Displaying publications 81 - 100 of 166 in total

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  1. Induction of MHC Class I HLA-A2 promoter by dengue virus occurs at the NFκB binding domains of the Class I Regulatory Complex
    Othman S, Rahman NA, Yusof R
    Virus Res, 2012 Jan;163(1):238-45.
    PMID: 22001567 DOI: 10.1016/j.virusres.2011.09.040
    Despite aggressive efforts in dengue research, the control of dengue diseases and discovery of therapeutics against them await complete elucidation of its complex immune-pathogenesis. Unlike many viruses that escape the host's immune responses by suppressing the major histocompatibility complex (MHC) Class I pathway, many Flaviviruses up-regulate the cell surface expression of MHC Class I complex. We recently reported MHC Class I HLA-A2 promoter activation by all serotypes of dengue virus (DV). The mechanism by which DV regulates this is further explored here in HepG2 human liver cell line. Using real-time PCR, evidence that, similar to infections by other Flaviviruses, DV infection has the ability to up-regulate the MHC Class I transcription and mRNA synthesis, is presented. The region responsive towards DV infection of all serotypes was mapped to the Class I Regulatory Complex (CRC) of the HLA-A2 promoter. Competition electrophoretic mobility shift assay (EMSA) with NFκB probe established the presence of specific DNA-protein complex in DV-infected nuclear extracts. Antibody-supershift assays identified the MHC Class I promoter activation by DV to occur through binding of p65/p50 heterodimers and p65 homodimers to κB1 and κB2 cis-acting elements, respectively, within the CRC, and not with the interferon consensus sequence (ICS). This study presents evidence of MHC Class I gene modulation by DV, hence providing a better understanding of dengue immune-pathogenesis that would consequently facilitate the discovery of antiviral therapeutics against dengue.
  2. Fulltext Incorporation of Hydroxyapatite into Glass Ionomer Cement (GIC) Formulated Based on Alumino-Silicate-Fluoride Glass Ceramics from Waste Materials
    Wan Jusoh WN, Matori KA, Mohd Zaid MH, Zainuddin N, Ahmad Khiri MZ, Abdul Rahman NA, et al.
    Materials (Basel), 2021 Feb 18;14(4).
    PMID: 33670465 DOI: 10.3390/ma14040954
    Glass ionomer cement (GIC) is a well-known restorative material applied in dentistry. The present work aims to study the effect of hydroxyapatite (HA) addition into GIC based on physical, mechanical and structural properties. The utilization of waste materials namely clam shell (CS) and soda lime silica (SLS) glass as replacements for the respective CaO and SiO2 sources in the fabrication of alumino-silicate-fluoride (ASF) glass ceramics powder. GIC was formulated based on ASF glass ceramics, polyacrylic acid (PAA) and deionized water, while 1 wt.% of HA powder was added to enhance the properties of the cement samples. The cement samples were subjected to four different ageing times before being analyzed. In this study, the addition of HA caused an increment in density and compressive strength results along with ageing time. Besides, X-ray Diffraction (XRD) revealed the formation of fluorohydroxyapatite (FHA) phase in HA-added GIC samples and it was confirmed by Fourier Transform Infrared (FTIR) analysis which detected OH‒F vibration mode. In addition, needle-like and agglomeration of spherical shapes owned by apatite crystals were observed from Field Emission Scanning Electron Microscopy (FESEM). Based on Energy Dispersive X-ray (EDX) analysis, the detection of chemical elements in the cement samples were originated from chemical compounds used in the preparation of glass ceramics powder and also the polyacid utilized in initiating the reaction of GIC.
  3. Fulltext Identification of natural antimicrobial agents to treat dengue infection: In vitro analysis of latarcin peptide activity against dengue virus
    Rothan HA, Bahrani H, Rahman NA, Yusof R
    BMC Microbiol, 2014;14:140.
    PMID: 24885331 DOI: 10.1186/1471-2180-14-140
    Although there have been considerable advances in the study of dengue virus, no vaccines or anti-dengue drugs are currently available for humans. Therefore, new approaches are necessary for the development of potent anti-dengue drugs. Natural antimicrobial peptides (AMPs) with potent antiviral activities are potential hits-to-leads for antiviral drug discovery. We performed this study to identify and characterise the inhibitory potential of the latarcin peptide (Ltc 1, SMWSGMWRRKLKKLRNALKKKLKGE) against dengue virus replication in infected cells.
  4. Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia
    Ghazali N, Rahman NA, Kannan TP, Ahmad A, Sulong S
    BMC Oral Health, 2023 Nov 29;23(1):945.
    PMID: 38031027 DOI: 10.1186/s12903-023-03464-3
    BACKGROUND: Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis.

    METHODS: This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7-13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software.

    RESULTS: The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023).

    CONCLUSION: The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.

  5. Fulltext Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine
    Xu Y, Yu S, Zou JW, Hu G, Rahman NA, Othman RB, et al.
    PLoS One, 2015;10(11):e0144171.
    PMID: 26636321 DOI: 10.1371/journal.pone.0144171
    The peptides derived from envelope proteins have been shown to inhibit the protein-protein interactions in the virus membrane fusion process and thus have a great potential to be developed into effective antiviral therapies. There are three types of envelope proteins each exhibiting distinct structure folds. Although the exact fusion mechanism remains elusive, it was suggested that the three classes of viral fusion proteins share a similar mechanism of membrane fusion. The common mechanism of action makes it possible to correlate the properties of self-derived peptide inhibitors with their activities. Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The model displayed 92% prediction accuracy with the Matthew's correlation coefficient of 0.84, obviously superior to those using physicochemical properties and amino acid decomposition as input. The predictive support vector machine model for self- derived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process.
  6. Identification of Novel Sesamol Dimers with Unusual Methylenedioxy Ring-Opening Skeleton and Evaluation of Their Antioxidant and Cytotoxic Activities
    Murthy S, Hazli UHAM, Kong KW, Mai CW, Leong CO, Rahman NA, et al.
    Curr Org Synth, 2019;16(8):1166-1173.
    PMID: 31984923 DOI: 10.2174/1570179416666191003095253
    BACKGROUND: Sesamol is a widely used antioxidant for the food and pharmaceutical industries. The oxidation products of this compound may be accumulated in foods or ingested. Little is known about its effect on human health.

    OBJECTIVE: It is of great interest to identify the oxidation products of sesamol that may be beneficial to humans. This study was undertaken to identify the oxidation products of sesamol and investigate their antioxidant and cytotoxic activities.

    MATERIALS AND METHODS: Using the ferricyanide oxidation approach, four oxidation products of sesamol (2, 3, 20 & 21) have been identified. Structural elucidation of these compounds was established on the basis of their detailed NMR spectroscopic analysis, mass spectrometry and x-ray crystallography. Additionally, a formation mechanism of compound 20 was proposed based on high-resolution mass spectrometry-fragmentation method. The antioxidant activities of these compounds were determined by the DPPH, FRAP, and ABTS assays. The in vitro antiproliferative activity of these compounds was evaluated against a panel of human cancer cell lines as well as non-cancerous cells.

    RESULTS: Two oxidation products of sesamol were found to contain an unusual methylenedioxy ring-opening skeleton, as evidenced by spectroscopic and x-ray crystallographic data. Among all compounds, 20 displayed impressive antiproliferative activities against a panel of human cancer cell lines yet remained non-toxic to noncancerous cells. The antioxidant activities of compound 20 are significantly weaker than sesamol as determined by the DPPH, FRAP, and ABTS assays.

    CONCLUSION: The oxidation products of sesamol could be a valuable source of bioactive molecules. Compound 20 may be used as a potential lead molecule for cancer studies.

  7. How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications
    Al-Obaidi JR, Jamaludin AA, Rahman NA, Ahmad-Kamil EI
    Planta, 2024 Mar 29;259(5):103.
    PMID: 38551683 DOI: 10.1007/s00425-024-04378-2
    Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.
  8. Helicobacter pylori eradication with short-term therapy leads to duodenal ulcer healing without the need for continued acid suppression therapy
    Goh KL, Navaratnam P, Peh SC, Wong NW, Chuah SY, Rahman NA, et al.
    Eur J Gastroenterol Hepatol, 1996 May;8(5):421-3.
    PMID: 8804868
    To determine whether duodenal ulcers continue to heal following successful Helicobacter pylori eradication with short-term eradication therapy without further acid suppression therapy.
  9. Fulltext Foot ulcers and their association with diabetic Charcot foot complications
    Rahman NA, Fauzi AA, Chung TY, Latif LA, Chan SC
    Aust J Gen Pract, 2020 2 3;49(1-2):48-53.
    PMID: 32008261 DOI: 10.31128/AJGP-07-19-4991
    BACKGROUND AND OBJECTIVES: Diabetic Charcot foot (DCF) can cause gross structural deformities of the foot and ankle. The main objective of this study was to identify complications of DCF and its associated factors.

    METHOD: This is a retrospective cohort study. Data on medical background, previous DCF treatment and complications were obtained. Multiple logistic regression analysis was performed to measure factors related to various complications of DCF.

    RESULTS: Ninety-eight patient records were retrieved. Of the 83 patients who were still alive, 75.9% (n = 63) had recurrent ulcers, 53.0% (n = 44) had undergone foot surgery and 45.8% (n = 38) had undergone amputation. Patients with a history of recurrent ulcers have the highest predilection to amputation (odds ratio: 8.5; 95% confidence interval: 1.8, 39.1).

    DISCUSSION: In terms of DCF complications, foot ulcers are an independent predictor of recurrent foot ulcers, foot surgery and amputation. Regular foot assessment of patients with DCF to prevent ulcers is strongly recommended.

  10. Fulltext Floating teeth appearance: A radiographic dilemma
    Rahman NA, Harun MH, Rahman SA, Mohammad NSA
    J Taibah Univ Med Sci, 2020 Apr;15(2):160-165.
    PMID: 32368214 DOI: 10.1016/j.jtumed.2020.02.005
    Gorham disease (GD) is an extremely rare disorder that is characterised by massive osteolysis of the affected bone with unknown aetiology and an unpredictable prognosis. Additionally, no standard treatment is available for GD. This article describes a case report of a 61-year-old Malay woman who was diagnosed with GD of the anterior mandible without a prior history of trauma. She presented with pain and mobility of the dentoalveolar segment for 3 months. The radiographic findings showed "floating teeth" with widening of the periodontal ligament space and localized area of bony destruction. Histopathologically, there was proliferation of numerous dilated endothelial-lined channels within the intertrabecular tissue. Some areas of bone were replaced by fibrous connective tissue giving rise to the appearance of a benign fibroosseous lesion. The patient was managed with simple removal of the affected bone segment under local anaesthesia, followed by prosthodontic rehabilitation. Healing of the surgical site was uneventful, and no recurrence was reported at the 3-year follow-up.
  11. Fulltext Flavonoids with M1 muscarinic acetylcholine receptor binding activity
    Swaminathan M, Chee CF, Chin SP, Buckle MJ, Rahman NA, Doughty SW, et al.
    Molecules, 2014 Jun 27;19(7):8933-48.
    PMID: 24979399 DOI: 10.3390/molecules19078933
    Muscarinic acetylcholine receptor-active compounds have potential for the treatment of Alzheimer's disease. In this study, a series of natural and synthetic flavones and flavonols was assayed in vitro for their ability to inhibit radioligand binding at human cloned M1 muscarinic receptors. Several compounds were found to possess competitive binding affinity (Ki=40-110 µM), comparable to that of acetylcholine (Ki=59 µM). Despite the fact that these compounds lack a positively-charged ammonium group under physiological conditions, molecular modelling studies suggested that they bind to the orthosteric site of the receptor, mainly through non-polar interactions.
  12. Fulltext Feeding Behaviour of Cynopterus sphinx (Pteropodidae) Under Captive Conditions
    Shafie NJ, Rahman NA, Sah SA, Rosely NF, Sufian M
    Trop Life Sci Res, 2014 Dec;25(2):53-9.
    PMID: 27073599 MyJurnal
    We examined the olfactory and visual abilities of megachiropteran bats, Cynopterus sphinx, for discrimination of the odour and shape of the banana fruit, Musa sp. We conducted the experiments in captive conditions by offering a selection of ripe bananas, blended bananas and artificial bananas. The behaviour of the bats was observed visually, and the percentage of activity and rest, duration of the first foraging bout, number of feeding attempts and the average duration of successful attempts was recorded for each bat. The bats exhibited an increased number of visits to ripe bananas and blended banana fruits. However, the artificial fruit did not evoke any response. Our study suggests that odour cues are more important than visual cues for the location of fruits by C. sphinx.
  13. Facial Fractures in Kajang Hospital, Malaysia: A 5-Year Review
    Rahman RA, Hussaini HM, Rahman NA, Rahman SR, Nor GM, Ai Idrus SM, et al.
    Eur J Trauma Emerg Surg, 2007 Feb;33(1):90-5.
    PMID: 26815981 DOI: 10.1007/s00068-007-5154-5
    The objective of this study was to determine the demographic data as well as other relevant data pertaining to the management of patients with maxillofacial injury in a Malaysian government regional hospital.
  14. Fabrication of electrospun cellulose/chitosan/ball-milled bone char membranes for efficient and selective sorption of Pb(II) from aqueous solutions
    Du X, Rashid SA, Abdullah LC, Rahman NA
    Environ Sci Pollut Res Int, 2023 Nov;30(51):110417-110430.
    PMID: 37783997 DOI: 10.1007/s11356-023-30213-4
    Separation materials have received increasing attention given their broad applications in the management of environmental pollution. It is desired to balance the contradiction between high separation efficiency and selectivity of separation materials. The integration of ball-milled bone chars with electrospun membranes might achieve this balance. In this study, electrospun cellulose/chitosan/ball-milled bone char (CL/CS/MB) membranes were by well-dispersing ball-milled bone chars with nanoscale size (98.9-167.5 nm) and developed porosity (40.2-373.1 m2/g) in the electrospinning solvent. The synergistic integration of distributed MBs (5.4-31.5 wt.% of loading hydroxyapatite on the membrane matrix) allowed the efficient sorption of Pb(II) with fast kinetics (20.0 min), excellent capacity (219.9 mg/g at pH 5.0, T 298 K), and favorable selectivity coefficients (2.76-6.79). The formation of minerals was dominant for the selective sorption of Pb(II) by combining the spectral analysis and quantitative determination. The surface complexation with O-/reductive N-species, the cation exchange with inorganic Ca2+, the electrostatic attraction with deprotonated O-, and the cation-π coordination with the aromatic carbon via the π-electrons should be not ignored for the capture of Pb(II). This work demonstrated the feasibility of electrospun CL/CS/MB membranes as a promising candidate for the remediation of aquatic pollutants.
  15. Evaluation of Microleakage Between Different Post and Core Systems Under Gradual Loading: an In-Vitro Study
    Salim NA, Muttlib NAA, Alawi R, Rahman NA, Ariffin Z
    Acta Stomatol Croat, 2018 Sep;52(3):218-226.
    PMID: 30510297 DOI: 10.15644/asc52/3/5
    Objective: This study aimed to compare the difference in marginal dye penetration between everStick, Parapost XP, Parapost fiber white and control groups under gradual loading.

    Materials and Methods: Sixty-eight human maxillary permanent incisors were divided into four groups. Each specimen was endodontically treated with step-back technique and prepared for each post system according to experimental groups, subsequently cemented in the canal. Composite resin cores were built and laboratory fabricated metal crowns were cemented. All specimens except those in the control group were subjected to thermal cycling. All groups were subjected to gradual loading from 0N-50N for 100 cycles. Specimens were sectioned transversely and the depths of dye penetration along the post were measured. Data were entered in SPSS ver. 22 and analyzed using two-way ANOVA test.

    Results: There was no significant difference in marginal dye penetration between each group (p-value>0.05). However, there was a significant difference in percentage of marginal dye penetration between all groups (p-value<0.05); post-hoc comparison showed significant difference between Fiber White and Control groups (p-value=0.009).

    Conclusion: All the groups showed dye penetration but the percentage was significant only between Parapost Fiber White and the control groups.

  16. Fulltext Enhancing flavonoid production by promiscuous activity of prenyltransferase, BrPT2 from Boesenbergia rotunda
    Liew YJM, Lee YK, Khalid N, Rahman NA, Tan BC
    PeerJ, 2020;8:e9094.
    PMID: 32391211 DOI: 10.7717/peerj.9094
    Flavonoids and prenylated flavonoids are active components in medicinal plant extracts which exhibit beneficial effects on human health. Prenylated flavonoids consist of a flavonoid core with a prenyl group attached to it. This prenylation process is catalyzed by prenyltranferases (PTs). At present, only a few flavonoid-related PT genes have been identified. In this study, we aimed to investigate the roles of PT in flavonoid production. We isolated a putative PT gene (designated as BrPT2) from a medicinal ginger, Boesenbergia rotunda. The deduced protein sequence shared highest gene sequence homology (81%) with the predicted homogentisate phytyltransferase 2 chloroplastic isoform X1 from Musa acuminata subsp. Malaccensis. We then cloned the BrPT2 into pRI vector and expressed in B. rotunda cell suspension cultures via Agrobacterium-mediated transformation. The BrPT2-expressing cells were fed with substrate, pinostrobin chalcone, and their products were analyzed by liquid chromatography mass spectrometry. We found that the amount of flavonoids, namely alpinetin, pinostrobin, naringenin and pinocembrin, in BrPT2-expressing cells was higher than those obtained from the wild type cells. However, we were unable to detect any targeted prenylated flavonoids. Further in-vitro assay revealed that the reaction containing the BrPT2 protein produced the highest accumulation of pinostrobin from the substrate pinostrobin chalcone compared to the reaction without BrPT2 protein, suggesting that BrPT2 was able to accelerate the enzymatic reaction. The finding of this study implied that the isolated BrPT2 may not be involved in the prenylation of pinostrobin chalcone but resulted in high yield and production of other flavonoids, which is likely related to enzyme promiscuous activities.
  17. Enhanced mannan-derived fermentable sugars of palm kernel cake by mannanase-catalyzed hydrolysis for production of biobutanol
    Shukor H, Abdeshahian P, Al-Shorgani NK, Hamid AA, Rahman NA, Kalil MS
    Bioresour Technol, 2016 Oct;218:257-64.
    PMID: 27372004 DOI: 10.1016/j.biortech.2016.06.084
    Catalytic depolymerization of mannan composition of palm kernel cake (PKC) by mannanase was optimized to enhance the release of mannan-derived monomeric sugars for further application in acetone-butanol-ethanol (ABE) fermentation. Efficiency of enzymatic hydrolysis of PKC was studied by evaluating effects of PKC concentration, mannanase loading, hydrolysis pH value, reaction temperature and hydrolysis time on production of fermentable sugars using one-way analysis of variance (ANOVA). The ANOVA results revealed that all factors studied had highly significant effects on total sugar liberated (P<0.01). The optimum conditions for PKC hydrolysis were 20% (w/v) PKC concentration, 5% (w/w) mannanase loading, hydrolysis pH 4.5, 45°C temperature and 72h hydrolysis time. Enzymatic experiments in optimum conditions revealed total fermentable sugars of 71.54±2.54g/L were produced including 67.47±2.51g/L mannose and 2.94±0.03g/L glucose. ABE fermentation of sugar hydrolysate by Clostridium saccharoperbutylacetonicum N1-4 resulted in 3.27±1.003g/L biobutanol.
  18. Enhanced fermentable sugar production from kitchen waste using various pretreatments
    Hafid HS, Rahman NA, Md Shah UK, Baharudin AS
    J Environ Manage, 2015 Jun 1;156:290-8.
    PMID: 25900092 DOI: 10.1016/j.jenvman.2015.03.045
    The kitchen waste fraction in municipal solid waste contains high organic matter particularly carbohydrate that can contribute to fermentable sugar production for subsequent conversion to bioethanol. This study was carried out to evaluate the influence of single and combination pretreatments of kitchen waste by liquid hot water, mild acid pretreatment of hydrochloric acid (HCl) and sulphuric acid (H2SO4) and enzymatic hydrolysis (glucoamylase). The maximum total fermentable sugar produced after combination pretreatment by 1.5% HCl and glucoamylase consisted of 93.25 g/L glucose, 0.542 g/L sucrose, 0.348 g/L maltose, and 0.321 g/L fructose. The glucose released by the combination pretreatment method was 0.79 g glucose/g KW equivalent to 79% of glucose conversion. The effects of the pre-treatment on kitchen waste indicated that the highest solubilization was 40% by the combination method of 1.5% HCl and glucoamylase. The best combination pre-treatment gave concentrations of lactic acid, acetic acid, and propionic acid of 11.74 g/L, 6.77 g/L, and 1.02 g/L, respectively. The decrease of aliphatic absorbance bands of polysaccharides at 2851 and 2923 cm(-1) and the increase on structures of carbonyl absorbance bands at 1600 cm(-1) reflects the progress of the kitchen waste hydrolysis to fermentable sugars. Overall, 1.5% HCl and glucoamylase treatment was the most profitable process as the minimum selling price of glucose was USD 0.101/g kitchen waste. Therefore, the combination pretreatment method was proposed to enhance the production of fermentable sugar, particularly glucose from kitchen waste as the feedstock for bioethanol production.
  19. Enantioselective organocatalytic Diels-Alder reactions: a density functional theory and kinetic isotope effects study
    Omar NY, Rahman NA, Zain SM
    J Comput Chem, 2011 Jul 15;32(9):1813-23.
    PMID: 21455954 DOI: 10.1002/jcc.21763
    The mechanism and enantioselectivity of the organocatalytic Diels-Alder reaction were computationally investigated by density functional theory at the B3LYP/6-31G(d) level of theory. The uncatalyzed Diels-Alder reaction was also studied to explore the effect of the organocatalyst on this reaction in terms of energetics, selectivity, and mechanism. The catalyzed reaction showed improved endo/exo selectivity, and the free energy of activation was significantly lowered in the presence of the catalyst. Both uncatalyzed and catalyzed reactions exhibited concerted asynchronous reaction mechanism with the degree of asynchronicity being more evident in the presence of the catalyst. The Corey's experimentally derived predictive selection rules for the outcome of the organocatalytic Diels-Alder reaction were also theoretically analyzed, and an excellent agreement was found between experiment and theory.
  20. Fulltext Effects of glucose, ethanol and acetic acid on regulation of ADH2 gene from Lachancea fermentati
    Yaacob N, Mohamad Ali MS, Salleh AB, Abdul Rahman NA
    PeerJ, 2016;4:e1751.
    PMID: 26989608 DOI: 10.7717/peerj.1751
    Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking. Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production. Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L. fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process. Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids.
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