In silico prediction of active RNA genes in legumes

Accumulating evidence suggests that non-coding RNAs (ncRNAs) play key roles in gene regulation and may form the basis of an inter-gene communication system. MicroRNAs are a class of small non-coding RNAs found in both plants and animals that regulate the expression of other genes. Identification and analysis of microRNAs enhances our understanding of the important roles that microRNAs play in this complex regulatory network. The work presented in this thesis constitutes the first large-scale prediction and characterization of both ncRNAs and miRNAs in the model legume Medicago truncatula and Lotus japonicus, and provides a basis for further research on elucidating ncRNA function in legume genomics..

Release of promoter-proximal paused Pol II in response to histone deacetylase inhibition

A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter-proximal paused RNA polymerase II (Pol II) into elongation is stimulated, whereas initiation is not. Although histone acetylation is elevated globally by HDAC inhibition, less than 100 genes respond within 10 min. These genes are highly paused, are strongly associated with the chromatin regulators NURF and Trithorax, display a greater increase in acetylation of the first nucleosomes than other genes, and become transcriptionally activated by HDAC inhibition. Among these rapidly up-regulated genes are HDAC1 (Rpd3) and subunits of HDAC-containing co-repressor complexes, demonstrating feedback regulation upon HDAC inhibition. Our results suggest that histone acetylation stimulates transcription of paused genes by release of Pol II into elongation, and that increased acetylation is not a consequence of their enhanced expression. We propose that HDACs are major regulators of Pol II pausing and that this partly explains the presence of HDACs at active genes

A network meta-analysis on the improvement of cognition in patients with vascular dementia by different acupuncture therapies

IntroductionThe second most prevalent cause of dementia is vascular dementia (VaD). Furthermore, acupuncture is a relatively safe and effective traditional therapy for individuals with VaD. We performed a network meta-analysis to assess the effectiveness and safety of various acupuncture therapies for VaD based on existing research.MethodsWe searched six electronic databases to screen for randomized controlled trials (RCTs) comparing different acupuncture treatments in VaD patients. The Cochrne tool (Review Manager 5.3) was used to evaluate the risk of bias of the included RCTs. Based on the Grading of Recommendations Assessment, Development and Evaluation framework, we assessed the confidence in the evidence using the Confidence In the results from Network Meta-Analysis approach. We used the frequency approach to perform the network meta-analysis. Data were analyzed using R 4.1.1.ResultsIn total, we included 46 eligible studies. The results of the network analysis showed that the combined interventions of moxibustion (MB) with body acupuncture (BA) (MB + BA) and electroacupuncture (EA) with scalp acupuncture (SA) with BA (EA + SA + BA) were more effective in improving cognitive functions and activities of daily living compared with SA or BA alone. However, in the subgroup analysis, EA + SA + BA showed better efficacy in short- and mid-term acupuncture compared with other acupuncture therapies.ConclusionCombined acupuncture therapy may be a safe and effective intervention for individuals with VaD, and MB + BA and EA + SA + BA appear to be the most effective interventions. However, because the analysis of this study was based on low-to-moderate evidence, there remains no strong supporting evidence. Thus, high-quality, large-scale, and long-term studies should be conducted in the future to assess the effectiveness and safety of acupuncture in VaD.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier: CRD42022354573

MicroRNA-145 Targets YES and STAT1 in Colon Cancer Cells

BACKGROUND: MicroRNAs (miRNAs) have emerged as important gene regulators and are recognized as key players in tumorigenesis. miR-145 is reported to be down-regulated in several cancers, but knowledge of its targets in colon cancer remains limited. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the role of miR-145 in colon cancer, we have employed a microarray based approach to identify miR-145 targets. Based on seed site enrichment analyses and unbiased word analyses, we found a significant enrichment of miRNA binding sites in the 3'-untranslated regions (UTRs) of transcripts down-regulated upon miRNA overexpression. Gene Ontology analysis showed an overrepresentation of genes involved in cell death, cellular growth and proliferation, cell cycle, gene expression and cancer. A number of the identified miRNA targets have previously been implicated in cancer, including YES, FSCN1, ADAM17, BIRC2, VANGL1 as well as the transcription factor STAT1. Both YES and STAT1 were verified as direct miR-145 targets. CONCLUSIONS/SIGNIFICANCE: The study identifies and validates new cancer-relevant direct targets of miR-145 in colon cancer cells and hereby adds important mechanistic understanding of the tumor-suppressive functions of miR-145

Y chromosome evidence confirms northeast Asian origin of Xinjiang Kazakhs and genetic influence from 18th century expansion of Kerey clan

AbstractThe Kazakhs of Xinjiang province are characterized by their nomadic lifestyle and patrilineal clan system. However, compared to Central Asian Kazakhs, a lack of Y chromosomal high-resolution analysis has hindered our understanding of the paternal history of modern Xinjiang Kazakhs.MethodsIn this study, we present the analysis of 110 Y-SNP data from 209 Altay Kazakhs and 201 Ili Kazakhs in Xinjiang, along with their previously reported 24 Y-STR loci data.Results and discussionWe found that the Y chromosome haplogroups exhibit greater diversity in Altay Kazakhs compared to Kazakhs in Kazakhstan, Russia, and other regions of China. Y-SNP-based PCA plots reveal that both the Altay and Ili Kazakhs are situated between the Turkic, Mongolia, and Tibeto-Burman clusters. The dominant haplogroup C2a1a3-F1918, which originated in northeast Asia during the Neolithic Age, accounts for nearly half of the Altay and Ili Kazakhs. The Y lineage network of C2a1a3-F1918 contained two subclusters. Approximately 60.6% of the Altay Kazakhs belong to the DYS448-23 subcluster, indicating their Kerey-Abakh ancestry. On the other hand, around three-quarters of the Ili Kazakhs belong to the DYS448-22 subcluster, suggesting their Kerey-Ashmaily heritage. Notably, the TMRCA ages of the DYS448-23 subcluster were calculated to be 289.4 ± 202.65 years, which aligns with the historical immigration of the Kerey clan back to the Altay Mountains after the defeat of the Dzungar by the Qing dynasty in the mid-18th century

Joint retrieval of growing season corn canopy LAI and leaf chlorophyll content by fusing Sentinel-2 and MODIS images

Continuous and accurate estimates of crop canopy leaf area index (LAI) and chlorophyll content are of great importance for crop growth monitoring. These estimates can be useful for precision agricultural management and agricultural planning. Our objectives were to investigate the joint retrieval of corn canopy LAI and chlorophyll content using filtered reflectances from Sentinel-2 and MODIS data acquired during the corn growing season, which, being generally hot and rainy, results in few cloud-free Sentinel-2 images. In addition, the retrieved time series of LAI and chlorophyll content results were used to monitor the corn growth behavior in the study area. Our results showed that: (1) the joint retrieval of LAI and chlorophyll content using the proposed joint probability distribution method improved the estimation accuracy of both corn canopy LAI and chlorophyll content. Corn canopy LAI and chlorophyll content were retrieved jointly and accurately using the PROSAIL model with fused Kalman filtered (KF) reflectance images. The relation between retrieved and field measured LAI and chlorophyll content of four corn-growing stages had a coefficient of determination (R2) of about 0.6, and root mean square errors (RMSEs) ranges of mainly 0.1-0.2 and 0.0-0.3, respectively. (2) Kalman filtering is a good way to produce continuous high-resolution reflectance images by synthesizing Sentinel-2 and MODIS reflectances. The correlation between fused KF and Sentinel-2 reflectances had an R2 value of 0.98 and RMSE of 0.0133, and the correlation between KF and field-measured reflectances had an R2 value of 0.8598 and RMSE of 0.0404. (3) The derived continuous KF reflectances captured the crop behavior well. Our analysis showed that the LAI increased from day of year (DOY) 181 (trefoil stage) to DOY 236 (filling stage), and then increased continuously until harvest, while the chlorophyll content first also increased from DOY 181 to DOY 236, and then remained stable until harvest. These results revealed that the jointly retrieved continuous LAI and chlorophyll content could be used to monitor corn growth conditions