Genome-Wide Functional Analysis of the Cotton Transcriptome by Creating an Integrated EST Database

A total of 28,432 unique contigs (25,371 in consensus contigs and 3,061 as singletons) were assembled from all 268,786 cotton ESTs currently available. Several in silico approaches [comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by Kyoto Encyclopedia of Genes and Genomes (KEGG)] were employed to investigate global functions of the cotton transcriptome. Cotton EST contigs were clustered into 5,461 groups with a maximum cluster size of 196 members. A total of 27,956 indel mutants and 149,616 single nucleotide polymorphisms (SNPs) were identified from consensus contigs. Interestingly, many contigs with significantly high frequencies of indels or SNPs encode transcription factors and protein kinases. In a comparison with six model plant species, cotton ESTs show the highest overall similarity to grape. A total of 87 cotton miRNAs were identified; 59 of these have not been reported previously from experimental or bioinformatics investigations. We also predicted 3,260 genes as miRNAs targets, which are associated with multiple biological functions, including stress response, metabolism, hormone signal transduction and fiber development. We identified 151 and 4,214 EST-simple sequence repeats (SSRs) from contigs and raw ESTs respectively. To make these data widely available, and to facilitate access to EST-related genetic information, we integrated our results into a comprehensive, fully downloadable web-based cotton EST database (www.leonxie.com)

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p<0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p<0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

Association of Red Blood Cell Distribution Width and Neutrophil-to-Lymphocyte Ratio with Calcification and Cardiovascular Markers in Chronic Kidney Disease

We aimed to investigate the association between Red Blood Cell Distribution Width (RDW) and Neutrophil-to-Lymphocyte Ratio (NLR), simple, rapidly assessed markers from the complete blood count with vascular calcification (VC)/stiffness and cardiovascular disease (CVD) in chronic kidney disease (CKD). Dephosphorylated, uncarboxylated matrix Gla-protein (dp-ucMGP), and central/peripheral hemodynamics' parameters were measured in 158 CKD patients, including Hemodialysis and Peritoneal Dialysis. Spearman's rho analysis showed that RDW correlated with C-reactive protein (CRP) (r = 0.29, p < 0.001), dp-ucMGP (r = 0.43, p = < 0.0001), central diastolic blood pressure (DBP) (r = -0.19, p = 0.02), and albuminuria (r = -0.17, p = 0.03). NLR correlated with the duration of CVD (r = 0.32, p < 0.001), CRP (r = 0.27, p = 0.01), dp-ucMGP (r = 0.43, p < 0.0001), central DBP (r = -0.32, p < 0.0001) and eGFR (r = -0.25, p = 0.04). In multiple regression models, circulating dp-ucMGP was an independent predictor of RDW (beta = 0.001, p = 0.001) and NLR (beta = 0.002, p = 0.002). In CKD patients, RDW and NLR are associated with traditional and novel markers of VC and CVD

In-vitro development of ovules obtained after pollination of cotton (Gossypium spp) flowers with pollen from okra (Abelmoschus esculentus L-Moench)

The in vitro response of ovules obtained after pollination of cotton flowers with pollen from Abelmoschus esculentus was studied. For this, 492 cotton flowers from five G. hirsutum varieties, four G. barbadense varieties and 10 F1 interspecific hybrids, were pollinated with pollen from A. esculentus and 5,069 ovules were cultured in vitro. From the cultured ovules, 69 embryos were isolated and 16 of them grew into plants. However, only three of them survived after transplantation. Finally, one plant which originated from the interspecific cross (B403 x Acala Sindos) x A. esculentus reached maturity. The mature plant (Pa0) had no morphological traits from A. esculentus. On the contrary, traits from both cotton species were observed. The flowcytometric analysis of the Pa0 plant indicated that it was hypoaneuploid. Root tip chromosome counts of its offsprings revealed a progressive chromosome increase from the Pa1 to Pa4 generation. Plants with 52 chromosomes or hypoaneuploids with a lower level of chromosomes (46-51) could be isolated from the Pa4 generation. These plants exhibited morphological traits from both cotton species and they were fertile. No signs of A. esculentus morphological characteristics were observed in these plants. It was concluded that aneuploid partial interspecific cotton plants could be produced after pollination of cotton interspecific hybrids with pollen from A. esculentus and application of an in-ovule embryo rescue technique

Induction of embryo development and fixation of partial interspecific lines after pollination of F-1 cotton interspecific hybrids (Gossypium barbadense x Gossypium hirsutum) with pollen from Hibiscus cannabinus

The possibility of inducing embryo development after pollination of F-1 interspecific cotton hybrids ( Gossypium barbadense x Gossypium hirsutum) and their reciprocals with pollen from Hibiscus cannabinus was investigated. For this, flowers of F-1 plants from 4 G. barbadense x G. hirsutum interspeci. c hybrids (B403 x Acala Sindos, Carnak x 4S, B403 x Coker 310, and Carnak x Acala Sindos) and their reciprocals grown in the field were pollinated with pollen from Hibiscus cannabinus. From the 443 pollinated flowers, 276 were left on the plant to grow naturally, and 167 were collected 5 days after pollination. Young ovules from the collected buds were cultured in vitro for embryo development. It was observed that, from the buds left to grow naturally on the mother plant, 21 bolls reached maturity. The mature bolls originated only from the 4 G. barbadense x G. hirsutum hybrids and contained 82 mature seeds. Finally, 38 plants (Pa0) were produced. From the in-ovule culture method, 10 young embryos were isolated from both G. barbadense x G. hirsutum and G. hirsutum x G. barbadense hybrids and finally 3 plants were produced. The plants produced from both approaches originated only from the G. barbadense x G. hirsutum hybrids. These plants exhibited morphological traits from both cotton species and they were partially fertile. No signs of H. cannabinus morphological traits were observed in the plants produced. Root-tip chromosome counts revealed that chromosome number among cells of the Pa0 plants ranged from 27 to 42 and the difference in chromosome number observed among cells of the same plant ranged from 1 to 3. The chromosome number, however, was increased progressively from generation to generation and in Pa3 it ranged from 46 to 52. Plants with 52 chromosomes were identified even from the Pa1 generation. In addition, flow cytometric analysis indicated that the parental plants had a similar DNA profile to the F-1 and F-2 interspecific hybrids but a different one from the Pa0 plants. Thus, alien pollination of cotton flowers from interspeci. c ( G. barbadense x G. hirsutum and reciprocals) hybrids with pollen from H. cannabinus most likely induced parthenogenetic (Pa) egg cell development which, after a progressive chromosome increase, produced fully fertile plants with most of the cells at the tetraploid or near-tetraploid level. It was concluded that a combination of the in situ boll development with an optimised in vitro ovule culture technique could establish the 'cannabinus method' in cotton, as a method for the production of genotype-independent partial interspecific lines