Modeling Microbial Communities: Perspective and Challenges.

Microbial communities are immensely important due to their widespread presence and profound impact on various facets of life. Understanding these complex systems necessitates mathematical modeling, a powerful tool for simulating and predicting microbial community behavior. This review offers a critical analysis of metabolic modeling and highlights key areas that would greatly benefit from broader discussion and collaboration.

MiR-34b promotes oxidative stress and induces cellular senescence through TWIST1 in human cervical cancer.

Purpose: The aim of this research was to elucidate the role of miR-34b in cervical cancer progression and the underlying mechanism behind the miR-34b-mediated tumor suppression. The study revealed the role of miR-34b as a senescence inducer and serves as a potential therapeutic target in developing combination therapy with senotherapeutics.

Methods: MiR-34b was ectopically expressed in cervical cancer cell lines using a tetracycline inducible system and its effects on cell viability, apoptosis, senescence, DNA damage and oxidative stress were studied using MTT assay, acridine orange/ ethidium bromide staining, senescence associated β-galactosidase assay, gamma H2AX foci staining assay, western blotting and specific dyes for the detection of total and individual ROS species.

Influence of endogenous and exogenous hormones on the cardiovascular response to lower extremity exercise and group III/IV activation in young females.

Oral contraceptive (OC) use can increase resting blood pressure (BP) in females as well as contribute to greater activation of group III/IV afferents during upper body exercise. It is unknown, however, whether an exaggerated BP response occurs during lower limb exercise in OC users. We sought to elucidate the group III/IV afferent activity-mediated BP and heart rate responses while performing lower extremity tasks during early and late follicular phases in young, healthy females.

Development and external validation of Indian population-specific Garbhini-GA2 model for estimating gestational age in second and third trimesters.

Background: A large proportion of pregnant women in lower and middle-income countries (LMIC) seek their first antenatal care after 14 weeks of gestation. While the last menstrual period (LMP) is still the most prevalent method of determining gestational age (GA), ultrasound-based foetal biometry is considered more accurate in the second and third trimesters. In LMIC settings, the Hadlock formula, originally developed using data from a small Caucasian population, is widely used for estimating GA and foetal weight worldwide as the pre-programmed formula in ultrasound machines.

SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format.

As genomics advances swiftly and its applications extend to diverse fields, bioinformatics tools must enable researchers and clinicians to work with genomic data irrespective of their programming expertise. We developed SCI-VCF, a Shiny-based comprehensive analysis utility to summarize, compare, inspect, analyse and design interactive visualizations of the genetic variants from the variant call format. With an intuitive graphical user interface, SCI-VCF aims to bridge the approachability gap in genomics that arises from the existing predominantly command-line utilities.

Antibody glycan quality predicted from CHO cell culture media markers and machine learning.

N-glycosylation can have a profound effect on the quality of mAb therapeutics. In biomanufacturing, one of the ways to influence N-glycosylation patterns is by altering the media used to grow mAb cell expression systems. Here, we explore the potential of machine learning (ML) to forecast the abundances of N-glycan types based on variables related to the growth media.

Chitosan alchemy: transforming tissue engineering and wound healing.

Chitosan, a biopolymer acquired from chitin, has emerged as a versatile and favorable material in the domain of tissue engineering and wound healing. Its biocompatibility, biodegradability, and antimicrobial characteristics make it a suitable candidate for these applications. In tissue engineering, chitosan-based formulations have garnered substantial attention as they have the ability to mimic the extracellular matrix, furnishing an optimal microenvironment for cell adhesion, proliferation, and differentiation.

Unveiling the versatility of gelatin methacryloyl hydrogels: a comprehensive journey into biomedical applications.

Gelatin methacryloyl (GelMA) hydrogels have gained significant recognition as versatile biomaterials in the biomedical domain. GelMA hydrogels emulate vital characteristics of the innate extracellular matrix by integrating cell-adhering and matrix metalloproteinase-responsive peptide motifs. These features enable cellular proliferation and spreading within GelMA-based hydrogel scaffolds.

DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein-protein complexes upon mutation.

Motivation: Protein-protein interactions underpin many cellular processes and their disruption due to mutations can lead to diseases. With the evolution of protein structure prediction methods like AlphaFold2 and the availability of extensive experimental affinity data, there is a pressing need for updated computational tools that can efficiently predict changes in binding affinity caused by mutations in protein-protein complexes.

Results: We developed a deep ensemble model that leverages protein sequences, predicted structure-based features, and protein functional classes to accurately predict the change in binding affinity due to mutations.

A finely balanced order-disorder equilibrium sculpts the folding-binding landscape of an antibiotic sequestering protein.

TipA, a MerR family transcription factor from , promotes antibiotic resistance by sequestering broad-spectrum thiopeptide-based antibiotics, thus counteracting their inhibitory effect on ribosomes. TipAS, a minimal binding motif which is expressed as an isoform of TipA, harbors a partially disordered N-terminal subdomain that folds upon binding multiple antibiotics. The extent and nature of the underlying molecular heterogeneity in TipAS that shapes its promiscuous folding-function landscape is an open question and is critical for understanding antibiotic-sequestration mechanisms.

Polymeric optical fiber biosensor with PAMAM dendrimer-based surface modification and PlGF detection for pre-eclampsia diagnosis.

Pre-eclampsia (PE) is a life-threatening complication that occurs during pregnancy, affecting a large number of pregnant women and newborns worldwide. Rapid, on-site and affordable screening of PE at an early stage is necessary to ensure timely treatment and minimize both maternal and neonatal morbidity and mortality rates. Placental growth factor (PlGF) is an angiogenic blood biomarker used for PE diagnosis.

A lateralized motor network in order to understand adaptation to visuomotor rotation.

The functional asymmetry between the two brain hemispheres in language and spatial processing is well documented. However, a description of difference in control between the two hemispheres in motor function is not well established. Our primary objective in this study was to examine the distribution of control in the motor hierarchy and its variation across hemispheres.

Driving towards digital biomanufacturing by CHO genome-scale models.

Genome-scale metabolic models (GEMs) of Chinese hamster ovary (CHO) cells are valuable for gaining mechanistic understanding of mammalian cell metabolism and cultures. We provide a comprehensive overview of past and present developments of CHO-GEMs and in silico methods within the flux balance analysis (FBA) framework, focusing on their practical utility in rational cell line development and bioprocess improvements. There are many opportunities for further augmenting the model coverage and establishing integrative models that account for different cellular processes and data for future applications.

Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station.

Background: The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board.

Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design.

Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein-protein and protein-ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently.

Design Principles for Biological Adaptation: A Systems and Control-Theoretic Treatment.

Establishing a mapping between (from and to) the functionality of interest and the underlying network structure (design principles) remains a crucial step toward understanding and design of bio-systems. Perfect adaptation is one such crucial functionality that enables every living organism to regulate its essential activities in the presence of external disturbances. Previous approaches to deducing the design principles for adaptation have either relied on computationally burdensome brute-force methods or rule-based design strategies detecting only a subset of all possible adaptive network structures.

Computational approaches for identifying disease-causing mutations in proteins.

Advancements in genome sequencing have expanded the scope of investigating mutations in proteins across different diseases. Amino acid mutations in a protein alter its structure, stability and function and some of them lead to diseases. Identification of disease-causing mutations is a challenging task and it will be helpful for designing therapeutic strategies.

Mechanism of drug resistance in HIV-1 protease subtype C in the presence of Atazanavir.

AIDS is one of the deadliest diseases in the history of humankind caused by HIV. Despite the technological development, curtailing the viral infection inside human host still remains a challenge. Therapies such as HAART uses a combination of drugs to inhibit the viral activity.

Evaluating oleaginous yeasts for enhanced microbial lipid production using sweetwater as a sustainable feedstock.

Background: Yeasts exhibit promising potential for the microbial conversion of crude glycerol, owing to their versatility in delivering a wide range of value-added products, particularly lipids. Sweetwater, a methanol-free by-product of the fat splitting process, has emerged as a promising alternative feedstock for the microbial utilization of crude glycerol. To further optimize sweetwater utilization, we compared the growth and lipid production capabilities of 21 oleaginous yeast strains under different conditions with various glycerol concentrations, sweetwater types and pH.

Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.

Membrane proteins play crucial roles in various cellular processes, and their interactions with other proteins in and on the membrane are essential for their proper functioning. While an increasing number of structures of more membrane proteins are being determined, the available structure data is still sparse. To gain insights into the mechanisms of membrane protein complexes, computational docking methods are necessary due to the challenge of experimental determination.

CarbDisMut: database on neutral and disease-causing mutations in human carbohydrate-binding proteins.

Protein-carbohydrate interactions are involved in several cellular and biological functions. Integrating structure and function of carbohydrate-binding proteins with disease-causing mutations help to understand the molecular basis of diseases. Although databases are available for protein-carbohydrate complexes based on structure, binding affinity and function, no specific database for mutations in human carbohydrate-binding proteins is reported in the literature.

The counteracting influence of 2-hydroxypropyl substitution and the presence of a guest molecule on the shape and size of the β-cyclodextrin cavity.

The aqueous solubility of β-cyclodextrin (β-CD), a cyclic carbohydrate comprising seven α-D-glucose molecules, is enhanced by 2-hydroxypropyl (2-HP) substitution of the hydroxyl groups at the CD rims. Our thorough analysis of the structural and solvation properties with different degrees of 2-hydroxypropyl substitution on β-CD using molecular dynamics simulations reveals that the solubility is enhanced at the cost of the structural distortion of the CD cyclic structure. Substitution at the secondary rim predominantly enhances the favourable interactions between CD and water by decreasing CD-CD hydrogen bonding and promoting CD-water hydrogen bonding.