The Prognostic and Therapeutic Potential of Fragile X Mental Retardation 1 (FMR1) Gene Expression in Prostate Adenocarcinoma: Insights into Survival Outcomes and Oncogenic Pathway Modulation.

Prostate adenocarcinoma (PRAD) is the second most common tumor associated with death. The role and mechanisms of the fragile X mental retardation 1 (FMR1) gene in PRAD remain unknown. We conducted an analysis of FMR1 expression in PRAD to determine its prognostic importance and connection to carcinogenic pathways such as PI3K_AKT_mTOR. Survival analyses were utilized to establish a correlation between FMR1 expression and patient outcomes. We used the integration of genomic data with bioinformatic predictions to predict the regulatory factors of the FMR1 gene in PRAD. Our data revealed that individuals with higher levels of FMR1 expression experience worse survival outcomes compared to those with lower expression (hazard ratio [HR] = 5.08, 95% confidence interval [CI] = 1.07 - 24, p = 0.0412). FMR1 expression was significantly higher in patients with advanced pathological tumor stages, particularly in the pT3 and pT4 combined stages and the pN1 nodal stage. Furthermore, patients with high Gleason scores (GSs) (combined GSs 8 and 9) exhibited increased levels of FMR1 expression. Our results further identify a possible regulatory link between FMR1 and key oncogenic pathways, including PI3K_AKT_mTOR, and predict the possible mechanism by which FMR1 is regulated in PRAD. Our data suggest that the FMR1 gene could serve as a biomarker for PRAD progression. However, in-depth investigations, including those with large patient samples and in vitro studies, are needed to validate this finding and understand the mechanisms involved.

Characterisation of Flavour Attributes in Egg White Protein Using HS-GC-IMS Combined with E-Nose and E-Tongue: Effect of High-Voltage Cold Plasma Treatment Time.

Egg white protein (EWP) is susceptible to denaturation and coagulation when exposed to high temperatures, adversely affecting its flavour, thereby influencing consumers' decisions. Here, we employ high-voltage cold plasma (HVCP) as a novel nonthermal technique to investigate its influence on the EWP's flavour attributes using E-nose, E-tongue, and headspace gas-chromatography-ion-mobilisation spectrometry (HS-GC-IMS) due to their rapidness and high sensitivity in identifying flavour fingerprints in foods. The EWP was investigated at 0, 60, 120, 180, 240, and 300 s of HVCP treatment time. The results revealed that HVCP significantly influences the odour and taste attributes of the EWP across all treatments, with a more significant influence at 60 and 120 s of HVCP treatment. Principal component analyses of the E-nose and E-tongue clearly distinguish the odour and taste sensors' responses. The HS-GC-IMS analysis identified 65 volatile compounds across the treatments. The volatile compounds' concentrations increased as the HVCP treatment time was increased from 0 to 300 s. The significant compounds contributing to EWP characterisation include heptanal, ethylbenzene, ethanol, acetic acid, nonanal, heptacosane, 5-octadecanal, decanal, p-xylene, and octanal. Thus, this study shows that HVCP could be utilised to modify and improve the EWP flavour attributes.

Allele frequency deviation (AFD) as a new prognostic model to predict overall survival in lung adenocarcinoma (LUAD).

BACKGROUND: Lung adenocarcinoma (LUAD) remains one of the world's most known aggressive malignancies with a high mortality rate. Molecular biological analysis and bioinformatics are of great importance as they have recently occupied a large area in the studies related to the identification of various biomarkers to predict survival for LUAD patients. In our study, we attempted to identify a new prognostic model by developing a new algorithm to calculate the allele frequency deviation (AFD), which in turn may assist in the early diagnosis and prediction of clinical outcomes in LUAD. METHOD: First, a new algorithm was developed to calculate AFD using the whole-exome sequencing (WES) dataset. Then, AFD was measured for 102 patients, and the predictive power of AFD was assessed using Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, and area under the curve (AUC). Finally, multivariable cox regression analyses were conducted to evaluate the independence of AFD as an independent prognostic tool. RESULT: The Kaplan-Meier analysis showed that AFD effectively segregated patients with LUAD into high-AFD-value and low-AFD-value risk groups (hazard ratio HR = 1.125, 95% confidence interval CI 1.001-1.26, p = 0.04) in the training group. Moreover, the overall survival (OS) of patients who belong to the high-AFD-value group was significantly shorter than that of patients who belong to the low-AFD-value group with 42.8% higher risk and 10% lower risk of death for both groups respectively (HR for death = 1.10; 95% CI 1.01-1.2, p = 0.03) in the training group. Similar results were obtained in the validation group (HR = 4.62, 95% CI 1.22-17.4, p = 0.02) with 41.6%, and 5.5% risk of death for patients who belong to the high and low-AFD-value groups respectively. Univariate and multivariable cox regression analyses demonstrated that AFD is an independent prognostic model for patients with LUAD. The AUC for 5-year survival were 0.712 and 0.86 in the training and validation groups, respectively. CONCLUSION: AFD was identified as a new independent prognostic model that could provide a prognostic tool for physicians and contribute to treatment decisions.

Characterization of a uronate dehydrogenase from Thermobispora bispora for production of glucaric acid from hemicellulose substrate.

A thermostable uronate dehydrogenase Tb-UDH from Thermobispora bispora was over-expressed in Escherichia coli using the T7 polymerase expression system. The Tb-UDH was purified by metal affinity chromatography, and gave a single band on SDS-PAGE. The maximum activity on glucuronic acid was found at 60 °C and pH 7.0. The purified enzyme retained over 58% of its activity after holding a pH ranging from 7.0 to 7.5 for 1 h at 60 °C. The Km and Vmax values of the purified Tb-UDH for Glucuronic acid (GluUA) were 0.165 mM and 117.7 U mg-1, respectively, those for galacturonic acid (GalUA) were 0.115 mM and 104.2 U mg-1, respectively, and those for NAD+ were 0.120 mM and 133.3 U mg-1, respectively; the turnover number (kcat) with GluUA as a substrate was higher than that with GalUA; however, the Michaelis constant (Km) for GalUA was lower than that for GluUA. After 60 min of incubation at 50 °C, Tb-UDH exhibited a conversion ratio for glucuronic acid to the glucaric acid of 84% on chemical reagent and 81.3% on hydrolysates from breech xylans formed by xylanase and α-glucuronidase. This work shows that biocatalytic routes have great potential for the conversion of hemicellulose substrate into value-added products derived from renewable biomass. TOC GRAPHIC: (A) The structure of the xylan is described and the site of action of the xylan degrading enzyme is indicated. (B) The effect of substrate concentration on recombinant Tb-UDH activity when galacturonic acid was used as substrate. (C) SDS-PAGE analysis of E. coli BL21 (DE3) harboring pET-20b(+) and pET-20b-Tb-UDH. (D) Oxidative conversion of glucuronic acid from a beechwood xylan to glucaric acid.

A novel carboxymethyl cellulose/gum xanthan and citric acid-based film that enhances the precision of blackcurrant anthocyanin-induced color detection for beef spoilage tracking.

Leveraging blackcurrant anthocyanin (BC) as an indicator and carboxymethyl cellulose (CMC), gum xanthan (GX), and citric acid (CA) as film fabricating materials, an innovative amine-responsive beef freshness intelligent film, known as CGC-BC, was successfully created. It was found that the physical characteristics, sensitivity to the biogenic amine reaction, and original color of the film were all highly influenced by the pH of the film-forming solutions. The film's freshness monitoring ability was assessed at 4, 25, and 35 °C, and various color changes were employed to monitor beef deterioration. ΔE values and the visual color difference of the low-concentration (SCG-BC-0.08 and SCG-BC-0.16) ammonia-sensitive indicator films demonstrated significant color changes than the high-concentration (SCG-BC-0.24 and SCG-BC-0.32) films. The films biodegradation (37.16 to 51.49%) ability was enhanced with increase in the proportions of BC. As the TVB-N and pH values of beef increased with the different temperatures and time and different color changes were observed from red to pink, black to brown, and yellow.

A new natural drying method for food packaging and preservation using biopolymer-based dehydration film.

A new method for the drying of beef and chicken meats at low temperatures (4 °C) was developed by using a composite film based on sodium carboxymethyl cellulose-gum Arabic (SG) with anthocyanins from Cinnamomum camphora fruit peel (ANC.P, 0, 1, 1.5 and 2%). After incorporation of ANC.P into SG, the physicochemical properties, morphological characteristics, melting, molecular, antioxidant and antimicrobial properties of the resulting dehydration films were improved. Film-dried beef and chicken slices showed higher values of dehydration ratio on day 6 (54.58% and 72.06%, respectively) compared with the control samples without film (4.55% and 7.04%, respectively). Results showed that SG-ANC.P film-dried meats exhibited more stable pH and color, higher rehydration rate, better sensory quality and microbial growth inhibition compared with SG film-dried samples and control samples, in which control samples showed the highest total viable count values (6.02 and 5.16 log CFU/mL for beef and chicken, respectively) during storage.

Impacts of nano-titanium dioxide toward Vallisneria natans and epiphytic microbes.

In this study, Vallisneria natans plants were exposed to 5 and 20 nm of titanium dioxide nanoparticles (TiO2 NPs) anatase and 600-1000 nm of bulk at 5 and 20 mg/L for 30 days. SEM images and EDX spectra revealed that epiphytic biofilms were more prone to TiO2 NPs adhesion than bare plant leaves. TiO2 NPs injured plant leaf cells, ruptured epiphytic diatoms membranes and increased the ratio of free-living microbes. The TN, NH4⁺-N and NO3--N concentrations significantly decreased, respectively, by 44.9%, 33.6%, and 23.6% compared to bulk treatments after 30 days due to macrophyte damage and a decline in diversity of epiphytic bacterial community and abundance of nitrogen cycle bacteria. TiO2 NPs size-dependent decrease in bacterial relative abundance was detected, including phylum Cyanobacteria, Planctomycetes, and Verrucomicrobia. Although TiO2 NPs increased eukaryotic diversity and abundance, abundances of Bacillariophyceae and Vampyrellidae classes and Gastrotricha and Phragmoplastophyta phylum decreased significantly under TiO2 NPs exposure compared to bulk and control. TiO2 NPs reduced intensities of interaction relationships among epiphytic microbial genera. This study shed new light on the potential effects of TiO2 NPs toxicity toward aquatic plants and epiphytic microbial communities and its impacts on nitrogen species removal in wetlands.

Prediction and evaluation of the 3D structure of Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and its interaction with palmitoleic acid or oleic acid: An integrated computational approach.

This study investigated the physicochemical properties and 3D structure of Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and its interaction with palmitoleic acid (POA) or oleic acid (OA) in macadamia oil. The 3D structure of MiAMP2 was constructed for the first time by ab initio modelling using the TrRosetta server. The results showed that MiAMP2 was highly hydrophilic and had seven disulfide bonds and higher α-helix and ß-sheet/turn contents. Molecular simulation showed that the hydrophobic pocket of MiAMP2 created a favourable environment for the binding of POA and OA. Free energy landscape and independent gradient model (IGM) analyses revealed that hydrogen bonds and van der Waals forces were the major driving forces stabilizing complexes formed by MiAMP2 and POA or OA. The present study provides a theoretical basis and new insight for the future development and utilization of macadamia nut protein in the food industry.

Large batch production of Galactooligosaccharides using ß-glucosidase immobilized on chitosan-functionalized magnetic nanoparticle.

ß-glucosidase (BglA) immobilization from Thermotoga maritima on magnetic nanoparticles (MNPs) functionalized with chitosan (Cs) were efficiently investigated to improve lactose conversion and galactooligosaccharides (GOS) production. We used a batch method in order to improve the conversion of lactose to GOS. The efficiency and yield of immobilization were 79% and immobilized BglA was effectively recycled via a magnetic separation procedure through a batch-wise GOS with no activity lessening. Furthermore, analyses were done through screening kinetics of enzyme activity, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Fourier transform infrared spectroscopy (FT-IR), and transmission electron microscopy (TEM). Proposed methodology of immobilization shows a potential application as it is stable which was proved through many methods including pH, temperature, heat treatment, storage, and kinetics of the enzyme. GOS and residual enzyme activity showed to be 28.76 and 40.44%, respectively. However, free enzyme synthesis of GOS yield was just 24% after 12 hr. This study proposed applying magnet in the immobilization process of BglA on Cs-MNPs to produce GOS as new method for immobilizing enzyme in a biostable and cost-efficient way. PRACTICAL APPLICATIONS: This paper focus on immobilization of BglA from T. maritima onto MNPs functionalized with CS to investigate their further possibility improving lactose conversion and GOS production. Interestingly, a successful immobilization of Tm-BglA on the substrates were achieved in Cs-MNPs. The obtained results from enzyme activity, SDS-PAGE, FT-IR, and TEM showed that the high binding capacity of BglA to Cs-MNPs was successfully obtained. Furthermore, the binding efficiency calculation indicated that the immobilized BglA-Cs-MNPs conserved 40.44% of its native activity at the end of its 6th repeated use. In addition, magnetic separation technique was successfully employed for reuse of the immobilized BglA for repetitive batch-wise GOS without significant loss of activity.

The nitrogen and phosphorus footprints of food products in Yemen over the last 57 years.

Food nitrogen (N) and phosphorus (P) footprints are indicators for determining the losses of N and P over food production (FP) and food consumption (FC) chain. Yemen is an interesting case because, given the country's heavy dependence on food imports, food insecurity, and poverty, the N footprint (NF) and P footprint (PF) could affect its future development. However, NF and PF over time have not yet been studied in Yemen. Therefore, this is the first paper to compute the NF and PF in Arabian Peninsula (a case study from Yemen) by an adjusted model of N-Calculator, by computing virtual N (VNFs) and virtual P (VPFs) factors for main foodstuffs. The NF (kg N cap-1 year-1) and PF (kg P cap-1 year-1) elevated from 5.56 and 1.20 in the 1960s to 15.2 and 4.79 during 2011-2017, respectively, while the national NF (Gg [109 g] N year-1) and national PF (Gg P year-1) increased from 27.7 and 6.77 in the 1960s to 358 and 122 during 2011-2017, respectively. Cereal was the largest contributor to the NF and PF in Yemen over the past 57 years. FP contributes approximately 80% and 86% of the total NF and PF during 2011-2017. Therefore, if possible, the best way for consumers and farmers in Yemen to decrease NF and PF is to focus efforts on increasing FP and FC of foodstuffs with less VNFs and VPFs. The consumption of vegetable-fruit, legumes, starchy, eggs, poultry, and fish should be increased as their NF and PF are low. However, people in Yemen suffer from shortage of resources and lack of awareness, and thus they do not have the opportunity to choose foodstuffs that are low in NF and PF. Accordingly, policymakers should encourage integrated approaches that introduce powerful tools for controlling crop and livestock production in conjunction with enhancements in nutrient use efficiency.

The Importance of Nitric Oxide as the Molecular Basis of the Hydrogen Gas Fumigation-Induced Alleviation of Cd Stress on Ganoderma lucidum.

Whether or not hydrogen gas (H2) can reduce cadmium (Cd) toxicity in Ganoderma lucidum has remained largely unknown. Here, we report that Cd-induced growth inhibition in G. lucidum was significantly alleviated by H2 fumigation or hydrogen-rich water (HRW), evaluated by lower oxidative damage and Cd accumulation. Moreover, the amelioration effects of H2 fumigation were better than of HRW in an optimum concentration of H2 under our experimental conditions. Further results showed that H2-alleviated growth inhibition in G. lucidum was accompanied by increased nitric oxide (NO) level and nitrate reductase (NR) activity under Cd stress. On the other hand, the mitigation effects were reversed after removing endogenous NO with its scavenger cPTIO or inhibiting H2-induced NR activity with sodium tungstate. The role of NO in H2-alleviated growth inhibition under Cd stress was proved to be achieved through a restoration of redox balance, an increase in cysteine and proline contents, and a reduction in Cd accumulation. In summary, these results clearly revealed that NR-dependent NO might be involved in the H2-alleviated Cd toxicity in G. lucidum through rebuilding redox homeostasis, increasing cysteine and proline levels, and reducing Cd accumulation. These findings may open a new window for H2 application in Cd-stressed economically important fungi.

Immobilization of ß-Glucosidase from Thermatoga maritima on Chitin-functionalized Magnetic Nanoparticle via a Novel Thermostable Chitin-binding Domain.

Enzyme immobilization is a powerful tool not only as a protective agent against harsh reaction conditions but also for the enhancement of enzyme activity, stability, reusability, and for the improvement of enzyme properties as well. Herein, immobilization of ß-glucosidase from Thermotoga maritima (Tm-ß-Glu) on magnetic nanoparticles (MNPs) functionalized with chitin (Ch) was investigated. This technology showed a novel thermostable chitin-binding domain (Tt-ChBD), which is more desirable in a wide range of large-scale applications. This exclusive approach was fabricated to improve the Galacto-oligosaccharide (GOS) production from a cheap and abundant by-product such as lactose through a novel green synthesis route. Additionally, SDS-PAGE, enzyme activity kinetics, transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FT-IR) revealed that among the immobilization strategies for Thermotoga maritime-ß-Glucosidase thermostable chitin-binding domain (Tm-ß-Glu-Tt-ChBD) on the attractive substrate; Ch-MNPs had the highest enzyme binding capacity and GOS production ratio when compared to the native enzyme. More interestingly, a magnetic separation technique was successfully employed in recycling the immobilized Tm-ß-Glu for repetitive batch-wise GOS without significant loss or reduction of enzyme activity. This immobilization system displayed an operative stability status under various parameters, for instance, temperature, pH, thermal conditions, storage stabilities, and enzyme kinetics when compared with the native enzyme. Conclusively, the GOS yield and residual activity of the immobilized enzyme after the 10th cycles were 31.23% and 66%, respectively. Whereas the GOS yield from native enzyme synthesis was just 25% after 12 h in the first batch. This study recommends applying Tt-ChBD in the immobilization process of Tm-ß-Glu on Ch-MNPs to produce a low-cost GOS as a new eco-friendly process besides increasing the biostability and efficiency of the immobilized enzyme.