Identification of biological signatures of cruciferous vegetable consumption utilizing machine learning-based global untargeted stable isotope traced metabolomics.

In recent years there has been increased interest in identifying biological signatures of food consumption for use as biomarkers. Traditional metabolomics-based biomarker discovery approaches rely on multivariate statistics which cannot differentiate between host- and food-derived compounds, thus novel approaches to biomarker discovery are required to advance the field. To this aim, we have developed a new method that combines global untargeted stable isotope traced metabolomics and a machine learning approach to identify biological signatures of cruciferous vegetable consumption.

Molecular tuning of sea anemone stinging.

Jellyfish and sea anemones fire single-use, venom-covered barbs to immobilize prey or predators. We previously showed that the anemone uses a specialized voltage-gated calcium (Ca) channel to trigger stinging in response to synergistic prey-derived chemicals and touch (Weir et al., 2020).

Niclosamide improves cancer immunotherapy by modulating RNA-binding protein HuR-mediated PD-L1 signaling.

Background: Immune checkpoint blockade (ICB) represents a revolutionary advance in cancer treatment but remains limited success in triple-negative breast cancer (TNBC). Here we aim to explore the mechanism of RNA-binding protein (RBP) HuR in cancer immune evasion by post-transcriptionally regulating PD-L1 and evaluate the potential of HuR inhibition to improve immune response.

Methods: The binding between HuR and PD-L1 mRNA was determined by ribonucleoprotein immunoprecipitation and RNA pull-down assays.

Hepatocyte-specific deletion of small heterodimer partner protects mice against acetaminophen-induced hepatotoxicity via activation of Nrf2.

Acetaminophen (APAP) overdose stands as the primary cause of acute liver failure in the United States. APAP hepatotoxicity involves hepatic glutathione (GSH) depletion and mitochondrial damage. To counteract the toxicity of APAP, the nuclear factor erythroid 2 like 2 (Nrf2) activates the expression of genes responsible for drug detoxification and GSH synthesis.

Small Heterodimer Partner Modulates Macrophage Differentiation during Innate Immune Response through the Regulation of Peroxisome Proliferator Activated Receptor Gamma, Mitogen-Activated Protein Kinase, and Nuclear Factor Kappa B Pathways.

Hepatic macrophages act as the liver's first line of defense against injury. Their differentiation into proinflammatory or anti-inflammatory subpopulations is a critical event that maintains a delicate balance between liver injury and repair. In our investigation, we explored the influence of the small heterodimer partner (SHP), a nuclear receptor primarily associated with metabolism, on macrophage differentiation during the innate immune response.

Molecular tuning of sea anemone stinging.

Jellyfish and sea anemones fire single-use, venom-covered barbs to immobilize prey or predators. We previously showed that the anemone uses a specialized voltage-gated calcium (Ca) channel to trigger stinging in response to synergistic prey-derived chemicals and touch (Weir et al., 2020).

Functional inhibition of the RNA-binding protein HuR sensitizes triple-negative breast cancer to chemotherapy.

Chemotherapy remains the standard treatment for triple-negative breast cancer (TNBC); however, chemoresistance compromises its efficacy. The RNA-binding protein Hu antigen R (HuR) could be a potential therapeutic target to enhance the chemotherapy efficacy. HuR is known to mainly stabilize its target mRNAs, and/or promote the translation of encoded proteins, which are implicated in multiple cancer hallmarks, including chemoresistance.

Hepatic transcriptome profiling reveals early signatures associated with disease transition from non-alcoholic steatosis to steatohepatitis.

Background And Aim: Non-alcoholic fatty liver disease (NAFLD) is becoming a leading cause of chronic liver disease worldwide. The molecular events that influence disease progression from non-alcoholic fatty liver (NAFL) to aggressive non-alcoholic steatohepatitis (NASH) remain incompletely understood, leading to lack of mechanism-based targeted treatment options for NASH. This study aims to identify early signatures associated with disease progression from NAFL to NASH in mice and humans.

Alignment-free sequence comparison for virus genomes based on location correlation coefficient.

Coronaviruses (especially SARS-CoV-2) are characterized by rapid mutation and wide spread. As these characteristics easily lead to global pandemics, studying the evolutionary relationship between viruses is essential for clinical diagnosis. DNA sequencing has played an important role in evolutionary analysis.

Geometric construction of viral genome space and its applications.

Understanding the relationships between genomic sequences is essential to the classification and characterization of living beings. The classes and characteristics of an organism can be identified in the corresponding genome space. In the genome space, the natural metric is important to describe the distribution of genomes.

Positional Correlation Natural Vector: A Novel Method for Genome Comparison.

Advances in sequencing technology have made large amounts of biological data available. Evolutionary analysis of data such as DNA sequences is highly important in biological studies. As alignment methods are ineffective for analyzing large-scale data due to their inherently high costs, alignment-free methods have recently attracted attention in the field of bioinformatics.

Rapid adaptation to elevated extracellular potassium in the pyloric circuit of the crab, .

Elevated potassium concentration ([K]) is often used to alter excitability in neurons and networks by shifting the potassium equilibrium potential () and, consequently, the resting membrane potential. We studied the effects of increased extracellular [K] on the well-described pyloric circuit of the crab . A 2.

A novel alignment-free method for HIV-1 subtype classification.

HIV-1 is the most common and pathogenic strain of human immunodeficiency virus consisting of many subtypes. To study the difference among HIV-1 subtypes in infection, diagnosis and drug design, it is important to identify HIV-1 subtypes from clinical HIV-1 samples. In this work, we propose an effective numeric representation called Subsequence Natural Vector (SNV) to encode HIV-1 sequences.

A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance.

Classification of DNA sequences is an important issue in the bioinformatics study, yet most existing methods for phylogenetic analysis including Multiple Sequence Alignment (MSA) are time-consuming and computationally expensive. The alignment-free methods are popular nowadays, whereas the manual intervention in those methods usually decreases the accuracy. Also, the interactions among nucleotides are neglected in most methods.

Expression, Regulation, and Function of the Calmodulin Accessory Protein PCP4/PEP-19 in Myometrium.

Objective: Calmodulin (CaM) plays a key role in the orchestration of Ca signaling events, and its regulation is considered an important component of cellular homeostasis. The control of uterine smooth muscle function is largely dependent on the regulation of Ca and CaM signaling. The objective of this study was to investigate the expression, function, and regulation of CaM regulatory proteins in myometrium during pregnancy.

Regulation of human placental drug transporters in HCV infection and their influence on direct acting antiviral medications.

Introduction: The objectives of this study were to determine how HCV infection affects placental drug transporters, and to determine the role of drug transporters on the cellular accumulation of direct-acting antiviral drugs in human trophoblasts.

Methods: Eighty-four ABC and SLC transporter genes were first screened in normal and HCV infected pregnant women using PCR profiler array. The changes in expression were confirmed by qPCR and Western blot.

A novel fast vector method for genetic sequence comparison.

With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny.

A novel alignment-free vector method to cluster protein sequences.

Classification of protein are crucial topics in biology. The number of protein sequences stored in databases increases sharply in the past decade. Traditionally, comparison of protein sequences is usually carried out through multiple sequence alignment methods.

Zika and Flaviviruses Phylogeny Based on the Alignment-Free Natural Vector Method.

Zika virus (ZIKV) is a mosquito-borne flavivirus. It was first isolated from Uganda in 1947 and has become an emergent event since 2007. However, because of the inconsistency of alignment methods, the evolution of ZIKV remains poorly understood.

Effect of prostaglandin E2 on multidrug resistance transporters in human placental cells.

Prostaglandin (PG) E2, a major product of cyclooxygenase (COX)-2, acts as an immunomodulator at the maternal-fetal interface during pregnancy. It exerts biologic function through interaction with E-prostanoid (EP) receptors localized to the placenta. The activation of the COX-2/PGE2/EP signal pathway can alter the expression of the ATP-binding cassette (ABC) transporters, multidrug resistance protein 1 [P-glycoprotein (Pgp); gene: ABCB1], and breast cancer resistance protein (BCRP; gene: ABCG2), which function to extrude drugs and xenobiotics from cells.