The TIGR Rice Genome Annotation Resource: improvements and new features

In The Institute for Genomic Research Rice Genome Annotation project (), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13 237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads

The Value of Peripheral Blood Leukocyte Parameters in the Early Diagnosis and Clinical Prognosis of Sepsis

Background. Early diagnosis of sepsis is the key to timely, targeted treatment. Cell population data (CPD) has been widely used in many diseases, but its predictive value for early diagnosis and the clinical outcome of sepsis remains unclear. Therefore, this paper discusses whether peripheral blood leukocyte parameters can be used as predictive indicators for early diagnosis and the clinical outcome of sepsis. Methods. A retrospective study of 45 patients with sepsis, 53 patients with nonseptic infections, and 86 healthy check-ups admitted to Gansu Provincial Hospital from January 2021 to June 2022 was done using a hematology analyzer. Results. The results of LYMPH#, HFLC#, IG#, NE-WX, LY-WX, LY-WY, and MO-WX showed better diagnostic efficiency in the sepsis group and nonseptic infection group. When the seven differential leukocyte parameters were used to establish diagnostic models, the sensitivity and specificity were 82.20% and 77.40%, respectively. Correlation analysis showed that LYMPH# and HFLC# were positively correlated with PCT (P<0.05). The clinical outcome of sepsis showed that the leukocyte parameters of discharged WBC and LY-X had better predictive efficacy. When the two differential leukocyte parameters were used to establish diagnostic models, the sensitivity and specificity were 90.90% and 100.00%. Cox regression analysis showed that leukocyte parameters of discharged WBC and LY-X were independent predictors of clinical outcomes (P<0.05). Conclusion. Leucocyte parameters HFLC#, IG#, NE-WX, LY-WX, LY-WY, and MO-WX had a certain auxiliary effect on the early diagnosis of sepsis leukocyte parameters of discharged WBC and LY-X were independent predictors of clinical outcomes in patients with sepsis. Therefore, peripheral blood leukocyte parameters may have predictive value for early diagnosis and the clinical outcome of sepsis, but large-scale retrospective studies are still needed to prove our preliminary results

Genetic determinants of IgG antibody response to COVID-19 vaccination.

Human humoral immune responses to SARS-CoV-2 vaccines exhibit substantial inter-individual variability and have been linked to vaccine efficacy. To elucidate the underlying mechanism behind this variability, we conducted a genome-wide association study (GWAS) on the anti-spike IgG serostatus of UK Biobank participants who were previously uninfected by SARS-CoV-2 and had received either the first dose (n&nbsp;= 54,066) or the second dose (n&nbsp;= 46,232) of COVID-19 vaccines. Our analysis revealed significant genome-wide associations between the IgG antibody serostatus following the initial vaccine and human leukocyte antigen (HLA) class II alleles. Specifically, the HLA-DRB1∗13:02 allele (MAF&nbsp;= 4.0%, OR&nbsp;= 0.75, p&nbsp;= 2.34e-16) demonstrated the most statistically significant protective effect against IgG seronegativity. This protective effect was driven by an alteration from arginine (Arg) to glutamic acid (Glu) at position 71 on HLA-DRβ1 (p&nbsp;= 1.88e-25), leading to a change in the electrostatic potential of pocket 4 of the peptide binding groove. Notably, the impact of HLA alleles on IgG responses was cell type specific, and we observed a shared genetic predisposition between IgG status and susceptibility/severity of COVID-19. These results were replicated within independent cohorts where IgG serostatus was assayed by two different antibody serology tests. Our findings provide insights into the biological mechanism underlying individual variation in responses to COVID-19 vaccines and highlight the need to consider the influence of constitutive genetics when designing vaccination strategies for optimizing protection and control of infectious disease across diverse populations