobacillus species were observed between the 2 groups (p < .001). Lactobacillus crispatus was more often found in the CV group (88.7%) than in the HC group (56.4%, p < .001). Compared with that in the HC group, the dominant L. crispatus strain in the CV group tended to produce more acid. CONCLUSIONS: The CV group carried a less diverse Lactobacillus species, vaginally. Lactobacillus crispatus was common to both CV and HC groups but demonstrated enhanced acid-producing capability in the CV group. The pathogenesis of CV may be based, in part, on an overgrowth of L. crispatus with enhanced acid-producing capability.

[Gene variant analysis of a fetus with autosomal recessive polycystic kidney disease].

OBJECTIVE: To explore the genetic basis for a fetus with autosomal recessive polycystic kidney disease (ARPKD). METHODS: Fetal tissue and peripheral blood samples were respectively obtained from the abortus and the couple. Following extraction of genomic DNA, genetic testing was carried out. RESULTS: The fetus was found to carry compound heterozygous variants of the PKHD1 gene, namely c.5336A>T (p.N1779I) and c.9455delA (p.N3152Tfs*10), which were respectively inherited from the husband and wife. CONCLUSION: The c.5336A>T and c.9455delA variants of the PKHD1 gene probably account for the ARPKD in the fetus. Above results have enabled genetic counseling and prenatal diagnosis for the couple.

Dual species transcript profiling during the interaction between banana (Musa acuminata) and the fungal pathogen Fusarium oxysporum f. sp. cubense.

BACKGROUND: Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneously assess the transcriptomes of pathogen and host. This method greatly helps to understand the responses of pathogen and host to each other and discover the potential pathogenic mechanism. RESULTS: Plantlets of two economically important banana cultivars, Foc TR4 less susceptible cultivar NK and susceptible cultivar BX, were used to research the Foc-banana interaction mechanism. Notably, the infected NK had more significantly up-regulated genes on the respiration machinery including TCA cycle, glyoxylate, glycerol, and glycolysis compared to BX at 27 h post inoculation (hpi). In addition, genes involved in plant-pathogen interaction, starch, sucrose, linolenic acid and sphingolipid metabolisms were uniquely more greatly induced in BX than those in NK during the whole infection. Genes related to the biosynthesis and metabolism of SA and JA were greatly induced in the infected NK; while auxin and abscisic acid metabolisms related genes were strongly stimulated in the infected BX at 27 hpi. Furthermore, most of fungal genes were more highly expressed in the roots of BX than in those of NK. The fungal genes related to pathogenicity, pectin and chitin metabolism, reactive oxygen scavenging played the important roles during the infection of Foc. CCP1 (cytochrome c peroxidase 1) was verified to involve in cellulose utilization, oxidative stress response and pathogenicity of fungus. CONCLUSION: The transcriptome indicated that NK had much faster defense response against Foc TR4 than BX and the expression levels of fungal genes were higher in BX than those in NK. The metabolisms of carbon, nitrogen, and signal transduction molecular were differentially involved in pathogen infection in BX and NK. Additionally, the putative virulence associated fungal genes involved in colonization, nutrition acquirement and transport provided more insights into the infection process of Foc TR4 in banana roots.