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  1. Fulltext De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read
    Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, et al.
    Gigascience, 2017 08 01;6(8):1-6.
    PMID: 28873963 DOI: 10.1093/gigascience/gix063
    One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.
    Matched MeSH terms: Perciformes/genetics*
  2. Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae
    Lopes-Lima M, Bolotov IN, Do VT, Aldridge DC, Fonseca MM, Gan HM, et al.
    Mol Phylogenet Evol, 2018 10;127:98-118.
    PMID: 29729933 DOI: 10.1016/j.ympev.2018.04.041
    Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritiferidae motivated a new search for other potential species of margaritiferids from members of Gibbosula and Lamprotula. Based on molecular and morphological analyses conducted on newly collected specimens from Vietnam, we here assign Gibbosula crassa to the Margaritiferidae. Additionally, we reanalyzed all diagnostic characteristics of the Margaritiferidae and examined museum specimens of Lamprotula and Gibbosula. As a result, two additional species are also moved to the Margaritiferidae, i.e. Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the taxonomy within the family. The present phylogeny reveals the division of Margaritiferidae into four ancient clades with distinct morphological, biogeographical and ecological characteristics that justify the division of the Margaritiferidae into two subfamilies (Gibbosulinae and Margaritiferinae) and four genera (Gibbosula, Cumberlandia, Margaritifera, and Pseudunio). The systematics of the Margaritiferidae family is re-defined as well as their distribution, potential origin and main biogeographic patterns.
    Matched MeSH terms: Bivalvia/genetics
  3. Fulltext Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics
    Cioffi MB, Ráb P, Ezaz T, Bertollo LAC, Lavoué S, Oliveira EA, et al.
    Int J Mol Sci, 2019 Sep 02;20(17).
    PMID: 31480792 DOI: 10.3390/ijms20174296
    Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA3/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.
    Matched MeSH terms: Fishes/genetics*
  4. Molecular characterization of Trichuris species isolated from humans, dogs and cats in a rural community in Peninsular Malaysia
    Mohd-Shaharuddin N, Lim YAL, Hassan NA, Nathan S, Ngui R
    Acta Trop, 2019 Feb;190:269-272.
    PMID: 30500371 DOI: 10.1016/j.actatropica.2018.11.026
    Trichuris trichiura (whipworm) are soil-transmitted helminths (STHs) that causing trichuriasis in human. Trichuris vulpis, a canine whipworm has also been reported occasionally in humans. However, an overlapping dimension in the morphology and due to limited external characters between both species may lead to the potential for misidentification. Although there has been an extensive study on the distribution of whipworm in both human and animal hosts, little is known about the molecular epidemiology of Trichuris species in both hosts. To investigate to characterize the whipworm species and to determine the genetic relationship between species infecting both humans and animals, we sequenced the small subunit ribosomal RNA (SSU rRNA) regions of Trichuris egg isolated from humans, dogs and cats in a rural community in Malaysia. A total of 524 fresh fecal samples were collected from humans and animals. The overall prevalence of Trichuris was 59.9% as determined by microscopy examination. The molecular analysis showed that 98.7% were identified as T. trichiura in the human fecal sample. Interestingly, 1.3% were identified as T. vulpis. As for animal fecal sample, 56.8% and 43.2% were identified as T. trichiura and T. vulpis, respectively. Phylogenetic and sequence analysis demonstrated that T. trichiura isolates were genetically distinct from T. vulpis isolates from both hosts. This finding implies that companion animals can be a reservoir and mechanical transmitter for T. trichiura infection in human and also highlighting the possible zoonotic potential of T. vulpis. This finding may also suggest that cross-transmission between humans and animal hosts in sympatric setting may be a source of infection in both hosts. More studies are needed to better understand the transmission dynamic and public health significance of Trichuris infection in both hosts.
    Matched MeSH terms: Trichuris/genetics*
  5. PLASMA MICRORNA-133А LEVEL IN PATIENTS WITH ESSENTIAL ARTERIAL HYPERTENSION
    Koval S, Snihurska I, Yushko K, Lytvynova O, Berezin A
    Georgian Med News, 2019 May.
    PMID: 31322515
    The aim of research was to investigate the plasma microRNA (miR-133а) level in patients with essential arterial hypertension (EAH). A total of 45 patients with EAH 2-3 degrees aged 52.14 ± 8.25 years and 21 healthy individuals (control group) with comparable age and sex distributions. The following frequency of risk factors was revealed among the examined patients: overweight (53%), dyslipidaemia (73%), pre-diabetes (13%), asymptomatic hyperuricemia (29%); hypertension-mediated organ damage: increased arterial stiffness (27%), left ventricular hypertrophy (55%), atherosclerotic plaque in the carotid artery (40%), microalbuminuria (15%), moderate stage of chronic kidney disease (22%) and cardiovascular diseases: stable ischemic heart disease (11%) and heart failure with preserved ejection fraction of NYHA functional class I (18%). The plasma miR-133a level was determined by polymerase chain reaction using "CFX96 Touch" detection system (BioRad) and "TaqMan microRNA Assay" and "TaqMan® Universal PCR Master Mix" reagents (Thermo Fisher Scientific, USA). It has been established that in patients with EAH the plasma level of miR-133a was significantly lower than in practically healthy individuals (0,182 [0,102; 0,301] ), vs (0,382 [0,198; 0,474]), p <0.05). It has also been revealed a significant decrease in the level of miR-133a in the blood plasma in patients with such organs damage as LVH (0,133 [0,099;0,184]) in comparison with patients without LVH (0,238 [0,155; 0,410]), p <0.05) and also significantly lower than in healthy subjects in the control group (0,382 [0,198; 0,474]), p<0.05). There were no statistically significant differences in the plasma levels of miR-133a in the group of patients with EAH, depending on the presence of risk factors, other organ damage and cardiovascular diseases. The findings suggest the significant role of reducing of plasma levels of miR-133a in the pathogenesis of hypertension itself and in pathological remodeling of the heart.
    Matched MeSH terms: MicroRNAs/genetics
  6. A review of Nipah and Hendra viruses with an historical aside
    Ksiazek TG, Rota PA, Rollin PE
    Virus Res, 2011 Dec;162(1-2):173-83.
    PMID: 21963678 DOI: 10.1016/j.virusres.2011.09.026
    The emergence of Hendra and Nipah viruses in the 1990s has been followed by the further emergence of these viruses in the tropical Old World. The history and current knowledge of the disease, the viruses and their epidemiology is reviewed in this article. A historical aside summarizes the role that Dr. Brian W.J. Mahy played at critical junctures in the early stories of these viruses.
    Matched MeSH terms: Plasmids/genetics; Viral Proteins/genetics; DNA, Complementary/genetics; Hendra Virus/genetics*; Nipah Virus/genetics*; Reverse Genetics/methods*
  7. Recent trends in cancer therapy: A review on the current state of gene delivery
    Yahya EB, Alqadhi AM
    Life Sci, 2021 Mar 15;269:119087.
    PMID: 33476633 DOI: 10.1016/j.lfs.2021.119087
    Cancer treatment has been always considered one of the most critical and vital themes of clinical issues. Many approaches have been developed, depending on the type and the stage of tumor. Gene therapy has the potential to revolutionize different cancer therapy. With the advent of recent bioinformatics technologies and genetic science, it become possible to identify, diagnose and determine the potential treatment using the technology of gene delivery. Several approaches have been developed and experimented in vitro and vivo for cancer therapy including: naked nucleic acids based therapy, targeting micro RNAs, oncolytic virotherapy, suicide gene based therapy, targeting telomerase, cell mediated gene therapy, and CRISPR/Cas9 based therapy. In this review, we present a straightforward introduction to cancer biology and occurrence, highlighting different viral and non-viral gene delivery systems for gene therapy and critically discussed the current and various strategies for cancer gene therapy.
    Matched MeSH terms: Neoplasms/genetics
  8. Autoinflammatory diseases in childhood, part 1: monogenic syndromes
    Navallas M, Inarejos Clemente EJ, Iglesias E, Rebollo-Polo M, Zaki FM, Navarro OM
    Pediatr Radiol, 2020 03;50(3):415-430.
    PMID: 32065272 DOI: 10.1007/s00247-019-04536-9
    Autoinflammatory diseases constitute a family of disorders defined by aberrant stimulation of inflammatory pathways without involving antigen-directed autoimmunity. They may be divided into monogenic and polygenic types. Monogenic autoinflammatory syndromes are those with identified genetic mutations, such as familial Mediterranean fever, tumor necrosis factor receptor-associated periodic fever syndrome (TRAPS), mevalonate kinase deficiency or hyperimmunoglobulin D syndrome, cryopyrin-associated periodic fever syndromes (CAPS), pyogenic arthritis pyoderma gangrenosum and acne (PAPA) syndrome, interleukin-10 and interleukin-10 receptor deficiencies, adenosine deaminase 2 deficiency and pediatric sarcoidosis. Those without an identified genetic mutation are known as polygenic and include systemic-onset juvenile idiopathic arthritis, idiopathic recurrent acute pericarditis, Behçet syndrome, chronic recurrent multifocal osteomyelitis and inflammatory bowel disease among others. Autoinflammatory disorders are defined by repeating episodes or persistent fever, rash, serositis, lymphadenopathy, arthritis and increased acute phase reactants, and thus may mimic infections clinically. Most monogenic autoinflammatory syndromes present in childhood. However, because of their infrequency, diverse and nonspecific presentation, and the relatively new genetic recognition, diagnosis is usually delayed. In this article, which is Part 1 of a two-part series, the authors update monogenic autoinflammatory diseases in children with special emphasis on imaging features that may help establish the correct diagnosis.
    Matched MeSH terms: Hereditary Autoinflammatory Diseases/genetics*
  9. On consanguineous marriages and the genetic load
    Chakraborty R, Chakravarti A
    Hum Genet, 1977 Apr 07;36(1):47-54.
    PMID: 870410
    It has been reported that studies of the genetic consequences of inbreeding should adopt a different strategy in populations having a relatively old inbreeding history and where inbreeding levels have varied over time. This contention is tested with a series of 39,495 single-birth records from Bombay, India, collected in a World Health Organization survey on congenital malformations. Our analysis reveals that: 1. the incidence of major malformations is significantly higher among the inbred offspring (1.34%) as compared to that among non-inbred ones (0,81%)--a finding at variance with a previous study in the same area; 2. the inbreeding effect on perinatal mortality (stillbirths and mortality during the first few days of life) is also found to be significant. In view of the above findings, the genetic load as disclosed by inbreeding is computed for perinatal mortality, major malformations and pooling these together. A + B, the measure of the number of lethal equivalents per gamete, is found to be at variance with other reports. Such variability can be ascribed to non-genetic factors. Supporting evidence collected from Brazil and Malaysia in the same survey is also presented.
    Matched MeSH terms: Genetics, Population*
  10. Fulltext Identification of a Newly Isolated Getah Virus in the China-Laos Border, China
    Li YY, Fu SH, Guo XF, Lei WW, Li XL, Song JD, et al.
    Biomed Environ Sci, 2017 Mar;30(3):210-214.
    PMID: 28427491 DOI: 10.3967/bes2017.028
    In this study, we isolated a virus strain (YN12031) from specimens of Armigeres subalbatus collected in the China-Laos border. BHK-21 cells infected with YN12031 exhibited an evident cytopathic effect (CPE) 32 h post-infection. The virus particles were spherical, 70 nm in diameter, and enveloped; they also featured surface fibers. Molecular genetic analysis revealed that YN12031 was closely related to alpha viruses such as Chikungunya virus and Sindbis virus, and located in the same clade as MM2021, the prototype of Getahvirus (GETV) isolated in Malaysia in 1955. Phylogenetic analysis of the E2 and capsid genes further revealed that YN12031 was located in the same clade as the Russian isolate LEIV/16275/Mag. Analysis of the homology of nucleotides and amino acids in the coding area and E2 gene demonstrated that the YN12031 isolated from the China-Laos border (tropical region) was related closest to the LEIV/16275/Mag isolate obtained in Russia (North frigid zone area) among other isolates studied. These results suggest that GETV can adapt to different geographical environments to propagate and evolve. Thus, strengthening the detection and monitoring of GETV and its related diseases is very crucial.
    Matched MeSH terms: Alphavirus/genetics*
  11. Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand
    Babaei N, Abdullah NA, Saleh G, Abdullah TL
    Mol Biol Rep, 2012 Nov;39(11):9869-77.
    PMID: 22752726
    Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.
    Matched MeSH terms: Curculigo/genetics*
  12. Fulltext Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction
    Azman A, Ng KK, Ng CH, Lee CT, Tnah LH, Zakaria NF, et al.
    Sci Rep, 2020 11 05;10(1):19112.
    PMID: 33154411 DOI: 10.1038/s41598-020-76092-4
    Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.
    Matched MeSH terms: Rhizophoraceae/genetics*
  13. Fulltext Detection of Laem-Singh virus in cultured Penaeus monodon shrimp from several sites in the Indo-Pacific region
    Sittidilokratna N, Dangtip S, Sritunyalucksana K, Babu R, Pradeep B, Mohan CV, et al.
    Dis Aquat Organ, 2009 Apr 27;84(3):195-200.
    PMID: 19565696 DOI: 10.3354/dao02059
    Laem-Singh virus (LSNV) is a positive-sense single-stranded RNA (ssRNA) virus that was recently identified in Penaeus monodon shrimp in Thailand displaying signs of slow growth syndrome. A total of 326 shrimp collected between 1998 and 2007 from countries in the Indo-Pacific region were tested by RT-PCR for evidence of LSNV infection. The samples comprised batches of whole postlarvae, and lymphoid organ, gill, muscle or pleopod tissue of juvenile, subadult and adult shrimp. LSNV was not detected in 96 P. monodon, P. japonicus or P. merguiensis from Australia or 16 P. monodon from Fiji, Philippines, Sri Lanka and Mozambique. There was no evidence of LSNV infection in 73 healthy juvenile P. vannamei collected during 2006 from ponds at 9 locations in Thailand. However, LNSV was detected in each of 6 healthy P. monodon tested from Malaysia and Indonesia, 2 of 6 healthy P. monodon tested from Vietnam and 39 of 40 P. monodon collected from slow-growth ponds in Thailand. A survey of 81 P. monodon collected in 2007 from Andhra Pradesh, India, indicated 56.8% prevalence of LSNV infection but no clear association with disease or slow growth. Phylogenetic analysis of PCR amplicons obtained from samples from India, Vietnam, Malaysia and Thailand indicated that nucleotide sequence variation was very low (>98% identity) and there was no clustering of viruses according to site of isolation or the health status of the shrimp. The data suggests that LSNV exists as a single genetic lineage and occurs commonly in healthy P. monodon in parts of Asia.
    Matched MeSH terms: RNA Viruses/genetics*
  14. Reducing the overwintering ability of Aedes albopictus by male release
    Hanson SM, Mutebi JP, Craig GB, Novak RJ
    J Am Mosq Control Assoc, 1993 Mar;9(1):78-83.
    PMID: 8468578
    Eggs of temperate Aedes albopictus populations are cold hardy and can diapause, but tropical populations are not cold hardy and cannot diapause. Heterozygotes possess intermediate diapause and cold hardiness. Males of a tropical strain from Malaysia with a distinctive genetic marker were released into an existing temperate population in East St. Louis, Illinois. Subsequent egg samples from the release site had genetic marker frequency of up to 24%. Reduced cold hardiness and decreased diapause incidence were also observed in the release site population. No such changes occurred at a nearby control site. The rank order of overwintering survival of eggs at the release site was: Aedes triseriatus > temperate Ae. albopictus > hybrid temperate/tropical Ae. albopictus > tropical Ae. albopictus. Eggs collected from the release population the next summer showed total absence of the genetic marker; presumably carriers were removed by the winter.
    Matched MeSH terms: Aedes/genetics*
  15. Cytogenetic evidence for two species within the current concept of the malaria vector Anopheles leucosphyrus in Southeast Asia
    Baimai V, Harbach RE, Sukowati S
    J Am Mosq Control Assoc, 1988 Mar;4(1):44-50.
    PMID: 3193098
    Karyotypes and crossing relationships were investigated for three allopatric populations of Anopheles leucosphyrus in Southeast Asia: South Kalimantan, Sumatra and Thailand. The mitotic karyotypes of these populations were similar to those previously observed in other species of the An. leucosphyrus group. Populations from Thailand and South Kalimantan exhibited telocentric and subtelocentric sex chromosomes, respectively, with a distinctive band of intercalary heterochromatin in the X chromosome. Strikingly different submetacentric X and Y chromosomes were observed in the population from Sumatra, and it seems likely that the evolution of these chromosomes occurred through the acquisition of constitutive heterochromatin. Sterile F1 males were observed in crosses between the Sumatra population and the populations from South Kalimantan and Thailand. No genetic incompatibility was observed in crosses between the latter two populations. We believe that the present concept of An. leucosphyrus includes two allopatric species, one inhabiting Borneo, West Malaysia and southern Thailand and one confined to Sumatra.
    Matched MeSH terms: Anopheles/genetics*
  16. Interspecific Cross-Mating Between Aedes aegypti and Aedes albopictus Laboratory Strains: Implication of Population Density on Mating Behaviors
    Marcela P, Hassan AA, Hamdan A, Dieng H, Kumara TK
    J Am Mosq Control Assoc, 2015 Dec;31(4):313-20.
    PMID: 26675452 DOI: 10.2987/moco-31-04-313-320.1
    Mating behavior between Aedes aegypti and Ae. albopictus, established colony strains were examined under laboratory conditions (30-cm(3) screened cages) for 5 consecutive days. The effect of selected male densities (30, 20, 10) and female density (20) on the number of swarming, mating pairs, eggs produced, and inseminated females were evaluated. Male densities significantly increased swarming behavior, mating pairs, and egg production of heterospecific females, but female insemination was reduced. Aedes aegypti males mate more readily with heterospecific females than do Ae. albopictus males. The current study suggests that Ae. aegypti males were not species-specific in mating, and if released into the field as practiced in genetically modified mosquito techniques, they may mate with both Ae. aegypti and Ae. albopictus females, hence reducing populations of both species by producing infertile eggs.
    Matched MeSH terms: Aedes/genetics
  17. Fulltext Whole gene transcriptomic analysis of PCB/biphenyl degrading Rhodococcus jostii RHA1
    Sha'arani S, Hara H, Araie H, Suzuki I, Mohd Noor MJM, Akhir FNM, et al.
    J Gen Appl Microbiol, 2019 Sep 14;65(4):173-179.
    PMID: 30686798 DOI: 10.2323/jgam.2018.08.003
    This study gives the first picture of whole RNA-Sequencing analysis of a PCB-degrading microbe, Rhodococcus jostii RHA1. Genes that were highly expressed in biphenyl-grown cells, compared with pyruvate-grown cells, were chosen based on the Reads Per Kilobase Million (RPKM) value and were summarized based on the criteria of RPKM ≥100 and fold change ≥2.0. Consequently, 266 total genes were identified as genes expressed particularly for the degradation of biphenyl. After comparison with previous microarray data that identified highly-expressed genes, based on a fold change ≥2.0 and p-value ≤0.05, 62 highly-expressed genes from biphenyl-grown cells were determined from both analytical platforms. As these 62 genes involve known PCB degradation genes, such as bph, etb, and ebd, the genes identified in this study can be considered as essential genes for PCB/biphenyl degradation. In the 62 genes, eleven genes encoding hypothetical proteins were highly expressed in the biphenyl-grown cells. Meanwhile, we identified several highly-expressed unannotated DNA regions on the opposite strand. In order to verify the encoded proteins, two regions were cloned into an expression vector. A protein was successfully obtained from one region at approximately 25 kDa from the unannotated strand. Thus, the genome sequence with transcriptomic analysis gives new insight, considering re-annotation of the genome of R. jostii RHA1, and provides a clearer picture of PCB/biphenyl degradation in this strain.
    Matched MeSH terms: Rhodococcus/genetics*
  18. Fulltext No Interaction Effect between Interleukin-6 Polymorphisms and Acid Ash Diet with Bone Resorption Marker in Postmenopausal Women
    Lim SY, Chan YM, Ramachandran V, Shariff ZM, Chin YS, Arumugam M
    Int J Environ Res Public Health, 2021 Jan 19;18(2).
    PMID: 33478001 DOI: 10.3390/ijerph18020827
    BACKGROUND: Evidence is growing that a high-acid diet might accelerate the rate of bone loss, and gene polymorphisms such as Interleukin 6 (IL6) -174G/C and -572G/C are related to bone deterioration. However, no study of the interaction between diet and IL6 polymorphisms has been conducted among Asians. Thus, the objective of this study was to determine whether IL6 gene polymorphisms modified the association between dietary acidity and the rate of bone resorption.

    METHODS: This cross-sectional study recruited 203 postmenopausal women (age ranged from 51 to 85 years old) in community settings. The dietary intakes of the participants were assessed using a validated interviewer-administered semi-quantitative food frequency questionnaire (FFQ), while dietary acid load (DAL) was estimated using net endogenous acid production (NEAP). Agena® MassARRAY genotyping analysis and serum collagen type 1 cross-linked C-telopeptide (CTX1) were used to identify the IL6 genotype and as a bone resorption marker, respectively. The interactions between diet and single-nucleotide polymorphisms (SNPs) were assessed using linear regressions.

    RESULTS: A total of 203 healthy postmenopausal women aged between 51 and 85 years participated in this study. The mean BMI of the participants was 24.3 kg/m2. In IL6 -174 G/C, all the participants carried the GG genotype, while the C allele was absent. Approximately 40% of the participants had a high dietary acid load. Dietary acid load (B = 0.15, p = 0.031) and the IL6 -572 CC genotype group (B = 0.14, p = 0.044) were positively associated with a higher bone resorption. However, there was no moderating effect of the IL6 genetic polymorphism on the relationship between and acid ash diet and bone resorption markers among the postmenopausal women (p = 0.79).

    CONCLUSION: High consumption of an acid ash diet and the IL6 -572 C allele seem to attribute to high bone resorption among postmenopausal women. However, our finding does not support the interaction effect of dietary acidity and IL6 (-174G/C and -572G/C) polymorphisms on the rate of bone resorption. Taken together, these results have given scientific research other candidate genes to focus on which may interact with DAL on bone resorption, to enhance planning for preventing or delaying the onset of osteoporosis among postmenopausal women.

    Matched MeSH terms: Interleukin-6/genetics
  19. Fulltext Major QTLs for Trunk Height and Correlated Agronomic Traits Provide Insights into Multiple Trait Integration in Oil Palm Breeding
    Teh CK, Ong AL, Mayes S, Massawe F, Appleton DR
    Genes (Basel), 2020 07 21;11(7).
    PMID: 32708151 DOI: 10.3390/genes11070826
    Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12-20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000-1500 seedling per cross, this low frequency could be easily compensated for during breeding selection.
    Matched MeSH terms: Arecaceae/genetics*
  20. Golden SusPtrit: a genetically well transformable barley line for studies on the resistance to rust fungi
    Yeo FK, Hensel G, Vozábová T, Martin-Sanz A, Marcel TC, Kumlehn J, et al.
    Theor Appl Genet, 2014 Feb;127(2):325-37.
    PMID: 24247233 DOI: 10.1007/s00122-013-2221-7
    KEY MESSAGE: We developed 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. Nonhost and partial resistance to Puccinia rust fungi in barley are polygenically inherited. These types of resistance are principally prehaustorial, show high diversity between accessions of the plant species and are genetically associated. To study nonhost and partial resistance, as well as their association, candidate gene(s) for resistance must be cloned and tested in susceptible material where SusPtrit would be the line of choice. Unfortunately, SusPtrit is not amenable to Agrobacterium-mediated transformation. Therefore, a doubled haploid (DH) mapping population (n = 122) was created by crossing SusPtrit with Golden Promise to develop a 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. We identified nine genomic regions occupied by resistance quantitative trait loci (QTLs) against four non-adapted rust fungi and P. hordei isolate 1.2.1 (Ph.1.2.1). Four DHs were selected for an Agrobacterium-mediated transformation efficiency test. They were among the 12 DH lines most susceptible to the tested non-adapted rust fungi. The most efficiently transformed DH line was SG062N (11-17 transformants per 100 immature embryos). The level of non-adapted rust infection on SG062N is either similar to or higher than the level of infection on SusPtrit. Against Ph.1.2.1, the latency period conferred by SG062N is as short as that conferred by SusPtrit. SG062N, designated 'Golden SusPtrit', will be a valuable experimental line that could replace SusPtrit in nonhost and partial resistance studies, especially for stable transformation using candidate genes that may be involved in rust-resistance mechanisms.
    Matched MeSH terms: Hordeum/genetics*
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