Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Tunnels in enzymes with buried active sites are key structural features allowing the entry of substrates and the release of products, thus contributing to the catalytic efficiency. Targeting the bottlenecks of protein tunnels is also a powerful protein engineering strategy. However, the identification of functional tunnels in multiple protein structures is a non-trivial task that can only be addressed computationally.

Exploring the potential of myo-inositol in thyroid disease management: focus on thyroid cancer diagnosis and therapy.

Thyroid cancer (TC) is a malignancy that is increasing in prevalence on a global scale, necessitating the development of innovative approaches for both diagnosis and treatment. Myo-inositol (MI) plays a crucial role in a wide range of physiological and pathological functions within human cells. To date, studies have investigated the function of MI in thyroid physiology as well as its potential therapeutic benefits for hypothyroidism and autoimmune thyroiditis.

An Enhanced Computational Approach Using Multi-kernel Positive Unlabeled Learning for Predicting Drug-target Interactions.

Background: In recent years, analyzing complex biological networks to predict future links in such networks has attracted the attention of many medical and computer science researchers. The discovery of new drugs is one of the application cases for predicting future connections in biological networks. The operation of drug-target interactions prediction (DTIP) can be considered a fundamental step in identifying potential interactions between drug and target to identify new drugs.

Hit discovery of potential CDK8 inhibitors and analysis of amino acid mutations for cancer therapy through computer-aided drug discovery.

Cyclin-dependent kinase 8 (CDK8) has emerged as a promising target for inhibiting cancer cell function, intensifying efforts towards the development of CDK8 inhibitors as potential cancer therapeutics. Mutations in CDK8, a protein kinase, are also implicated as a primary factor associated with tumor formation. In this study, we identified potential inhibitors through virtual screening for CDK8 and single amino acid mutations in CDK8, namely D173A (Aspartate 173 mutate to Alanine), D189N (Aspartate 189 mutate to Asparagine), T196A (Threonine 196 mutate to Alanine) and T196D (Threonine 196 mutate to Aspartate).

Machine Learning-Guided Protein Engineering.

Recent progress in engineering highly promising biocatalysts has increasingly involved machine learning methods. These methods leverage existing experimental and simulation data to aid in the discovery and annotation of promising enzymes, as well as in suggesting beneficial mutations for improving known targets. The field of machine learning for protein engineering is gathering steam, driven by recent success stories and notable progress in other areas.

Colorimetric bacteria sensing of Pseudomonas aeruginosa using gold nanoparticle probes.

Background: Due to the advantages of molecular methods over biochemical methods, the use of molecular methods for diagnosing nosocomial infections such as Pseudomonas can be an appropriate and rapid way to choose the right diagnosis and treatment of infection and prevent further complications caused by the infection. The present article provides a description of the development of a nanoparticle-based detection technique for sensitive and specific deoxyribonucleic acid-based diagnostic of Pseudomonas aeruginosa. Specific thiolated oligonucleotide probes for one of the hypervariable regions of the 16S rDNA gene were designed and applied for colorimetric detection of the bacteria.

DTIP-TC2A: An analytical framework for drug-target interactions prediction methods.

Identifying drug-target interactions through computational methods is raised an important and key step in the process of drug discovery and drug-oriented research during the last years. In addition to the advantages of existing computational methods, there are also challenges that affect methods' efficiency and provide obstacles in the direction of developing these computational methods. However, the literature suffers from lacking a comprehensive and comparative analysis concerning drug-target interactions prediction (DTIP) focusing on the analysis of technical and challenging aspects.

Simple innovative adaptor to improve genome walking with convenient PCR.

Background: Various polymerase chain reaction (PCR)-based methods have been applied for the development of genome walking (GW) technique. These methods which could be based on the application of restriction enzymes or primers have various efficiencies to identify the unknown nucleotide sequences. The present study was conducted to design a new innovative double-strand adaptor using MAP30 gene sequence of Momordica charantia plant as a model to improve genome walking with convenient PCR.

Chromium Supplementation; Negotiation with Diabetes Mellitus, Hyperlipidemia and Depression.

Chromium (Cr) is an essential trace element which found naturally in a daily diet and available in the form of supplementary tablets to boost disorders like diabetes mellitus (DM) and functions like lipid metabolism and beneficial on depression too. Diabetes is one of the most prevalent endocrine diseases or in other words, the most severe metabolic syndrome (MS), which associated with high production of free-radicals which is out of bodies detoxifying machine capacity or high oxidative stress (HOS), vasculitis and elevated lipid profile. many research papers and clinical trials published about the significance of chromium on biological activities, pre and post clinical.

Moiré Flat Bands in Twisted Double Bilayer Graphene.

We investigate twisted double bilayer graphene (TDBG), a four-layer system composed of two AB-stacked graphene bilayers rotated with respect to each other by a small angle. Our ab initio band structure calculations reveal a considerable energy gap at the charge-neutrality point that we assign to the intrinsic symmetric polarization (ISP). We then introduce the ISP effect into the tight-binding parametrization and perform calculations on TDBG models that include lattice relaxation effects down to very small twist angles.

DTIP: A Comparative Analytical Framework for Chemogenomic Drugtarget Interactions Prediction.

Background: Prediction of drug-target interactions is an essential step in drug discovery. Given drug-target interactions network, the objective of this task is to predict probable missing edges from known interactions. Computationally predicting drug-target interactions is an appropriate alternative for the time-consuming and costly experimental process of drug-target interaction prediction.

Gold nanoparticle biosensors, a novel application in gene transformation and expression.

The conventional techniques of PCR, Southern blot, northern blot, in situ hybridization, and RNase protection assay have long been used to investigate transformation and expression of genes, but most of them are time-consuming and have relatively low sensitivity. In recent years, applying biosensors for molecular identification of biomolecules has been expanding significantly. Hence in this study, Zabol melon was used as a model plant to introduce new DNA and RNA-based biosensors for confirming gene transformation and expression.

Thiol-Capped Gold Nanoparticle Biosensors for Rapid and Sensitive Visual Colorimetric Detection of Klebsiella pneumoniae.

In the last few years, gold nanoparticle biosensors have been developed for rapid, precise, easy and inexpensive with high specificity and sensitivity detection of human, plant and animal pathogens. Klebsiella pneumoniae serotype K2 is one of the common gram-negative pathogens with high prevalence. Therefore, it is essential to provide the effective and exclusive method to detect the bacteria.

Simultaneous Expression of GUS and Actin Genes by Using the Multiplex RT-PCR and Multiplex Gold Nanoparticle Probes.

Gene expression analysis is considered to be extremely important in many different biological researches. DNA-based diagnostic test, which contributes to DNA identification, has higher specificity, cost, and speed than some biochemical and molecular methods. In this study, we try to use the novel nano technology approach with Multiplex RT-PCR and Gold nano particular probes (GNPs-probes) in order to get gene expression in Curcumas melons.

Thiolated AuNP probes and multiplex PCR for molecular detection of Staphylococcus epidermidis.

The emergence of nanotechnology in biology helps to apply the gold nanoparticle probes for fast and accurate identification of pathogens compared to the time-consuming and non-precise phenotypic methods. In this study, two molecular methods have been established for the accurate identification of staphylococcus epidermidis from other coagulase-negative staphylococci. Multiplex PCR was performed using designed primers for Gmk2 and pta housekeeping genes, and SESB specific gene of S.

Temporal Super Resolution Enhancement of Echocardiographic Images Based on Sparse Representation.

A challenging issue for echocardiographic image interpretation is the accurate analysis of small transient motions of myocardium and valves during real-time visualization. A higher frame rate video may reduce this difficulty, and temporal super resolution (TSR) is useful for illustrating the fast-moving structures. In this paper, we introduce a novel framework that optimizes TSR enhancement of echocardiographic images by utilizing temporal information and sparse representation.

An efficient Agrobacterium-mediated transformation of strawberry cv. Camarosa by a dual plasmid system.

An Agrobacterium-mediated transformation method was applied to introduce the luciferase reporter gene under the control of the CaMV35S promoter in the pGreen0049 binary vector into strawberry cv. Camarosa. The in vitro regeneration system of strawberry leaves to be used in the transformation was optimized using different TDZ concentrations in MS medium.

Breaking-off tissue specific activity of the oil palm metallothionein-like gene promoter in T(1) seedlings of tomato exposed to metal ions.

Metallothioneins (MTs) are cysteine-rich metal-binding proteins that are involved in cell growth regulation, transportation of metal ions and detoxification of heavy metals. A mesocarp-specific metallothionein-like gene (MT3-A) promoter was isolated from the oil palm (Elaeis guineensis Jacq). A vector construct containing the MT3-A promoter fused to the β-glucuronidase (GUS) gene in the pCAMBIA 1304 vector was produced and used in Agrobacterium-mediated transformation of tomato.