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The breastfeeding period until the barn is dry makes dairy cows vulnerable to bacterial attacks that can lead to udder infection. Infected bacteria in cows trigger an innate immune system reaction, including a cytokine rash and chemotactic. This activity aimed to analyze the gene expression profile of cytokines and chemokines in the blood of dairy cows infected with subclinical mastitis. Six genes are used: the TLR group (TLR 2 and TLR 4), the cytokine group (IL1A and IL6), and the chemokines group (IL8 and CXCR1). The expression was derived from the isolation of mRNA in the blood of 10 healthy cows infected with sub-clinical mastitis by RT-PCR. Sub-clinical mastitis control was conducted using the California Mastitis Test (CMT) method. Expression of immune marker genes IL6, IL8, TLR2, TLR4, and CXCR1 was observed more in healthy cow blood samples than in cows exhibiting signs of mastitis. whereas the IL1A gene is approximately equal between the two conditions. Inflammation of breast tissue in dairy cows modulates the expression of a number of genes associated with the innate immune system. [ABSTRACT FROM AUTHOR]

Type 2 diabetes mellitus is multifactorial disease characterized by hyperglycaemia condition that can be induced by high diets in carbohydrates and/or MSG. Diabetic nephropathy is a complication that often occurs in DM patients. Environmental and genetic factors play roles in histopathological changes in kidney organs and changes in gene expression responsible for glucose metabolism. The aim of the study is to examine the effect of high diet carbohydrate and/or MSG on changes in kidney histopathology and PPAR-ɣ gene expression. Forty Swiss Webster male mice with the age of 7-week-old were divided into 1 control group (A) and 3 groups induced with high carbohydrate 71% (B), MSG 10% (C), mixture of carbohydrates 71% and MSG 10% (J) for 14 weeks. Termination was conducted to remove the kidneys for histopathological procedures and muscle to shows changes in PPAR-ɣ gene expression through polymerase-chain reaction (PCR). Both results analysed with ImageJ application and tested with one-way anova. The results is thickening of glomerular basement membrane (GBM) was found which characterized by narrowing capsular spaces in group B (0,013 µm), group C(0,010 µm), and group J(0,008 µm) compared to group A (0,016 µm) with significant results between group p value<0,05. Average ratio PPAR-y gene expression values to housekeeping gene GAPDH in group A (1,48), group B (1,38), group C (1,30) and group J (1,37) with non-significant difference between groups p value>0.05. Hyperglycaemia condition induced by high diet carbohydrates and/or MSG resulted in thickening GBM in kidneys, whereas expression of PPAR-ɣ gene in the muscle did not show significant change. [ABSTRACT FROM AUTHOR]

Immunomodulatory effect of lactoferrin (LF) against Salmonella Typhimurium infected mice. The parameters used to assess the orally administered LF on bacterial fecal shedding and liver colonization, also interleukin-12 (IL-12) gene expression in jejunal tissue using real time-PCR technique (RT-qPCR) in Salmonella Typhimurium infected mice. Balb/c mice were divided into four equal groups, mice in G1 and G3 given orally a volume of 0.2 ml containing 0.2 mg/mouse of LF for ten days as a control group. On day 5, G3 were infected with 0.2 ml/ mouse of S. Typhimurium sublethal dose. G 2 Infected with S. Typhimurium and sacrificed at days 5 and 10 post-infection. Group 4 as a negative control. The results of bacterial fecal shedding and liver colonization in G3 were significantly lower than that of G2. IL-12 mRNA gene expression results on day 5 showed significantly lower expression in G2 than that of lactoferrin. Mice in G1 had a significant increase in gene expression on day 10. Inversely, G2 showed a significant decrease in gene expression on day 10, while G3 showed no significant difference on day 10. The results showed that LF ameliorates immune response, increasing IL-12, an essential key link to activate adaptive immunity. [ABSTRACT FROM AUTHOR]

Enterococcus faecalis is one of the most common causes of nosocomial infections among Enterococcus species Enterococci have many virulence factors that contribute to adherence to host cells, facilitate tissue invasion, and cause tissue damage. This study is designed to demonstrate the relation between the expression of endocarditis and biofilm-associated pili among E. faecalis isolates and biofilm formation. Biofilm formation by eight clinical E. faecalis isolates was detected by microtiter assay, the isolates showed differences in their ability in biofilm production. Four isolates produced strong biofilm, and three were moderate biofilm producers. While one isolate obtained from the wound was a non-producer. One Step RT-PCR was used to measure the expression of the pili genes related to biofilms and endocarditis (epbA, epbC), the E. faecalis isolates had different ebpA and ebpC gene expression. The root canal isolate (21R) had a high expression of ebpA in comparison with the control isolate and the urine isolate (19U) followed by the root canal (21R) showed a high expression of ebpC genes in comparison with the control isolate. There is a strong correlation between the production of biofilm and gene expression of virulence factor, ebpA (r=0.838) while ebpC correlated non-significantly with biofilm formation (r=0.7143). [ABSTRACT FROM AUTHOR]

Lateral intakes are used for both irrigation networks and farm water transport and distribution. In this investigation, three-dimensional (3D) numerical model of a rectangular lateral intake's flow field in the subcritical flow regime is used to conduct CFD analysis, with FLOW-3D software used to simulate the phenomena, a k-ω model utilised to simulate the turbulence of the flow field, and a volume of fluid scheme used to simulate changes in the free surface (VOF). The primary objective of this research was to determine the applicability of FLOW-3D software and to find a novel formula for predicting the dimensions of the separation zone that arises at the inlet of branch channel by employing a state-of-the-art computing modelling technique known as gene expression programming (GEP). Three statistical parameters, the determination coefficient (R2), the mean absolute error (MAE), and the root mean square error (RMSE), were then used to select the model offering the most accurate estimate of separation zone size. The results showed that the numerical model accurately described the flow field, while the GEP model's derived formula was the most accurate predictor of the size of the separated area. GEP also offered the unique property of giving both the explicit and compressed arithmetic terms required for this purpose. [ABSTRACT FROM AUTHOR]

Trypsin plays a crucial role in processing recombinant precursor insulins, especially in removing a peptide linker or a peptide spacer by cleaving the peptide after a lysine or arginine residue. To reduce the cell toxicity of the expressed trypsin and increase the secretory expression, we developed a strategy for producing a recombinant bovine trypsinogen using the methylotrophic yeast Pichia pastoris. The expression cassette contains the gene encoding a truncated α-mating factor from Saccharomyces cerevisiae with a cleavage site for a Kex2 endoprotease, a short propeptide having the cleavage site for autolysis (DDDDK), followed by the sequence for the active trypsin. Furthermore, based on a 3D structure model, we constructed a variant of bovine trypsin, which would have a higher specificity in cleaving a polypeptide after a lysine residue rather than an arginine. Clones resistant to zeocin could be isolated and checked using PCR with primers specific to AOX1 to integrate the expression cassette into the genome of P. pastoris and to identify Mut phenotypes. Trypsinogen secretion into the supernatant was demonstrated using SDS-PAGE, with which a single band of the secreted trypsinogen with a molecular weight of approximately 25 kDa was detected. The method described here represents an initial step in developing "halal" trypsin, particularly for its application in the production of recombinant insulin and its analogs. [ABSTRACT FROM AUTHOR]

Colon cancer, along with lung, prostate, and breast cancer, is one of the most common types of cancer globally and is regarded as one of the world's leading causes of death. In therapy for this common illness, substantial progress has been achieved recently. Adjuvant chemotherapy is effective, specifically in stage III patients, and surgery was tailored for the most outstanding results with the least amount of morbidity. Several novel target-oriented medications are being evaluated, and some of them (cetuximab and bevacizumab, for example) have already shown high activity/efficacy, primarily when used in conjunction with chemotherapy. To get the best results, it is necessary to provide current recommendations for treating these patients in medical trials and daily practices. This research seeks to use a person's gene expression to determine whether or not they have colon cancer. This information is used by the Logistic Regression, Naive–Bayes Algorithm and Catboost Algorithm to predict human colon cancer. The learning classification dataset included 7457 gene expression levels from 36 patients, 18 of whom were healthy and 18 of whom were malignant. [ABSTRACT FROM AUTHOR]

Background: Patients with COVID-19 have dysregulation in immunity response, like cytokine storm, lymphopenia, and a raised number of CD4 and CD8 T cells exhausted. These characteristics could lead to increase in mortality rates. Aim: The aim of this study measured the rate of TIM -3 mRNA expression which is considered an exhausted marker of CD8 T cells that associated with progression of disease, Material and method: 30 patients were diagnosed as infected with COVID-19 symptoms and require Intensive care units (ICU): 18 females and 14 males in the age range (22-82), the positive COVID-19 was detected via a positive real-time PCR on the specimens of the respiratory tract that had a collection from the Teaching Hospital in Al-Diwaniyah in the period from (September 2021 - March 2022), the Control group includes (17 blood sample) (8 males and 9 females) with age range (20-80 year), the blood sample undergoes to extract RNA to measurement amount of TIM3 by using reverse transcription real-time PCR. Result: the data in the study indicated the mean of the TIM -3 gene was increased statical significantly (1.3±0.6) in COVID-19 patients compared with the mean TIM -3 (0.6±0.3) in the Control group at significant (P≤0.05). [ABSTRACT FROM AUTHOR]

Therapy to cure a persistent infection of the Hepatitis B Virus (HBV) is needed to suppress viral replication. Current therapy with nucleoside analogues does not destroy HBV covalently closed circular DNA (cccDNA). A new strategy using Base Editing is required to tackle this viral latent infection. We designed guide RNAs (gRNAs) to target the pre-S and S genes of HBV for the development of antiviral, based on the dominant HBV genotype in Indonesia. The conserved regions of HBV, pre-S and S genes were used to determine a selected target of the Cas9-mediated base editing system. Base Editing (BE)-Designer web-based software to designed gRNA and SnapGene to visualized the expression vector. We identified 5 candidate sequences, including 3 sequences in the pre-S and 2 sequences in the S gene. These target sequences show no mismatches and GC contains between 45-60%. In addition, the gRNA sequences were checked in Nucleotide BLAST tools (NCBI) to prevent the off-target effect and ensure the differences with the human genome. This study provides the candidate target sequences to be developed in antiviral therapy. The utility and efficiency of the candidate sequences need to be evaluated in viral gene expression by in vitro HBV infection systems. [ABSTRACT FROM AUTHOR]

The number of cases of blood cancer has increased in a scary way due to a failure in prediction. Filter feature selection is a crucial technique for the microarray gene expression analysis. Univariate filters are particularly appealing due to their simplicity and efficiency. This study aims to compare six univariate filters according to the number of selected features and the classification accuracy using three different types of classifiers: support vector machine, naive bayes and artificial neural network. This study used leukemia datasets in both binary and multi-class formats to investigate the performance of the studied filters. [ABSTRACT FROM AUTHOR]

There has been a lot of interest in reverse engineering gene regulatory networks from gene expression data. In order to deal with a wide range of problems, a variety of models and methodologies have been developed. Although these strategies are focused on particular biological and experimental systems, they often require experimental data that is difficult or impossible to collect. More genetic disruption and higher-throughput sequencing data make it possible to create more complete methods for inferring gene regulation networks. In order to infer gene regulatory networks from perturbed gene expression data, we provide in this paper an approach based on Euclidean distance and the Bayesian mean average method. Existing methods were compared to the new one, and the results indicate that the new method performs better. [ABSTRACT FROM AUTHOR]

Appearance of genes in the cells of an entity regulates its function and structure. Often, the activity of one nucleic acid influences the venture of a group of other nucleic acid, such linked nucleic acid form a gene regulatory network. Identifying the groups of genes that are co-regulated is an important task in bioinformatics. In the current study, we propose a approach using Correlation, Mutual Information and K-Means clustering for inference of gene regulatory network's from gene expression data. The results are differentiating with existing methods and show a quality execution. [ABSTRACT FROM AUTHOR]

Plant resilience to drought stress requires a complex mechanism that involves controls of gene expression. Understanding its molecular regulation becomes critical to find the best strategy to improve plant tolerance to drought. Functional genomics has been a popular method to understand gene functions. In this study, an Ac/Ds transposon-mediated mutant library has been constructed previously to identify genes that might be involved in regulating drought tolerance in rice. From the screening activities of the mutant library using PEG6000 treatments, a mutant line has been selected as one of the drought-tolerant candidates. Further analysis was done to identify the location of Ds transposon in the rice genome. After performing a TAIL-PCR method, one of the flanking regions of Ds insertion was isolated, cloned, and sequenced. It was revealed that the Ds transposon element had been inserted into the last exon of a gene from the family of pentatricopeptide repeat protein (PPR) located at chromosome 11. Interestingly, a sequence of a putative natural antisense transcript (NAT) was also identified in the reverse direction of this gene. From a survey through bioinformatics, five genes were found to be located nearby the insertion site, including Os11g0131200, Os11g0131300, Os11g0131400, Os11g0131500, and Os11g0131600. However, most of these genes have not been functionally characterized in rice. Further investigations are still needed to reveal which gene plays the key role in the tolerance mechanism and whether disruption of the NAT sequence affects rice tolerance to drought. [ABSTRACT FROM AUTHOR]

Pregnancy-associated genes contribute to antiluteolytic mechanisms in cattle corpus luteum. Early luteolysis (days 12–14) was associated with differential expression of a number of genes in the corpus luteum, including Mx1 gene that was induced by interferon-tau (IFNT) as the main signal for maternal recognition of pregnancy in ruminants. This gene may be used as a gene target for the early detection method of cattle pregnancy. The objective of this study is to clone and express Mx1 gene in Escherichia coli systems to produce Mx1 antigenic protein that can be used to develop antibody polyclonal for early pregnancy detection. The 733 bp of Mx1 gene was obtained via artificial gene synthesis gBlock and was cloned into pJET 1.2/Blunt cloning vector. Then, Mx1 gene was constructed using the pET-32b expression vector in BamHI-HindIII restriction sites to generate the pET-Mx1 plasmid. The gene was fused with a nucleotides sequence encoding Trx-tag, His-tag, and S-tag producing ∼45 kDa of recombinant Mx1. Gene expression in the construct was controlled by the T7 promoter and Trx-tag start codon through IPTG induction. Results showed that E. coli carrying pET-Mx1 overexpressed a 45 kDa protein in induced culture as a soluble protein that was expressed in periplasm. Dot blot analysis using anti his ensures that E. coli expresses a recombinant Mx1 protein that can be used for the development of polyclonal antibodies. [ABSTRACT FROM AUTHOR]

Waste is a big global issue that has a substantial influence on the environment and human health. One type of waste that is notoriously difficult to decompose and requires a considerable amount of time to degrade is polyethylene terephthalate (PET) plastic. Due to its remarkably persistent properties, the accumulation of PET waste poses a major threat to the ecosystem. Several attempts have been made to address the problem of PET plastic waste, one of which is to use an enzymatic approach to accelerate the decomposition of PET. PET hydrolase (PETase), found in Ideonella sakaiensis, is a potential agent for the biodegradation of PET. In this study, we used a synthetic biological approach (synthetic DNA) to develop a PETase biocatalyst, in which the PETase gene was chemically synthesized, cloned into a pET-22b vector, and then expressed in E. coli BL21 (DE3) with IPTG induction. During the construction process, the mutated N-terminal pelB signal sequence was included with the expectation that the end-product PETase could be either secreted into periplasmic or excreted to the culture medium. Several different extraction methods were utilized, including intracellular (cytoplasmic), periplasmic, and extracellular extraction. In addition, Western Blot Analysis was carried out to confirm that the target protein had been expressed. The pET22b(+)-petase was verified using restriction enzymes, and the result showed that the gene was properly cloned. The SDS-PAGE and western blot result showed that the pET22b-IsPETase has been successfully expressed and secreted, but the amount is still low so that further optimization needs to be done. [ABSTRACT FROM AUTHOR]

Polyethylene terephthalate (PET) is widely used as raw material for clear, strong, and lightweight plastics that have been exploited in the packaging market. Although the use of plastics makes human's life easier, their waste has become a major environmental problem. Recycling plastics-based waste is still expensive and highly energy consuming. Recently two steps synergic degradation of PET has been discovered in Ideonella sakaiensis in which PET is converted into mono-(2-hydroxyethyl) terephthalic acid (MHET) catalyzed by PETase, and MHET is further hydrolyzed into terephthalic acid and ethylene glycol catalyzed by MHETase. This discovery offers a promising and eco-friendlier solution to the global environmental crisis of plastic pollution. In this work, we have cloned the MHETase gene synthetically designed based on IsMHETase. The synthetic gene was codon optimized for protein expression in Escherichia coli. Aiming to obtain extracellular MHETase, the recombinant enzyme was produced in E. coli BL21 (DE3) and its secretion was mediated by a mutated pelB signal sequence. Expression of MHETase was induced by IPTG at 37°C for 5 h. Intracellular, periplasmic, and extracellular fractions were extracted using different methods. Intracellular and periplasmic fraction was obtained from a lysate of sonicated and osmotic shocked cells, respectively, while extracellular fraction was yielded from concentrated cell free culture. Those three fractions were further analyzed by SDS-PAGE and Western Blot using anti-6X HisTag antibodies. We found that the recombinant MHETase was majority expressed as inclusion bodies and distinctively observed after purification of solubilized protein. Western Blot analysis of solubilized fraction showed a stronger signal at ~62 kDa than soluble intracellular protein fraction. Active MHETase were observed in refolded protein fraction and generated 0.4015 U.mL-1 of esterase activity. [ABSTRACT FROM AUTHOR]

The plant produces excessive amounts of hydrogen peroxide (H2O2) in response to environmental stress H2O2 which causes oxidative stress and cellular damage. To cope with oxidative stress, plants express the Ascorbate peroxidase (APX) enzyme for scavenging excessive amounts of H2O2 in the cell. Among eight APX isozymes in Arabidopsis, APX2 is less studied in response to heavy metal stress. In the present study, we isolate two T-DNA insertion mutants from collection resources, named apx2-1 and apx2-2. The T-DNA was inserted in the first and fifth exon of the APX2 gene in the apx2-1 and apx2-2 mutant plants, respectively. RNA expression analysis shows that the APX2 transcript was undetectable in the mutants, indicating that both were knock-out mutants. Overexpression lines were also generated by expressing APX2 cDNA under the control of constitutive promoter 35S-CaMV in Arabidopsis. Under normal conditions, without any stress treatment that can induce the expression of endogenous AtAPX2 protein, overexpression and mutant lines did not show any distinctive phenotype compared to their WT. However, when plants were challenged with heavy metals nickel, both apx2-1 and apx2-2 showed growth retardation, browning, and died compared to WT, indicating that the mutant is more susceptible compared to WT. The browning leaves indicated that plants were dying because of the accumulation of H2O2. However, the overexpression line has more green leaves than WT and mutants under nickel treatment, indicating that the overexpression line is more tolerant to nickel than WT and mutants. This finding indicates that APX2 possibly plays a role in scavenging H2O2 due to heavy metal stress, especially nickel. APX2 can be used as a candidate gene for producing heavy metal tolerant plants in phytoremediation studies. [ABSTRACT FROM AUTHOR]

Rice is one of the world's most consumed food crops, and productivity is significantly affected by environmental conditions, such as soil salinity. Due to the gradual rising of sea level, the development of salinity-tolerant rice is crucial to maintain food security, especially in coastal zones. Two homozygous transgenic rice lines (IR411-17-10-2 and IR411-19-06-1) harboring the OsActin::AtAVP1 gene were evaluated for their salinity tolerance during the vegetative stage by measuring the projected shoot area (PSA) and the leaf K+/Na+ ratio under normal and salt stress (120 mM NaCl) conditions. To overcome the laborious and time-consuming nature of conventional measurement, the plant's shoot area was measured automatically using the LemnaTec 3D Scanalyzer system. The basic principle of this image-based phenotyping is the conversion of shoot image pixels into Projected Shoot Area (PSA) by LemnaTec Grid software. The phenotyping was done for 28 days. Non-transgenic IR64 and a null line were also grown as negative controls for comparison. Under normal and salt conditions, the projected shoot area of IR411-17-10-2 was similar to both controls, while the projected shoot area of IR411-19-06-1 was lower than both controls. Another common parameter for salt tolerance is leaf ionic ratio (K+/Na+). The K+/Na+ ratio of transgenic lines was compared to IR64 and null controls to see any significant differences. The K+/Na+ ratio of both transgenic lines was similar to that of IR64 and null controls under normal and salt stress conditions. These findings may indicate that constitutive expression of AtAVP1 in rice c.v IR64 does not have any significant effects on the plant's performance and salt tolerance at the early vegetative stage. These findings should be further validated by gene expression analyses before any firm conclusion can be drawn. [ABSTRACT FROM AUTHOR]

D-tagatose is an isomer of L-fructose and around 92% as sweet as sugar. Therefore, it can be used as a low-calorie sweetener that demonstrates an anti-hyperglycemic effect. D-tagatose can be produced through enzymatic conversion of D-galactose by the enzyme L-arabinose isomerase (L-AIs; EC 5.3.1.4). Hence, we describe the expression of L-AI from the hyper-thermophilic bacterium Thermotoga thermarum in Escherichia coli. The araA gene encoding the L-AI from T. thermarum (L-TTAI) was subcloned into the pRHA-vector for the expression in E. coli NiCo21 under the control of a rhamnose-tightly regulated promoter. The His6-tagged enzyme was successfully expressed after the induction with L-rhamnose and subsequently purified using immobilized metal-chelate affinity chromatography (IMAC) on TALON™-matrix. The SDS-PAGE result revealed that the enzyme has a molecular weight of approximately 56 kDa, corresponding to the molecular weight calculated based on its amino acid sequence. The molecular characteristics of the L-TTAI were compared to other bacterial L-arabinose isomerases. [ABSTRACT FROM AUTHOR]

Cancer is still being a problem for health around the world. Sargassum sp. and Padina sp. potential as anticancer because it contains bioactive compounds that are believed to be able to overcome several health problems including as antioxidants, anti-inflammatory and anticancer. The purpose of this study was to determine the activity of the ethanol extract of Sargassum sp., Padina sp. and taurine on cytotoxic, antiproliferative, and p53 expression tests on HeLa cervical cancer cells. Extraction of Sargassum sp and Padina sp was carried out by maceration method, using ethanol analyze as solvent. The concentrations used were 625 ppm, 1250 ppm, 1875 ppm, and 2500 ppm. Evaluation of cell viability using IC50 values observed from the MTT Assay method. The antiproliferation test was determined by the doubling time value. Measurement of p53 gene expression using RT-PCR. The results showed that the ethanolic extracts of Sargassum sp., Padina sp., and taurine were cytotoxic, anti-proliferative and able to increase p53, as evidenced by the decreased percentage of cell viability, longer doubling time than control and increased p53 gene expression in each treatment. So it can be concluded that the ethanolic extracts of Sargassum sp., Padina sp., and taurine have the potential to be developed as anticancer agents in HeLa cervical cancer. [ABSTRACT FROM AUTHOR]

The study's purpose was to investigate the effect of the expression pattern of microRNA-122 (miRNA-122) in patients with diabetes, hypertension, and patients who have diabetes and hypertension together compared to healthy control subjects, compared each other, and study its effect on stimulating inflammatory factors related to a metabolic disorder of these diseases. Blood samples were obtained from thirty patients with type 2 diabetes mellitus (T2DM), thirty patients with hypertension (HTN), thirty patients with T2DM+HTN, and thirty healthy people as control groups. Lipid profiles were determined by using an ARCHITECT c4000 clinical chemistry analyzer. Whole blood hemoglobinA1c and serum C-reactive protein (C-RP) levels were measured by the sandwich immunodetection method. Serum tumor necrosis factor-alpha (TNF-α) level was measured by enzyme-linked immunosorbent assay (ELISA). The expression of serum miRNA-122 was screened using the quantitative polymerase chain reaction (qPCR). The results revealed a substantial rise in TNF-α levels in each patient group when compared to the control group (p<0.05), indicating that there is no meaningful difference between the two groups. CRP levels are significantly higher in the T2DM and T2DM+HTN groups than in the control and HTN groups (p<0.05). When comparing patient groups to control groups, miRNA-122 gene expression was substantially higher in the patients (p<0.05). According to the data, miRNA-122 expression is implicated in the etiology of metabolic illnesses such as T2DM and HTN, or in people who have both. Increased expression of miRNA-122 stimulates inflammation in individuals with metabolic disorders, especially those with T2DM. [ABSTRACT FROM AUTHOR]

Toward sustainable resource development, bioprocess technology using useful organisms such as yeast (Saccharomyces cerevisiae) is expected to be developed. Microorganisms in large-scale fermenters and high-concentration cultures on an industrial scale are sometimes exposed to hypoxic conditions. Hypoxic environments are not particularly uncommon for environmental microorganisms. Uncovering the biological responses under such hypoxic conditions is a critical issue of understanding the degree of microbial adaptation and scale-up of microbial production. To find time-series trends of gene expression patterns in yeast under hypoxic conditions, this study applied the dynamic topic model, which is a method of latent semantic analysis used in the field of natural language processing, to statistically analyze the "trends of gene expressions." This approach visualized rank changes in time-series gene expression. Especially, several cell wall related genes were dramatically changed ranks under hypoxic conditions. This method extracts trends in the time-series expression profiles of yeast under hypoxic conditions, and the rank variation in the trends reveals temporal shifts in gene expression among hypoxia-responsive gene sets. This approach could provide new insights into the gene regulatory systems under hypoxic conditions in yeast. [ABSTRACT FROM AUTHOR]

The presence of residues of the herbicide glyphosate in poultry feed is a fairly common problem. Our experiments were carried out in the vivarium of LLC "BIOTROF +" on broilers of the cross "Ross 308". For the experiment, the birds were divided into 3 groups: 1 control group, which received a diet without additives, diet with the addition of glyphosate and the strain of the microorganism Bacillus sp.GL-8. The analysis of gene expression of the caecum of the intestines of broilers was carried out using quantitative PCR with reverse transcription. For the analysis of mRNA expression, specific primers were selected for the following prostaglandin genes studied: PTGER3, PTGER4, PTGR1, PTGDS and PTGES Amplification reactions were performed using SsoAdvanced ™ Universal SYBR® Green Supermix (Bio-Rad) For the first time in our study, the impact of glyphosates on poultry occurs, including through changes in the activity of key genes associated with prostaglandin metabolism Glyphosate introduced into bird feed in an amount corresponding to I eat one MPC, acted as an inducer of prostaglandin receptor gene expression (PTGER3 and PTGER4), prostaglandin catabolism (PTGR1) and prostaglandin synthesis (PTGDS and PTGES) in the caeca of the intestine of broilers. Thus, the levels of mRNA expression of the PTGER3 gene and the PTGER4 gene when exposed to glyphosate (group 2) were activated 1.87 and 1.91 times compared with the control group 1, PTGDS and PTGES genes - 1.35 times, PTGR1 gene - 1.87 times (P≤0.05). In the future, the PTGER3, PTGER4, PTGDS, and PTGR1 genes can be used as possible therapeutic targets for toxicosis caused, in particular, by feed glyphosates. The probiotic strain of Bacillus sp. GL-8 probably restored the microbiota, thereby enhancing its protective effect against toxicants, in particular, its metabolic functions of biodegradation. This was expressed in the "smoothing" of the level of PTGR1 gene activity to the level of the control group, as well as a decrease in the activity of PTGDS, PTGES, and PTGER3. Positive shifts in the change in transcription of prostaglandin genes under the influence of a strain of a probiotic microorganism indicate the prospect of using probiotics as a tool for leveling physiological imbalance against the background of feed contamination with toxic substances. [ABSTRACT FROM AUTHOR]

Despite the widespread use of microbiological plant growth stimulators, the molecular genetic basis of their effects is not well understood. In this regard, this article presents research data on the effect of microbiological growth stimulants on the level of cotton gene expression in the field. The obtained results indicate that the positive effect of the used stimulants (Rizokom-1, Micro-1 and Khosil) on the salt tolerance of the Porloq-4 cotton variety is due to the influence on the level of expression of genes for the synthesis of sugars, proline and unsaturated fatty acids. It was also found that these stimulants affect the level of expression of genes for nitrogen and phosphorus metabolism and the synthesis of cell wall polysaccharides, which explains their positive effect on fiber yield and quality. [ABSTRACT FROM AUTHOR]

The Kidney cancer in recent times has shown global dominance in worldwide incidences. Renal cell carcinoma includes kidney renal clear cell carcinoma (KIRC) and kidney renal papillary cell carcinoma (KIRP). KIRP is a relatively rare type and not many studies and research is being done in that area. Our study will be shading light on correlation with epigenetics and DNA repair genes in KIRP. DNA damage repair genes work as mechanism for repairing damaged or mutated genes. Here we have studied 36 significantly important DNA repair genes in KIRP in which we have identified 2 genes NEIL1 and LIG4. Clinical data suggested that low expression of DNA repair genes immensely affect malignance of tumour in cancer which is backed by data available in KP-plotter showing high expression of NEIL1 and LIG4 in KIRP showing better survival probability while we got lower mRNA expression in tumour samples using publicly available software such as TIMER and GEPIA to further identify the reason behind the low mRNA expression we screened for hyper-methylation of both the genes to validate them as targets of epigenetic inactivation in KIRP. Overall, we predict that NEIL1 and LIG4 are hyper-methylated in KIRP which reduces the expression of the genes leading to more severity. [ABSTRACT FROM AUTHOR]

Despite the recent advances in novel therapeutic approaches, breast cancer is still the most common cancer among women. It remains a leading cause of cancer death for them after lung cancer. Due to their reversible nature, epigenetic modification is one of the attractive targets in cancer treatment. In breast cancer, epigenetic changes are widely recognized, specifically RASGAP proteins activity, which control cell growth by inhibiting RAS signaling mechanism in a normal cell. Dysregulation of RASGAPs gene is critical to the development and progression of breast tumors; therefore, epigenetic regulation of RASGAPs gene represents a very promising treatment strategy. Despite its clinical relevance, the mechanism which leads to breast tumor growth is still unclear. Here, we analyzed the RASGAPs gene using the cancer genomics database to understand the reason behind low expression of RASGAP tumor suppression genes in breast cancer. Our analyzed data from different cancer genomics datasets identified that the DAB2IP gene was very low expressed in breast cancer & its subtypes. Our analysis detected an association of promoter methylation rather than mutation as a cause behind the downregulation of DAB2IP gene in luminal subtypes of breast cancer that deserves further investigation. [ABSTRACT FROM AUTHOR]

The method of evaluating the physical traits of living creatures by generating essential proteins is known as gene expression. Translation and transcription are the two processes in gene expression. Gene Expression can be captured from DNA or RNA using a variety of approaches. High-throughput gene expression (NGS) data is having multiple advantages over the traditional gene expression dataset. Still one of the major disadvantages of NGS data is it is complex, comprising a large number of genes with few samples; among these thousands of significant genes, disease-causing genes must be identified. This issue should be solved by lowering the data source's dimension to a manageable level. Machine learning (ML) has proven its potential in the research areas of disease identification, and genomics in recent years. Many Machine Learning-based Gene Selection techniques have been described in the literature, to improve dimensionality reduction precision. In this work, a unique clinical support system based on the Relief-Cuckoo Search (CS)-Random Forest (RF) hybrid multi-stage significant gene identification technique is proposed for significant gene selection from the next-generation sequencing (NGS) dataset. This work can be helpful for the accurate identification of sepsis and the relevant genes associated with it, which helps early detection of the disease. This hybrid feature selection technique could be beneficial in later stages of disease treatment, such as disease diagnosis and drug development. The accuracy of the proposed model is 95.23 % which can be helpful for further analysis of various infectious diseases and thus helps the diagnosis procedure more convenient. [ABSTRACT FROM AUTHOR]

Machine learning is a part of artificial intelligence and its optimization techniques are allows system to learn from past example and identify pattern from large dataset. This criteria are well suited for researchers for doing their research on medical application, genomic measurements and it cause to machine learning techniques are used in cancer diagnosis and detection. Recent year machine learning has been applied to cancer prediction and prognosis. This latter approach growing trend towards an artificial neural network. ANN ensemble is a learning platform in which a number of neurons work together to solve a problem. Our approach is used to identify adenocarcinoma cancer diseases from gene expression data samples obtained from bodies that are to be diagnosed in this research. Last decades Next-generation sequencing (NGS) technology has been expanded with advantages in the reliability, data interpretation and costs, sequencing chemistry. Such large improvements can make NGS clinically practical, and NGS technology is presently being developed for use in the field of oncolo-gy. Various clinical applications are discussed, including DNA-sequencing-based mutation detection in inherited cancer syndromes, RNA-sequencing-based detection of spliceogenic variants, DNA-sequencing-based risk modi-fiers and application for pre-implantation genetic diagnosis, and cancer somatic mutation analysis. In this study, neural network classifiers were used to determine patient carcinoma cancer status. Applied neural network architecture is based on a two-level architecture, with each individual network having two outputs based on the normal cell sample or cancer cell sample according to our dataset. [ABSTRACT FROM AUTHOR]

Dementia is a chronic or progressive syndrome characterized by impaired cognitive capacity from Alzheimer's disease in which the expression of the Caspase-9 and Calm1 genes is one of the genes that play a role in this disease. This study aims to see gene expression of Caspase-9 and Calm1 in rat models of Alzheimer's disease after the addition of Mesenchymal Stem Cell Wharton Jelly (MSC-WJ). The treatment group consisted of a control, AlCl3, MSC-WJ, and a combination of AlCl3 and MSC-WJ. All treatment groups were tested using the Realtime PCR (RT-PCR) method. All experimental groups were analyzed using the one-way ANOVA test using SPSS. If the p-value <0.05, then this value is considered significant. The results showed that the giving of MSC-WJ had a significant effect on the expression of the Caspase-9 gene with a p-value of 0.044 but didn't have a significant on the expression of the Calm1 gene expression with a p-value of 0.761. The conclusion of this study showed that the administration of MSC-WJ affects the gene expression of Caspase-9 a gene that plays a role in the apoptosis of cells but has no effect on the gene expression Calm1 as a gene involved in calcium signaling. [ABSTRACT FROM AUTHOR]

There are promising results in the use of platelet-rich plasma (PRP) for tissue repair and degenerative diseases application. However, the variability in the methodology for its obtaining may cause different and opposing findings in the literature. Particularly, the choice of the anticoagulant is the first definition to be made. In this study, blood was collected with sodium citrate (SC), ethylenediaminetetraacetic acid (EDTA), and Heparin. Growth factors release TGF-β quantification was performed using the ELISA method, and the effects of PRP on synovial membrane-mesenchymal stromal cell (SM-MSC) culture differentiation gene expression was evaluated using RT-qPCR analysis. Based on the result, PRP obtained with anticoagulant sodium citrate resulted in higher TGF-β concentration, compared to another anticoagulant. Moreover, the RT-qPCR analysis of level expression of chondrogenic marker gene SOX9 was higher in the 15% PRP group, while osteogenic marker gene RUNX2 was higher in the 10% PRP group than 5%, 15%, 20% PRP, and control group. In conclusion, our results show that PRP obtained with anticoagulant sodium citrate may affect the differentiation activity of synovial membrane-derived mesenchymal stem cells in vitro. [ABSTRACT FROM AUTHOR]

Pyrrolnitrin is one of the antifungal compounds produced by Serratia plymuthica UBCF_13. Pyrrolnitrin biosynthesis involves a gene cluster consisting of four genes, namely prnA, prnB, prnC, and prnD. In this study, we assessed two of the four gene expression levels, prnA, and prnD. This study evaluated the influence of Colletotrichum gloeosporioides toward and expression levels of prnA and prnD genes in UBCF_13. The method used was RT-qPCR to compare the expression levels of prnA and prnD genes in single culture and coculture. The results of this study showed that the C. gloiosporioides affected the transcription of both prnA and prnD genes in UBCF_13, but the expression levels of both genes are different. The fungi C. gloiosporioides was able to decrease the expression of prnA and prnD genes on day forth and on day sixth it was able to increase the expression of both genes, but only the prnD gene increased its expression almost 2-fold. [ABSTRACT FROM AUTHOR]

The bacterium Serratia plymuthica strain UBCF_13 is a biocontrol agent that has the potential to inhibit the pathogenic fungus C. gloeosporioides. S. plymuthica produces several antifungal compounds, such as oocydin A. The biosynthesis of oocydin A involves 23 genes, namely oocA to oocW genes. However, only a few genes play a crucial role in the biosynthesis of oocydin A, such as oocE and oocO genes. This study was conducted to determine the changes in the expression levels of the oocE and oocO genes of S. plymuthica strain UBCF_13 against the presence of C. gloeosporioides. The method used is qRT-PCR. The culture treatment consisted of single culture and co-culture with the age of bacteria from each culture was 4, 8 and 12 days. The results showed that the presence of the pathogenic fungus C. gloeosporioides could increase the expression of the oocE gene and decrease the expression of the oocO gene in S. plymuthica UBCF_13 because the oocE and oocO genes have different regulatory pathways. The expression of the oocO gene is under the control of Quorum Sensing (QS) and its regulation is regulated by the RpoS gene, while the regulation of the oocE gene is still unknown. [ABSTRACT FROM AUTHOR]

This study was conducted at technical college of Mussaib / Department of Technical Animal production in cooperation with Jessar Al-Mussaib Company for Biological Studies which located in Baghdad / Karrada Dakhla for studying and investigating caspase3 gene expression and its relationship with follicles in the ovaries of Iraqi local sheep. For this enquiry, (47) female reproductive genital were collected from Karbala and Babylon butchery for two seasons: the reproductive season including October and November months of 2020, while out of reproductive season including the months of June and July of 2021. Follicle's size was measured, and a biopsy of tissue was taken from the surface of the ovary to investigate caspase3 gene expression. The obtained results indicated that there are no significant differences between out and during the reproductive season for the caspase 3 gene expression, however for relative expression of the caspase 3 gene, the results exhibited decreasing during reproductive season (0.939) in comparison with the expression of the gene out of the season, in conclusion, caspase 3 decrease during reproductive season while it increase during out of reproductive season. [ABSTRACT FROM AUTHOR]

Use of gene expression data from microarrays can be used to identify and treat a variety of diseases. There are duplicated high-dimensional feature genes in the microarray gene expression data, as well as smaller training and test samples. Lung cancer strikes the elderly the worst. Only a small fraction of persons diagnosed with lung cancer are under the age of 45. When a person is discovered, they are typically over the age of 70. Lung cancer is the most common kind of cancer. This study aims to find the best classifier for Lung cancer gene data to identify normal and abnormal patterns. The statistical characteristics of precision, accuracy, GDR, recall, and f-measure were used to compare the performance of the four classifiers. Extracted information is categorized using PCA, Detrend FA, EM, and Detrend FA with EM classifiers. PCA and Detrend FA. When using the EM Classifier, Detrend FA beats the competition, achieving an accuracy of 93.36% and a GDR of 84.68%. [ABSTRACT FROM AUTHOR]

Presenilin2 (PSEN2) genes and A Disintegrin and Metalloproteinase 10 (ADAM10) genes are responsible for the amyloid precursor protein sequence of proteolytic cleavage and the subsequent formation of amyloid β peptides. A total of 18 RNA samples from the brain cortex and hippocampal regions of an adult group (10-12 years old; 4 female) and an old group (>15 years old; 5 females) of Cynomolgus monkey (Macaca fascicularis) were analyzed using RT-qPCR. There were no differences in PSEN2 mRNA expression in the cortex (p=0.063), significant differences in the hippocampus (p=0.010) in between groups. There were no significant differences in ADAM10 mRNA expression between old and adult group (p=0.200) and also between hippocampus and cortex (p=0.827). The overall PSEN2 expression level was higher in the adult group and correlated with early onset Alzheimer's disease (EOAD) characteristics in relatively young individuals. ADAM10 mRNA expression level was higher in the adult group and in the hippocampus. PSEN2 expression level was higher in the adult group and ADAM10 expression level was lower in old group, similar to that found in human Alzheimer's disease. Alteration in PSEN2 and ADAM10 expression may be a risk factor for Alzheimer's disease correlated to regulation of neuronal plasticity, amyloid precursor protein processing, and tau aggregation. [ABSTRACT FROM AUTHOR]

Colorectal carcinoma (CRC) ranks as the third-highest cause of mortality with a short survival rate. Significantly, the prevalence of CRC among Indonesian was markedly increased in the last decade. The late diagnosis and severity of patients due to metastasis are the significant contributors to the high mortality. In addition, it is suggested that some potential proteins related to metastasis may induce epithelial-mesenchymal transition (EMT) and patient death. This preliminary study seeks to evaluate the expression of metastasis protein including Snail, ZEB-1, Twist, and Slug in Indonesian CRC samples. In this case study, seven fresh tumor samples were processed for total RNA isolation, followed by gene expression analysis using the real-time quantitative polymerase chain reaction method. A similar Snail, ZEB-1, Twist, and Slug expression pattern is observed in subjects with stadium III-IV. Those genes expression significantly increased in-stadium III and decreased gradually in the next stadium. The interaction between all metastatic genes enhances the degradation of extracellular matrix (ECM) in the early stage of metastasis by inhibiting the adhesion protein expression E-cadherin. Hence, the profiling of metastatic protein expression in the early stages of CRC is urgently required to prevent CRC progression and increase patient survival rate. [ABSTRACT FROM AUTHOR]

Clustering technique used to analyzing and compiling similar data depending on some characteristics. Divides data of interest into a relatively small number of or homogeneous groups, this technology is used in many applications. One reason it's so frequently used is that it can work on a dataset without prior knowledge. This is why clustering is feasible for real-world applications. Gene expression data have been clustered and shown to help reveal the normal structure of the data, cellular processes, gene functions, extracting valuable information from occult data. Info on gene expression hides crucial information, because of the intricacy of biological networks and the huge number of genes involved. Therefore, clustering strategies are the top step in addressing these issues, and they are needed to identify interesting patterns and to scout natural structures in the underlying data. The discovery of homology is another advantage of data on gene expression clustering. This review looks at the different clustering algorithms applied to analyze gene code trim to discover, and supply valuable information about the best clustering strategy for ensuring consistency and precision in the research process. [ABSTRACT FROM AUTHOR]

Colorectal carcinoma one of most incidence and dangerous cancer around the world. The aim of current study to investigate the association between any molecular aberration in PIK3CA gene, exon 20 and PIK protein expression in colorectal carcinoma development. Methods; The current study achieved in two lines, Molecular study which achieved in advanced researches laboratory in biology department, Faculty of Sciences / University of Kufa, while immunohistochemical study was achieved in histopathology department, faculty of Medicine / University of Kufa. Only Iraqi patients were included in the current study who diagnosed through period extend from 01 December 2019 to 30 February 2021 and any patients diagnosed before or after this period were excluded. Also any samples without case report were excluded. The present study included 103 cases divided into two groups, patients group were included 50 cases with colorectal carcinoma(adenocarcinoma) and 53 cases with other non-adenocarcinoma such as hyperplastic polyp and colitis. According to gender, a study was included 61 male and 42 female. According to patients ages. the average was(50-89) years. The samples were collected from AL-Sader medical city in AL-Najaf province and Medical city in Baghdad province. Blood samples and tissues samples were collected from each 103 patients after enter the hospital(s) and have report of colonoscopy or CT-scan. blood samples were used in molecular line to (DNA extraction and sequencing). Tissues sample were confirmed by H&E examination and from these 102 cases only 50 cases with and other cases were excluded from a study. Breast carcinoma used as positive control for PIK3CA. Results: 27 cases (54%) given positive for staining with PIK3CA antibodies, but with normal genotype in sequencing. Therefore, there was no any correlation between colorectal carcinoma development and any aberration in PIK3CA gene –Exon 20 in current study. According to relation between colorectal carcinoma grades and positive and negative for PIK3CA, 15 cases(44%) in grade I, 8 cases (67%) in grade II and 4 cases (100%) were given positive for PIK3CA. There is positive correlation between grades and both ages and positive and negative cases(P =0.173 and sig=0.229) (P 0.312, sig 0.027) respectively. while, Negative correlation found between gender with both age and grades (p= -0.304, sig= 0.032) (P -0.365, sig=0.009) respectively. Also the negative correlation found between positive or negative cases for PIK3CA with both age and gender (P -0.196, sig 0.172)(P -0.201, sig 0.162) respectively. Conclusion: Due to relation between molecular study of PIK3CA Exon 20 and IHC study of PIK3CA expression, we don't found any relation between PIK3CA expression in patients with colorectal carcinoma and genetic aberration in PIK3CA gene, exon 20. According to relation between PIK3CA score index and grades, increase in PIK3CA score index directly Proportional with advance in grade of colorectal carcinoma. According to grades and cases with positive or negative cases, found numbers of cases that give positive for PIK3CA Abs increase with advance in grades.., There is positive correlation between grades and both ages and positive and negative cases for PIK3CA. while, Negative correlation found between gender with both age and grades. Also the negative correlation found between positive or negative cases for PIK3CA with both age and gender. [ABSTRACT FROM AUTHOR]

With the advancement of genomic engineering and genetic modification techniques, the uptake of computational tools to design guide RNA increased drastically. Searching for genomic targets to design guides with maximum on-target activity (efficiency) and minimum off-target activity (specificity) is now an essential part of genome editing experiments. Today, a variety of tools exist that allow the search of genomic targets and let users customize their search parameters to better suit their experiments. Here we present an overview of different ways to visualize these searched CRISPR target sites along with specific downstream information like primer design, restriction enzyme activity and mutational outcome prediction after a double-stranded break. We discuss the importance of a good visualization summary to interpret information along with different ways to represent similar information effectively. [ABSTRACT FROM AUTHOR]

Exosomes are a type of vesicle with the constituents from the viable cells, which can secrete the exosome included. They can be produced, conveyed and uptaken by different and distant cells, and affect the function and behavior of the recipient cells. Mesenchymal stem cell-derived exosomes (MSC-EXO), among all exosomes derived, gain uncommon consideration because of its potential of tissue repair and regeneration in all kinds of disease treatment. Studies have shown that, indeed, MSC-EXO presents its strong ability to inhibit inflammation, scar formation and promote skin repairing of human skins. Those abilities are proven to be highly relatable to the special miRNAs that exist in the MSC-EXO, which they function through manipulating the interpretation of the protein during the process of gene expression. This review highlights the investigation of therapeutic potential of MSC-EXO on human skin, as well as the relations between the various miRNAs in MSC-EXO and skin tissue repair and regeneration. [ABSTRACT FROM AUTHOR]

Background: Progression in the severity of metabolic syndrome (MetS) contributes to the development of cardiovascular disease. It leads to changes in the histological structure of the heart, known as cardiac fibrosis. Cardiac fibrosis can be identified from the high levels of the profibrotic molecule, such as activin-a and collagen-1. Aim: This study aims to determine the effect of therapy chlorogenic acid (CGA) from green coffee and epigallocatechin-3-gallate (EGCG) from green tea extract on activin-1 and collagen-1 gene expression the rat MetS model. Methods: Twenty-five male MetS rats (Sprague-Dawley) were divided into two control groups and three therapy groups (n=5). The administration of the CGA 200mg/kgbw and EGCG 300mg/kgbw were given orally. After eight weeks of treatment, rats were euthanized, then mRNA expression of activin-1 and collagen-1 were measured. Results: There is a significant effect of giving CGA and EGCG a therapy to suppress the activin-a (P-value= 0.001) and collagen-1 (P-value= 0.016) gene expressions in the rat MetS model. The correlation between the two genes expression shows a positive association. Conclusion: This study shows that CGA and EGCG are potential agents to prevent cardiac fibrosis as a clinical manifestation in metabolic syndrome. [ABSTRACT FROM AUTHOR]

The gram positive bacterium Staphylococcus aureus (S. aureus) is responsible for many diseases including toxic shock syndromes and food toxicity caused by the exotoxins that S. aureus releases. SEA and SEB are the best characterized out of more than 20 Staphylococcal enterotoxins. Treatment with Peganum Harmala seeds alcoholic extract can result in effect the gene expression of SEA gene, due to its antibacterial effects. This study focused on the seed extract of P. harmala, 20 grams of dried and powdered seeds of peganum harmala were extracted and 125 Staphylococcus aureus samples were screened. All of the isolates are previously confirmed using differential and selective media. From the isolates bacteria genomic DNA was extracted and the SEA gene was identified by using conventional PCR with specific primers. One S. aureus of the isolates was found to be SEA gene positive. The results of sensitivity test of S. aureus isolates to 3 concentrations of Peganum Harmala extract was determined using disc diffusion method, at concentrations of 500, 250 and 50 mg/ml has inhibit the S.aureus by 2.1 mm, 1mm and no antimicrobial activity respectively. The result of RT-PCR Showed that SEA gene at 50 concentrations is expressed 0.40 times less than the control, at 250 concentrations is expressed 0.15 times less than the control and at 500 concentrations is expressed 0.06 less than the control. [ABSTRACT FROM AUTHOR]

Staphylococcus epidermidis has been many virulence agents which instantly prompt damage to its host tissues. The capability to forming a biofilm is considered one of the most major virulence agents for many types of bacteria included S. epidermidis to supporting any illness. A biofilm is usually formed by attached microbial cells sessile within a matrix of extracellular polymeric substances (EPS). EPS has been consisted of; proteins arranged from one to two percentage including enzymes, RNA, and DNA less than one percent, while the polysaccharides were one to two and the main remaining composition is, water up to 97% that is liable to the movement of nutrients inside the biofilm components. Current knowledge leads to small RNAs (sRNAs) bis- (3'-5')-cyclic di-guanosine monophosphate (c-di-GMP) and quorum sensing (QS) as the primary arranger of bacterial biofilms formation. QS-controlled genes constituted about 10% of the total bacterial genome. Biofilm composition is reliant on the stimulation of certain genes expression that leads to the starting point of biofilm foundation. So, the present study aimed to study the impact of Al2O3 & Fe3O4 nanoparticles on extracellular matrix-binding protein (embp), autolysin E (atlE), and Tntercellular adhesion protein C (icaC) genes expression level which are involved in biofilm-forming of S. epidermidis bacteria. By using real-time quantitative polymerase chain reaction (RT-qPCR) assay. The result showed significantly impact (P < 0.05) of Al2O3 & Fe3O4 nanoparticles on expression levels of (embp), (atlE), and (icaC) genes. [ABSTRACT FROM AUTHOR]

The process of forming sex in the fetal phase involves many complexes and genes. The gene that plays the most important role in gender formation is the SRY gene or usually called the Sex Determining Y gene. However, the role of epigenetic regulation is beginning to be discovered concerning the determination of human gonads. Epigenetic regulation is the process of gene expression or phenotypic changes in an individual caused by non-genetic factors without changes in the basic DNA sequence. Epigenetic mechanisms enable organisms to integrate genomic and environmental information to change gene activity and produce a specific phenotype. Changes in gene expression allow cells to specialize and keep their identity during development. This is critical for determining gender. In addition, epigenetics can also contribute to several disorders of sexual development. These findings encourage further research to develop sex determination techniques through epigenetic analysis. [ABSTRACT FROM AUTHOR]

Gene expression is essential to life and occurs through the processes of transcription of mRNA in the nucleus, export of transcripts to the cytoplasm through the nuclear pore complex (NPC), and translation of the mRNA into protein in the cytosol. The budding yeast S. cerevisiae is a eukaryotic model system used to explore the regulation of mRNA export. Transcripts are able to exit the nucleus through interaction with Mex67 which binds mRNA via adaptor proteins and allows crossing through NPCs. However, during heat shock (42°C) known adaptor proteins are rendered dysfunctional thus halting general mRNA export. Under these conditions, specific transcripts are able to exit the nucleus to enable the cell to response to stress. For example, SSA4 encodes a chaperone, which helps denatured proteins refold following heat shock is able to selectively export in response to stress. However, the mechanism for this selective export is not understood. I hypothesize that an unknown adaptor protein recruits Mex67 to allow for its selective export from the nucleus. In order to test this hypothesis, I have cloned a pair of vectors to be used as phenotypic reporters for SSA4 export. These reporters include the ADE3 ORF and SSA4 regulatory sequence (promoter, 5' and 3' UTRs). We anticipated that these reporters would yield red yeast cells if selectively exported during heat shock conditions. Analysis of the first reporter plasmids indicated that the plasmids weren't fully cloned as expected, and subsequent experiments aimed at generating the proper clones did not produce clear results to continue the project. In the future, this project will be reimagined using CRISPR technology which aims to integrate the LacZ gene into the SSA4 locus. The new method has the potential to similarly serve as a colorimetric assay while eliminating previous issues of leaky expression and false positive results. [ABSTRACT FROM AUTHOR]

Microarray or gene expression profiling is conducted in a single experiment with different types of cells or tissue samples to evaluate and compare the extent of gene expression. The role of classifying the sample in question is more promising as the microarray dataset is disrupted due to the dimensional component, with a limited number of samples together with incorrect and noise genes. This is most important for the screening and diagnosis of a sample of breast cancer. The method of gene selection is currently being formulated to classify a few numbers of significant genes that are correlated with the extremely predictive process in the classification field. To carry out this method, a revolutionary genetic selection algorithm, namely the minimal Redundancy Maximal Significance (mRMR), is devised and integrated with the Gene Weight Imperialist Competitive Algorithm (GWICA), mRMR-GWICA, to classify insightful genes from the microarray-containing profile. The ground-breaking approach relies on the parallel Progressive Inductive Subspace Ensemble Clustering (PPISEC) algorithm to measure the precision of the classification of the known genes. PPISEC-WICA algorithm has three key steps: Improved Support Vector Machine (ISVM) classifier and Incremental Ensemble Member Chosen (IEMC) by GWICA are used to pick the centroid values and to execute the gene expression data clustering a structured cut algorithm is suggested. Experimental findings reveal that the formulated PPISEC system performs well on data containing the expression of the gene for breast cancer relative to conventional clustering ensemble approaches. This design is applied in a dataset comprising the gene expression dataset (GSE45827) which is collected from breast-cancer-gene-expression-cumida. The outputs of the clustering method are determined based on certain metrics such as precision, recall, f-measurement, accuracy, Adjusted Rand Index (ARI), and Normalized Mutual Information (NMI). The clustering design is implemented by implementing the MATLAB simulation environment in the R2014a edition. [ABSTRACT FROM AUTHOR]

Toll-IL1 receptor (TLR) and TIR signaling pathway genes (IRAK4, MyD88) deficiencies are an inborn error of the innate immune system. Defect in these two genes results in improper downstream signaling of the TLR and TIR pathways which is the important step for the activation of innate and adaptive immune systems. This study aimed to complement the differentially expressed genes (DEGs) innate immune response of patients with inborn errors in Toll-IL1 receptor signaling pathway (IRAK4, MyD88 deficiencies) compared to healthy subjects, identify their functions and molecular pathways. In order to identify key genes, enriched pathways, and important modules in the patients with such inborn innate immune system errors data for gene expression profiles (GSE25742) were downloaded from the GEO database, and bioinformatics analysis was made. In total 500 DEGs were identified. Among them, 191 (38.2%) genes were up-regulated and 309 (61.8%) genes were down-regulated. Gene ontology (GO) and KEGG pathway enrichment analysis of target genes was performed. Furthermore, we reviewed some relevant core genes such as TNF, IL1B, TLR2, MMP9, SPL1, ITAGAX, HCK, Lyn, CXCL1, and FPR2 by using gene-gene interaction network analysis, which may contribute to a better understanding of the molecular mechanisms of the inborn error of innate immunity or TLR signaling. Whereas six clusters were identified by MCODE. These genes and pathways repotted might provide a new perspective for revealing the underlying pathological mechanisms and therapy strategy for inborn error in Tool like receptor signaling pathways and other inborn errors of the innate immune system. [ABSTRACT FROM AUTHOR]

In this paper, we have described the production of 3-Hydroxypropanoic acid using glycerol as a key intermediate in the presence of engineered microbes. 3-hydroxypropanoic acid (3-HP) is an important interface chemical that is in great need around the world. 3-HP can be generated from a variety of renewable energy sources. Acrylic acid and its several derivatives are made from it as a starting material 3-hydroxypropanoic acid (3-HP) is a highly sought-after platform chemical, used in bioplastics in their polymerized state. Many microbes naturally have biosynthetic pathways for producing 3-HP, and some of these pathways have been inserted into commonly used cell factories like Saccharomyces cerevisiae and Escherichia coli. Recent advances in synthetic biology and metabolic engineering have resulted in more effective methods for bio-production of 3-HP. Among them are novel methods for implementing heterologous pathways, rational enzyme engineering, precise gene expression control, carbon flux redirection based on in silico predictions from genome- scale metabolic models, and fermentation state optimization. Despite extensive research into 3-HP production in existing industrially applicable cell factories, modern production methods have not yet achieved the standards required for commercialization. In this paper, we compare yields and titers obtained in various microbial cell factories, as well as possible methods for achieving industrially important cell factories, to assess the current state of 3-HP bio-production. [ABSTRACT FROM AUTHOR]

Here we report about molecular genetic markers development and primer pairs selection for studying effects of heavy metal pollution on gene expression levels of the Baikal endemic sponges. We selected four genes as targets for marker development: Metal Regulatory Transcription Factor 1, Glutathione-s-transferase mu class, Copper transporting ATPase 1 and Copper chaperone for superoxide dismutase since as it was previously shown for other aquatic invertebrates these genes expression levels can be affected by high concentration of heavy metals. We have developed and successfully tested specific primer pairs for these genes. Developed markers will be further used for analysis of heavy metal pollution effects on gene expression levels of endemic Baikal sponges. [ABSTRACT FROM AUTHOR]

THD-Tricluster method is a triclustering analysis with a biclustering-based approach. The THD-Tricluster method uses the Shifting-and-Scaling Similarity (SSSim) value to form a bicluster first and shows it by forming a tricluster. The SSSim value uses Shifting-and-Scaling Correlation to use an interface with shifting and scaling patterns as well as intertemporal coherence and compares it with the threshold value. THD-Tricluster method was performed on treatment response data to interferon-beta therapy in multiple sclerosis patients. The optimal scenario is a scenario with a coverage value scenario that uses the highest threshold value. In this scenario, there are two types of tricluster, namely the tricluster which has a collection of genes in responsive patients and patients who are not responsive to therapy. The differences collection of genes in both tricluster can be used by medical professionals in the development of interferon-beta therapy treatments to create a therapy response on multiple sclerosis disease. [ABSTRACT FROM AUTHOR]