Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Alfalfa is an excellent leguminous forage crop that is widely cultivated worldwide, but its yield and quality are often affected by drought and soil salinization. Hyperosmolality-gated calcium-permeable channel (OSCA) proteins are hyperosmotic calcium ion (Ca2+) receptors that play an essential role in regulating plant growth, development, and abiotic stress responses. However, no systematic analysis of the OSCA gene family has been conducted in alfalfa. In this study, a total of 14 OSCA genes were identified from the alfalfa genome and classified into three groups based on their sequence composition and phylogenetic relationships. Gene structure, conserved motifs and functional domain prediction showed that all MsOSCA genes had the same functional domain DUF221. Cis-acting element analysis showed that MsOSCA genes had many cis-regulatory elements in response to abiotic or biotic stresses and hormones. Tissue expression pattern analysis demonstrated that the MsOSCA genes had tissue-specific expression; for example, MsOSCA12 was only expressed in roots and leaves but not in stem and petiole tissues. Furthermore, RT–qPCR results indicated that the expression of MsOSCA genes was induced by abiotic stress (drought and salt) and hormones (JA, SA, and ABA). In particular, the expression levels of MsOSCA3, MsOSCA5, MsOSCA12 and MsOSCA13 were significantly increased under drought and salt stress, and MsOSCA7, MsOSCA10, MsOSCA12 and MsOSCA13 genes exhibited significant upregulation under plant hormone treatments, indicating that these genes play a positive role in drought, salt and hormone responses. Subcellular localization results showed that the MsOSCA3 protein was localized on the plasma membrane. This study provides a basis for understanding the biological information and further functional analysis of the MsOSCA gene family and provides candidate genes for stress resistance breeding in alfalfa

Exogenous Proline Improves Salt Tolerance of Alfalfa through Modulation of Antioxidant Capacity, Ion Homeostasis, and Proline Metabolism

Alfalfa (Medicago sativa L.) is an important forage crop, and its productivity is severely affected by salt stress. Although proline is a compatible osmolyte that plays an important role in regulating plant abiotic stress resistance, the basic mechanism of proline requires further clarification regarding the effect of proline in mitigating the harmful effects of salinity. Here, we investigate the protective effects and regulatory mechanisms of proline on salt tolerance of alfalfa. The results show that exogenous proline obviously promotes seed germination and seedling growth of salt-stressed alfalfa. Salt stress results in stunted plant growth, while proline application alleviates this phenomenon by increasing photosynthetic capacity and antioxidant enzyme activities and decreasing cell membrane damage and reactive oxygen species (ROS) accumulation. Plants with proline treatment maintain a better K+/Na+ ratio by reducing Na+ accumulation and increasing K+ content under salt stress. Additionally, proline induces the expression of genes related to antioxidant biosynthesis (Cu/Zn-SOD and APX) and ion homeostasis (SOS1, HKT1, and NHX1) under salt stress conditions. Proline metabolism is mainly regulated by ornithine-δ-aminotransferase (OAT) and proline dehydrogenase (ProDH) activities and their transcription levels, with the proline-treated plants displaying an increase in proline content under salt stress. In addition, OAT activity in the ornithine (Orn) pathway rather than Δ1-pyrroline-5-carboxylate synthetase (P5CS) activity in the glutamate (Glu) pathway is strongly increased under salt stress, made evident by the sharp increase in the expression level of the OAT gene compared to P5CS1 and P5CS2. Our study provides new insight into how exogenous proline improves salt tolerance in plants and that it might be used as a significant practical strategy for cultivating salt-tolerant alfalfa

Analysis of Xpert MTB/RIF results in retested patients with very low initial bacterial loads: A retrospective study in China

Background: The Xpert MTB/RIF (Xpert) assay has been widely used to diagnose suspected active tuberculosis (TB) and rifampicin-resistant TB cases. Despite its excellent performance record, false-positive Xpert rifampicin (RIF) resistance results are obtained for specimens with extremely low bacterial loads. Objective: We aimed to study the feasibility of repeat Xpert testing as a strategy for reducing the odds of obtaining false-positive results when testing paucibacillary TB patients. Methods: We enrolled previously tested TB patients with very low initial bacterial loads from May 2016 to February 2022 for Xpert retesting. A total of 251 TB patients were retested using the Xpert assay. Results: RIF resistance was noted in 65 (25.9 %) patients when tested by Xpert at initial diagnosis. Only 107 (42.6 %) of 251 patients tested positive for MTB when retested via Xpert. The majority (98.6 %) of RIF-susceptible cases were still susceptible to RIF when retested. Initial Xpert testing yielded 35 positive results for MTB in the RIF-resistant group, of whom 25 (71.4 %) still exhibited RIF resistance when retested. All culture-positive MTB isolates in the RIF-susceptible group were also RIF-susceptible by phenotypic DST. In the RIF-resistant group, 10 of 14 culture-positive MTB isolates exhibited RIF resistance, of which 4 isolates were deemed RIF-susceptible by phenotypic DST. The proportion of double mutations within the MTB rpoB RRDR sequence, as detected by hybridization of Xpert D and E probes, was significantly higher in the RIF-susceptible group than in the RIF-susceptible group. Conclusions: Our results demonstrated that initial RIF-susceptible results were more accurate than RIF-resistant results. Additionally, patients with double mutations that delayed probe D/E hybridization were more likely to have false-positive Xpert results. Our findings emphasize that repeat Xpert MTB/RIF testing is necessary for TB patients with extremely low bacterial loads who are at high risk for RIF-resistant TB

Systemic Inflammatory Biomarkers Predict Survival of Patients Treated With Tyrosine Kinase Inhibitors for Metastatic Renal Cell Carcinoma

Objective We aimed to retrospectively investigate whether the neutrophil to lymphocyte ratio (NLR) and the monocyte to lymphocyte ratio (MLR) can predict the prognosis of patients with metastatic renal cell carcinoma (mRCC) treated with sunitinib or sorafenib. Methods We retrospectively identified 210 patients with mRCC treated with sunitinib or sorafenib from 2007 to 2017 at Fudan University- and Hexi University-affiliated hospitals. Overall survival (OS) and progression-free survival (PFS) were evaluated using the Kaplan–Meier method. Multivariate regression analysis was used to evaluate predictors of PFS and OS. Results Low NLR (<2.85) and MLR (<.30) were strongly associated with increased PFS and OS. Multivariable analyses verified that the NLR and MLR were both independent prognostic factors. Additionally, the NLR was negatively correlated with CD8 + and CD4 + T-cell infiltration in tumors. Conclusion In patients with mRCC treated with sunitinib and sorafenib, an NLR <2.85 and MLR <.30 was associated with superior PFS and OS, which may be related to the reduced lymphocytic infiltration of tumors

Table_2_Efficacy of comprehensive unit-based safety program to prevent ventilator associated-pneumonia for mechanically ventilated patients in China: A propensity-matched analysis.docx

BackgroundVentilator-associated pneumonia (VAP) is the most common healthcare-associated infection (HAI) in patients with mechanical ventilation. VAP is largely preventable, and a comprehensive unit-based safety program (CUSP) has effectively reduced HAI. In this study, we aim to comprehensively investigate the effect of implementing the CUSP in patients requiring mechanical ventilation.MethodsIn this uncontrolled before-and-after trial conducted in two intensive care unit (ICU) settings in China, patients requiring invasive mechanical ventilation were enrolled. Patients were divided into two groups based on the implementation of CUSP. The primary outcome was the incidence of VAP. The secondary outcomes were the time from intubation to VAP, days of antibiotic use for VAP treatments, rate of other infection, length of stay (LOS) in ICU, hospital LOS, and safety culture score. Joinpoint regression analysis was used to test the changes in trends of VAP rate for statistical significance. Propensity score matching (1:1 matching) was used to reduce the potential bias between CUSP and no CUSP groups. Univariate and multivariate logistic/linear regression analyses were performed to evaluate the association between the use of CUSP and clinical outcomes. This study was registered at the Chinese Clinical Trial Registry (chictr.org.cn), registration number: ChiCTR1900025391.ResultsA total of 1,004 patients from the transplant ICU (TICU) and 1,001 patients from the surgical ICU (SICU) were enrolled in the study from January 2016 to March 2022. Before propensity score matching, the incidences of VAP decreased from 35.1/1,000 ventilator days in the no CUSP group to 12.3/1,000 ventilator days in the CUSP group in the TICU setting (adjusted odds ratio [OR], 0.30; 95% confidence interval [CI], 0.15–0.59). The results of the joinpoint regression analysis confirmed that the implementation of CUSP significantly decreased the incidences of VAP. After propensity score matching in TICU setting, the CUSP group reported a lower incidence of VAP (30.4 vs. 9.7‰, P = 0.003; adjusted OR = 0.26, 95% CI: 0.10–0.76), lower wound infection (3.4 vs. 0.9%, P = 0.048; adjusted OR = 0.73, 95% CI: 0.50–0.95), shorter ICU LOS [3.5(2.3–5.3) vs. 2.5(2.0–4.5) days; P = 0.003, adjusted estimate = −0.34, 95% CI: −0.92 to −0.14], and higher safety culture score (149.40 ± 11.74 vs. 153.37 ± 9.74; P = 0.002). Similar results were also observed in the SICU setting between the no CUSP and CUSP group.ConclusionsThe implementation of CSUP for patients receiving mechanical ventilation could significantly reduce the incidences of VAP, and other infections, prolong the time until the VAP occurrence, reduces the days of antibiotic use for VAP, shorten the ICU and hospital LOS, and enhance the awareness of safety culture.</p

Table_3_Efficacy of comprehensive unit-based safety program to prevent ventilator associated-pneumonia for mechanically ventilated patients in China: A propensity-matched analysis.docx

BackgroundVentilator-associated pneumonia (VAP) is the most common healthcare-associated infection (HAI) in patients with mechanical ventilation. VAP is largely preventable, and a comprehensive unit-based safety program (CUSP) has effectively reduced HAI. In this study, we aim to comprehensively investigate the effect of implementing the CUSP in patients requiring mechanical ventilation.MethodsIn this uncontrolled before-and-after trial conducted in two intensive care unit (ICU) settings in China, patients requiring invasive mechanical ventilation were enrolled. Patients were divided into two groups based on the implementation of CUSP. The primary outcome was the incidence of VAP. The secondary outcomes were the time from intubation to VAP, days of antibiotic use for VAP treatments, rate of other infection, length of stay (LOS) in ICU, hospital LOS, and safety culture score. Joinpoint regression analysis was used to test the changes in trends of VAP rate for statistical significance. Propensity score matching (1:1 matching) was used to reduce the potential bias between CUSP and no CUSP groups. Univariate and multivariate logistic/linear regression analyses were performed to evaluate the association between the use of CUSP and clinical outcomes. This study was registered at the Chinese Clinical Trial Registry (chictr.org.cn), registration number: ChiCTR1900025391.ResultsA total of 1,004 patients from the transplant ICU (TICU) and 1,001 patients from the surgical ICU (SICU) were enrolled in the study from January 2016 to March 2022. Before propensity score matching, the incidences of VAP decreased from 35.1/1,000 ventilator days in the no CUSP group to 12.3/1,000 ventilator days in the CUSP group in the TICU setting (adjusted odds ratio [OR], 0.30; 95% confidence interval [CI], 0.15–0.59). The results of the joinpoint regression analysis confirmed that the implementation of CUSP significantly decreased the incidences of VAP. After propensity score matching in TICU setting, the CUSP group reported a lower incidence of VAP (30.4 vs. 9.7‰, P = 0.003; adjusted OR = 0.26, 95% CI: 0.10–0.76), lower wound infection (3.4 vs. 0.9%, P = 0.048; adjusted OR = 0.73, 95% CI: 0.50–0.95), shorter ICU LOS [3.5(2.3–5.3) vs. 2.5(2.0–4.5) days; P = 0.003, adjusted estimate = −0.34, 95% CI: −0.92 to −0.14], and higher safety culture score (149.40 ± 11.74 vs. 153.37 ± 9.74; P = 0.002). Similar results were also observed in the SICU setting between the no CUSP and CUSP group.ConclusionsThe implementation of CSUP for patients receiving mechanical ventilation could significantly reduce the incidences of VAP, and other infections, prolong the time until the VAP occurrence, reduces the days of antibiotic use for VAP, shorten the ICU and hospital LOS, and enhance the awareness of safety culture.</p

Table_1_Efficacy of comprehensive unit-based safety program to prevent ventilator associated-pneumonia for mechanically ventilated patients in China: A propensity-matched analysis.docx

BackgroundVentilator-associated pneumonia (VAP) is the most common healthcare-associated infection (HAI) in patients with mechanical ventilation. VAP is largely preventable, and a comprehensive unit-based safety program (CUSP) has effectively reduced HAI. In this study, we aim to comprehensively investigate the effect of implementing the CUSP in patients requiring mechanical ventilation.MethodsIn this uncontrolled before-and-after trial conducted in two intensive care unit (ICU) settings in China, patients requiring invasive mechanical ventilation were enrolled. Patients were divided into two groups based on the implementation of CUSP. The primary outcome was the incidence of VAP. The secondary outcomes were the time from intubation to VAP, days of antibiotic use for VAP treatments, rate of other infection, length of stay (LOS) in ICU, hospital LOS, and safety culture score. Joinpoint regression analysis was used to test the changes in trends of VAP rate for statistical significance. Propensity score matching (1:1 matching) was used to reduce the potential bias between CUSP and no CUSP groups. Univariate and multivariate logistic/linear regression analyses were performed to evaluate the association between the use of CUSP and clinical outcomes. This study was registered at the Chinese Clinical Trial Registry (chictr.org.cn), registration number: ChiCTR1900025391.ResultsA total of 1,004 patients from the transplant ICU (TICU) and 1,001 patients from the surgical ICU (SICU) were enrolled in the study from January 2016 to March 2022. Before propensity score matching, the incidences of VAP decreased from 35.1/1,000 ventilator days in the no CUSP group to 12.3/1,000 ventilator days in the CUSP group in the TICU setting (adjusted odds ratio [OR], 0.30; 95% confidence interval [CI], 0.15–0.59). The results of the joinpoint regression analysis confirmed that the implementation of CUSP significantly decreased the incidences of VAP. After propensity score matching in TICU setting, the CUSP group reported a lower incidence of VAP (30.4 vs. 9.7‰, P = 0.003; adjusted OR = 0.26, 95% CI: 0.10–0.76), lower wound infection (3.4 vs. 0.9%, P = 0.048; adjusted OR = 0.73, 95% CI: 0.50–0.95), shorter ICU LOS [3.5(2.3–5.3) vs. 2.5(2.0–4.5) days; P = 0.003, adjusted estimate = −0.34, 95% CI: −0.92 to −0.14], and higher safety culture score (149.40 ± 11.74 vs. 153.37 ± 9.74; P = 0.002). Similar results were also observed in the SICU setting between the no CUSP and CUSP group.ConclusionsThe implementation of CSUP for patients receiving mechanical ventilation could significantly reduce the incidences of VAP, and other infections, prolong the time until the VAP occurrence, reduces the days of antibiotic use for VAP, shorten the ICU and hospital LOS, and enhance the awareness of safety culture.</p

Genotypic Diversity Analysis of <i>Mycobacterium tuberculosis</i> Strains Collected from Beijing in 2009, Using Spoligotyping and VNTR Typing

<div><p>Background</p><p>Tuberculosis (TB) is a serious problem in China. While there have been some studies on the nationwide genotyping of <i>Mycobacterium tuberculosis</i> (<i>M. tuberculosis</i>), there has been little detailed research in Beijing, the capital of China, which has a huge population. Here, <i>M. tuberculosis</i> clinical strains collected in Beijing during 2009 were genotyped by classical methods.</p><p>Methodology/Principal Findings</p><p>Our aim was to analyze the genetic diversity of <i>M. tuberculosis</i> strains within the Beijing metropolitan area. We characterized these strains using two standard methods, spoligotyping (n = 1585) and variable number of tandem repeat (VNTR) typing (n = 1053). We found that the most prominent genotype was Beijing family genotype. Other genotypes included the MANU, T and H families etc. Spoligotyping resulted in 137 type patterns, included 101 unclustered strains and 1484 strains clustered into 36 clusters. In VNTR typing analysis, we selected 12-locus (QUB-11b, MIRU10, Mtub21, MIRU 23, MIRU39, MIRU16, MIRU40, MIRU31, Mtub24, Mtub04, MIRU20, and QUB-4156c) and named it 12-locus (BJ) VNTR. VNTR resulted in 869 type patterns, included 796 unclustered strains and 257 strains clustered into 73 clusters. It has almost equal discriminatory power to the 24-locus VNTR.</p><p>Conclusions/Significance</p><p>Our study provides a detailed characterization of the genotypic diversity of <i>M. tuberculosis</i> in Beijing. Combining spoligotyping and VNTR typing to study the genotyping of <i>M. tuberculosis</i> gave superior results than when these techniques were used separately. Our results indicated that Beijing family strains were still the most prevalent <i>M. tuberculosis</i> in Beijing. Moreover, VNTR typing analyzing of <i>M. tuberculosis</i> strains in Beijing was successfully accomplished using 12-locus (BJ) VNTR. This method used for strains genotyping from the Beijing metropolitan area was comparable. This study will not only provide TB researchers with valuable information for related studies, but also provides guidance for the prevention and control of TB in Beijing.</p></div