Browsing by Author "Liyana Azmi"
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Publication Aldehyde-alcohol Dehydrogenase Forms A High-order Spirosome Architecture Critical For Its Activity(Nature Publishing Group, 2019) ;Gijeong Kim ;Liyana Azmi ;Seongmin Jang ;Taeyang Jung ;Hans Hebert ;Andrew J. Roe ;Olwyn ByronJi-Joon SongAldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity. - Some of the metrics are blocked by yourconsent settings
Publication Bridging Science And Religion – Treatment Of Depressed Muslim Patients Using Islamic Integrated Cognitive Behavioural Therapy(Universiti Sains Islam Malaysia, 2020) ;Siti Nur Ainina Mohd Yusoff ;Amira Raudhah ;Nathratul Ayeshah ZulkifliLiyana AzmiMental illness, particularly depression, is an increasing health problem for many people from all walks of life. Both conventional and non-conventional therapies for mental illnesses including depression have been and are still being put to practice. An alternative method for treatment of depressed patients, particularly Muslims, is through the combination of Cognitive Behavioural Therapy with Islamic values, which is known as Islamic Integrated Cognitive Behavioural Therapy. This review discusses the benefits, limitations and future propects of Islamic Integrated Cognitive Behavioural Therapy particularly in treating Muslims with depression. - Some of the metrics are blocked by yourconsent settings
Publication Calicivirus VP2 Forms A Portal-like Assembly Following Receptor Engagement(Nature Publishing Group, 2019) ;Michaela J. Conley ;Marion McElwee ;Liyana Azmi ;Mads Gabrielsen ;Olwyn Byron ;Ian G. GoodfellowDavid BhellaTo initiate infection, many viruses enter their host cells by triggering endocytosis following receptor engagement. However, the mechanisms by which non-enveloped viruses escape the endosome are poorly understood. Here we present near-atomic-resolution cryo-electron microscopy structures for feline calicivirus both undecorated and labelled with a soluble fragment of its cellular receptor, feline junctional adhesion molecule A. We show that VP2, a minor capsid protein encoded by all caliciviruses1,2, forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly—which was not detected in undecorated virions—is formed of twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface. Local rearrangement at the portal site leads to the opening of a pore in the capsid shell. We hypothesize that the portal-like assembly functions as a channel for the delivery of the calicivirus genome, through the endosomal membrane, into the cytoplasm of a host cell, thereby initiating infection. VP2 was previously known to be critical for the production of infectious virus3; our findings provide insights into its structure and function that advance our understanding of the Caliciviridae. - Some of the metrics are blocked by yourconsent settings
Publication Effect of Circadian Rhythm Disturbance on the Human Musculoskeletal System and the Importance of Nutritional Strategies(MDPI, 2023) ;Norsham Juliana ;Liyana Azmi ;Nadia Mohd Effendy ;Nur Islami Mohd Fahmi Teng ;Izuddin Fahmy Abu ;Nur Nabilah Abu Bakar ;Sahar Azmani ;Noor Anisah Abu Yazit ;Suhaini KadimanSrijit DasThe circadian system in the human body responds to daily environmental changes to optimise behaviour according to the biological clock and also influences various physiological processes. The suprachiasmatic nuclei are located in the anterior hypothalamus of the brain, and they synchronise to the 24 h light/dark cycle. Human physiological functions are highly dependent on the regulation of the internal circadian clock. Skeletal muscles comprise the largest collection of peripheral clocks in the human body. Both central and peripheral clocks regulate the interaction between the musculoskeletal system and energy metabolism. The skeletal muscle circadian clock plays a vital role in lipid and glucose metabolism. The pathogenesis of osteoporosis is related to an alteration in the circadian rhythm. In the present review, we discuss the disturbance of the circadian rhythm and its resultant effect on the musculoskeletal system. We also discuss the nutritional strategies that are potentially effective in maintaining the system’s homeostasis. Active collaborations between nutritionists and physiologists in the field of chronobiological and chrononutrition will further clarify these interactions. This review may be necessary for successful interventions in reducing morbidity and mortality resulting from musculoskeletal disturbances. - Some of the metrics are blocked by yourconsent settings
Publication High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE(John Wiley and Sons Ltd, 2020) ;Liyana Azmi ;Eilis C. Bragginton ;Ian T. Cadby ;Olwyn Byron ;Andrew J. Roe ;Andrew L. LoveringMads GabrielsenThe bifunctional alcohol/aldehyde dehydrogenase (AdhE) comprises both an N-terminal aldehyde dehydrogenase (AldDH) and a C-terminal alcohol dehydrogenase (ADH). In vivo, full-length AdhE oligomerizes into long oligomers known as spirosomes. However, structural analysis of AdhE is challenging owing to the heterogeneity of the spirosomes. Therefore, the domains of AdhE are best characterized separately. Here, the structure of ADH from the pathogenic Escherichia coli O157:H7 was determined to 1.65 Å resolution. The dimeric crystal structure was confirmed in solution by small-angle X-ray scattering. Keywords: alcohol dehydrogenase; AdhE; Escherichia coli - Some of the metrics are blocked by yourconsent settings
Publication Impact of Rapid Vaccination on Sars-Cov-2 Genomic Diversity: An Intervention to Minimise the Public Burden of the Pandemic(Malaysian Journal of Public Health Medicine, 2023) ;Amirah Azzeri ;Shuhaila Mat-Sharani ;Danish A/L Kumareahsan ;Ismatul Nurul Asyikin Ismail ;Muhamad Arif Mohamad JamaliLiyana AzmiGlobal sharing of SARS-CoV-2 sequences enabled comprehensive analyses of COVID-19 genomic diversity and demographics. Yet, regional genomic surveillance is often neglected, leading to the possible oversight of novel mutations by public health authorities. Our study used the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyse infection patterns in the state of Negeri Sembilan, and compare infection patterns to the state of Selangor, in Malaysia. We discuss the impact of rapid vaccination on resulting single nucleotide variants (SNVs) and identified novel sporadic mutations may affect viral fitness and pathogenicity. Four hundred and seventeen SARS-CoV-2 sequences extracted from Negeri Sembilan from July 2021 until June 2022. Infection patterns based on pangolin lineages from Negeri Sembilan was compared to infections of the same period from Selangor. SNVs from the spike protein were sorted by frequency, with the lowest frequency variant submitted for functional prediction using PredictSNP. Negeri Sembilan exhibited a comparable infection pattern to Selangor, but with fewer Omicron sequences which was postulated to occur due to the rapid vaccination strategies by Negeri Sembilan. Omicron outbreaks were associated with eased lockdowns and policy changes in December 2021. From our extracted data, seventy novel SNVs in the spike protein of SARS-CoV-2 were extracted from this study. In silico predictions indicated five of the SNVs (S221L, L226S, V826L, C1240F and C1243F) to may cause functional defects to the spike protein. Rapid sequencing and analysis will aid policymaking for public health controls by detecting potential outbreaks within transient variants. - Some of the metrics are blocked by yourconsent settings
Publication Molecular Dynamic Simulations Of Mlac Inhibition By Antibiotic In Escherichia Coli(Malaysian Society for Biochemistry and Molecular Biology, 2023) ;Umairah Ramli ;Muhamad Arif Mohamad Jamali ;Ismatul Nurul Asyikin Ismail ;Fatin Hilyani MohamadLiyana AzmiAntimicrobial resistance has emerged as a global public health concern. Gram-negative bacteria such as Escherichia coli (E. coli) pose a significant threat to human health due to their increasing antibiotic resistance. For instance, Shiga toxin-producing E. coli (STEC) is a strain that produces toxins that cause damage to the lining of the intestines and kidneys. Antibiotic exposures to STEC would induce the hemolytic uraemic syndrome and bloody diarrhea, a potentially fatal-condition to the patient. The outer membrane architecture in Gram-negatives, specifically the OmpC–Mla complex, maintains the outer membrane lipid asymmetry. The MlaC protein transfers phospholipids from outer membranes to inner membranes and ensures the integrity of the membrane. Inactivation of MlaC protein increases the penetrability of OM and increases the antibiotic’s sensitivity. Therefore, screening for inhibitor compounds that can bind and inhibit the function of MlaC is a viable strategy for antibiotic development.This study aims to understand the interactions of four types of inhibitors in MlaC protein from E. coli via docking and molecular dynamic (MD) simulation. The four types of inhibitors namely albacarcin V, clorobiocin, 1-N,4-N-bis(3- phenylphenyl)piperazine-1,4-dicarboxamide (piperazine dicarboxamide) and -2-[2-[(6- oxobenzo[c]chromen-2-yl)carbamoyl]phenyl]benzoic acid (salicylanilide benzoate). The docking showed that the inhibitors fit into the lipid pocket of MlaC. MD for each system run at 100 ns showed that the system has stable Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and reasonable Radius of Gyration (Rg) value. The RMSD, RMSF and Rg were comparable to the native phospholipid binding in the crystal structure, which suggests the potential use of these four types of inhibitors. Salicylanilide benzoate was revealed to be the most stable in complex with MlaC, with the least deviation, least fluctuation, and most compact throughout the simulation - Some of the metrics are blocked by yourconsent settings
Publication Physical Parameters Influence The Microbial Quality Of Indoor Air In Research Laboratories: A Report From Malaysia(Elsevier, 2023) ;Kuilan Yogeswaran ;Liyana Azmi ;Subha Bhassu ;Hafizah N. IsaMuhamad Afiq AzizThe quality of air conditioning and ventilation systems in laboratories is vital to ensure optimum health of the users and guarantee the accuracy of experiments conducted. Moreover, recent studies show that the average quality of air conditioning and ventilation systems in labs can pose health risks to occupants. The study aims to examine the relationship between physical parameters and microbial pollutants in research laboratories' indoor air quality (IAQ) by quantifying and characterising the bacteria and fungi in the indoor environment of research laboratories using the settle plate method; whereby our Petri dishes containing media are exposed to the air for sample collection. This study was conducted over the course of 3 day at three different research laboratories: Virology Lab (VL), Genetic Lab (GL), and Aquatic Lab (AL). The physical parameters such as air temperature, humidity and carbon dioxide were measured using FLUKE 975 air meter, whereas the microbial parameters were assessed using the settle plate method with Tryptone Soya agar and Sabouraud Dextrose agar for the bacterial and fungal count, respectively. Our results showed that the high temperature and relative humidity, exceeded the standard threshold for temperature (23–26 C) and relative humidity (40–70%) set by the Department of Occupational Safety and Health (DOSH). Additionally, because of poor air conditioning and ventilation system maintenance, there were high total bacterial counts in GL (CFU/m3 234.34 30.93) and total fungal counts in VL (CFU/m3 589.34 53.03). We also showed that the most commonly isolated bacteria and fungi in research laboratories were Staphylococcus spp. (72.2%) and Cladosporium spp. (76.7%). conclusion, we reported that there was a correlation between the physical parameters and microbial pollutants in the research laboratories. Therefore, regular monitoring of indoor air quality (IAQ) parameters and maintenance of the air conditioning and ventilation system should be carried out to ensure a good and safe indoor environment in research laboratories. - Some of the metrics are blocked by yourconsent settings
Publication The Upshot Of Covid-19 On Malaysian Research(Universiti Sains Islam Malaysia, 2020-10-15) ;Hafizah Noor IsaLiyana AzmiCOVID-19 has changed the global dynamics in many aspects. The infectious nature of the disease has forced global lockdown in many countries, thereby causing disruptions in our daily lives, including work. Particularly for research, hindrances to travel and the sudden increase of attention of COVID-19 itself has changed many aspects of research. In Malaysia, this is no exception as many researchers, scientists, academicians, and students try to research the midst of the pandemic. With a focus on Malaysia, we discuss the pros and cons of research that have come with global shutdowns, shifts in grant focus and how scientists are coping with the massive lifechanges imposed by COVID-19.