DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.

Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Traditional prediction methods, dependent on homology and sequence similarity, often fail to predict functions for novel proteins and proteins without known homologs.

Prognostic value of the ratio of pretreatment carcinoembryonic antigen to tumor volume in rectal cancer.

Background: As a commonly used biomarker in rectal cancer (RC), the prognostic value of carcinoembryonic antigen (CEA) remains underexplored. This study aims to evaluate the prognostic value of pretreatment CEA/tumor volume in RC.

Methods: This retrospective study included patients who underwent pretreatment magnetic resonance imaging (MRI) with histologically confirmed primary rectal adenocarcinoma from November 2012 to April 2018.

Corrigendum: Association of CT-based delta radiomics biomarker with progression-free survival in patients with colorectal liver metastases undergo chemotherapy.

[This corrects the article DOI: 10.3389/fonc.2022.

Suppressing ASPARTIC PROTEASE 1 prolongs photosynthesis and increases wheat grain weight.

The elongation of photosynthesis, or functional staygreen, represents a feasible strategy to propel metabolite flux towards cereal kernels. However, achieving this goal remains a challenge in food crops. Here we report the cloning of wheat CO assimilation and kernel enhanced 2 (cake2), the mechanism underlying the photosynthesis advantages and natural alleles amenable to breeding elite varieties.

Suppression of ZEAXANTHIN EPOXIDASE 1 restricts stripe rust growth in wheat.

Reducing losses caused by pathogens is an effective strategy for stabilizing crop yields. Daunting challenges remain in cloning and characterizing genes that inhibit stripe rust, a devastating disease of wheat (Triticum aestivum) caused by Puccinia striiformis f. sp.

HSP90.2 promotes CO assimilation rate, grain weight and yield in wheat.

Wheat fixes CO by photosynthesis into kernels to nourish humankind. Improving the photosynthesis rate is a major driving force in assimilating atmospheric CO and guaranteeing food supply for human beings. Strategies for achieving the above goal need to be improved.

Hormone-response transcriptional landscapes of wheat seedlings and the development of a JA fluorescent reporter.

Wheat is an essential energy and protein source for humans. Climate change brings daunting challenges to wheat yield through environmental stresses, in which phytohormones play critical roles. Nevertheless, the comprehensive understanding of wheat phytohormone responses remains elusive.

Association of CT-Based Delta Radiomics Biomarker With Progression-Free Survival in Patients With Colorectal Liver Metastases Undergo Chemotherapy.

Unlabelled: Predicting the prognosis of patients in advance is conducive to providing personalized treatment for patients. Our aim was to predict the therapeutic efficacy and progression free survival (PFS) of patients with liver metastasis of colorectal cancer according to the changes of computed tomography (CT) radiomics before and after chemotherapy.

Methods: This retrospective study included 139 patients (397 lesions) with colorectal liver metastases who underwent neoadjuvant chemotherapy from April 2015 to April 2020.

Mild phototherapy mediated by manganese dioxide-loaded mesoporous polydopamine enhances immunotherapy against colorectal cancer.

One of the main challenges in applying the immune checkpoint blockade to treat colorectal cancer (CRC) is the immunosuppressive tumor microenvironment. Owing to its excellent cancer cell killing ability and immune activation, mild photothermal therapy (PTT) has shown bright promise to sensitize tumors to immune checkpoint inhibition through turning the immunologically "cold" tumors into "hot" ones. Herein, a mild photothermal effect-assisted theragnostic nanodrug (MnO@MPDA-PEG NPs) is developed by incorporating MnO into PEGylated-mesoporous polydopamine nanoparticles (MPDA-PEG NPs).

Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.).

Background: GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted.

Function in Lipid Biosynthesis Is Required for Arbuscular Mycorrhizal Symbiosis in Rice.

Arbuscular mycorrhiza (AM) is a mutualistic symbiosis formed between most land plants and Glomeromycotina fungi. During symbiosis, plants provide organic carbon to fungi in exchange for mineral nutrients. Previous legume studies showed that the () gene is necessary for transferring lipids from plants to AM fungi (AMF) and is also likely to play a "signaling" role at the root surface.

Molecular mapping of the gene(s) conferring resistance to Soybean mosaic virus and Bean common mosaic virus in the soybean cultivar Raiden.

In the soybean cultivar Raiden, both a SMV-resistance gene and a BCMV-resistance gene were fine-mapped to a common region within the Rsv1 complex locus on chromosome 13, in which two CC-NBS-LRR resistance genes (Glyma.13g184800 and Glyma.13g184900) exhibited significant divergence between resistant and susceptible cultivars and were subjected to positive selection.

An Update on the Evolution of Glucosyltransferase () Genes in .

In many caries-promoting species, glucosyltransferases (Gtfs) are recognized as key enzymes contributing to the modification of biofilm structures, disruption of homeostasis of healthy microbiota community and induction of caries development. It is therefore of great interest to investigate how genes have evolved in In this study, we conducted a comprehensive survey of genes among 872 genomes of 37 species and identified genes from 364 genomes of 18 species. To clarify the relationships of these genes, 45 representative sequences were used for phylogenic analysis, which revealed two clear clades.

Hydrogen-Rich Saline Ameliorates Hepatic Ischemia-Reperfusion Injury Through Regulation of Endoplasmic Reticulum Stress and Apoptosis.

Objective: To evaluate the effect of hydrogen-rich saline (HS) on hepatic ischemia-reperfusion (I/R) injury.

Methods: Forty rats were randomly allocated into five groups: one sham group (control group), one group treated with 20 min of ischemia and normal saline (NS; I/R1 + NS group), one group treated with 20 min of ischemia and HS (I/R1 + HS group), one group treated with 60 min of ischemia and NS (I/R2 + NS group), and one group treated with 60 min of ischemia and HS (I/R2 + HS group). After reperfusion for 6 h, hepatic function, oxidative stress, pathological changes, and apoptosis of hepatic cells were evaluated.

Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review.

MicroRNAs (MiRNAs) play multiple crucial regulating roles in cell which can regulate one third of protein-coding genes. MiRNAs participate in the developmental and physiological processes of human body, while their aberrant adjustment will be more likely to trigger diseases such as cancers, kidney disease, central nervous system diseases, cardiovascular diseases, diabetes, viral infections and so on. What's worse, for the detection of miRNAs, their small size, high sequence similarity, low abundance and difficult extraction from cells impose great challenges in the analysis.