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A review on the origin of multidrug-resistant Salmonella and perspective of tailored phoP gene towards avirulence

Gangathraprabhu B, Kannan S, Santhanam G, Suryadevara N, Maruthamuthu M

Microb Pathog, 2020 Oct;147:104352.
PMID: 32592823 DOI: 10.1016/j.micpath.2020.104352

Salmonellosis continues to remain a health problem as the causative organism Salmonella spp. developed resistance to many of the antibiotics. As per World Health Organization (WHO), it is estimated that enteric fever, accounts for almost 16 million cases annually and over 600,000 deaths worldwide. Recent data revealed that the multi-drug resistance (MDR) rate of enteric fever was as high as 70% in Asian countries, as compared with the overall reported incidence of 50%. Emergence of MDR typhoid fever demands the use of newer antibiotics which also not offer promising effect in recent days. Effective antimicrobial therapy is required to control morbidity and prevent death from typhoid fever. The studies on PhoP/Q regulation revealed it as a best-characterized transcriptional regulation; a two-component system required for Salmonella pathogenesis which controls the expression of more than 40 genes. The PhoP DNA binding proteins possess positively charged amino acids such as arginine, lysine and histidine which present in the DNA binding site. Prevention of PhoP binding in phoP box may ultimately prevent the expression of many regulatory mechanism which plays vital role in Salmonella virulence. Deepness study of PhoP protein and various mutation swots may offer effectual controlling of MDR Salmonella.

Matched MeSH terms: Amino Acids
Fulltext Mutations causing streptomycin resistance in Mycobacterium tuberculosis isolates of Sabah

Cheronie Shely Stanis, Myo Thura Zaw, Zainal Arifin Mustapha, Nor Amalina Emran, Richard Avoi, Jiloris Frederick Dony, et al.

Malaysian Journal of Medicine and Health Sciences, 2019;15(106):22-22.
MyJurnal

Introduction: Tuberculosis (TB) still remains a public health problem worldwide and the emergence of drug resistant TB (DR-TB) has worsened the situation as it is difficult and expensive to treat. The characterization of the genetic mutations underlying streptomycin resistance may be helpful in developing rapid detection methods which may guide clinicians in making therapeutic decisions. The aim of this study is to detect mutations causing streptomycin (STR) resistance in Mycobacterium tuberculosis isolates from Sabah. Methods: Susceptibility testing was carried out in MGIT system for 42 Mycobacterium tuberculosis clinical isolates. The drug resistant isolates were subject to whole genome sequencing and in-silico analysis was performed to detect the mutations in the sequence of the rpsL gene known to confer resistance to anti-tuberculous drugs. Results: Of the 42 positive isolates, 27 (64.3%) are shown to be susceptible towards first line drugs (FLDs) while 15 (35.7%) isolates were mono- and multiple resistant to the FLDs. Our findings reveal that the isolate 145 possess mutations at codon 43 within rpsL gene with amino acid change A to G (K43R). Conclusion: Findings from this study enable us to expand our knowledge of mutations causing drug resistance in Mycobacterium tuberculosis and the point mutations, which can be used as the potential marker for detection of drug resistant isolates.

Matched MeSH terms: Amino Acids
Interaction of monomeric Ebola VP40 protein with a plasma membrane: A coarse-grained molecular dynamics (CGMD) simulation study

Mohamad Yusoff MA, Abdul Hamid AA, Mohammad Bunori N, Abd Halim KB

J Mol Graph Model, 2018 Jun;82:137-144.
PMID: 29730487 DOI: 10.1016/j.jmgm.2018.04.010

Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles in oligomerization, budding and egress from the host cell. VP40 exists predominantly as a monomer at the inner leaflet of the plasma membrane, and has been suggested to interact with negatively charged lipids such as phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylserine (PS) via its cationic patch. The hydrophobic loop at the C-terminal domain has also been shown to be important in the interaction between the VP40 and the membrane. However, details of the molecular mechanisms underpinning their interactions are not fully understood. This study aimed at investigating the effects of mutation in the cationic patch and hydrophobic loop on the interaction between the VP40 monomer and the plasma membrane using coarse-grained molecular dynamics simulation (CGMD). Our simulations revealed that the interaction between VP40 and the plasma membrane is mediated by the cationic patch residues. This led to the clustering of PIP2 around the protein in the inner leaflet as a result of interactions between some cationic residues including R52, K127, K221, K224, K225, K256, K270, K274, K275 and K279 and PIP2 lipids via electrostatic interactions. Mutation of the cationic patch or hydrophobic loop amino acids caused the protein to bind at the inner leaflet of the plasma membrane in a different orientation, where no significant clustering of PIP2 was observed around the mutated protein. This study provides basic understanding of the interaction of the VP40 monomer and its mutants with the plasma membrane.

Matched MeSH terms: Amino Acids
Fulltext Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: The case for COVID-19

Ab Ghani NS, Emrizal R, Makmur H, Firdaus-Raih M

Comput Struct Biotechnol J, 2020;18:2931-2944.
PMID: 33101604 DOI: 10.1016/j.csbj.2020.10.013

Structures of protein-drug-complexes provide an atomic level profile of drug-target interactions. In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. We were able to identify 22 target sites for the repositioning of 16 approved drug compounds as potential therapeutics for COVID-19. Using the same approach, we were also able to investigate the potentially promiscuous binding of the 16 compounds to off-target sites that could be implicated in toxicity and side effects that had not been provided by any previous studies. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. The intention of this work is not to explicitly identify candidate compounds but to present how an integrated drug repositioning and potential toxicity pipeline using side chain similarity searching algorithms are of great utility in epidemic scenarios involving novel pathogens. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed.

Matched MeSH terms: Amino Acids
Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica

Tan IKP, Foong CP, Tan HT, Lim H, Zain NA, Tan YC, et al.

J Biotechnol, 2020 Apr 10;313:18-28.
PMID: 32171790 DOI: 10.1016/j.jbiotec.2020.03.006

The polyhydroxyalkanoate (PHA) producing capability of four bacterial strains isolated from Antarctica was reported in a previous study. This study analyzed the PHA synthase genes and the PHA-associated gene clusters from the two antarctic Pseudomonas isolates (UMAB-08 and UMAB-40) and the two antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) through whole-genome sequence analysis. The Pseudomonas isolates were found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively. On the other hand, the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis was detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment showed that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. PHA biosynthesis and in vitro PhaC enzymatic assay results showed that this uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-60 is funtional. This report adds new knowledge to the PHA synthase database as we describe scarce information of PHA synthase genes and PHA-associated gene clusters from the antarctic bacterial isolates (extreme and geographically isolated environment) and comparing with those from non-antarctic PHA-producing bacteria.

Matched MeSH terms: Amino Acids
Global Transcriptome Analysis of Gracilaria changii (Rhodophyta) in Response to Agarolytic Enzyme and Bacterium

Lim EL, Siow RS, Abdul Rahim R, Ho CL

Mar Biotechnol (NY), 2016 Apr;18(2):189-200.
PMID: 26631182 DOI: 10.1007/s10126-015-9680-6

Many bacterial epiphytes of agar-producing seaweeds secrete agarase that degrade algal cell wall matrix into oligoagars which elicit defense-related responses in the hosts. The molecular defense responses of red seaweeds are largely unknown. In this study, we surveyed the defense-related transcripts of an agarophyte, Gracilaria changii, treated with β-agarase through next generation sequencing (NGS). We also compared the defense responses of seaweed elicited by agarase with those elicited by an agarolytic bacterium isolated from seaweed, by profiling the expression of defense-related genes using quantitative reverse transcription real-time PCR (qRT-PCR). NGS detected a total of 391 differentially expressed genes (DEGs) with a higher abundance (>2-fold change with a p value <0.001) in the agarase-treated transcriptome compared to that of the non-treated G. changii. Among these DEGs were genes related to signaling, bromoperoxidation, heme peroxidation, production of aromatic amino acids, chorismate, and jasmonic acid. On the other hand, the genes encoding a superoxide-generating NADPH oxidase and related to photosynthesis were downregulated. The expression of these DEGs was further corroborated by qRT-PCR results which showed more than 90 % accuracy. A comprehensive analysis of their gene expression profiles between 1 and 24 h post treatments (hpt) revealed that most of the genes analyzed were consistently upregulated or downregulated by both agarase and agarolytic bacterial treatments, indicating that the defense responses induced by both treatments are highly similar except for genes encoding vanadium bromoperoxidase and animal heme peroxidase. Our study has provided the first glimpse of the molecular defense responses of G. changii to agarase and agarolytic bacterial treatments.

Matched MeSH terms: Amino Acids, Aromatic
Transcriptome-Guided Identification of Carbohydrate Active Enzymes (CAZy) from the Christmas Island Red Crab, Gecarcoidea natalis and a Vote for the Inclusion of Transcriptome-Derived Crustacean CAZys in Comparative Studies

Gan HM, Austin C, Linton S

Mar Biotechnol (NY), 2018 Oct;20(5):654-665.
PMID: 29995174 DOI: 10.1007/s10126-018-9836-2

The Christmas Island red crab, Gecarcoidea natalis, is an herbivorous land crab that consumes mostly fallen leaf litter. In order to subsist, G. natalis would need to have developed specialised digestive enzymes capable of supplying significant amounts of metabolisable sugars from this diet. To gain insights into the carbohydrate metabolism of G. natalis, a transcriptome assembly was performed, with a specific focus on identifying transcripts coding for carbohydrate active enzyme (CAZy) using in silico approaches. Transcriptome sequencing of the midgut gland identified 70 CAZy-coding transcripts with varying expression values. At least three newly discovered putative GH9 endo-β-1,4-glucanase ("classic cellulase") transcripts were highly expressed in the midgut gland in addition to the previously characterised GH9 and GH16 (β-1,3-glucanase) transcripts, and underscoring the utility of whole transcriptome in uncovering new CAZy-coding transcripts. A highly expressed transcript coding for GH5_10 previously missed by conventional screening of cellulase activity was inferred to be a novel endo-β-1,4-mannase in G. natalis with in silico support from homology modelling and amino acid alignment with other functionally validated GH5_10 proteins. Maximum likelihood tree reconstruction of the GH5_10 proteins demonstrates the phylogenetic affiliation of the G. natalis GH5_10 transcript to that of other decapods, supporting endogenous expression. Surprisingly, crustacean-derived GH5_10 transcripts were near absent in the current CAZy database and yet mining of the transcriptome shotgun assembly (TSA) recovered more than 100 crustacean GH5_10s in addition to several other biotechnological relevant CAZys, underscoring the unappreciated potential of the TSA database as a valuable resource for crustacean CAZys.

Matched MeSH terms: Amino Acids
Fulltext Untargeted and Targeted Metabolomic Profiling of Australian Indigenous Fruits

Lim V, Gorji SG, Daygon VD, Fitzgerald M

Metabolites, 2020 Mar 19;10(3).
PMID: 32204361 DOI: 10.3390/metabo10030114

Selected Australian native fruits such as Davidson's plum, finger lime and native pepperberry have been reported to demonstrate potent antioxidant activity. However, comprehensive metabolite profiling of these fruits is limited, therefore the compounds responsible are unknown, and further, the compounds of nutritional value in these native fruits are yet to be described. In this study, untargeted and targeted metabolomics were conducted using the three fruits, together with assays to determine their antioxidant activities. The results demonstrate that targeted free and hydrolysed protein amino acids exhibited high amounts of essential amino acids. Similarly, important minerals like potassium were detected in the fruit samples. In antioxidant activity, Davidson's plum reported the highest activity in ferric reducing power (FRAP), finger lime in antioxidant capacity (ABTS), and native pepperberry in free radical scavenging (DPPH) and phosphomolybdenum assay. The compounds responsible for the antioxidant activity were tentatively identified using untargeted GC×GC-TOFMS and UHPLC-QqQ-TOF-MS/MS metabolomics. A clear discrimination into three clusters of fruits was observed using principal component analysis (PCA) and partial least squares (PLS) analysis. The correlation study identified a number of compounds that provide the antioxidant activities. GC×GC-TOFMS detected potent aroma compounds of limonene, furfural, and 1-R-α-pinene. Based on the untargeted and targeted metabolomics, and antioxidant assays, the nutritional potential of these Australian bush fruits is considerable and supports these indigenous fruits in the nutraceutical industry as well as functional ingredients for the food industry, with such outcomes benefiting Indigenous Australian communities.

Matched MeSH terms: Amino Acids, Essential
Genome Organization of Escherichia Phage YD-2008.s: A New Entry to Siphoviridae Family

Sellvam D, Lau NS, Arip YM

Trop Life Sci Res, 2018 Mar;29(1):37-50.
PMID: 29644014 DOI: 10.21315/tlsr2018.29.1.3

Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales. Genomic sequence analyses revealed phage YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content. Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome, using bioinformatics annotation software; Rapid Annotation using Subsystem Technology (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are classified as hypothetical proteins and there are two unidentified proteins. Even though majority of the coded putative proteins have high amino acids similarities to phages from the genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its' own distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.

Matched MeSH terms: Amino Acids
Fulltext Genome organization of Eschrichia phage YD-2008.s: a new entry to siphoviridae family

Sellvam, Dharmela, Yahya Mat Arip, Nyok, Sean Lau

Trop Life Sci Res, 2018;29(1):37-50.
MyJurnal

Malaysia is one of the countries that are loaded with mega biodiversity which
includes microbial communities. Phages constitute the major component in the microbial
communities and yet the numbers of discovered phages are just a minute fraction of
its population in the biosphere. Taking into account of a huge numbers of waiting to be
discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s
was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile
flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae
family under the order of Caudovirales. Genomic sequence analyses revealed phage
YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content.
Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome,
using bioinformatics annotation software; Rapid Annotation using Subsystem Technology
(RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are
classified as hypothetical proteins and there are two unidentified proteins. Even though
majority of the coded putative proteins have high amino acids similarities to phages from the
genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its’ own
distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the
growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.

Matched MeSH terms: Amino Acids
Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey

Saepuloh U, Iskandriati D, Pamungkas J, Solihin DD, Mariya SS, Sajuthi D

Trop Life Sci Res, 2020 Oct;31(3):47-61.
PMID: 33214855 DOI: 10.21315/tlsr2020.31.3.4

Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in Asian macaques. It is a potential confounding variable in biomedical research. SRV-2 also provides a valuable viral model compared to other retroviruses which can be used for understanding many aspects of retroviral-host interactions and immunosuppression, infection mechanism, retroviral structure, antiretroviral and vaccine development. In this study, we isolated the gene encoding reverse transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf ET1006) and predicted the three dimensional structure model using the iterative threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT Mf ET1006 consisted of 547 amino acids at nucleotide position 3284-4925 of whole genome SRV-2. The polymerase active site located in the finger/palm subdomain characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template modelling score (TM-score 0.90 ± 0.06) and root mean square deviation (RMSD) 4.7 ± 3.1Å, indicating that this model can be trusted and the accuracy can be seen from the appearance of protein folding in tertiary structure. The superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 (HIV-1) RT were performed to predict the structural in details and to optimise the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 0.911, RMSD 1.85 Å, and coverage of 0.953. This preliminary study of SRV-2 RT Mf ET1006 structure modelling is intriguing and provide some information to explore the molecular characteristic and biochemical mechanism of this enzyme.

Matched MeSH terms: Amino Acids
Fulltext Extraction and characterization of pepsin-solubilized collagen from the body wall of crown-of-thorns Starfish (Acanthaster planci)

Tan, C. C., Karim, A. A., Latiff, A. A., Gan, C. Y., Ghazali, F. C.

International Food Research Journal, 2013;20(6):3013-3020.
MyJurnal

Pepsin-solubilized collagen (PSC) was extracted from the body wall of crown-of-thorns starfish (COTS) (Acanthaster planci) using pepsin digestion in 0.5 M acetic acid. The electrophoretic pattern of PSC showed that it consisted of two α chains (α1 and α2 chains). In addition, the peptide mapping showed that there were some differences in peptide patterns among PSC, calf skin collagen and salmon skin collagen. This suggested that the primary structure of the PSC was different from calf skin collagen and salmon skin collagen. Furthermore, Fourier transform infrared spectroscopy (FTIR) investigation showed the existence of triple helical structure in PSC, suggesting that the triple helical structure was well preserved during the extraction of collagen from COTS. The denaturation temperature of PSC was 33.0°C, which was comparable with mammalian collagen. In addition, the amino acid composition analysis showed that the imino acid content of PSC was similar to mammalian collagen but it was higher than other marine collagen. This suggested that the imino acid content might contributed the denaturation temperature of collagen. The results in this study suggest that PSC from the underutilized COTS has potential to be exploited in various commercial applications.

Matched MeSH terms: Amino Acids
Different patterns of pfcrt and pfmdr1 polymorphism in Plasmodium falciparum isolates from Tehama region, Yemen

Atroosh WM, Al-Mekhlafi HM, Al-Jasari A, Sady H, Dawaki SS, Elyana FN, et al.

PeerJ, 2016;4:e2191.
PMID: 27478699 DOI: 10.7717/peerj.2191

Introduction. Despite the efforts of the malaria control programme, malaria morbidity is still a common health problem in Yemen, with 60% of the population at risk. Plasmodium falciparum is responsible for 99% of malaria cases. The emergence in Yemen of parasite resistance to chloroquine (CQ) prompted the adoption of artemisinin combination therapy (ACT) in 2009, which involves the use of artesunate plus sulphadoxine-pyrimethamine (AS + SP). However, CQ was retained as the drug of choice for vivax malaria. To assess the impact of the change in the malaria treatment policy five years after its introduction, the present study investigated the mutations in the CQ resistance transporter (pfcrt) and multidrug resistance 1 (pfmdr1) genes. Method. A molecular investigation of 10 codons of pfcrt (72-76, 220, 271, 326, 356, and 371) and five codons of pfmdr1 (86, 184, 1034, 1042, and 1246) was conducted on P. falciparum isolates from districts with the highest malaria endemicity in the Hodeidah and Al-Mahwit governorates in Tehama region, Yemen. A total of 86 positive cases of falciparum monoinfection were investigated for the presence of mutations related to CQ and other antimalarials using a PCR-RFLP assay. Results. There was a wide prevalence of pfcrt gene mutations with the pfcrt 76T CQ resistance marker being predominant (97.7%). The prevalence of other pfcrt mutations varied from high (75E: 88%) to moderate (74I: 79.1%, 220S: 69.8%, 271E and 371I: 53.5%) or low (326S: 36%, 72S: 10.5%). Mutated pfcrt 72-76 amino acids haplotypes were highly prevalent (98.8%). Among these, the CVIET classic, old-world African/Southeast Asian haplotype was the most predominant, and was mostly found in the isolates from the Khamis Bani Saad district of Al-Mahwit (93.1%) and the AdDahi district of Hodeidah (88.9%). However, it was only found in 26.3% of the isolates from the Bajil district of Hodeidah. Surprisingly, the SVMNT new-world South American haplotype was exclusively detected in 9.3% of the isolates from the Bajil district of Hodeidah. Mutations at Y184F of pfmdr1 were found in all isolates (100%) from all districts. The mutation for codons 1034C and 86Y were found only in the isolates from the AdDahi and Khamis Bani Saad districts. Overall, the AdDahi and Khamis Bani Saad districts were similar in terms of carrying most of the mutations in the pfcrt and pfmdr1 genes, while there was a lower prevalence of mutation in the isolates from the Bajil district. Conclusion. The high prevalence of mutations in pfcrt 5 years after the official cessation of CQ use against P. falciparum suggests that there is sustained CQ pressure on P. falciparum isolates in the study area. Moreover, the low prevalence of mutations in the pfmdr1 gene could be a good indicator of the high susceptibility of P. falciparum isolates to antimalarials other than CQ. A new strategy to ensure the complete nationwide withdrawal of CQ from the private drug market is recommended.

Matched MeSH terms: Amino Acids
Fulltext Potential use of Malaysian rubber (Hevea brasiliensis) seed as food, feed and biofuel

International Food Research Journal, 2010;17(3):527-534.
MyJurnal

Rubber seed as a waste product from rubber plantations contains nutritive values that can be harnessed
as food for human, feed for animals or biofuel for energy. Proximate analysis showed moisture content of
3.99%, protein content of 17.41 g/100g, fat content of 68.53 ± 0.04 g/100g and ash content of 3.08 ± 0.01
g/100g. Amino acid in rubber seed is high in Glutamic acid (16.13%) and low in Cysteine (0.78%). Despite its potential as a source of protein, fresh rubber seeds contain a toxic factor, cyanogenetic glucoside (186 mg/kg). FAME analysis indicated that rubber seed oil is high in oleic, linoleic and linolenic acid. The fuel potential of rubber seed (585.41 kJ/kg) is in reasonable agreement with ASTM.

Matched MeSH terms: Amino Acids
Fulltext Effect of thermal treatment on the biochemical composition of tropical honey samples

Chua, L. S., Adnan, N. A., Abdul-Rahaman, N. L., Sarmidi, M. R.

International Food Research Journal, 2014;21(2):773-778.
MyJurnal

Honey is usually subjected to filtration and heating for bottling before commercialization. However, there is no standard procedure available for thermal treatment on honey. Honey is thermally heated at various temperature and duration based on individual experience to prolong the shelf life of honey in the market. The heating methods might decrease the biochemical components such as nutrients, enzymatic activities and vitamins to certain extent. In addition to water reduction, thermal treatment on sugar rich honey usually accompanied by the formation of 5-hydroxymethylfurfural (HMF). In the present study, the biochemical components in three commonly consumed honey in Malaysia, namely tualang, gelam and acacia honey were investigated before and after thermal treatment at 90oC for 30 min. The short period of heating time was found to degrade nutrients, enzymatic activities and water soluble vitamins in honey. The degradation of protein and enzyme via proteolytic digestion had attributed to the increase of free amino acids in honey. Based on the multivariate analysis, the most thermally affected biochemical components are crude fat, panthotenic acid (Vitamin B5) and diastase activity which explain for 86.4% of the total variance. The kinetic studies on the HMF formation revealed that the honey samples followed zero order kinetic model for the first 60 min of heating at 90oC. The findings indicate that the temperature and duration of heating during honey processing is essential to be investigated according to the honey origin. The initial biochemical composition of honey would affect the kinetic profile of HMF formation.

Matched MeSH terms: Amino Acids
Fulltext Phenotypic MicroArray (PM) profiles (carbon sources and sensitivity to osmolytes and pH) of Campylobacter jejuni ATCC 33560 in response to temperature

Tang, J.Y.H., Carlson, J., Mohamad Ghazali, F., Saleha, A.A., Nishibuchi, M., Nakaguchi, Y., et al.

International Food Research Journal, 2010;17(4):837-844.
MyJurnal

The present study aimed to provide an insight of C. jejuni ATCC 33560 phenotype profiles (carbon sources and sensitivity to osmolytes and pH) using Phenotypic MicroArray (PM) system in response to optimal and suboptimal temperature. C. jejuni ATCC 33560 showed utilization carbon sources from amino acids and carboxylates but not from sugars. C. jejuni ATCC 33560 is sensitive to NaCl at 2% and above but showed survival in a wide range of food preservatives (sodium lactate, sodium phosphate, sodium benzoate, ammonium sulphate and sodium nitrate). When incubated at suboptimal temperature, no phenotype loss was observed in carbon source plates. Phenotype loss of C. jejuni ATCC 33560 was observed in sodium chloride (1%), sodium sulphate (2-3%), sodium formate (1%), sodium lactate (7-12%), sodium phosphate pH7 (100mM and 200mM), ammonium sulphate pH8 (50mM), sodium nitrate (60mM, 80mM and 100mM), sodium nitrite (10mM), and growth in pH5. The phenotypic profile from present study will provide a better insight related to survival of C. jejuni ATCC 33560.

Matched MeSH terms: Amino Acids
Fulltext Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase

Ker DS, Pang SL, Othman NF, Kumaran S, Tan EF, Krishnan T, et al.

PeerJ, 2017;5:e2961.
PMID: 28265494 DOI: 10.7717/peerj.2961

BACKGROUND: Sesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment.
METHODS: The enzyme was purified in two steps using affinity and size exclusion chromatography. Enzyme assays were performed using the malachite green assay and enzymatic product was identified using gas chromatography-mass spectrometry (GC-MS) analysis. Sequence analysis of PmSTS was performed using multiple sequence alignment (MSA) against plant sesquiterpene synthase sequences. The homology model of PmSTS was generated using I-TASSER server.
RESULTS: Our findings suggest that the recombinant PmSTS is mainly expressed as inclusion bodies and soluble aggregate in the E. coli protein expression system. However, the addition of 15% (v/v) glycerol to the protein purification buffer and the removal of N-terminal 24 amino acids of PmSTS helped to produce homogenous recombinant protein. Enzyme assay showed that recombinant PmSTS is active and specific to the C15 substrate FPP. The optimal temperature and pH for the recombinant PmSTS are 30 °C and pH 8.0, respectively. The GC-MS analysis further showed that PmSTS produces β-sesquiphellandrene as a major product and β-farnesene as a minor product. MSA analysis revealed that PmSTS adopts a modified conserved metal binding motif (NSE/DTE motif). Structural analysis suggests that PmSTS may binds to its substrate similarly to other plant sesquiterpene synthases.
DISCUSSION: The study has revealed that homogenous PmSTS protein can be obtained with the addition of glycerol in the protein buffer. The N-terminal truncation dramatically improved the homogeneity of PmSTS during protein purification, suggesting that the disordered N-terminal region may have caused the formation of soluble aggregate. We further show that the removal of the N-terminus disordered region of PmSTS does not affect the product specificity. The optimal temperature, optimal pH, Km and kcat values of PmSTS suggests that PmSTS shares similar enzyme characteristics with other plant sesquiterpene synthases. The discovery of an altered conserved metal binding motif in PmSTS through MSA analysis shows that the NSE/DTE motif commonly found in terpene synthases is able to accommodate certain level of plasticity to accept variant amino acids. Finally, the homology structure of PmSTS that allows good fitting of substrate analog into the catalytic active site suggests that PmSTS may adopt a sesquiterpene biosynthesis mechanism similar to other plant sesquiterpene synthases.

Matched MeSH terms: Amino Acids
Genetic Diversity and Phylogenetic Relationships of Cytochrome C Oxidase Subunit I in Cimex hemipterus (Hemiptera: Cimicidae) Populations in Malaysia

Seri Masran SNA, Ab Majid AH

J Med Entomol, 2017 Jul 01;54(4):974-979.
PMID: 28399302 DOI: 10.1093/jme/tjw227

The tropical bed bug is scientifically recognized as a significant public health problem. While there is an increased awareness about their resurgence by medical and life science committees, efficient bed bug management still remains unresolved. The solution may soon arise, as information about bed bugs' infestation dynamics and systematics are becoming more distinguishable. Recent developments in studies about bed bugs are based on molecular intervention by determining their genetic variation and phylogeography. The aim of this study is to assess the phylogenetic relationships and genetic diversity among the populations of tropical bed bugs inhabiting Malaysia. A molecular genotyping study was conducted with 22 tropical bed bug populations composed of three individuals per population. The mitochondrial (COI) gene was used as a marker. The data obtained were analyzed using the T-Coffee, ClustalX, MEGA 6.0, and PAUP software. The results showed one main monophyletic clade that consisted of two groups: Ch01 and Ch02. Ch02 consists of samples from the Bandar Hilir population, differing from the other populations studied by one singleton base. However, as there were no changes in the amino acid, this singleton genetic variation was considered to have no effect on genetic differentiation. Ch01 shows similarity with some sequence of Cimex hemipterus (F.) from Thailand, suggesting an international diversity connection. The disparity index apparently suggests that all isolates are homogeneous populations and are supported by the low value of the mean pairwise distance between isolates. This study will increase the knowledge about phylogeographic diversity of tropical bed bug in Malaysia.

Matched MeSH terms: Amino Acids
Fulltext Transcriptome profiling of sulfate deprivation responses in two agarophytes Gracilaria changii and Gracilaria salicornia (Rhodophyta)

Lee WK, Namasivayam P, Ong Abdullah J, Ho CL

Sci Rep, 2017 04 24;7:46563.
PMID: 28436444 DOI: 10.1038/srep46563

Seaweeds survive in marine waters with high sulfate concentration compared to those living at freshwater habitats. The cell wall polymer of Gracilaria spp. which supplies more than 50% of the world agar is heavily sulfated. Since sulfation reduces the agar quality, it is interesting to investigate the effects of sulfate deprivation on the sulfate contents of seaweed and agar, as well as the metabolic pathways of these seaweeds. In this study, two agarophytes G. changii and G. salicornia were treated under sulfate deprivation for 5 days. The sulfate contents in the seaweed/agar were generally lower in sulfate-deprivated samples compared to those in the controls, but the differences were only statistically significant for seaweed sample of G. changii and agar sample of G. salicornia. RNA sequencing (RNA-Seq) of sulfate-deprivated and untreated seaweed samples revealed 1,292 and 3,439 differentially expressed genes (DEGs; ≥1.5-fold) in sulfate-deprivated G. changii and G. salicornia, respectively, compared to their respective controls. Among the annotated DEGs were genes involved in putative agar biosynthesis, sulfur metabolism, metabolism of sulfur-containing amino acids, carbon metabolism and oxidative stress. These findings shed light on the sulfate deprivation responses in agarophytes and help to identify candidate genes involved in agar biosynthesis.

Matched MeSH terms: Amino Acids
Fulltext Mini review : the effects of food processing on biogenic amines formation

Chong, C.Y., Abu Bakar, F., Russly, A.R., Jamilah, B., Mahyudin, N.A.

International Food Research Journal, 2011;18(3):-.
MyJurnal

Biological amines are nitrogenous compounds that occur naturally in wide variety of food. Histamine, putrescine, cadavarine, tyramine, spermine, spermidine, tryptamine and β-phenylethylamine are the biogenic amines that are normally present in foods. Although the biogenic amines play some important physiological functions but high level of amines can cause toxicological effects. High amount of amines can be produced by bacteria during amino acids decarboxylation and have been identified as one of the important agent causing seafood intoxication. Temperature is the major factor for controlling the biogenic amines formation in food. The effects of other alternatives are also discussed including salting, packaging, irradiation, high pressure processing and the use of starter culture. A variety of techniques can be combined together to control the microbial growth and enzyme activity during processing and storage for better shelf life extension and food safety.

Matched MeSH terms: Amino Acids

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