R. Howard, E. Abotsi, Elbert L Jansen Van Rensburg
et al.
This review is written from the perspective of scientists working in lignocellulose bioconversion in a developing country and the aim of this review is to remind ourselves and other scientists working in related areas of lignocellulose research of the enormous economic potential of the bioprocessing of residual plant materials generally regarded as “waste”, and secondly to highlight some of the modern approaches which potentially could be used to tackle one of the major impediments, namely high enzyme cost, to speed-up the extensive commercialisation of the lignocellulose bioprocessing. Key words : lignocellulose, bioconversion, enzyme cost. African Journal of Biotechnology Vol. 2 (12), pp. 602-619, December 2003
In this study, we implement thiol termination on the surface of few-nanometer-sized silicon carbide (SiC) nanoparticles (NPs) to enable further applications, such as fluorescent biomarkers. Various spectroscopic techniques are employed to monitor the effectiveness of the surface treatment. A thiol-Michael addition reaction is performed by conjugating 4-arm PEGmaleimide molecules to the thiol groups of SiC NPs, further demonstrating the reactivity of thiol-terminated SiC NPs, which also acts as a protection layer against oxidation. These fluorescent thiolated SiC NPs, both with and without conjugated molecules, are directly applicable as bioinert probes. Since SiC NPs can potentially host room-temperature fluorescent defect quantum bits, our results are an important step to realize a bioinert, ultrasmall quantum sensor bioagents, which may open new avenues in biotechnology.
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in biophysics, biotechnology, and medicine. One effective approach to uncovering photoactive processes is through computational methods. These techniques provide atomic-level insights into the structural, electronic, and dynamic changes that occur upon light absorption. By employing these methods, we can gain a better understanding of processes that are challenging to capture experimentally, such as chromophore isomerization and protein conformational changes. Here, we provide a brief overview of the different families of photoactive proteins and the computational methods used to study them, including bioinformatics, molecular dynamics, and enhanced sampling. Our review can serve as an introduction to computational methods for studying light-activated molecular processes, specifically targeting researchers beginning their journey in this field.
Clear and effective explanations are essential for human understanding and knowledge dissemination. The scope of scientific research aiming to understand the essence of explanations has recently expanded from the social sciences to machine learning and artificial intelligence. Explanations for machine learning decisions must be impactful and human-like, and there is a lack of large-scale datasets focusing on human-like and human-generated explanations. This work aims to provide such a dataset by: extracting sentences that indicate explanations from scientific literature among various sources in the biotechnology and biophysics topic domains (e.g. PubMed's PMC Open Access subset); providing a multi-class notation derived inductively from the data; evaluating annotator consensus on the emerging categories. The sentences are organized in an openly-available dataset, with two different classifications (6-class and 3-class category annotation), and the 3-class notation achieves a 0.667 Krippendorf Alpha value.
Polycyclic aromatic hydrocarbons (PAHs) are recognized carcinogens that enter the food chain through pre-existing environmental contamination (air, water, soil), and their formation and accumulation during food preparation and processing involve high temperatures. We established a modified QuEChERS GC-MS method that couples <i>n</i>-hexane-saturated acetonitrile containing 1% toluene with a freeze-out step. Compared to the previously reported ACN QuEChERS protocol, this method enhanced PAH desorption and suppressed lipid interference across four matrices. The method linearity (R<sup>2</sup> ≥ 0.99), limit of detection (LOD, from 0.03 to 0.20 μg/kg), limit of quantitation (LOQ, from 0.10 to 0.60 μg/kg), and intra-/inter-day precision (≤5.7% RSD) all satisfied AOAC criteria. The modified QuEChERS reduced solvent consumption and shortened preparation time compared to other conventional extraction methods. The developed method was applied to 302 retail food samples, and <i>Kezuribushi</i> was found to have the highest concentration of the 4PAHs, reaching 22.0 µg/kg. Risk assessment based on EFSA’s margin-of-exposure (MOE) approach identified grilled chicken feet (MOE = 7604) as a potential health concern, as this value falls below EFSA’s threshold of 10,000 for potential risk characterization. The validated method enables sensitive and scalable monitoring of PAHs in complex food matrices within the tested matrices and conditions.
Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we proposed a novel method that utilized autoencoder shaped models to explore the protein embedding space, and generate novel peptide analogs by leveraging protein language models. The proposed method requires only a single sequence of interest, avoiding the need for large datasets. Our results show significant improvements over baseline models in similarity indicators of peptide structures, descriptors and bioactivities. The proposed method validated through Molecular Dynamics simulations on TIGIT inhibitors, demonstrates that our method produces peptide analogs with similar yet distinct properties, highlighting its potential to enhance peptide screening processes.
Konstantin S. Kolegov, Irina V. Vodolazskaya, Andrei V. Eserkepov
et al.
The ability to control the morphology of the nanotube deposit formed during the evaporation of a sessile droplet on a substrate is of theoretical and practical interest. Such deposits are required for various applications including nanotechnology, medicine, biotechnology, and optronics. In the experiment of Zhao et al. [J. Colloid Interface Sci. 440, 68 (2015)], an annular deposit was formed near the contact line. The deposition geometry is caused by the coffee ring effect. This deposit is unusual in its morphology. It changes gradually in space from a disordered structure in the inner part of the ring to an aligned structure of nanotubes close to the periphery. To understand the mechanisms that lead to this, we have developed a mathematical model that takes into account the effects of advection, diffusion, and electrostatic interactions on particle transport. Results of numerical calculations have confirmed that all these factors together have an influence on the formation of such a variable morphology. Qualitative agreement with the experiment is shown for some values of the model parameters.
Afsha Fatima Qadri, Sibhghatulla Shaikh, Ye Chan Hwang
et al.
Glycyrrhiza uralensis is a traditional herbal medicine with significant bioactivity. This study investigated the effect of G. uralensis crude water extract (GU-CWE) on nitric oxide synthase 2 (NOS2) expression during myogenesis. GU-CWE treatment increased myoblast differentiation by downregulating NOS2 and upregulating myogenic regulatory factors (MYOD, MYOG, and MYH). Notably, this effect was supported by an observed decrease in NOS2 expression in the gastrocnemius tissues of mice treated with GU-CWE. In addition, GU-CWE treatment and NOS2 knockdown were associated with reductions in reactive oxygen species levels. We further elucidate the role of the NOS2 gene in myoblast differentiation, demonstrating that its role was expression dependent, being beneficial at low expression but detrimental at high expression. High NOS2 gene expression induced oxidative stress, whereas its low expression impaired myotube formation. These findings highlight that the modulation of NOS2 expression by G. uralensis can potentially be use for managing muscle wasting disorders.