Biochemical Properties Research Articles

Conditional Optimization of Single Cell Protein Production from Crude Oil by <i>Pseudomonas aeruginosa</i>

The study was carried out to investigate the possible biodegradation of crude oil as a carbon by the bacterium <i>Pseudomonas aeruginosa</i> isolated from marine environment (Ras El-Menkar- Benghazi- Libya) using basal yeast extract protease peptone-3 (BYP) enriched medium. The isolated bacterium was identified and characterized according to its cultural condition and microbial biochemical properties. Different experiments were developed throughout this study to stimulate bacterial growth and production of single cell protein (SCP). The results show that the optimal concentration of crude oil as a carbon source for the highest bacterial growth (1.14g/l), and production of SCP (0.65g/l; 57.02% of the biomass dry weight) was 1%. This was required to utilize up to 50.6% of oil as a carbon source. As to the nitrogen source, the optimal concentration of ammonium chloride was 0.1%, in which the bacterial growth and SCP production increased to 1.23 g/l and 0.67 g/l respectively. The stimulating effects of organic and inorganic factors on the bacterial growth and SCP production was also tested. Addition of inorganic nutrients such as potassium phosphate (0.05%), magnesium sulphate (0.01%), and organic nutrient in the form of yeast extract (0.1%) to the fermentation medium slightly promoted the bacterial growth which reflected positively on SCP production and the percentage of the consumed crude oil, (>57%) at final pH value of 8.0. The obtained results indicated that the isolated<i> Pseudomonas aeruginosa</i> posses the ability to utilize the crude oil and use it as a carbon for bacterial growth and production of SCP.

Gilded vaterite particles: Synthesis, optical characterization, and label-free imaging

Inorganic nanoparticles are capable of accommodating multiple biomedical modalities, making them prime candidates for realizing light-responsive theranostic carriers. Within this realm, merging the benefits of diverse platforms promises the development of new functionalities, broadening the range of applications. While vaterite, a polymorph of calcium carbonate, is known for its structural versatility and chemical modifiability, gold nanoparticles are recognized for their unique optical properties. Here we explore a new mesoscopic particle, gilded vaterite, which encompasses the advantages of both platforms. A flexible synthesis method is developed and optimized, demonstrating the capability to obtain high-yield fabrication of vaterite particles with controllable form factors alongside tailored surface coverage with gold. Uniform reproducible distributions of gold nanoparticles of up to 80 nm in diameter, with coverage above 40%, were demonstrated. Optical properties of gilded vaterite particles were explored, revealing strong peaks, which built up owing to the resonant hybridization of near-field coupled plasmonic resonances. Confocal microscopy of cells was utilized to explore potential applications of gilded vaterite with tunable optical properties in the realm of label-free imaging. Strong light scattering from vaterite carriers, taken up by cells, alongside the fluorescence from stained cells, was observed via reflectance confocal microscopy. This dual-channel approach allows for simultaneous observation of the particles and their biological environment. Tunable optical and biochemical properties of gilded vaterite promote this perspective platform towards accommodating new modalities and thus becoming an intrinsically optical-responsive multifunctional system.

Functionalized Collagen I Membranes as a Bruch's Membrane Mimetic for Outer Retinal In Vitro Models.

Physiologically relevant in vitro models of the human outer retina are required to better elucidate the complex interplay of retinal tissue layers and investigate their role in retinal degenerative disorders. Materials currently used to mimic the function of Bruch's membrane fail to replicate a range of important structural, mechanical, and biochemical properties. Here, we detail the fabrication of a surface-functionalized, fibrous collagen I membrane. We demonstrate its ability to better replicate a range of important material properties akin to the function of human Bruch's membrane when compared with a commonly utilized synthetic polyethylene terephthalate alternative. We further reveal the ability of this membrane to support the culture of the ARPE-19 cell line, as well as human pluripotent stem cell-derived RPE-like cells and human umbilical vein endothelial cells. This material could provide greater physiological relevance to the native Bruch's membrane than current synthetic materials and further improve the outcomes of in vitro outer retinal models.

Physical, antibacterial, blood coagulation, and healing promotion evaluations of chitosan derivative-based composite films

Chitosan is a potentially suitable material for wound dressing, but is undesirably water-insoluble. Although chitosan can be modified to produce water-soluble derivatives, the best chitosan derivative for wound dressings remains unclear. The present study introduced three water-soluble chitosan derivatives, namely, carboxymethyl chitosan, quaternized chitosan (QCS), and carboxymethyl quaternized chitosan, and explored the physical properties, biochemical properties, and wound care effectiveness of films of these derivatives. The QCS-based film exhibited higher absorption ability, mechanical properties, water-vapor permeability, electroconductivity, and antioxidant capacity than the other films. Most importantly, the cationic quaternary ammonium groups facilitated the antibacterial activity (>95 %) and blood coagulant capacity of the QCS-based film. As this film also promoted wound healing, it presented as an ideal candidate for wound dressings.

Individual mangrove trees provide alternative reef fish habitat on backreefs

Mangrove trees occur in a variety of geomorphic and sedimentary settings. Yet, studies investigating their role as habitat providers often focus on the most common biophysical types, such as deltaic, estuarine, open coast or lagoonal mangroves on soft sediments, disregarding less typical environments. Here, we investigated the influence of individual mangrove trees growing on a consolidated backreef system (Laucala Bay, Fiji) on habitat use by reef fishes. Combining field surveys and an experiment, we quantified the extent to which reef mangrove trees serve as habitat for solitary or shoaling reef fishes. Using mangrove tree mimics, we disentangled effects attributable to the physical structure of trees from those related to their bio-chemical properties. We found that fish numbers were 3.7 times higher within close proximity to the mangrove trees than at control sites and correlated significantly with root system perimeter. The roots of larger trees sheltered aggregations of juveniles and adults at incoming and high tides. Mangrove trees and mimics attracted fishes alike. We show that mangrove trees on backreefs provide habitat for shoaling and adult reef fishes in addition to serving as nursery areas, an ecosystem service otherwise lacking on backreef areas with low structural complexity.

ETIOPATHOGENETIC REASONING OF URETHRAL MICROBIOTA REHABILITATION IN PATIENTS WITH ACUTE INFECTIOUS URETHRITIS

The microbiota of the male genitourinary tract is a complex dynamic system that has not been sufficiently studied. Unlike the microbiome of the female urethral mucosa, which is constantly changing, the taxonomic composition and population level of the male urethral microbiome is more stable and independent of age. The aim of the study. To improve the results of treatment of patients with inflammatory processes of the urethra by determining the taxonomic composition, population level and microscopic indicators of the "macroorganism-microbiome" ecosystem of the microbiota of the urethra in men with acute urethritis.Material and methods. The taxonomic composition and population level of the first portion of urine of 69 sexually mature men (average age 34.8±7.14 years) with acute infectious (nonspecific) urethritis were investigated. Isolation of conditionally pathogenic bacteria was carried out by the bacteriological method using optimal nutrient media, their pH, temperature and cultivation time for each taxon. The identification of isolated pure cultures was carried out according to morphological, tinctorial, cultural, biochemical properties, as well as signs of pathogenicity and antigenic structure. To determine the mechanisms of colonization of the mucous membrane of the urethra by conditionally pathogenic microorganisms, the microecological method was used.Research results. According to the taxonomic composition and the level of microecological indicators of the "macroorganism-microbiome" ecosystem of the urethra microbiota (Margalef's species richness index, Whittaker's species diversity index, and Simpson's and Berger-Parker's species dominance indices), vulgar (common), hemolytic, and enteropathogenic Escherichia coli, coagulase-positive staphylococcus. The leading role in the formation of urethritis is played by ordinary enterobacteria - E. coli, a slightly smaller etiological role in the formation of urethritis in men belongs to S. aureus (less by 17.83%), E. coli Hly+ (less by 28.35%), enteropathogenic Escherichia coli (by 83.12%). Other microorganisms have a minimal etiological role. Conclusions. Acute urethritis in men is a polyetiological disease. Enterobacteria E. coli, E. coli Hly+, enteropathogenic Escherichia coli, K. pneumoniae, S. aureus, S. epidermidis, S. viridans are involved in the formation of the inflammatory process of the urethra. The leading causative agents of acute urethritis in men are E. coli, S. aureus, E. coli Hly+, enteropathogenic escherichia, which belong to uropathogenic escherichia.

Evaluation of Turkish shallot genetic resources for morphological, biochemical and sensory properties

Evaluation of Turkish shallot genetic resources for morphological, biochemical and sensory properties

Physcomitrium patens flavodiiron proteins form heterotetrametric complexes

Flavodiiron proteins (FLVs) catalyze the reduction of oxygen to water by using electrons from Photosystem I (PSI). In several photosynthetic organisms such as cyanobacteria, green algae, mosses and gymnosperms, FLV-dependent electron flow protects PSI from over-reduction and consequent damage especially under fluctuating light conditions. In this work we investigated biochemical and structural properties of FLVA and FLVB from the model moss Physcomitrium patens. The two proteins, expressed and purified from Escherichia coli, bind both iron and flavin cofactors and show NAD(P)H oxidase activity as well as oxygen reductase capacities. Moreover, the co-expression of both FLVA and FLVB, coupled to a tandem affinity purification procedure with two different affinity tags, enabled the isolation of the stable and catalytically active FLVA/B hetero tetrameric protein complex with cooperative nature. The multimeric organization was shown to be stabilized by inter-subunit disulfide bonds. This investigation provides valuable new information on the biochemical properties of FLVs, with new insights into their in vivo activity.

Bioremediation of heavy metals by an unexplored bacterium, Pseudoxanthomonas mexicana strain GTZY isolated from aerobic-biofilm wastewater system.

We prompted to characterize a wastewater bacterium, Pseudoxanthomonas mexicana GTZY, that efficiently transforms toxic mercury and arsenic, explores its bioremediation capability, and reveals their relevant gene resistance operons. The isolated strain was characterized by its phylogenetic, biochemical, and phenotypic properties. The strain GTZY potentially removed 84.3% of mercury and their mercury volatilization (Hg(II) to Hg(0)) was confirmed using the X-ray film method, and its respective merA gene was PCR amplified. In addition, strain GTZY efficiently removed arsenate (68.5%) and arsenite (63.2%), and showed resistance up to > 175 and > 55mM, respectively. Their genomic annotations disclosed the linkage of Tn2-transposon and int1 in both ends of mer operon (merAPTR). The co-existence of arsP and arsH proteins in its intrinsic ars operon (arsCPRH) was extremely diverse from its ancestral species. We believe that the mercury resistance-conferring mer operon of P. mexicana GTZY presumably derived horizontally from other species in the reactor, while the arsenic resistance-conferring intrinsic ars operon was highly diversified and evolved from its ancestral species. By considering the potential of the strain GTZY to transform heavy metals, this can be used to recover contaminated sites.

Kiphynet: an online network simulation tool connecting cellular kinetics and physiological transport.

Human metabolism is sustained by functional networks that operate at diverse scales. Capturing local and global dynamics in the human body by hierarchically bridging multi-scale functional networks is a major challenge in physiological modeling. To develop an interactive, user-friendly web application that facilitates the simulation and visualization of advection-dispersion transport in three-dimensional (3D) microvascular networks, biochemical exchange, and metabolic reactions in the tissue layer surrounding the vasculature. To help modelers combine and simulate biochemical processes occurring at multiple scales, KiPhyNet deploys our discrete graph-based modeling framework that bridges functional networks existing at diverse scales. KiPhyNet is implemented in Python based on Apache web server using MATLAB as the simulator engine. KiPhyNet provides the functionality to assimilate multi-omics data from clinical and experimental studies as well as vascular data from imaging studies to investigate the role of structural changes in vascular topology on the functional response of the tissue. With the network topology, its biophysical attributes, values of initial and boundary conditions, parameterized kinetic constants, biochemical species-specific transport properties such as diffusivity as inputs, a user can use our application to simulate and view the simulation results. The results of steady-state velocity and pressure fields and dynamic concentration fields can be interactively examined. KiPhyNet provides barrier-free access to perform time-course simulation experiments by building multi-scale models of microvascular networks in physiology, using a discrete modeling framework. KiPhyNet is freely accessible at http://pallab.cds.iisc.ac.in/kiphynet/ and the documentation is available at https://deepamahm.github.io/kiphynet_docs/ .

Standardization of Process Variables for the Development of Osmo-dehydrated Coconut Haustorium

Background: Coconut (Cocos nucifera L.) is considered a highly valuable and beneficial perennial crop in our country. The basal portion of the coconut embryo enlarges during germination and forms a spongy structure, haustorium, which is an excellent source of essential nutrients. Since consumer preference is shifting towards healthy food and processed coconut products have immense scope in this sector, the study was conducted to standardize the process variables for osmo-dehydration of coconut haustorium and to evaluate the nutritional qualities of the osmo-dehydrated product. Methods: The present study involved the development of osmo-dehydrated coconut haustorium by standardizing the process variables, viz., osmotic solution concentration and immersion time. Mass transfer, physical, biochemical and sensory parameters were analysed to evaluate the nutritional qualities and consumer acceptance. Result: The results on biochemical properties revealed that an increase in concentration and time of immersion increased TSS, total sugar, reducing sugar, ash and mineral content. The process variables were standardized for the development of osmo-dehydrated coconut haustorium with optimum mass transfer characters, better nutritional qualities and consumer acceptance, which has application in the food industry.

The unusual structural properties and potential biological relevance of switchback DNA

Synthetic DNA motifs form the basis of nucleic acid nanotechnology. The biochemical and biophysical properties of these motifs determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.

Rheological and Biochemical Properties of Blood in Runners: A Preliminary Report

Purpose: Physical activity induces numerous modifications in the morphological, rheological, and biochemical properties of blood. The purpose of this study was to evaluate changes in blood rheological and biochemical indicators among runners. Also, we assessed how the rheological and biochemical properties of blood in people who practised running characterised the range and direction of exercise modifications and allowed for the diagnosis of transient adaptive effects. Methods: This study included 12 athletes who regularly trained in middle- and long-distance running (6–8 times a week) and presented a high sports level (national and international class). The athletes performed a 30 min warm-up consisting of 15 min of jogging and exercises. After a 10 min rest, they completed a 3 km run with submaximal effort. Blood samples were collected at baseline and after the effort. Results: No statistically significant changes were revealed in erythrocyte, leukocyte, platelet, iron, ferritin, transferrin, erythropoietin, or C-reactive protein concentrations in the examined runners. The same applied to the elongation index at a shear stress within the range of 0.30–60.00 Pa, amplitude and total extent of aggregation, aggregation half-life, and aggregation index. A significant increase (within standard limits) was only observed in fibrinogen concentration after running. Conclusions: The lack of post-exercise changes in blood rheological and biochemical indicators in the investigated runners points at an efficient haemorheological system. This, in turn, reflects well-executed training and remarkably well-trained adaptive systems responsible for regeneration.

In Silico Deciphering of the Potential Impact of Variants of Uncertain Significance in Hereditary Colorectal Cancer Syndromes.

Colorectal cancer (CRC) ranks third in terms of cancer incidence worldwide and is responsible for 8% of all deaths globally. Approximately 10% of CRC cases are caused by inherited pathogenic mutations in driver genes involved in pathways that are crucial for CRC tumorigenesis and progression. These hereditary mutations significantly increase the risk of initial benign polyps or adenomas developing into cancer. In recent years, the rapid and accurate sequencing of CRC-specific multigene panels by next-generation sequencing (NGS) technologies has enabled the identification of several recurrent pathogenic variants with established functional consequences. In parallel, rare genetic variants that are not characterized and are, therefore, called variants of uncertain significance (VUSs) have also been detected. The classification of VUSs is a challenging task because each amino acid has specific biochemical properties and uniquely contributes to the structural stability and functional activity of proteins. In this scenario, the ability to computationally predict the effect of a VUS is crucial. In particular, in silico prediction methods can provide useful insights to assess the potential impact of a VUS and support additional clinical evaluation. This approach can further benefit from recent advances in artificial intelligence-based technologies. In this review, we describe the main in silico prediction tools that can be used to evaluate the structural and functional impact of VUSs and provide examples of their application in the analysis of gene variants involved in hereditary CRC syndromes.

Salmonella Prevalence and antibiotic resistance profile in raw poultry meat sold in North Lebanon: Insights from the COVID-19 pandemic and economic crisis

Salmonella-related foodborne illness is a significant public health concern, with the primary source of human infection being animal-based food products, particularly chicken meat. Lebanon is currently experiencing a dual crisis: the COVID-19 pandemic and an unprecedented economic crisis, which has resulted in substantial challenges to the public health system and food safety. This study aims to assess the prevalence and antibiotic resistance profile of Salmonella in raw poultry meat sold in North Lebanon during this dual crisis. A cross-sectional study was carried out between May 2021 and April 2022 across six different districts in North Lebanon. A total of 288 whole, unprocessed chickens were examined. The isolation and identification of Salmonella isolates were done based on cultural and biochemical properties. All isolates were subjected to antimicrobial susceptibility testing and phenotypic assays for Extended-Spectrum Beta-lactamase (ESBL) detection. The prevalence of Salmonella in raw poultry meat purchased in North Lebanon reached 18.05 % (52/288). The dry season and chilled chicken were significantly associated with an increased risk of Salmonella contamination (P < 0.05). Additionally, 34.61 % of the isolates were potential ESBL producers, and 57.69 % exhibited multidrug resistance (MDR). This study highlights the existence of MDR in chicken meat in North Lebanon, posing a potential health risk if undercooked chicken meat is consumed. This emphasizes the importance of the implementation of preventive strategies and hygienic procedures throughout the food chain to reduce the risk of Salmonella spp. contamination in chicken meats and its potential transmission to humans.

Sequence, Structure, and Functional Space of Drosophila De Novo Proteins.

During de novo emergence, new protein coding genes emerge from previously nongenic sequences. The de novo proteins they encode are dissimilar in composition and predicted biochemical properties to conserved proteins. However, functional de novo proteins indeed exist. Both identification of functional de novo proteins and their structural characterization are experimentally laborious. To identify functional and structured de novo proteins in silico, we applied recently developed machine learning based tools and found that most de novo proteins are indeed different from conserved proteins both in their structure and sequence. However, some de novo proteins are predicted to adopt known protein folds, participate in cellular reactions, and to form biomolecular condensates. Apart from broadening our understanding of de novo protein evolution, our study also provides a large set of testable hypotheses for focused experimental studies on structure and function of de novo proteins in Drosophila.

Impact of Harvesting Time on Grain Yield, Physicochemical Attributes, and 2-Acetyl-1-pyrroline Biosynthesis in Aromatic Rice

Achieving a consistent grain yield while preserving persistent aroma remains a substantial challenge in aromatic rice production in Bangladesh. To address this challenge, a field experiment was conducted at the agronomy research area of Sher-e-Bangla Agricultural University, Dhaka-1207, between 15 June 2022, and 25 November 2022 (Aman season). This study aimed to evaluate the influence of harvesting time on aromatic rice performance. The experiment, following a randomized complete block design with three replications, involved two factors: factor 1 comprised various rice varieties [Bangladesh Rice Research Institute (BRRI) dhan34, BRRI dhan70, BRRI dhan80, and Tulshimala], and factor 2 comprised three harvesting times [3, 4, and 5 weeks after flowering (WAF)]. Results revealed significant impacts of variety and/or harvesting time on grain yield, physicochemical characteristics, and aroma of aromatic rice. Notably, Tulshimala and BRRI dhan80 exhibited superior milling quality, biochemical properties, and aroma characteristics among the aromatic rice types. BRRI dhan70 and BRRI dhan80 displayed higher grain yield when harvested at 5 WAF. However, Tulshimala and BRRI dhan80 showed superiority in grain 2-acetyl-1-pyrroline (2-AP) concentration when harvested 3 or 4 WAF. Earlier harvesting at 3 and 4 WAF resulted in higher percentages of grain 2-AP (60.22% and 53.96%, respectively) compared with later harvesting at 5 WAF (used as check). In conclusion, varying harvesting times markedly impact the yield, physiochemical characteristics, and aroma of aromatic rice varieties, with earlier harvesting beneficial for aroma retention in Tulshimala and BRRI Dhan80 and later harvesting for increased economic yield in BRRI dhan70 and BRRI dhan80.

Enhancing Solanum lycopersicum Resilience: Bacterial Cellulose Alleviates Low Irrigation Stress and Boosts Nutrient Uptake.

The use of natural-origin biomaterials in bioengineering has led to innovative approaches in agroforestry. Bacterial cellulose (BC), sharing the same chemical formula as plant-origin cellulose (PC), exhibits significantly different biochemical properties, including a high degree of crystallinity and superior water retention capacity. Previous research showed that natural-origin glucose-based chitin enhanced plant growth in both herbaceous and non-herbaceous plants. In this study, we produced BC in the laboratory and investigated its effects on the substrate and on Solanum lycopersicum seedlings. Soil amended with BC increased root growth compared with untreated seedlings. Additionally, under limited irrigation conditions, BC increased global developmental parameters including fresh and dry weight, as well as total carbon and nitrogen content. Under non-irrigation conditions, BC contributed substantially to plant survival. RNA sequencing (Illumina®) on BC-treated seedlings revealed that BC, despite its bacterial origin, did not stress the plants, confirming its innocuous nature, and it lightly induced genes related to root development and cell division as well as inhibition of stress responses and defense. The presence of BC in the organic substrate increased soil availability of phosphorus (P), iron (Fe), and potassium (K), correlating with enhanced nutrient uptake in plants. Our results demonstrate the potential of BC for improving soil nutrient availability and plant tolerance to low irrigation, making it valuable for agricultural and forestry purposes in the context of global warming.

Soluble Human Lectins at the Host-Microbe Interface.

Human lectins are integral to maintaining microbial homeostasis on the skin, in the blood, and at mucosal barriers. These proteins can recognize microbial glycans and inform the host about its microbial status. In accordance with their roles, their production can vary with tissue type. They also can have unique structural and biochemical properties, and they can influence microbial colonization at sites proximal and distal to their tissue of origin. In line with their classification as innate immune proteins, soluble lectins have long been studied in the context of acute infectious disease, but only recently have we begun to appreciate their roles in maintaining commensal microbial communities (i.e., the human microbiota). This review provides an overview of soluble lectins that operate at host-microbe interfaces, their glycan recognition properties, and their roles in physiological and pathological mechanisms.

Leucine-Rich Repeat Kinases.

Activating mutations in leucine-rich repeat kinase 2 (LRRK2) represent the most common cause of monogenic Parkinson's disease. LRRK2 is a large multidomain protein kinase that phosphorylates a specific subset of the ∼65human Rab GTPases, which are master regulators of the secretory and endocytic pathways. After phosphorylation by LRRK2, Rabs lose the capacity to bind cognate effector proteins and guanine nucleotide exchange factors. Moreover, the phosphorylated Rabs cannot interact with their cognate prenyl-binding retrieval proteins (also known as guanine nucleotide dissociation inhibitors) and, thus, they become trapped on membrane surfaces. Instead, they gain the capacity to bind phospho-Rab-specific effector proteins, such as RILPL1, with resulting pathological consequences. Rab proteins also act upstream of LRRK2 by controlling its activation and recruitment onto membranes. LRRK2 signaling is counteracted by the phosphoprotein phosphatase PPM1H, which selectively dephosphorylates phospho-Rab proteins. We present here our current understanding of the structure, biochemical properties, and cell biology of LRRK2 and its related paralog LRRK1 and discuss how this information guides the generation of LRRK2 inhibitors for the potential benefit of patients.