Role of GDF-15 in diabetic nephropathy: mechanisms, diagnosis, and therapeutic potential.

Purpose: Growth differentiation factor 15 (GDF-15) is a cytokine involved in regulating homeostasis, and its expression is up-regulated in response to injury, stress, and inflammation. This study explored the role of GDF-15 in diabetic nephropathy (DN), a severe complication of diabetes mellitus, and its potential as a biomarker for disease progression.

Methods: As a member of the transforming growth factor-β superfamily, GDF-15 exhibits its renal protective functions primarily through its anti-inflammatory effects and the up-regulation of other renal protective factors.

The Transpeptidase Sortase A Binds Nucleic Acids and Mediates Mammalian Cell Labeling.

Wild-type sortase A is an important virulence factor displaying a diverse array of proteins on the surface of bacteria. This protein display relies on the transpeptidase activity of sortase A, which is widely engineered to allow protein ligation and protein engineering based on the interaction between sortase A and peptides. Here an unknown interaction is found between sortase A from Staphylococcus aureus and nucleic acids, in which exogenously expressed engineered sortase A binds oligonucleotides in vitro and is independent of its canonical transpeptidase activity.

A top variant identification pipeline for protein engineering.

Understanding the fitness of protein variants with combinatorial mutations is critical for effective protein engineering. In this issue of Cell Systems, Chu et al. present TopVIP, a top variant identification pipeline that enables accurate picking of the greatest number of best-performing protein variants with high-fitness leveraging zero-shot predictor and low-N iterative sampling.

Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing.

The increasing emergence of Cas9 variants has attracted broad interest, as these variants were designed to expand CRISPR applications. New Cas9 variants typically feature higher editing efficiency, improved editing specificity, or alternative PAM sequences. To select Cas9 variants and gRNAs for high-fidelity and efficient genome editing, it is crucial to systematically quantify the editing performances of gRNAs and develop prediction models based on high-quality datasets.

Comparison of transcriptome-wide N6-methyladenosine profiles from healthy trio families reveals regulator-mediated methylation alterations.

The N6-methyladenosine (m6A) modification is a highly conserved RNA modification found in eukaryotic messenger RNAs (mRNAs). It plays a vital role in regulating various biological processes. Dysregulation of m6A modifications has been linked to a range of complex genetic diseases in humans.

Clinical Severity of SARS-CoV-2 Variants during COVID-19 Vaccination: A Systematic Review and Meta-Analysis.

Due to the variation in the SARS-CoV-2 virus, COVID-19 exhibits significant variability in severity. This presents challenges for governments in managing the allocation of healthcare resources and prioritizing health interventions. Clinical severity is also a critical statistical parameter for researchers to quantify the risks of infectious disease, model the transmission of COVID-19, and provide some targeted measures to control the pandemic.

Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.

Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample.

Achieved low-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio predicts the pathophysiological evolution of lipid-rich plaques in acute coronary syndromes: an optical coherence tomography study.

Background: As a novel lipoprotein ratio, baseline low-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio (LHR) is closely related to the clinical outcomes of acute coronary syndromes (ACS) after percutaneous coronary intervention. However, the pathophysiological impact of achieved LHR (aLHR) on the evolution of non-culprit lipid-rich plaques has not been systematically explored.

Methods: Between September 2013 and December 2018, ACS patients with both baseline and 1-year follow-up optical coherence tomography (OCT) examinations were included in current study.

Optimized minimal genome-wide human sgRNA library.

Genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-based knockout screening is revolting the genetic analysis of a cellular or molecular phenotype in question but is challenged by the large size of single-guide RNA (sgRNA) library. Here we designed a minimal genome-wide human sgRNA library, H-mLib, which is composed of 21,159 sgRNA pairs assembled based on a dedicated selection strategy from all potential SpCas9/sgRNAs in the human genome. These sgRNA pairs were cloned into a dual-gRNA vector each targeting one gene, resulting in a compact library size nearly identical to the number of human protein-coding genes.

Multiobjective Multitasking Optimization With Decomposition-Based Transfer Selection.

Multiobjective multitasking optimization (MTO) needs to solve a set of multiobjective optimization problems simultaneously, and tries to speed up their solution by transferring useful search experiences across tasks. However, the quality of transfer solutions will significantly impact the transfer effect, which may even deteriorate the optimization performance with an improper selection of transfer solutions. To alleviate this issue, this article suggests a new multiobjective multitasking evolutionary algorithm (MMTEA) with decomposition-based transfer selection, called MMTEA-DTS.

Identification of SARS-CoV-2 PLpro and 3CLpro human proteome substrates using substrate phage display coupled with protein network analysis.

Viral proteases play key roles in viral replication, and they also facilitate immune escape by proteolyzing diverse target proteins. Deep profiling of viral protease substrates in host cells is beneficial for understanding viral pathogenesis and for antiviral drug discovery. Here, we utilized substrate phage display coupled with protein network analysis to identify human proteome substrates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteases, including papain-like protease (PLpro) and 3C-like protease (3CLpro).

Deep sampling of gRNA in the human genome and deep-learning-informed prediction of gRNA activities.

Life science studies involving clustered regularly interspaced short palindromic repeat (CRISPR) editing generally apply the best-performing guide RNA (gRNA) for a gene of interest. Computational models are combined with massive experimental quantification on synthetic gRNA-target libraries to accurately predict gRNA activity and mutational patterns. However, the measurements are inconsistent between studies due to differences in the designs of the gRNA-target pair constructs, and there has not yet been an integrated investigation that concurrently focuses on multiple facets of gRNA capacity.

Effect of Induction Therapy With Olamkicept vs Placebo on Clinical Response in Patients With Active Ulcerative Colitis: A Randomized Clinical Trial.

Importance: Olamkicept, a soluble gp130-Fc-fusion-protein, selectively inhibits interleukin 6 (IL-6) trans-signaling by binding the soluble IL-6 receptor/IL-6 complex. It has anti-inflammatory activities in inflammatory murine models without immune suppression.

Objective: To assess the effect of olamkicept as induction therapy in patients with active ulcerative colitis.

PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation.

CRISPR technology holds significant promise for biological studies and gene therapies because of its high flexibility and efficiency when applied in mammalian cells. But endonuclease (e.g.

Automatic assessment of calcified plaque and nodule by optical coherence tomography adopting deep learning model.

Optical coherence tomography (OCT) has become the best imaging tool to assess calcified plaque and nodule. However, every OCT pullback has numerous images, and artificial analysis requires too much time and energy. Thus, it is unsuitable for clinical application.

Impact of mass rapid antigen testing for SARS-CoV-2 to mitigate Omicron outbreaks in China.

We analysed the effectiveness of various non-pharmaceutical interventions in containing the 2022 Omicron outbreak in China. The results show that the Rapid Antigen Test contributed to containing the outbreak, reducing the reproduction number by 0.788 (95% CI:−0.

Tissue-Characteristic Expression of Mouse Proteome.

The mouse is a valuable model organism for biomedical research. Here, we established a comprehensive spectral library and the data-independent acquisition-based quantitative proteome maps for 41 mouse organs, including some rarely reported organs such as the cornea, retina, and nine paired organs. The mouse spectral library contained 178,304 peptides from 12,320 proteins, including 1678 proteins not reported in previous mouse spectral libraries.

An in-library ligation strategy and its application in CRISPR/Cas9 screening of high-order gRNA combinations.

Simultaneous targeting multiple genes is a big advantage of CRISPR (clustered regularly interspaced short palindromic repeats) genome editing but challenging to achieve in CRISPR screening. The crosstalk among genes or gene products is a common and fundamental mechanism to ensure cellular stability and functional diversity. However, the screening approach to map high-order gene combinations to the interesting phenotype is still lacking.

Reproduction Number of the Omicron Variant Triples That of the Delta Variant.

COVID-19 remains a persistent threat, especially with the predominant Omicron variant emerging in early 2022, presenting with high transmissibility, immune escape, and waning. There is a need to rapidly ramp up global vaccine coverage while enhancing public health and social measures. Timely and reliable estimation of the reproduction number throughout a pandemic is critical for assessing the impact of mitigation efforts and the potential need to adjust for control measures.

Feasibility and Safety of Very-Low Contrast Combined Ringer's Solution in Optical Coherence Tomography Imaging.

Background: Optical coherence tomography (OCT) is an important modality used in coronary intervention. However, OCT requires a high amount of contrast media, limiting its extensive application in clinical practice. This study compared OCT images of coronary lesions obtained using contrast media and very-low contrast combined Ringer's solution (VLCCR) in patients with acute coronary syndrome (ACS).

New Chromatin Run-On Reaction Enables Global Mapping of Active RNA Polymerase Locations in an Enrichment-free Manner.

The development of a simple and cost-effective method to map the distribution of RNA polymerase II (RNPII) genome-wide at a high resolution is highly beneficial to study cellular transcriptional activity. Here we report a mutation-based and enrichment-free global chromatin run-on sequencing (mGRO-seq) technique to locate active RNPII sites genome-wide at near-base resolution. An adenosine triphosphate (ATP) analog named -allyladenosine triphosphate (aATP) was designed and could be incorporated into nascent RNAs at RNPII-located positions during a chromatin run-on reaction.

Single-cell transcriptome analysis uncovers the molecular and cellular characteristics of thin endometrium.

Infertility is a social and medical problem around the world and the incidence continues to rise. Thin endometrium (TE) is a great challenge of infertility treatment, even by in vitro fertilization and embryo transfer. It is widely believed that TE impairs endometrium receptivity.

Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer.

Background: Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity-however, most predicted enhancer regions remain to be functionally tested.

Methods: We analyzed 132 epigenomic histone modification profiles of 18 primary gastric cancer (GC) samples, 18 normal gastric tissues, and 28 GC cell lines using Nano-ChIP-seq technology.

Association Between Echocardiographic Non-invasive Myocardial Work Indices and Myocardial Fibrosis in Patients With Dilated Cardiomyopathy.

To analyze the association between global myocardial work indices evaluated by non-invasive left ventricular (LV) pressure-strain loop (PSL) and LV myocardial fibrosis in patients with dilated cardiomyopathy (DCM). A total of 57 patients with DCM were included in this prospective study. Global work index (GWI), global constructive work (GCW), global wasted work (GWW), global work efficiency (GWE) and global longitudinal strain (GLS) were measured using LVPSL.