Reconstructions of genome-scale metabolic networks from different organisms have become popular in recent years. Metabolic engineering can simulate the reconstruction process to obtain desirable phenotypes. In previous studies, optimization algorithms have been implemented to identify the near-optimal sets of knockout genes for improving metabolite production. However, previous works contained premature convergence and the stop criteria were not clear for each case. Therefore, this study proposes an algorithm that is a hybrid of the ant colony optimization algorithm and flux balance analysis (ACOFBA) to predict near optimal sets of gene knockouts in an effort to maximize growth rates and the production of certain metabolites. Here, we present a case study that uses Baker's yeast, also known as Saccharomyces cerevisiae, as the model organism and target the rate of vanillin production for optimization. The results of this study are the growth rate of the model organism after gene deletion and a list of knockout genes. The ACOFBA algorithm was found to improve the yield of vanillin in terms of growth rate and production compared with the previous algorithms.
The small ubiquitin-like modifier (SUMO) is implicated in various cellular activities, including transcriptional regulation. We previously showed that the yeast activator Gcn4 becomes sumoylated during activation, facilitating its eventual promoter eviction and transcriptional shut off. Here we show that the corepressor Tup1 is sumoylated, at two specific lysines, under various stress conditions. Mutation of these sites has no effect on Tup1 recruitment or RNAP II promoter occupancy immediately following induction. However, Tup1 levels subsequently decrease, while RNAP II and transcription increase in Tup1 mutant cells. Consistent with this, a Tup1 mutant displaying increased sumoylation led to reduced transcription. We also show that coordinated sumoylation of Gcn4 and Tup1 enhances Gcn4 promoter eviction and that multiple Tup1-interacting proteins become sumoylated after stress. Together, our studies provide evidence that coordinated sumoylation of Gcn4, Tup1 and likely other factors dampens activated transcription by stabilizing Tup1 binding and stimulating Gcn4 and RNAP II removal.
Pregnant women are susceptible to vaginal colonization and infection by yeast. The purpose of the study was to determine the prevalence of Candida spp in high vaginal swabs of pregnant women and their antifungal susceptibility.
Mekanisme pengambilan dan penghasilan asid amino bagi mikroorganisma psikrofil yang bermandiri dan berpoliferasi
pada persekitaran sejuk melampau masih belum difahami sepenuhnya. Objektif kajian ini ialah untuk mengenal pasti
gen yang terlibat dalam penjanaan asid amino bagi yis psikrofil, Glaciozyma antarctica serta menentukan pengekspresan
gen tersebut semasa kehadiran dan kekurangan asid amino dalam medium pertumbuhan. Pengenalpastian gen telah
dilakukan melalui penjanaan penanda jujukan terekspres (ESTs) daripada dua perpustakaan cDNA yang dibina daripada
sel yang dikultur dalam medium pertumbuhan kompleks dan medium pertumbuhan minimum tanpa asid amino. Sebanyak
3552 klon cDNA daripada setiap perpustakaan dipilih secara rawak untuk dijujuk menghasilkan 1492 transkrip unik
(medium kompleks) dan 1928 transkrip unik (medium minimum). Analisis pemadanan telah mengenl pasti gen mengekod
protein yang terlibat di dalam pengambilan asid amino bebas, biosintesis asid amino serta gen yang terlibat dengan
kitar semula asid amino berdasarkan tapak jalan yang digunakan oleh yis model, Saccharomyces cerevisiae. Analisis
pengekspresan gen menggunakan kaedah RT-qPCR menunjukkan pengekspresan gen mengekod protein yang terlibat di
dalam pengambilan asid amino bebas iaitu permease adalah tinggi pada medium kompleks manakala pengekspresan
kebanyakan gen mengekod protein yang terlibat dalam kitar semula dan biosintesis asid amino adalah tinggi di dalam
medium minimum. Kesimpulannya, gen yang terlibat dalam penjanaan dan pengambilan asid amino bagi mikroorganisma
psikrofil adalah terpulihara seperti mikroorganisma mesofil dan pengekspresan gen-gen ini adalah diaruh oleh kehadiran
atau ketiadaan asid amino bebas pada persekitaran.
Previously, we synthesized triazoloquinazolines 1-14 and characterized their structure. In this study, we aimed to evaluate the in vitro activity of the targets 1-14 as α-glucosidase inhibitors using α-glucosidase enzyme from Saccharomyces cerevisiae type 1. Among the tested compounds, triazoloquinazolines 14, 8, 4, 5, and 3 showed the highest inhibitory activity (IC50 = 12.70 ± 1.87, 28.54 ± 1.22, 45.65 ± 4.28, 72.28 ± 4.67, and 83.87 ± 5.12 μM, respectively) in relation to that of acarbose (IC50 = 143.54 ± 2.08 μM) as a reference drug. Triazoloquinazolines were identified herein as a new class of potent α-glucosidase inhibitors. Molecular docking results envisaged the plausible binding interaction between the target triazoloquinazolines and α-glucosidase enzyme and indicated considerable interaction with the active site residues.
Automated methods for reconstructing biological networks are becoming increasingly important in computational systems biology. Public databases containing information on biological processes for hundreds of organisms are assisting in the inference of such networks. This paper proposes a multiobjective genetic algorithm method to reconstruct networks related to metabolism and protein interaction. Such a method utilizes structural properties of scale-free networks and known biological information about individual genes and proteins to reconstruct metabolic networks represented as enzyme graph and protein interaction networks. We test our method on four commonly-used protein networks in yeast. Two are networks related to the metabolism of the yeast: KEGG and BioCyc. The other two datasets are networks from protein-protein interaction: Krogan and BioGrid. Experimental results show that the proposed method is capable of reconstructing biological networks by combining different omics data and structural characteristics of scale-free networks. However, the proposed method to reconstruct the network is time-consuming because several evaluations must be performed. We parallelized this method on GPU to overcome this limitation by parallelizing the objective functions of the presented method. The parallel method shows a significant reduction in the execution time over the GPU card which yields a 492-fold speedup.
Cyclopoid copepod has a potential as live feed that can provide ornamental fish larvae with energy and essential nutrients, and promote their growth and survival, as well as affect their colouration. However, the nutrition, growth and nutritional requirements of this species are poorly understood. This research focuses on comparing the efficacy of enrichment types on copepods towards the growth rate, survival rate and colouration of Pterophyllum scalare larvae. The enrichment of copepods consists of four enrichment procedures (rice bran, palm kernel cake (PKC),Chlorella and yeast). This study was carried out over 50 days and the growth rate, survival rate and colouration (growth rate, survival rate, SGR and colouration) were used to evaluate the responses of P. scalare larvae towards different enrichment methods. Specific growth rates (8.0161 ± 1.4928 %; P = 0.775) and survival rates (66.667 ± 5.337%; P = 0.815) of fish larvae were found to not be significantly different (P = 0.775, P = 0.815; P >0.05). However, the colouration of the fish larvae was affected by the types of enrichment used (P
Eukaryotic cells contain translation-associated mRNA surveillance pathways which prevent the production of potentially toxic proteins from aberrant mRNA translation events. We found that loss of mRNA surveillance pathways in mutants deficient in nonsense-mediated decay (NMD), no-go decay (NGD) and nonstop decay (NSD) results in increased protein aggregation. We have isolated and identified the proteins that aggregate and our bioinformatic analyses indicates that increased aggregation of aggregation-prone proteins is a general occurrence in mRNA surveillance mutants, rather than being attributable to specific pathways. The proteins that aggregate in mRNA surveillance mutants tend to be more highly expressed, more abundant and more stable proteins compared with the wider proteome. There is also a strong correlation with the proteins that aggregate in response to nascent protein misfolding and an enrichment for proteins that are substrates of ribosome-associated Hsp70 chaperones, consistent with susceptibility for aggregation primarily occurring during translation/folding. We also identified a significant overlap between the aggregated proteins in mRNA surveillance mutants and ageing yeast cells suggesting that translation-dependent protein aggregation may be a feature of the loss of proteostasis that occurs in aged cell populations.
Green coffee beans are stored for a certain period and under certain conditions until they are finally utilized. The storage period may depend on customer demand while the storage conditions depend on where the coffee beans are stored. Thus, this research emphasizes the physicochemical changes that occur in Liberica coffee beans during storage under the Malaysian
climate (average temperature and relative humidity of 29.33ºC and 71.75% respectively). The changes in the physico-chemical (coffee size, mass, densities, colour, proximate analysis, sucrose, chlorogenic acid content) and microbiological (yeast and mould count) properties were evaluated during eight months of storage. After the storage, the physical properties of the coffee changed as the coffee beans expanded in size, reduced in mass and density and became brighter in colour. Changes in the chemical properties were also detected where the moisture decreased and the ash content increased. In addition, the sucrose level was found to decrease with a corresponding increase in chlorogenic acid. During storage, the counts of yeast and mould were reduced. Model equations describing the changes in the properties were developed. The overall conclusion was that the coffee beans reduced in quality during storage.
In this study polymerase chain reaction (PCR) was used to identify yeast in domestic ragi obtained
from two local markets in Sarawak and Pahang. These ragi are normally used as a dry starter in food fermentation (tapai) for Pahang (ST2) and Sarawak (ST3) and tuak (ST1) which is an alcoholic drink in Sarawak. Universal primer, NL1 and NL4 were used as a primer in this study to amplify D1/D2 fragment. Based on the result from the sequencing and after the BLAST search of the nucleotide sequences, the strain was confirmed as Candida glabrata (FN424108.) partial 26S rRNA gene, strain IMUFRJ 51955 for ST1, Saccharomyces cerevisiae(EU285514.1) isolate 35 26S ribosomal RNA gene, partial sequence for ST2 sample and Candida glabrata (FN393990.1) partial 26S rRNA gene, strain MUCL 51244 for ST3. All these strains were found in domestic ragi used for food fermentation.
Evaluation on the physicochemical and sensory properties of wheat flour doughnuts substituted with banana flour (BF) was investigated. Wheat flour was substituted with green banana (Musa paradisiaca var. Awak) flour at 0% (control), 10%, 20% and 30% levels in yeast-raised doughnut prepared by the straight dough method. Chemical (moisture, fat, protein, ash, carbohydrate, crude fibre, total dietary fibre and caloric content), physical (volume, specific volume and colour) and sensory evaluation were conducted on all samples. Chemical analyses result indicated a higher percentage of total dietary fibre and caloric content in doughnut substituted with BF than the control. Colour evaluation showed that the dough, crust and crumb of doughnut with BF ranged from 68.97 ± 0.59 – 84.78 ± 0.16 (red – yellow quadrant). The change from light to darker colour correlated with the amount of BF added. Results also showed that the volume and specific volume was significantly affected (p < 0.05) by levels of BF substituted. Doughnut substituted with 20% BF showed the highest score in overall acceptability (6.71 ± 1.40).
The objective of this study was to determine microbiological quality of gulai tempoyak paste (GTP) added with three different leaf; Vietnamese coriander, turmeric and asam gelugor. The GTP was cooked for 10 minutes with control temperature (60-70°C) and the leaf were added at 2, 5 and 8 minutes during the cooking time to give exposure times of 8, 5 and 2 minutes of the leaf to GTP. GTP without addition of leaf was treated as control and all the prepared GTPs were stored at 30°C for 2 days before analysed using total plate count (TPC) and yeast and mould count (YMC). The addition of asam gelugor leaf to GTP for 5 minutes of the cooking period significantly (p > 0.05) reduced TPC (log10 3.54 CFU/g) compared to Vietnamese coriander (log10 4.67 CFU/g) and turmeric leaf (log10 4.70 CFU/g). Asam gelugor leaf also showed a significant difference in TPC reduction (log10 4.44 CFU/g) when added to GTP for 8 minutes compared to Vietnamese coriander (log10 5.10 CFU/g), but was insignificant to turmeric leaf (log10 4.71 CFU/g). In conclusion, there are significant effects on microbiological quality of GTP when added with Vietnamese coriander, turmeric and asam gelugor leaf at different exposure time based on TPC and YMC.
Extremely low temperatures present various challenges to life that include ice formation and effects on metabolic capacity. Psyhcrophilic microorganisms typically have an array of mechanisms to enable survival in cold temperatures. In this study, we sequenced and analysed the genome of a psychrophilic yeast isolated in the Antarctic region, Glaciozyma antarctica. The genome annotation identified 7857 protein coding sequences. From the genome sequence analysis we were able to identify genes that encoded for proteins known to be associated with cold survival, in addition to annotating genes that are unique to G. antarctica. For genes that are known to be involved in cold adaptation such as anti-freeze proteins (AFPs), our gene expression analysis revealed that they were differentially transcribed over time and in response to different temperatures. This indicated the presence of an array of adaptation systems that can respond to a changing but persistent cold environment. We were also able to validate the activity of all the AFPs annotated where the recombinant AFPs demonstrated anti-freeze capacity. This work is an important foundation for further collective exploration into psychrophilic microbiology where among other potential, the genes unique to this species may represent a pool of novel mechanisms for cold survival.
Cashew (Anacardium occidentale L.) leaf is traditionally used to treat skin infections. Although many flavonols have been identified from its leaf extract, their inhibitory effects on skin pathogens are not yet determined. The aims of this study were to determine the antimicrobial (against skin pathogenic microbes) and antioxidant activities of four flavonol glycosides from the crude extract and three flavonol aglycones from the hydrolyzed extract. The hydrolyzed extract was found to show higher activities than the crude extract. Myricetin showed the highest activity against all the tested bacteria and yeast with the lowest Minimum Inhibition Concentration (MIC) of 7.81 μg/mL on Corynebacterium minutissimum ATCC23348. Myricetin also exhibited good primary antioxidant activities with the effective concentration with 50% of activity (EC50) values ranged between 2.23 μg/mL and 6.40 μg/mL. The highest secondary antioxidant activity was indicated by myricetin-3-O-rhamnoside. Thus, myricetin can be considered as a bioactive compound of the hydrolyzed extract.
The Zingiber zerumbet rhizomes are traditionally used to treat fever, and the in vitro inhibitory effect of ethyl acetate extract from Zingiber zerumbet rhizomes (EAEZZR) against DENV2 NS2B/NS3 (two non-structural proteins, NS2 and NS3 of dengue virus type 2) has been reported earlier. This study was carried out to establish an acute toxicity profile and evaluate the anti-fever (anti-pyretic) activities of EAEZZR in yeast-induced fever in rats. The major compound of EAEZZR, zerumbone, was isolated using chromatographic methods including column chromatography (CC) and preparative thin-layer chromatography (PTLC). Additionally, the structure of zerumbone was elucidated using nuclear magnetic resonance (NMR), liquid chromatography mass spectrometer-ion trap-time of flight (LCMS-IT-TOF), infrared (IR), and ultraviolet (UV) spectroscopy. The toxicity of EAEZZR was evaluated using Organization for Economic Cooperation and Development Test Guideline 425 (OECD tg-425) with minor modifications at concentrations EAEZZR of 2000 mg/kg, 3000 mg/kg, and 5000 mg/kg. Anti-fever effect was determined by yeast-induced fever (pyrexia) in rats. The acute toxicity study showed that EAEZZR is safe at the highest 5000 mg/kg body weight dose in Sprague Dawley rats. Rats treated with EAEZZR at doses of 125, 250, and 500 mg/kg exhibited a significant reduction in rectal temperature (TR) in the first 1 h. EAEZZR at the lower dose of 125 mg/kg showed substantial potency against yeast-induced fever for up to 2 h compared to 0 h in controls. A significant reduction of TR was observed in rats treated with standard drug aspirin in the third through fourth hours. Based on the present findings, ethyl acetate extract of Zingiber zerumbet rhizomes could be considered safe up to the dose of 5000 mg/kg, and the identification of active ingredients of Zingiber zerumbet rhizomes may allow their use in the treatment of fever with dengue virus infection.
Newly synthesized benzimidazole hydrazone derivatives 1-26 were evaluated for their α-glucosidase inhibitory activity. Compounds 1-26 exhibited varying degrees of yeast α-glucosidase inhibitory activity with IC50 values between 8.40 ± 0.76 and 179.71 ± 1.11 μM when compared with standard acarbose. In this assay, seven compounds that showed highest inhibitory effects than the rest of benzimidazole series were identified. All the synthesized compounds were characterized by different spectroscopic methods adequately. We further evaluated the interaction of the active compounds with enzyme with the help of docking studies.
Oil palm trunk (OPT) sap was utilized for growth and bioethanol production by Saccharomycescerevisiae with addition of palm oil mill effluent (POME) as nutrients supplier. Maximum yield (YP/S) was attained at 0.464g bioethanol/g glucose presence in the OPT sap-POME-based media. However, OPT sap and POME are heterogeneous in properties and fermentation performance might change if it is repeated. Contribution of parametric uncertainty analysis on bioethanol fermentation performance was then assessed using Monte Carlo simulation (stochastic variable) to determine probability distributions due to fluctuation and variation of kinetic model parameters. Results showed that based on 100,000 samples tested, the yield (YP/S) ranged 0.423-0.501g/g. Sensitivity analysis was also done to evaluate the impact of each kinetic parameter on the fermentation performance. It is found that bioethanol fermentation highly depend on growth of the tested yeast.
Ethanol was produced via the simultaneous saccharification and fermentation (SSF) of dilute sodium hydroxide treated corn stover. Saccharification was achieved by cultivating either Phanerochaete chrysosporium or Gloeophyllum trabeum on the treated stover, and fermentation was then performed by using either Saccharomyces cerevisiae or Escherichia coli K011. Ethanol production was highest on day 3 for the combination of G. trabeum and E. coli K011 at 6.68 g/100g stover, followed by the combination of P. chrysosporium and E. coli K011 at 5.00 g/100g stover. SSF with S. cerevisiae had lower ethanol yields, ranging between 2.88 g/100g stover at day 3 (P. chrysosporium treated stover) and 3.09 g/100g stover at day 4 (G. trabeum treated stover). The results indicated that mild alkaline pretreatment coupled with fungal saccharification offers a promising bioprocess for ethanol production from corn stover without the addition of commercial enzymes.
A drastic improvement in the analysis of gene expression has lead to new discoveries in bioinformatics research. In order to analyse the gene expression data, fuzzy clustering algorithms are widely used. However, the resulting analyses from these specific types of algorithms may lead to confusion in hypotheses with regard to the suggestion of dominant function for genes of interest. Besides that, the current fuzzy clustering algorithms do not conduct a thorough analysis of genes with low membership values. Therefore, we present a novel computational framework called the "multi-stage filtering-Clustering Functional Annotation" (msf-CluFA) for clustering gene expression data. The framework consists of four components: fuzzy c-means clustering (msf-CluFA-0), achieving dominant cluster (msf-CluFA-1), improving confidence level (msf-CluFA-2) and combination of msf-CluFA-0, msf-CluFA-1 and msf-CluFA-2 (msf-CluFA-3). By employing double filtering in msf-CluFA-1 and apriori algorithms in msf-CluFA-2, our new framework is capable of determining the dominant clusters and improving the confidence level of genes with lower membership values by means of which the unknown genes can be predicted.
Utilization of macroalgae biomass for bioethanol production appears as an alternative source to lignocellulosic materials. In this study, for the first time, Amberlyst (TM)-15 was explored as a potential catalyst to hydrolyze carbohydrates from Eucheuma cottonii extract to simple reducing sugar prior to fermentation process. Several important hydrolysis parameters were studied for process optimization including catalyst loading (2-5%, w/v), reaction temperature (110-130°C), reaction time (0-2.5 h) and biomass loading (5.5-15.5%, w/v). Optimum sugar yield of 39.7% was attained based on the following optimum conditions: reaction temperature at 120°C, catalyst loading of 4% (w/v), 12.5% (w/v) of biomass concentration and reaction time of 1.5h. Fermentation of the hydrolysate using Saccharomyces cerevisiae produced 0.33 g/g of bioethanol yield with an efficiency of 65%. The strategy of combining heterogeneous-catalyzed hydrolysis and fermentation with S. cerevisiae could be a feasible strategy to produce bioethanol from macroalgae biomass.