Analysis of the Transmission of SARS-CoV-2 Delta VOC in Yantai, China, August 2021.

Objective: Starting 31 July 2021, a SARS-CoV-2 outbreak occurred in Yantai, Shandong Province. The investigation showed that this outbreak was closely related to the epidemic at Nanjing Lukou Airport. In view of the fact that there were many people involved in this outbreak and these people had a complex activity area, the transmission route cannot be analyzed by simple epidemiological investigation. Here we combined the SARS-COV-2 whole-genome sequencing with epidemiology to determine the epidemic transmission route of Yantai. Methods: Thirteen samples of SARS-CoV-2 outbreak cases from 31 July to 4 August 2021 were collected and identified by fluorescence quantitative PCR, then whole-genome deep sequencing based on NGS was performed, and the data were analyzed and processed by biological software. Results: All sequences were over 29,000 bases in length and all belonged to B.1.617.2, which was the Delta strain. All sequences shared two amino acid deletions and 9 amino acid mutations in Spike protein compared with reference sequence NC_045512.2 (Wuhan virus strain). Compared with the sequence of Lukou Airport Delta strain, the homology was 99.99%. In order to confirm the transmission relationship between patients, we performed a phylogenetic tree analysis. The results showed that patient 1, patient 2, and patient 9 belong to an independent branch, and other patients have a close relationship. Combined with the epidemiological investigation, we speculated that the epidemic of Yantai was transmitted by two routes at the same time. Based on this information, our prevention and control work was carried out in two ways and effectively prevented the further spread of this epidemic.

Study on Influencing Factors of Frailty in Elderly Patients with Type II Diabetes.

The purpose of this study was to analyze the influencing factors of frailty in elderly patients with type II diabetes. 332 elderly patients with type II diabetes admitted to our hospital from May 2018 to December 2019 were selected as the study subjects. The degree of frailty was evaluated by the Fried fragility phenotype scale, and the general information and the clinical data of patients were collected by inquiry and questionnaire survey. After that, all the data were analyzed by SPSS 20.0. Univariate analysis showed that there were significant differences in age, medication types, dietary habits, exercise tolerance, exercise capacity, body balance, coordination ability, urinary incontinence, anxiety, etc., in elderly patients with type II diabetes who suffered from different degrees of frailty (P < 0.01). In addition, there were significant differences in the presence of coronary heart disease, heart failure, atrial fibrillation, pulmonary diseases, osteoarticular diseases, anemia, and other blood diseases of elderly patients with type II diabetes who suffered from different degrees of frailty (P < 0.01). Multiple Logistic regression analyses indicated that weakened exercise tolerance, reduced exercise capacity, atrial fibrillation, anemia, and other blood diseases were the influencing factors of the frailty in elderly patients with type II diabetes. The degree of frailty in elderly patients with diabetes is affected by many factors, such as exercise tolerance, exercise capacity, atrial fibrillation, anemia, and other blood diseases; thus, reasonable intervention should be implemented for elderly patients with type II diabetes according to the influencing factors so as to effectively relieve frailty.

Copy-number variation in goat genome sequence: A comparative analysis of the different litter size trait groups.

Copy number variation (CNV), as an important component of genomic structural variation (SV), plays essential roles in phenotypic variability, disease susceptibility and species evolution. To investigate whether critical CNVs exist in dairy goats with differing fecundity, we performed genome-wide sequencing of two populations of Laoshan dairy goats with large differences in litter size. After reference genome aligning, CNV calling, and annotation, we screened identified CNVs in the high-fecundity (HF) and low-fecundity (LF) groups to identify discrepant CNVs and their distribution within the genome. Prolactin-related protein 1 and 6 (PRP1 and PRP6), important factors regulating reproductive processes, were demonstrated to be duplicated in the HF group. In summary, based on the differences in CNVs between goats with differing litter sizes, it suggests CNVs may contribute to litter size in Laoshan dairy goats.

Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing.

Genome flanking regions surrounding transcription start sites (TSSs) are critical for the regulation of gene expression, containing many translational regulatory elements. To investigate whether critical single nucleotide polymorphisms (SNPs) exist around TSSs in the dairy goat genome, we performed high throughput DNA sequencing to compare two dairy goat groups with discrepant litter sizes. After genome mapping, SNP calling, and annotation, we screened the SNPs within 2kb scales surrounding annotated TSSs in high fecundity (HF) and low fecundity (LF) groups, respectively. We attempted to identify distinct SNPs and motifs near the TSSs in both groups. The SNPs near the TSSs most were consistent; 318 new SNPs were uncovered in the HF group, of which 305 were heterozygote SNPs, 13 were homozygote SNPs, and majority of which were distributed on chromosome 2 and 29. After validation by Sanger sequencing we found that a SNP in CHI16: 27612330 C>A in the PSEN2 gene presented an A/A genotype in the HF group and an A/A or A/C genotype in the LF group. In conclusion, our study provides insightful information into the dairy goat genomic variations surrounding TSSs, which may contribute to enhanced litter size. Based on comparison studies of SNPs exist around transcription start sites between high fecundity group and low fecundity group. Our finding provides insights concerning the goat litter size phenotypic and will promote future goat breeding.

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus).

Dairy goats are one of the most utilized domesticated animals in China. Here, we selected extreme populations based on differential fecundity in two Laoshan dairy goat populations. Utilizing deep sequencing we have generated 68.7 and 57.8 giga base of sequencing data, and identified 12,458,711 and 12,423,128 SNPs in the low fecundity and high fecundity groups, respectively. Following selective sweep analyses, a number of loci and candidate genes in the two populations were scanned independently. The reproduction related genes CCNB2, AR, ADCY1, DNMT3B, SMAD2, AMHR2, ERBB2, FGFR1, MAP3K12 and THEM4 were specifically selected in the high fecundity group whereas KDM6A, TENM1, SWI5 and CYM were specifically selected in the low fecundity group. A sub-set of genes including SYCP2, SOX5 and POU3F4 were localized both in the high and low fecundity selection windows, suggesting that these particular genes experienced strong selection with lower genetic diversity. From the genome data, the rare nonsense mutations may not contribute to fecundity, whereas nonsynonymous SNPs likely play a predominant role. The nonsynonymous exonic SNPs in SETDB2 and CDH26 which were co-localized in the selected region may take part in fecundity traits. These observations bring us a new insights into the genetic variation influencing fecundity traits within dairy goats.

Association of ß2-microglobulin with the prognosis of non-Hodgkin's lymphoma: a meta analysis.

OBJECTIVE: The influence of ß2-microglobulin (ß2-MG) on the prognosis of non-Hodgkin's lymphoma (NHL) remains controversial. This study performed meta-analyses to evaluate the prognostic value of ß2-MG on the overall survival (OS) of NHL. METHODS: Through a search of relevant literature in PubMed, EMbase, Science Direct, OVID and Wanfang databases from 1980-2013, the hazard ratios (HRs) of OS between the normal ß2-MG group and the increased ß2-MG group were retrieved, and the results were combined using a fixed effect model and a random effect model. Subgroup analyses were performed based on univariate and multivariate analysis results, and sensitivity analyses were performed to estimate the changes of the combined HRs. In addition, funnel plots and fail-safe numbers were used to estimate publication bias. RESULTS: A total of 17 qualified publications were included, with a cumulative total of 2,479 cases. The result of heterogeneity examination showed that there was heterogeneity among all studies (P < 0.001, I(2) = 87%). In the random effect model, the combined HR was 2.71 (95% confidence interval [CI]: 1.91-3.85). The result of the total effect examination was statistically significant (Z = 5.59, P < 0.001). CONCLUSION: The increased ß2-MG level was an independent risk factor for the prognosis of NHL.

Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice.

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F(1) super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression (SAGE) revealed 1183 differentially expressed genes (DGs), among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F(1) hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F(1) hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci (QTL), a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

A transcriptomic analysis of superhybrid rice LYP9 and its parents.

By using a whole-genome oligonucleotide microarray, designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid rice LYP9 and its parental cultivars 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total genes set collectively from 7 tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicles at filling stage. Clustering results showed that the F1 hybrid's expression profiles resembled those of its parental lines more than that which lies between the 2 parental lines. Out of the total gene set, 7,078 genes are shared by all sampled tissues and 3,926 genes (10.6% of the total gene set) are differentially expressed genes (DG). As we divided DG into those between the parents (DG(PP)) and between the hybrid and its parents (DG(HP)), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DG(HP) rather than in DG(PP). In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes.

Cell-wall invertases from rice are differentially expressed in Caryopsis during the grain filling stage.

Cell-wall invertase plays an important role in sucrose partitioning between source and sink organs in higher plants. To investigate the role of cell-wall invertases for seed development in rice (Oryza sativa L.), cDNAs of three putative cell-wall invertase genes OsCIN1, OsCIN2 and OsCIN3 were isolated. Semi-quantitative reverse transcription-polymerase chain reaction analysis revealed different expression patterns of the three genes in various rice tissues/organs. In developing caryopses, they exhibited similar temporal expression patterns, expressed highly at the early and middle grain filling stages and gradually declined to low levels afterward. However, the spatial expression patterns of them were very different, with OsCIN1 primarily expressed in the caryopsis coat, OsCIN2 in embryo and endosperm, and OsCIN3 in embryo. Further RNA in situ hybridization analysis revealed that a strong signal of OsCIN2 mRNA was detected in the vascular parenchyma surrounding the xylem of the chalazal vein and the aleurone layer, whereas OsCIN3 transcript was strongly detected in the vascular parenchyma surrounding the phloem of the chalazal vein, cross-cells, the aleurone layer and the nucellar tissue. These data indicate that the three cell-wall invertase genes play complementary/synergetic roles in assimilate unloading during the grain filling stage. In addition, the cell type-specific expression patterns of OsCIN3 in source leaf blades and anthers were also investigated, and its corresponding physiological roles were discussed.

Cloning and expression analysis of rice sucrose transporter genes OsSUT2M and OsSUT5Z.

Two sucrose transporter (SUT) cDNAs, OsSUT2M and OsSUT5Z, were isolated from rice (Oryza sativa L.) by reverse transcription polymerase chain reaction (RT-PCR). Sequencing results indicate they are 1,531 bp and 1,635 bp in length including complete open reading frame 1,506 bp and 1,608 bp, which encode 502 amino acids and 536 amino acids, respectively. The TopPred program suggested that both sucrose transporter proteins, OsSUT2M and OsSUT5Z, consist of potentially 12 transmembrane domains. Semi-quantitative RT-PCR was carried out to investigate the gene expression patterns of OsSUT2M and OsSUT5Z. In vegetative organs, transcripts of OsSUT2M were higher in source leaf blades than in other organs at the same development stage, whereas transcripts of OsSUT5Z were less traceable in all organs investigated. In reproductive organs, both transcripts of these two genes were high in panicles from the booting stage to 7 days after flowering (DAF) and then sharply declined. The potential physiology functions of these two sucrose transporters are discussed.