Combined genome and transcriptome analysis of elite fiber quality in Gossypium barbadense.

Gossypium barbadense, which is one of several species of cotton, is well-known for its superior fiber quality. However, the genetic basis of its high-quality fiber remains largely unexplored. Here, we re-sequenced 269 G. barbadense accessions. Phylogenetic structure analysis showed that the set of accessions were clustered into three groups, G1 and G2 mainly included modern cultivars from Xinjiang, China, and G3 was related to widely introduced accessions in different regions worldwide. A genome-wide association study of five fiber quality traits across multiple field environments identified a total of 512 qtls (main effect QTLs) and 94 qtlEs (QTL-by-environment interactions) related to fiber quality, of which 292 qtls and 57 qtlEs co-located with previous studies. We extracted the genes located in these loci and performed expression comparison, local association analysis, and introgression segment identification. The results showed that high expression of hormone-related genes during fiber development, introgressions from G. hirsutum, and the recombination of domesticated elite allelic variation, were three major contributors to improve fiber quality of G. barbadense. In total, 839 candidate genes with encoding region variation associated with elite fiber quality were mined. We confirmed that haplotype GB_D03G0092H traced from G. hirsutum introgression, with a 1-bp deletion leading to a frameshift mutation compared with GB_D03G0092B, significantly improved fiber quality. GB_D03G0092H localized in the plasma membrane, while GB_D03G0092B in both the nucleus and plasma membrane. Overexpression of GB_D03G0092H in Arabidopsis (Arabidopsis thaliana) significantly improved the elongation of longitudinal cells. Our study systematically reveals the genetic basis of the superior fiber quality of G. barbadense and provides elite segments and gene resources for breeding high-quality cotton cultivars.

Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola.

The RNA-targeting type VI CRISPR-Cas effector complexes are widely used in biotechnology applications such as gene knockdown, RNA editing, and molecular diagnostics. Compared with Cas13a from mesophilic organisms, a newly discovered Cas13a from thermophilic bacteria Thermoclostridium caenicola (TccCas13a) shows low sequence similarity, high thermostability, and lacks pre-crRNA processing activity. The thermostability of TccCas13a has been harnessed to make a sensitive and robust tool for nucleic acid detection. Here we present the structures of TccCas13a-crRNA binary complex at 2.8 Å, and TccCas13a at 3.5 Å. Although TccCas13a shares a similarly bilobed architecture with other mesophilic organism-derived Cas13a proteins, TccCas13a displayed distinct structure features. Specifically, it holds a long crRNA 5'-flank, forming extensive polar contacts with Helical-1 and HEPN2 domains. The detailed analysis of the interaction between crRNA 5'-flank and TccCas13a suggested lack of suitable nucleophile to attack the 2'-OH of crRNA 5'-flank may explain why TccCas13a fails to cleave pre-crRNA. The stem-loop segment of crRNA spacer toggles between double-stranded and single-stranded conformational states, suggesting a potential safeguard mechanism for target recognition. Superimposition of the structures of TccCas13a and TccCas13a-crRNA revealed several conformational changes required for crRNA loading, including dramatic movement of Helical-2 domain. Collectively, these structural insights expand our understanding into type VI CRISPR-Cas effectors, and would facilitate the development of TccCas13a-based applications.

Effects of Osimertinib Combined With Pulmonary Rehabilitation and Health Care Training on Pulmonary Function, Complications, and Quality of Life in Patients After Radical Resection of Lung Cancer.

Objective: To explore the effects of osimertinib combined with pulmonary rehabilitation and health care training on pulmonary function, complications, and the quality of life (QOL) in patients after radical resection of lung cancer. Methods: The data of 120 patients with radical resection of lung cancer admitted to The First Affiliated Hospital of Zhengzhou University from February 2020 to February 2021 were retrospectively analyzed. According to the order of admission, they were equally divided into group p and group q. All patients were given pulmonary rehabilitation and health care training, and group p was treated with osimertinib, while group q received the treatment of pemetrexed combined with cisplatin. The pulmonary function, the incidence of complications, and QOL between the two groups were compared. Results: Compared with group q, the pulmonary function was higher (P < 0.001), the incidence of complications was significantly lower (P < 0.05), and QOL scores were markedly higher in group p after treatment (P < 0.001). Conclusion: The combination of osimertinib and pulmonary rehabilitation and health care training can improve the pulmonary function of patients with non-small cell lung cancer (NSCLC) with radical resection of lung cancer, and reduce their postoperative morbidity, thereby improving their QOL, which is conducive to reducing the patient's and society's medical burden.

Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance.

Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.

A Calmodulin-Like Gene (GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense.

Sea Island cotton (Gossypium barbadense) is world-renowned for its superior natural fiber. Although fiber strength is one of the most important fiber quality traits, genes contributing to fiber strength are poorly understood. Production of sea island cotton also is inextricably linked to improving its relatively low yield, thus enhancing the importance of joint improvement of both fiber quality and yield. We used genomic variation to uncover the genetic evidence of trait improvement resulting from pedigree breeding of Sea Island cotton. This pedigree was aimed at improving fiber strength and yielded an elite cultivar, XH35. Using a combination of genome-wide association study (GWAS) and selection screens, we detected 82 putative fiber-strength-related genes. Expression analysis confirmed a calmodulin-like gene, GbCML7, which enhanced fiber strength in a specific haplotype. This gene is a major-effect gene, which interacts with a minor-effect gene, GbTUA3, facilitating the enhancement of fiber strength in a synergistic fashion. Moreover, GbCML7 participates in the cooperative improvement of fiber strength, fiber length, and fiber uniformity, though a slight compromise exists between the first two of these traits and the latter. Importantly, GbCML7 is shown to boost yield in some backgrounds by increasing multiple yield components to varying degrees, especially boll number. Our work provides valuable genomic evidence and a key genetic factor for the joint improvement of fiber quality and yield in Sea Island cotton.

Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense).

BACKGROUND: Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton. RESULTS: In this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in "cellular and biological process". In addition, "xylem development" and "response to hormone" pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality. CONCLUSIONS: The present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.

Crosstalk between cytokinin and ethylene signaling pathways regulates leaf abscission in cotton in response to chemical defoliants.

Abscission is a process that allows plants to shed tissues or organs via cell separation, and occurs throughout the life cycle. Removal of leaves through the use of chemical defoliants is very important for mechanical harvesting of cotton (Gossypium hirsutum). However, our knowledge of the molecular mechanisms of the defoliation response involved is limited. In this study, RNA-seq was conducted in order to profile the differentially expressed genes (DEGs) between cultivars X50 (sensitive to chemical defoliants) and X33 (relatively insensitive) at different time points after treatment with thidiazuron and ethephon (TE). A total of 2434 DEGs were identified between the two cultivars across the different time-points. Functional categories according to GO and KEGG analyses revealed that plant hormone signal transduction and zeatin biosynthesis were involved in the response to TE. Cytokinin oxidase/dehydrogenase (CKX) genes and ethylene-related genes were up-regulated following TE treatment, and were associated with increased level of ethylene, especially in cultivar X50. Down-regulation of GhCKX3 resulted in delayed defoliation and a reduced ethylene response. The results show that crosstalk between cytokinin and ethylene regulates cotton defoliation, and provide new insights into the molecular mechanisms underlying the mode of action of defoliants in cotton.

The Development of Biologically Important Spirooxindoles as New Antimicrobial Agents.

BACKGROUND: Antibiotic resistance is one of the biggest threats to global health today, leading to higher medical costs and increased mortality. Because of the emergence and rapid spread of new resistance mechanisms globally, a growing number of infections are becoming harder to treat as the antibiotics used to treat them become less effective. Therefore, the development of new effective antimicrobial agents is still urgently needed. In last decades, a large number of structurally novel spirooxindoles have been synthesized mainly based on the ylide intermediates generated in situ and further assessed for their antimicrobial activity against different types of bacteria, leading to the discovery of some potent lead compounds with antimicrobial potentials. OBJECTIVE: The aim of this review to submarize recent advances on the synthesis, structure- activity relationship studies (SARs) and antimicrobial activity of spirooxindoles. METHODS: Peer-reviewed research work on spirooxindoles with antimicrobial activity were downloaded from bibliographic databases and analyzed based on their chemoptypes. RESULTS: 50 papers were retrieved from the literature databases, of which 20 papers described the synthesis and antimicrobial activity of spirooxindoles. CONCLUSION: This review highlights the importance of spirooxindoles as potential antimicrobial agents. The antimicrobial activity of spirooxindoles against different types of bacteria is less studied, mainly centering on primary antimicrobial assessment, some of these compounds have showed interesting antimicrobial activity. However, the current study is only limited to primary antimicrobial assessment, no detailed modes of action are investigated.

Ambient fine particles (PM2.5 ) attenuate collagen-induced platelet activation through interference of the PLCγ2/Akt/GSK3ß signaling pathway.

AIMS: It has been proven that carbon nanoparticles or diesel exhaust particles stimulate platelet activation. However, the effect of fine particle matter (PM2.5 ) on platelet activation remains unknown, which motivates this study. METHODS: PM2.5 samples were collected in an urban area of Zhengzhou, China. To study the morphological characteristics and the mass concentrations of trace elements of PM2.5 samples, a filed-emission scanning electron microscope, the Image-J software, and an inductively coupled plasma mass spectrometry were used. Washed human platelets or platelet-rich-plasma were used to study the effect of PM2.5 on platelet aggregation, P-selectin expression, or platelet signaling pathways. The cytotoxicity in platelets exposed to PM2.5 was evaluated by a lactate dehydrogenase assay kit. In addition, platelet adhesion and spreading were studied on collagen-coated surfaces in stable conditions. RESULTS: The filed-emission scanning electron microscope scanning showed that PM2.5 samples varied in shape and size distributions. The mean equivalent spherical diameter of these particles was 1.97 ± 0.04 µm, of which 82.40% were particles with equivalent spherical diameters of less than 2.5 µm. The mass concentration of Ca was higher than that of other elements. The other elements followed the trend of Al>Fe>Zn>Mg>Pb>K>Mn>Cu>Ti>Ba>As>Sr>Sn>Sb>Cd>B>Se>Mo>Ag>Ni>TI>V>Co. Furthermore, pretreatment of PM2.5 significantly inhibited rather than potentiated collagen-induced platelet aggregation and P-selectin expression, whereas it had no significant effect on ADP-induced platelet aggregation and P-selectin expression. The lactate dehydrogenase analysis showed trivial cytotoxic effect of PM2.5 exposure on platelets. Pretreatment of PM2.5 inhibited platelet adhesion on immobilized collagen-coated surfaces; however, it almost did not impact the platelet spreading. Immunoblotting analysis indicated that PM2.5 reduced collagen-induced phosphorylation of phospholipase C gamma-2 (PLCγ2) at Tyr759, Akt at Ser473, and glycogen synthase kinase 3ß (GSK3ß) at Ser9. CONCLUSIONS: PM2.5 attenuated collagen-induced platelet aggregation, α-granule secretion and adhesion, with the potential mechanism of impairing PLCγ2, Akt, and GSK3ß signaling. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 530-540, 2017.

Diagnostic value of bronchoalveolar lavage fluid and serum tumor markers for lung cancer.

OBJECTIVE: To analyze the changes of bronchoalveolar lavage fluid (BALF) and serum tumor markers in lung cancer. MATERIALS AND METHODS: Fifty patients with lung cancer (study group) and 50 cases with benign lung lesions (control group) were selected from May, 2010 to May, 2013. The observation group included squamous cell carcinoma subgroup (n = 25), adenocarcinoma subgroup (n = 19), and small cell undifferentiated carcinoma subgroup (n = 6). The carcinoembryonic antigen (CEA), neuron-specific enolase (NSE), and cytokeratin 19 fragment (CYFRA21-1) concentration were compared; and the comparisons among subgroups were also performed. RESULTS: Three kinds of tumor markers in BALF and serum of the observation group were higher than that of the control group. NSE concentration of small.cell lung cancer was the highest, CYFRA21.1 concentration was highest in the squamous cell carcinoma, and CEA concentration was highest in the adenocarcinoma group; the former increased more significantly. CONCLUSION: BALF and serum NSE, CEA, and CYFRA21.1 elevated in lung cancer, which had prompt value for pathology, especially significant for BALF.

Investigations of the total flavonoids extracted from flowers of Abelmoschus manihot (L.) Medic against α-naphthylisothiocyanate-induced cholestatic liver injury in rats.

ETHNOPHARMACOLOGY RELEVANCE: The decoction of the flowers of Abelmoschus manihot (L.) Medic was traditionally used for the treatment of jaundice and various types of chronic and acute hepatitis in Anhui and Jiangsu Provinces of China for hundreds of years. Phytochemical studies have indicated that total flavonoids extracted from flowers of A. manihot (L.) Medic (TFA) were the major constituents of the flowers. Our previous studies have investigated the hepatoprotective effects of the TFA against carbon tetrachloride (CCl4) induced hepatocyte damage in vitro and liver injury in vivo. This study aimed to investigate the protective effects and mechanisms of TFA on α-naphthylisothiocyanate (ANIT)-induced cholestatic liver injury in rats. MATERIAL AND METHODS: The hepatoprotective activities of TFA (125, 250 and 500mg/kg) were investigated on ANIT-induced cholestatic liver injury in rats. The serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) were used as indices of hepatic cell damage and measured. Meanwhile, the serum levels of alkaline phosphatase (ALP), gamma-glutamyltransferase (GGT), total bilirubin (TBIL), direct bilirubin (DBIL), and total bile acid (TBA) were used as indices of biliary cell damage and cholestasis and evaluated. Hepatic malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), glutathione transferase (GST), tumor necrosis factor-α (TNF-α) and nitric oxide (NO) were measured in the liver homogenates. The bile flow in 4h was estimated and the histopathology of the liver tissue was evaluated. Furthermore, the expression of transporters, bile salt export pump (BSEP), multidrug resistance-associated protein 2 (MRP2), and Na(+)-taurocholate cotransporting polypeptide (NTCP) were studied by western blot and reverse transcription-quantitative real-time polymerase chain reaction (RT-PCR) to elucidate the protective mechanisms of TFA against ANIT-induced cholestasis. RESULTS: The oral administration of TFA to ANIT-treated rats could reduce the increases in serum levels of ALT, AST, LDH, ALP, GGT, TBIL, DBIL and TBA. Decreased bile flow by ANIT was restored with TFA treatment. Concurrent administration of TFA reduced the severity of polymorphonuclear neutrophil infiltration and other histological damages, which were consistent with the serological tests. Hepatic MDA and GSH contents in liver tissue were reduced, while SOD and GST activities, which had been suppressed by ANIT, were elevated in the groups pretreated with TFA. With TFA intervention, levels of TNF-α and NO in liver were decreased. Additionally, TFA was found to increase the expression of liver BSEP, MRP2, and NTCP in both protein and mRNA levels in ANIT-induced liver injury with cholestasis. CONCLUSION: TFA exerted protective effects against ANIT-induced liver injury. The possible mechanisms could be related to anti-oxidative damage, anti-inflammation and regulating the expression of hepatic transporters. It layed the foundation for the further research on the mechanisms of cholestasis as well as the therapeutic effects of A. manihot (L.) Medic for the treatment of jaundice.