ORCID Profile
0000-0001-7200-3102
Current Organisations
Institute for Medical Research
,
University of Tasmania
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Publisher: MDPI AG
Date: 17-01-2023
DOI: 10.3390/TROPICALMED8020069
Abstract: Leptospirosis is a common zoonotic disease in tropical and subtropical countries. It is considered an emerging disease in Malaysia and is a notifiable disease. This study was conducted to characterize Malaysian isolates from human, animal and environmental s les via MLST and rrs2 sequencing in an attempt to develop a Malaysian genotypic database. An existing polymerase chain reaction (PCR)-based MLST scheme was performed to facilitate subsequent sequencing. Out of 46 extracted DNA, 36 had complete MLST profiles whereby all six genes were lified and sequenced. Most of the pathogenic Leptospira genotypes with full MLST profiles were L. interrogans serogroup Bataviae (n = 17), followed by L. borgpetersenii serogroup Javanica (n = 9), L. interrogans serogroup Sejroe (n = 2), L. interrogans serogroup Australis (n = 2), L. kirschneri (n = 2), L. interrogans serogroup Grippotyphosa (n = 1) and L. interrogans serogroup Pyrogenes (n = 3). Two s les (R3_SER/17 and R4_SER/17) were not closely related with any of the reference strains. For the s les with incomplete MLST profiles, leptospiral speciation was conducted through rrs2 analysis, in which four s les were identified as L. borgpetersenii, five s les were closely related to L. kmetyi and one s le was known as L. yasudae. This study shows that molecular approaches that combine both MLST and rrs2 sequencing have great potential in the comprehensive characterization of pathogenic Leptospira because they can be performed directly from cultured and clinical s les.
Publisher: Mary Ann Liebert Inc
Date: 11-2019
DOI: 10.1089/HUM.2019.021
Abstract: Safe delivery of CRISPR/Cas endonucleases remains one of the major barriers to the widespread application of
Publisher: Springer Science and Business Media LLC
Date: 04-08-2023
DOI: 10.1186/S13023-023-02848-6
Abstract: Pompe disease is a rare glycogen storage disorder caused by deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA), leading to glycogen deposition in multiple tissues. Infantile-onset Pompe disease (IOPD) patients present within the first year of life with profound hypotonia and hypertrophic cardiomyopathy. Treatment with enzyme replacement therapy (ERT) has significantly improved survival for this otherwise lethal disorder. This study aims to describe the clinical and molecular spectrum of Malaysian IOPD patients, and to analyze their long term treatment outcomes. Seventeen patients diagnosed with IOPD between 2000 and 2020 were included in this retrospective cohort study. Clinical and biochemical data were collated and analyzed using descriptive statistics. GAA enzyme levels were performed on dried blood spots. Molecular analysis of the GAA gene was performed by polymerase chain reaction and Sanger sequencing. Structural modelling was used to predict the effect of the novel mutations on enzyme structure. Our cohort had a median age of presentation of 3 months and median age of diagnosis of 6 months. Presenting features were hypertrophic cardiomyopathy (100%), respiratory insufficiency (94%), hypotonia (88%), failure to thrive (82%), feeding difficulties (76%), and hepatomegaly (76%). Fourteen different mutations in the GAA gene were identified, with three novel mutations, c.1552-14_1552-1del, exons 2–3 deletion and exons 6–10 deletion. The most common mutation identified was c.1935C A p.(D645E), with an allele frequency of 33%. Sixteen patients received ERT at the median age of 7 months. Overall survival was 29%. Mean age of death was 17.5 months. Our longest surviving patient has atypical IOPD and is currently 20 years old. This is the first study to analyze the genotype and phenotype of Malaysian IOPD patients, and has identified the c.1935C A p.(D645E) as the most common mutation. The three novel mutations reported in this study expands the mutation spectrum for IOPD. Our low survival rate underscores the importance of early diagnosis and treatment in achieving better treatment outcomes.
Publisher: Hindawi Limited
Date: 13-09-2022
DOI: 10.1155/2022/5870092
Abstract: Background. Glycogen storage disease type 1a (GSD1a) is a rare autosomal recessive metabolic disorder characterized by hypoglycaemia, growth retardation, lactic acidosis, hepatomegaly, hyperlipidemia, and nephromegaly. GSD1a is caused by a mutation in the G6PC gene encoding glucose-6-phosphatase (G6Pase) an enzyme that catalyses the hydrolysis of glucose-6-phosphate (G6P) to phosphate and glucose. Objective. To elaborate on the clinical findings, biochemical data, molecular genetic analysis, and short-term prognosis of 13 GSD1a patients in Malaysia. Methods. The information about 13 clinically classified GSD1a patients was retrospectively studied. The G6PC mutation analysis was performed by PCR-DNA sequencing. Results. Patients were presented with hepatomegaly (92%), hypoglycaemia (38%), poor weight gain (23%), and short stature (15%). Mutation analysis revealed nine heterozygous mutations eight previously reported mutations (c.155 A T, c.209 G A, c.226 A T, c.248 G A, c.648 G T, c.706 T A, c.1022 T A, c.262delG) and a novel mutation (c.325 T C). The most common mutation found in Malaysian patients was c.648 G T in ten patients (77%) of mostly Malay ethnicity, followed by c.248 G A in 4 patients of Chinese ethnicity (30%). A novel missense mutation (c.325 T C) was predicted to be disease-causing by various in silico software. Conclusions. The establishment of G6PC molecular genetic testing will enable the detection of presymptomatic patients, assisting in genetic counselling while avoiding the invasive methods of liver biopsy.
Publisher: Wiley
Date: 06-03-2020
DOI: 10.1002/JCLA.23254
Abstract: Serum protein electrophoresis (SPE) is a widely used laboratory technique to diagnose patients with multiple myeloma (MM) and other disorders related to serum protein. In patients with MM, abnormal monoclonal protein can be detected by SPE and further characterized using immunofixation electrophoresis (IFE). There are several semi‐automated agarose gel‐based systems available commercially for SPE and IFE. In this study, we sought to evaluate the analytical performance of fully automated EasyFix G26 (EFG26) and semi‐automated HYDRASYS 2 SCAN (H2SCAN) for both SPE and IFE. Both instruments were operated according to manufacturer's instructions. S les used include a commercially available normal control serum (NCS) and patients' specimens. The following were evaluated: precision and comparison studies for SPE, and reproducibility and comparison studies for IFE. Statistical analyses were performed using Microsoft Excel. For SPE repeatability study, our results showed that EFG26 has higher coefficient of variation (%CV) compared with H2SCAN for both s les except for monoclonal component with %CV of 0.97% and 1.18%, respectively. Similar results were obtained for SPE reproducibility study except for alpha‐1 (4.16%) and beta (3.13%) fractions for NCS, and beta fractions (5.36%) for monoclonal s le. Subsequently, reproducibility for IFE was 100% for both instruments. Values for correlation coefficients between both instruments ranged from 0.91 to 0.98 for the five classic bands. Both instruments demonstrated good analytical performance characterized by high precision, reproducibility and correlation.
Publisher: Springer Science and Business Media LLC
Date: 25-09-2020
DOI: 10.1038/S41467-020-18715-Y
Abstract: Precision genome engineering has dramatically advanced with the development of CRISPR/Cas base editing systems that include cytosine base editors and adenine base editors (ABEs). Herein, we compare the editing profile of circularly permuted and domain-inlaid Cas9 base editors, and find that on-target editing is largely maintained following their intradomain insertion, but that structural permutation of the ABE can affect differing RNA off-target events. With this insight, structure-guided design was used to engineer an SaCas9 ABE variant (microABE I744) that has dramatically improved on-target editing efficiency and a reduced RNA-off target footprint compared to current N-terminal linked SaCas9 ABE variants. This represents one of the smallest AAV-deliverable Cas9-ABEs available, which has been optimized for robust on-target activity and RNA-fidelity based upon its stereochemistry.
Publisher: Public Library of Science (PLoS)
Date: 23-05-2019
Publisher: Cold Spring Harbor Laboratory
Date: 07-06-2022
DOI: 10.1101/2022.06.07.495067
Abstract: Directed evolution uses cycles of gene ersification and selection to generate proteins with novel properties. While traditionally directed evolution is performed in prokaryotic systems, recently a mammalian directed evolution system (viral evolution of genetically actuating sequences, or “VEGAS”) has been described. Here we report that the VEGAS system has major limitations precluding its use for directed evolution. The primary technical issue with the VEGAS system is an immediate contamination with “cheater” particles that bypass directed evolution circuits. By sequencing we find these cheater particles contain Sindbis structural genes instead of the intended directed evolution target transgene. These cheaters outcompete the VEGAS transgenes within 2 rounds of transduction but cannot themselves activate synthetic circuits that drive expression of Sindbis structural genes, preventing directed evolution c aigns. Similar results have been obtained in independent labs. Taken together, the VEGAS system does not work as described and, without significant redesign to suppress cheaters, cannot be used for mammalian directed evolution c aigns.
Publisher: American Chemical Society (ACS)
Date: 11-10-2022
DOI: 10.1021/ACSSYNBIO.2C00460
Abstract: Directed evolution uses cycles of gene ersification and selection to generate proteins with novel properties. While traditionally directed evolution is performed in prokaryotic systems, recently a mammalian directed evolution system (viral evolution of genetically actuating sequences, or "VEGAS") has been described. Here we report that the VEGAS system has major limitations that preclude its use for directed evolution. The deconstructed Sindbis virus (SINV) genome that comprises the VEGAS system could no longer promote Sindbis structural gene (SSG)-dependent viral replication. Moreover, viral particles generated using the VEGAS system rapidly lost the target directed evolution transgene, and instead, "cheater" particles, primarily containing RNA encoding SINV structural components, arose. By sequencing, we found that this contamination came from RNA provided during initial SINV packaging, not RNA derived from the VEGAS system. Of note, both the structural RNA and target transgenes used in the VEGAS system contain viral packaging sequences. The impact of SINV "cheater" particles could be potentially overcome in the context of a robust VEGAS circuit, but since SSG complementation is also defective in the VEGAS system, selection for authentic evolution products is not currently possible. Similar results have been obtained in independent laboratories. Taken together, these results show that the VEGAS system does not work as described and, without significant redesign, cannot be used for mammalian directed evolution c aigns.
Publisher: MDPI AG
Date: 11-08-2023
DOI: 10.3390/TROPICALMED8080409
Abstract: Dengue virus serotype 4 (DENV-4) has been the rarest circulating serotype in Malaysia, resulting in it being an understudied area. A recent observation from institutional surveillance data indicated a rapid increase in DENV-4-infected cases. The present study aimed to investigate the resurgence of DENV-4 in relation to the demographic, clinical and genomic profiles of 75 retrospective dengue s les. First, the demographic and clinical profiles obtained between 2017 and July 2022 were statistically assessed. S les with good quality were subjected to full genome sequencing on the Illumina Next Seq 500 platform and the genome data were analysed for the presence of mutations. The effect of the mutations of interest was studied via an in silico computational approach using SWISS-MODEL and AlphaFold2 programs. The predominance of DENV-4 was discovered from 2021 to 2022, with a prevalence of 64.3% (n = 9/14) and 89.2% (n = 33/37), respectively. Two clades with a genetic ergence of 2.8% were observed within the dominant genotype IIa. The majority of DENV-4-infected patients presented with gastrointestinal symptoms, such as vomiting (46.7%), persistent diarrhoea (30.7%) and abdominal pain (13.3%). Two mutations, His50Tyr and Pro144Ser, located at the wing domain of the NS1 protein were discovered to be unique to the recently sequenced DENV-4.
Publisher: Springer Science and Business Media LLC
Date: 14-06-2019
No related grants have been discovered for Mohd Khairul Nizam Mohd Khalid.