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  1. Fulltext Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host
    Ahn M, Anderson DE, Zhang Q, Tan CW, Lim BL, Luko K, et al.
    Nat Microbiol, 2019 05;4(5):789-799.
    PMID: 30804542 DOI: 10.1038/s41564-019-0371-3
    Bats are special in their ability to host emerging viruses. As the only flying mammal, bats endure high metabolic rates yet exhibit elongated lifespans. It is currently unclear whether these unique features are interlinked. The important inflammasome sensor, NLR family pyrin domain containing 3 (NLRP3), has been linked to both viral-induced and age-related inflammation. Here, we report significantly dampened activation of the NLRP3 inflammasome in bat primary immune cells compared to human or mouse counterparts. Lower induction of apoptosis-associated speck-like protein containing a CARD (ASC) speck formation and secretion of interleukin-1β in response to both 'sterile' stimuli and infection with multiple zoonotic viruses including influenza A virus (-single-stranded (ss) RNA), Melaka virus (PRV3M, double-stranded RNA) and Middle East respiratory syndrome coronavirus (+ssRNA) was observed. Importantly, this reduction of inflammation had no impact on the overall viral loads. We identified dampened transcriptional priming, a novel splice variant and an altered leucine-rich repeat domain of bat NLRP3 as the cause. Our results elucidate an important mechanism through which bats dampen inflammation with implications for longevity and unique viral reservoir status.
    Matched MeSH terms: Chiroptera/genetics; Influenza, Human/genetics; Influenza A virus/genetics; Interleukin-1beta/genetics; Inflammasomes/genetics; Middle East Respiratory Syndrome Coronavirus/genetics; NLR Family, Pyrin Domain-Containing 3 Protein/genetics
  2. Description of the female of Simulium (Gomphostilbia) aziruni (Diptera: Simuliidae) and its genetic relationships with members of the Simulium gombakense species-group
    Ya'cob Z, Takaoka H, Low VL, Tan TK, Sofian-Azirun M
    Acta Trop, 2019 May;193:66-70.
    PMID: 30807749 DOI: 10.1016/j.actatropica.2019.02.023
    Simulium (Gomphostilbia) aziruni Takaoka, Hashim & Chen was described initially based only on a pupa and a mature larva collected from Peninsular Malaysia. Herein, we describe the morphological characters of the female of S. aziruni for the first time. It resembles those of the other members of the Simulium gombakense species-group by the genital fork with a distinct projection directed medioposteriorly from each arm and claw with a large basal tooth. Cytochrome c oxidase I (COI) barcoding analysis indicates that S. aziruni is the sister species of S. maleewongae, but both are distantly separated by a genetic distance of 4.9%.
    Matched MeSH terms: Simuliidae/genetics*
  3. Obesity an overview: Genetic conditions and recent developments in therapeutic interventions
    Vasanth Rao VRB, Candasamy M, Bhattamisra SK
    Diabetes Metab Syndr, 2019 05 07;13(3):2112-2120.
    PMID: 31235145 DOI: 10.1016/j.dsx.2019.05.004
    Obesity is a complex disorder that is linked to many coexisting disorders. Recent epidemiological data have suggested that the prevalence of obesity is at an all-time high, growing to be one of the world's biggest problems. There are several mechanisms on how individuals develop obesity which includes genetic and environmental factors. Not only does obesity contribute to other health issues but it also greatly affects the quality of life, physical ability, mental strength and imposes a huge burden in terms of healthcare costs. Along with that, obesity is associated with the risk of mortality and has been shown to reduce the median survival rate. Obesity is basically when the body is not able to balance energy intake and output. When energy intake exceeds energy expenditure, excess calories will be stored as fat leading to weight gain and eventually obesity. The therapeutic market for treating obesity is composed of many different interventions from lifestyle intervention, surgical procedures to pharmacotherapeutic approaches. All of these interventions have their respective benefits and disadvantages and are specifically prescribed to a patient based on the severity of their obesity as well as the existence of other health conditions. This review discusses the genetic and environmental causes of obesity along with the recent developments in anti-obesity therapies.
    Matched MeSH terms: Obesity/genetics*
  4. Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives
    Neoh HM, Tan XE, Sapri HF, Tan TL
    Infect Genet Evol, 2019 10;74:103935.
    PMID: 31233781 DOI: 10.1016/j.meegid.2019.103935
    Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.
    Matched MeSH terms: Bacteria/genetics
  5. Fulltext Genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis from Malaysia
    Tan JL, Simbun A, Chan KG, Ngeow YF
    Sci Data, 2020 05 05;7(1):135.
    PMID: 32371951 DOI: 10.1038/s41597-020-0475-x
    Mycobacterium tuberculosis (MTB) is commonly used as a model to study pathogenicity and multiple drug resistance in bacteria. These MTB characteristics are highly dependent on the evolution and phylogeography of the bacterium. In this paper, we describe 15 new genomes of multidrug-resistant MTB (MDRTB) from Malaysia. The assessments and annotations on the genome assemblies suggest that strain differences are due to lineages and horizontal gene transfer during the course of evolution. The genomes show mutations listed in current drug resistance databases and global MTB collections. This genome data will augment existing information available for comparative genomic studies to understand MTB drug resistance mechanisms and evolution.
    Matched MeSH terms: Mycobacterium tuberculosis/genetics*
  6. Fulltext Phylogenetic relationships of Pseudo-nitzschia subpacifica (Bacillariophyceae) from the Mexican Pacific, and its production of domoic acid in culture
    Quijano-Scheggia SI, Olivos-Ortiz A, Garcia-Mendoza E, Sánchez-Bravo Y, Sosa-Avalos R, Salas Marias N, et al.
    PLoS One, 2020;15(4):e0231902.
    PMID: 32330168 DOI: 10.1371/journal.pone.0231902
    Pseudo-nitzschia is a cosmopolitan genus, some species of which can produce domoic acid (DA), a neurotoxin responsible for the Amnesic Shellfish Poisoning (ASP). In this study, we identified P. subpacifica for the first time in Todos Santos Bay and Manzanillo Bay, in the Mexican Pacific using SEM and molecular methods. Isolates from Todos Santos Bay were cultivated under conditions of phosphate sufficiency and deficiency at 16°C and 22°C to evaluate the production of DA. This toxin was detected in the particulate (DAp) and dissolved (DAd) fractions of the cultures during the exponential and stationary phases of growth of the cultures. The highest DA concentration was detected during the exponential phase grown in cells maintained in P-deficient medium at 16°C (1.14 ± 0.08 ng mL-1 DAd and 4.71 ± 1.11 × 10-5 ng cell-1 of DAp). In P-sufficient cultures DA was higher in cells maintained at 16°C (0.25 ± 0.05 ng mL-1 DAd and 9.41 ± 1.23 × 10-7 ng cell-1 of DAp) than in cells cultured at 22°C. Therefore, we confirm that P. subpacifica can produce DA, especially under P-limited conditions that could be associated with extraordinary oceanographic events such as the 2013-2016 "Blob" in the northeastern Pacific Ocean. This event altered local oceanographic conditions and possibly generated the presence of potential harmful species in areas with economic importance on the Mexican Pacific coast.
    Matched MeSH terms: Diatoms/genetics*
  7. Emmer wheat (Triticum dicoccon Schrank) improves water use efficiency and yield of hexaploid bread wheat
    Ma'arup R, Trethowan RM, Ahmed NU, Bramley H, Sharp PJ
    Plant Sci, 2020 Jun;295:110212.
    PMID: 32534607 DOI: 10.1016/j.plantsci.2019.110212
    Emmer wheat (Triticum dicoccon Schrank) is a potential source of new genetic diversity for the improvement of hexaploid bread wheat. Emmer wheat was crossed and backcrossed to bread wheat and 480 doubled haploids (DHs) were produced from BC1F1 plants with hexaploid appearance derived from 19 crossses. These DHs were screened under well-watered conditions (E1) in 2013 to identify high-yielding materials with similar phenology. One-hundred and eighty seven DH lines selected on this basis, 4 commercial bread wheat cultivars and 9 bread wheat parents were then evaluated in extensive field experiments under two contrasting moisture regimes in north-western NSW in 2014 and 2015. A significant range in the water-use-efficiency of grain production (WUEGrain) was observed among the emmer derivatives. Of these, 8 hexaploid lines developed from 8 different emmer wheat parents had significantly improved intrinsic water-use-efficiency (WUEintr) and instantaneous water-use-efficiency (WUEi) compared to their bread wheat recurrent parents. Accurate and large scale field-based phenotyping was effective in identifying emmer wheat derived lines with superior performance to their hexaploid bread wheat recurrent parents under moisture stress.
    Matched MeSH terms: Triticum/genetics
  8. Bacterial endosymbiont inhabiting Leucaena leucocephala leaves and their antioxidant and antidiabetic potential
    Chigurupati S, Vijayabalan S, Selvarajan KK, Alhowail A, Kauser F
    J Complement Integr Med, 2020 Dec 22;18(2):319-325.
    PMID: 34187119 DOI: 10.1515/jcim-2020-0203
    OBJECTIVES: Research on endosymbionts is emerging globally and is considered as a potential source of bioactive phytochemicals. The present study examines the antioxidant and antidiabetic of the endophytic crude extract isolated from Leucaena leucocephala leaves.

    METHODS: Endophytic bacteria were isolated from the leaves of L. leucocephala and 16S rRNA gene sequencing was used to establish their identity. The in vitro antioxidant effect of endophytic crude extract (LL) was evaluated using 2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) free radical scavenging methods. The in vitro antidiabetic properties of LL were evaluated using α-amylase and α-glucosidase enzyme inhibition assay.

    RESULTS: The isolated endophytic bacteria were identified as Cronobacter sakazakii. LL displayed potent free radical scavenging effect against ABTS and DPPH radicals with an inhibitory concentration 50% (IC50) value of 17.49 ± 0.06 and 11.3 ± 0.1 μg/mL respectively. LL exhibited α-amylase and α-glucosidase inhibition with an IC50 value of 23.3 ± 0.08 and 23.4 ± 0.1 μg/mL respectively compared to the standard drug (acarbose). Both glucose loaded normoglycemic rats and STZ induced diabetic rats treated with LL (200 mg/kg) exhibited a considerable reduction in blood glucose levels p<0.01 after 8 h of treatment when compared to normal and diabetic control rats respectively.

    CONCLUSIONS: Thus, the study shows that LL has a wellspring of natural source of antioxidants, and antidiabetic agents and phytoconstituents present in endophytes could be the rich source for bioactive compounds.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  9. Fulltext Medical genetics in developing countries in the Asia-Pacific region: challenges and opportunities
    Thong MK, See-Toh Y, Hassan J, Ali J
    Genet Med, 2018 10;20(10):1114-1121.
    PMID: 30093710 DOI: 10.1038/s41436-018-0135-0
    Advances in genetic and genomic technology changed health-care services rapidly in low and middle income countries (LMICs) in the Asia-Pacific region. While genetic services were initially focused on population-based disease prevention strategies, they have evolved into clinic-based and therapeutics-oriented service. Many LMICs struggled with these noncommunicable diseases and were unprepared for the needs of a clinical genetic service. The emergence of a middle class population, the lack of regulatory oversight, and weak capacity-building in medical genetics expertise and genetic counseling services led to a range of genetic services of variable quality with minimal ethical oversight. Some of the current shortcomings faced include the lack of awareness of cultural values in genetic health care, the variable stages of socioeconomic development and educational background that led to increased demand and abuse of genetics, the role of women in society and the crisis of gender selection, the lack of preventive and care services for genetic and birth defects, the issues of gene ethics in medicine, and the lack of understanding of some religious controversies. These challenges provide opportunities for both developing and developed nations to work together to reduce the inequalities and to ensure a caring, inclusive, ethical, and cost-effective genetic service in the region.
    Matched MeSH terms: Genetics, Medical/trends*
  10. Improved protection from velogenic Newcastle disease virus challenge following multiple immunizations with plasmid DNA encoding for F and HN genes
    Loke CF, Omar AR, Raha AR, Yusoff K
    Vet Immunol Immunopathol, 2005 Jul 15;106(3-4):259-67.
    PMID: 15963824
    Specific-pathogen free (SPF) chickens were inoculated with the plasmid constructs encoding the fusion (F) and haemagglutinin-neuraminidase (HN) glycoproteins of Newcastle disease virus (NDV), either individually or in combination and challenged with velogenic NDV. The antibody level against NDV was measured using commercial enzyme linked immunosorbent assay (ELISA). In the first immunization regimen, SPF chickens inoculated twice with NDV-F or NDV-HN constructs elicited antibody responses 1 week after the second injection. However, the levels of the antibody were low and did not confer significant protection from the lethal challenge. In addition, administration of the plasmid constructs with Freund's adjuvant did not improve the level of protection. In the second immunization regimen, chickens inoculated twice with the plasmid constructs emulsified with Freund's adjuvant induced significant antibody titers after the third injection. Three out of nine (33.3%) chickens vaccinated with pEGFP-HN, five of ten (50.0%) chickens vaccinated with pEGFP-F and nine of ten (90.0%) chickens vaccinated with combined pEGFP-F and pEGFP-HN were protected from the challenge. No significant differences in the levels of protection were observed when the chickens were vaccinated with linearized pEGFP-F. The results suggested that more than two injections with both F and HN encoding plasmid DNA were required to induce higher level of antibodies for protection against velogenic NDV in chickens.
    Matched MeSH terms: DNA, Viral/genetics; Newcastle disease virus/genetics*; Plasmids/genetics; Viral Fusion Proteins/genetics; Viral Vaccines/genetics; HN Protein/genetics; Vaccines, DNA/genetics
  11. Population data of six Alu insertions in indigenous groups from Sabah, Malaysia
    Kee BP, Chua KH, Lee PC, Lian LH
    Ann Hum Biol, 2012 Nov-Dec;39(6):505-10.
    PMID: 22989108 DOI: 10.3109/03014460.2012.719548
    The present study is the first to report the genetic relatedness of indigenous populations of Sabah, Malaysia, using a set of Indel markers (HS4.32, TPA25, APO, PV92, B65 and HS3.23). The primary aim was to assess the genetic relationships among these populations and with populations from other parts of the world by examining the distribution of these markers.
    Matched MeSH terms: Ethnic Groups/genetics*
  12. Alpha 1-protease inhibitor (PI) subtypes in seven populations of east Asia
    Saha N
    Ann Hum Biol, 1990 5 1;17(3):229-34.
    PMID: 2337328
    The distribution of serum alpha 1-protease inhibitor (PI) or alpha 1-antitrypsin (alpha 1AT) subtypes was determined by thin-layer isoelectric focusing in a group of 1233 individuals from six Mongoloid populations of East Asia and Dravidian Indians. The sample comprised 385 Chinese from Singapore and 151 Chinese from the Fujien province; 126 Malays; 243 Filipinos; 112 Thais; 56 Koreans and 160 Dravidian Indians. The frequency of PiM1 ranged from 0.65 in the Thais to 0.81 in the Fujien Chinese. The highest frequency of PiM2 was found in the Dravidian Indians (0.28) followed by the Thais (0.25). The frequency of PiM3 was found to vary from 0.03 to 0.07 in these populations. A low frequency of PiF (0.01 to 0.02) and PiS (0.01 to 0.04) was also observed in the Mongoloid populations but absent in the Indians. The PiZ allele was completely absent in all these populations. The phenotypic distribution of PI subtypes was at Hardy-Weinburg equilibrium in all the populations.
    Matched MeSH terms: alpha 1-Antitrypsin/genetics*
  13. Distribution of transferrin (Tf) subtypes in several Mongoloid populations of East Asia
    Saha N
    Ann Hum Biol, 1987 7 1;14(4):349-56.
    PMID: 3662433
    The distribution of serum transferrin subtypes was determined by PAG electrophoresis and isoelectric focussing in a group of 2288 individuals from 10 Mongoloid populations of East Asia. The sample comprised 857 Chinese from different localities: Singapore (239), Malaysia (228), Taiwan (265), Hong Kong (65), Fouzhou (60); Koreans (332), Filipinos (281), Thais (455), Malays (335) and Indonesians (28). The frequencies of TfC1 varied from 0.73 to 0.79 in the Chinese and from 0.76 to 0.83 in the other Mongoloid populations. TfC3 was observed at a frequency of 0.02 in the Koreans and Chinese from Fouzhou. TfDChi was present in a low frequency (0.01 to 0.03) in all the populations. A low frequency of TfB was also present in all the populations. The phenotypic distribution of transferrin subtypes was at Hardy-Weinberg equilibrium in all the populations.
    Matched MeSH terms: Transferrin/genetics*
  14. Fulltext Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application
    Gan Z, Roslan MAM, Abd Shukor MY, Halim M, Yasid NA, Abdullah J, et al.
    Biosensors (Basel), 2022 Oct 25;12(11).
    PMID: 36354431 DOI: 10.3390/bios12110922
    Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.
    Matched MeSH terms: Mammals/genetics
  15. Fragmented population structure of plasmodium falciparum in a region of declining endemicity
    Anthony TG, Conway DJ, Cox-Singh J, Matusop A, Ratnam S, Shamsul S, et al.
    J Infect Dis, 2005 May 1;191(9):1558-64.
    PMID: 15809916
    The population genetic structure of Plasmodium falciparum differs between endemic regions, but the characteristics of a population recently fragmented by effective malaria control have been unknown.
    Matched MeSH terms: Plasmodium falciparum/genetics*
  16. Fulltext Prevalence and management of aphids (Hemiptera: Aphididae) in different wheat genotypes and their impact on yield and related traits
    Hafeez F, Abbas M, Zia K, Ali S, Farooq M, Arshad M, et al.
    PLoS One, 2021;16(10):e0257952.
    PMID: 34644343 DOI: 10.1371/journal.pone.0257952
    Wheat (Triticum aestivum L.) production is significantly altered by the infestation of sucking insects, particularly aphids. Chemical sprays are not recommended for the management of aphids as wheat grains are consumed soon after crop harvests. Therefore, determining the susceptibility of different wheat genotypes and selecting the most tolerant genotype could significantly lower aphid infestation. This study evaluated the susceptibility of six different wheat genotypes ('Sehar-2006', 'Shafaq-2006', 'Faisalabad-2008', 'Lasani-2008', 'Millat-2011' and 'Punjab-2011') to three aphid species (Rhopalosiphum padi Linnaeus, Schizaphis graminum Rondani, Sitobion avenae Fabricius) at various growth stages. Seed dressing with insecticides and plant extracts were also evaluated for their efficacy to reduce the incidence of these aphid species. Afterwards, an economic analysis was performed to compute cost-benefit ratio and assess the economic feasibility for the use of insecticides and plant extracts. Aphids' infestation was recorded from the seedling stage and their population gradually increased as growth progressed towards tillering, stem elongation, heading, dough and ripening stages. The most susceptible growth stage was heading with 21.89 aphids/tiller followed by stem elongation (14.89 aphids/tiller) and dough stage (13.56 aphids/tiller). The genotype 'Punjab-2011' recorded the lower aphid infestation than 'Faisalabad-2008', 'Sehar-2006', 'Lasani-2008' and 'Shafaq-2006'. Rhopalosiphum padi appeared during mid-February, whereas S. graminum and S. avenae appeared during first week of March. Significant differences were recorded for losses in number of grains/spike and 1000-grain weight among tested wheat genotypes. The aphid population had non-significant correlation with yield-related traits. Hicap proved the most effective for the management of aphid species followed by Hombre and Husk among tested seed dressers, while Citrullus colocynthis L. and Moringa oleifera Lam. plant extracts exhibited the highest efficacy among different plant extracts used in the study. Economic analysis depicted that use of Hombre and Hicap resulted in the highest income and benefit cost ratio. Therefore, use of genotype Punjab-2011' and seed dressing with Hombre and Hicap can be successfully used to lower aphid infestation and get higher economic returns for wheat crop.
    Matched MeSH terms: Triticum/genetics*
  17. Efficacy and Safety of Hepatitis B Virus Vaccination Following Hepatitis B Immunoglobulin Withdrawal After Liver Transplantation
    Jo HS, Khan JF, Han JH, Yu YD, Kim DS
    Transplant Proc, 2021 Dec;53(10):3016-3021.
    PMID: 34740450 DOI: 10.1016/j.transproceed.2021.09.038
    BACKGROUND: Hepatitis B immunoglobulin (HBIG) and oral nucleoside/nucleotide analogs have been the mainstay of hepatitis B virus (HBV) prophylaxis after liver transplantation. However, long-term HBIG administration could have disadvantages, such as an increase in medical costs and the development of mutant HBV strains. This study aimed to investigate the safety and efficacy of HBV vaccination after the withdrawal of HBIG after liver transplantation.

    METHODS: This prospective open-label single-arm observational clinical trial enrolled 41 patients who underwent liver transplantation between 2010 and 2016 because of a condition related to chronic HBV infection. At the time of enrollment, all patients had taken entecavir and discontinued HBIG administration. When hepatitis B surface antibody titer was undetectable after the withdrawal of HBIG, a recombinant HBV vaccine was injected intramuscularly at month 0, 1, and 6.

    RESULTS: After excluding 5 patients who dropped out and 2 patients who had a persistent hepatitis B surface antibody titer, 9 (26.5%) of 34 patients had a positive vaccination response. The median hepatitis B surface antibody titer at seroconversion was 86 (12-1000) IU/L, and those at the end of follow-up were 216 (30-1000) IU/L. No patients experienced HBV recurrence during the study period. Sex (female, odds ratio 32.91 [1.83-592.54], P = .018) and the dosing interval of HBIG before withdrawal (≥90 days, 16.21 [1.21-217.31], P = .035) were independent contributing factors for positive response to the vaccination.

    CONCLUSION: HBV vaccination still deserves consideration as active immunoprophylaxis after liver transplantation because it could provide added immunity to nucleoside/nucleotide analogs monotherapy with excellent cost-effectiveness.

    Matched MeSH terms: Hepatitis B virus/genetics
  18. Fulltext Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber
    Adedze YMN, Lu X, Xia Y, Sun Q, Nchongboh CG, Alam MA, et al.
    Sci Rep, 2021 02 16;11(1):3872.
    PMID: 33594240 DOI: 10.1038/s41598-021-83313-x
    Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line '9930' and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
    Matched MeSH terms: Cucumis sativus/genetics*
  19. The Potential Role of miRNAs as Predictive Biomarkers in Neurodevelopmental Disorders
    Juvale IIA, Che Has AT
    J Mol Neurosci, 2021 Jul;71(7):1338-1355.
    PMID: 33774758 DOI: 10.1007/s12031-021-01825-7
    Neurodevelopmental disorders are defined as a set of abnormal brain developmental conditions marked by the early childhood onset of cognitive, behavioral, and functional deficits leading to memory and learning problems, emotional instability, and impulsivity. Autism spectrum disorder, attention-deficit/hyperactivity disorder, Tourette syndrome, fragile X syndrome, and Down's syndrome are a few known examples of neurodevelopmental disorders. Although they are relatively common in both developed and developing countries, very little is currently known about their underlying molecular mechanisms. Both genetic and environmental factors are known to increase the risk of neurodevelopmental disorders. Current diagnostic and screening tests for neurodevelopmental disorders are not reliable; hence, individuals with neurodevelopmental disorders are often diagnosed in the later stages. This negatively affects their prognosis and quality of life, prompting the need for a better diagnostic biomarker. Recent studies on microRNAs and their altered regulation in diseases have shed some light on the possible role they could play in the development of the central nervous system. This review attempts to elucidate our current understanding of the role that microRNAs play in neurodevelopmental disorders with the hope of utilizing them as potential biomarkers in the future.
    Matched MeSH terms: Autism Spectrum Disorder/genetics; Attention Deficit Disorder with Hyperactivity/genetics; Down Syndrome/genetics; Fragile X Syndrome/genetics; Tourette Syndrome/genetics; MicroRNAs/genetics; Neurodevelopmental Disorders/genetics
  20. Fulltext Modelling infectious diseases with herd immunity in a randomly mixed population
    Law KB, M Peariasamy K, Mohd Ibrahim H, Abdullah NH
    Sci Rep, 2021 10 18;11(1):20574.
    PMID: 34663839 DOI: 10.1038/s41598-021-00013-2
    The conventional susceptible-infectious-recovered (SIR) model tends to magnify the transmission dynamics of infectious diseases, and thus the estimated total infections and immunized population may be higher than the threshold required for infection control and eradication. The study developed a new SIR framework that allows the transmission rate of infectious diseases to decline along with the reduced risk of contact infection to overcome the limitations of the conventional SIR model. Two new SIR models were formulated to mimic the declining transmission rate of infectious diseases at different stages of transmission. Model A utilized the declining transmission rate along with the reduced risk of contact infection following infection, while Model B incorporated the declining transmission rate following recovery. Both new models and the conventional SIR model were then used to simulate an infectious disease with a basic reproduction number (r0) of 3.0 and a herd immunity threshold (HIT) of 0.667 with and without vaccination. Outcomes of simulations were assessed at the time when the total immunized population reached the level predicted by the HIT, and at the end of simulations. Further, all three models were used to simulate the transmission dynamics of seasonal influenza in the United States and disease burdens were projected and compared with estimates from the Centers for Disease Control and Prevention. For the simulated infectious disease, in the initial phase of the outbreak, all three models performed expectedly when the sizes of infectious and recovered populations were relatively small. As the infectious population increased, the conventional SIR model appeared to overestimate the infections even when the HIT was achieved in all scenarios with and without vaccination. For the same scenario, Model A appeared to attain the level predicted by the HIT and in comparison, Model B projected the infectious disease to be controlled at the level predicted by the HIT only at high vaccination rates. For infectious diseases with high r0, and at low vaccination rates, the level at which the infectious disease was controlled cannot be accurately predicted by the current theorem. Transmission dynamics of infectious diseases with herd immunity can be accurately modelled by allowing the transmission rate of infectious diseases to decline along with the reduction of contact infection risk after recovery or vaccination. Model B provides a credible framework for modelling infectious diseases with herd immunity in a randomly mixed population.
    Matched MeSH terms: Communicable Diseases/genetics
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