Publications by authors named "Nguyen Ngoc Lan"

60 Publications

Biliary atresia combined Wilson disease identified by whole exome sequencing in Vietnamese patient with severe liver failure.

Medicine (Baltimore) 2022 Jan;101(2):e28547

Institute of Genome Research, Vietnam Academy of Science and Technology, 18 - Hoang Quoc Viet Str., Caugiay, Hanoi, Vietnam.

Rationale: Hepatobiliary diseases such as biliary atresia (BA), Wilson disease, and progressive familial intrahepatic cholestasis are common causes of morbidity and mortality in young children. Affected patients progress rapidly to end-stage cirrhosis and require liver transplantation or die. Mutations in many genes have been identified to play an important role in the pathogenesis of hepatobiliary diseases.

Patient Concerns And Diagnosis: In this study, we identified mutations in an 8-year-old girl who had severe liver failure. The patient was first diagnosed with BA at 2.5 months of age and has undergone Kasai surgery to connect the umbilical cord and jejunum. After that, the patient suddenly had unusual developments with symptoms of jaundice, acute liver failure with hemolysis. She was tested and diagnosed with Wilson disease.

Interventions And Outcomes: She was treated according to the regimen for a patient with Wilson disease but had abnormal progress leading to severe liver failure. Genetic analysis was performed by whole exome sequencing and Sanger sequencing methods. The genetic analysis revealed that the patient had a homozygous mutation (p.Gly17Glyfs77∗) in the KRT18 gene, a double heterozygous mutation (p.Ser105∗ and p.Pro992Leu) in the ATP7B gene, and a homozygous variant (p.Val444Ala) in the ABCB11 gene. In silico prediction of mutations indicated that these mutations are the cause of the severe liver failure in the patient.

Lesson: This is a rare clinical case of a BA patient combined with Wilson disease. Our results suggested that whole exome sequencing is an effective diagnostic tool and emphasizes the importance of early diagnosis and appropriate management to save lives and prevent serious complications in the patient.
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http://dx.doi.org/10.1097/MD.0000000000028547DOI Listing
January 2022

The role of p.Val444Ala variant in the ABCB11 gene and susceptibility to biliary atresia in Vietnamese patients.

Medicine (Baltimore) 2021 Nov;100(47):e28011

Institute of Genome Research, Vietnam Academy of Science and Technology, Vietnam.

Abstract: Biliary atresia (BA) is the most serious type of obstructive cholangiopathy that occurs in infants. BA can be the cause of death in children under 2 years if untreated early. However, the etiology of the disease is not known. BA is considered to be the result of the destruction of the bile duct system including the accumulation of bile acids. The bile salt export pump, a transporter protein encoded by the ABCB11 gene, plays the main role in the exportation and accumulation of bile acids. The p.Val444Ala variant in this gene is known to be associated with many cholestatic diseases. However, to date no study have been performed to evaluate the association of this variant with susceptibility to the risk of BA. In this study, we aimed to identify the frequency of p.Val444Ala variant and the risk of BA in Vietnamese patients.The polymerase chain reaction (PCR)- restriction fragment length polymorphism method was used to determine the frequency of alleles c.1331T>C (p.Val444Ala, rs2287622) in the ABCB11 gene in 266 Vietnamese patients with BA and 150 healthy people. The gene segment containing the variant was amplified by PCR with specific primers, after that the PCR products were cut by HaeIII restriction enzyme and analyzed on agarose gel to determine the genotypes. The frequency of alleles was assessed statistically to determine the association between these alleles and the risk of disease in patients.In our study, the frequency of alleles c.1331T>C (p.Val444Ala, rs2287622) in the ABCB11 gene was investigated the first time in the patients with BA. The results showed that CC and TC genotypes were significantly different between BA patients and healthy people (P < .01), and the C allele was associated with an increased risk of BA (odds ratio = 2.47; 95% confidence interval: 1.84-3.32; P < .01). The initial results of clinical, biochemical, and genetic analysis in our study suggested that the p.Val444Ala variant in the ABCB11 gene may be a susceptibility factor for the disease in Vietnamese patients with BA. These results provided new insights into the role of this ABCB11 variant in the pathogenesis of BA.
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http://dx.doi.org/10.1097/MD.0000000000028011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8615439PMC
November 2021

Molecular Genetics, Clinical Characteristics, and Treatment Outcomes of K-Channel Neonatal Diabetes Mellitus in Vietnam National Children's Hospital.

Front Endocrinol (Lausanne) 2021 9;12:727083. Epub 2021 Sep 9.

Department of Endocrinology, Metabolism and Genetics, Vietnam National Children's Hospital, Hanoi, Vietnam.

Background: Neonatal diabetes mellitus (NDM) is defined as insulin-requiring persistent hyperglycemia occurring within the first 6 months of life, which can result from mutations in at least 25 different genes. Activating heterozygous mutations in genes encoding either of the subunits of the ATP-sensitive K channel (K channel; or ) of the pancreatic beta cell are the most common cause of permanent NDM and the second most common cause of transient NDM. Patients with NDM caused by K channel mutations are sensitive to sulfonylurea (SU) treatment; therefore, their clinical management can be improved by replacing insulin with oral agents.

Patients And Methods: Seventy patients were diagnosed with NDM between May 2008 and May 2021 at Vietnam National Children's Hospital, and molecular genetic testing for all genes known to cause NDM was performed at the Exeter Genomic Laboratory, UK. Patients with or mutations were transferred from insulin to oral SU. Clinical characteristics, molecular genetics, and annual data relating to glycemic control, SU dose, severe hypoglycemia, and side effects were collected. The main outcomes of interest were SU dose, SU failure (defined as permanent reintroduction of daily insulin), and glycemic control (HbA1c).

Results: Fifty-four of 70 patients (77%) with NDM harbored a genetic mutation and of these; 27 (50%) had activating heterozygous mutations in or . A total of 21 pathogenic mutations were identified in the 27 patients, including 13 mutations in and 8 mutations in . Overall, 51% had low birth weight (below 3rd percentile), 23 (85%) were diagnosed before 3 months of age, and 23 (85%) presented with diabetic ketoacidosis. At diagnosis, clinical and biochemical findings (mean ± SD) were pH 7.16 ± 0.16; , 7.9 ± 7.4 mmol/L; BE, -17.9 ± 9.1 mmol/L; HbA1C, 7.98% ± 2.93%; blood glucose, 36.2 ± 12.3 mmol/L; and C-peptide median, 0.09 (range, 0-1.61 nmol/l). Twenty-six patients were successfully transferred from insulin to SU therapy. In the remaining case, remission of diabetes occurred prior to transfer. Glycemic control on SU treatment was better than on insulin treatment: HbA1c and blood glucose level decreased from 7.58% ± 4.63% and 19.04 ± 14.09 mmol/L when treated with insulin to 5.8 ± 0.94% and 6.87 ± 3.46 mmol/L when treated with SU, respectively.

Conclusions: This is the first case series of NDM patients with mutations reported in Vietnam. SU is safe in the short term for these patients and more effective than insulin therapy, consistent with all studies to date. This is relevant for populations where access to and cost of insulin are problematic, reinforcing the importance of genetic testing for NDM.
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http://dx.doi.org/10.3389/fendo.2021.727083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8458931PMC
September 2021

Polymorphism of Gene in Vietnamese Gastric Cancer Patients: A Multicenter Case-Control Study.

Front Oncol 2021 31;11:694977. Epub 2021 Aug 31.

Biochemistry Department, Hanoi Medical University, Hanoi, Vietnam.

Background: A few studies revealed that the polymorphisms of gene have a role and significance as a susceptible factor contributing to gastric cancer. To better understand the roles of two genotype polymorphisms of rs4072037 and rs2070803 in the development of gastric cancer in Vietnamese population, a multicenter, large-sample, case-control study was conducted to investigate the potential association of these single-nucleotide polymorphisms (SNPs) of gene with gastric cancer risk and to evaluate the combination factors in relation with these SNPs.

Methods: This case-control study included 302 gastric cancer patients and 304 controls at four national medical hospitals between 2016 and 2018. All participants were interviewed for sociodemographic characteristics, smoking and drinking status, and personal and family history of gastric diseases. Genotyping was done using polymerase chain reaction-restriction fragment length polymorphism analysis. The association of SNPs with gastric cancer was explored using logistic regression models.

Results: AA genotype for rs4072037 was significantly associated with increased gastric cancer. Those with AA genotype had higher gastric cancer risk than had patients with AG (OR: 2.09, 95% CI: 1.48-2.96) and a combination of AG+GG (OR: 1.85, 95% CI: 1.33-2.56). In rs2070803, GG genotype increased gastric cancer risk when compared with AG (OR: 1.97, 95% CI: 1.39-2.80) and AG+AA (OR: 1.71, 95% CI: 1.23-2.39). AG genotypes in both SNPs decreased gastric cancer risk when compared with homogenous genotype, more specifically AA (OR: 0.51, 95% CI: 0.35-0.72) and GG (OR: 0.58, 95% CI: 0.35-0.97). These genotypes in combination with above-60-year-old age, male gender, alcoholism, and personal history of gastric disease were also significantly elevated risk factors for gastric cancer.

Conclusions: rs4072037 and rs2070803 of genes are two genotypic risk factors for gastric cancer. Those in combination with gender, family history, smoking, and drinking habits significantly increase the risk of gastric cancer.
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http://dx.doi.org/10.3389/fonc.2021.694977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439541PMC
August 2021

Anti-inflammatory norclerodane diterpenoids and tetrahydrophenanthrene from the leaves and stems of Dioscorea bulbifera.

Fitoterapia 2021 Sep 12;153:104965. Epub 2021 Jun 12.

Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Viet Nam. Electronic address:

Chemical investigation of the leaves and stems of Dioscorea bulbifera resulted in isolation of 10 compounds, including three new norclerodane diterpenoids, diosbulbiferins A (1) and B (2) and diosbulbiferinoside A (3), and one new natural congener, diosbulbiferin C (4), along with one new tetrahydrophenanthrene, diosbulbinone (8). Their structures were elucidated by comprehensive analyses of spectroscopic methods, including NMR and mass spectra. The absolute configurations of compounds 1-3 and 8 were deduced by time-dependent density functional theory (TD-DFT) electronic circular dichroism (ECD) spectroscopic analyses. In addition, cytotoxic effects against MCF-7, HepG2, and SK-Mel-2 cancer cells and in vitro anti-inflammatory effects of the isolated compounds in LPS-stimulated BV2 microglial cells were also reported.
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http://dx.doi.org/10.1016/j.fitote.2021.104965DOI Listing
September 2021

Identification of three novel mutations in PCNT in vietnamese patients with microcephalic osteodysplastic primordial dwarfism type II.

Genes Genomics 2021 02 18;43(2):115-121. Epub 2021 Jan 18.

Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.

Background: Primordial dwarfism (PD) is a group of genetically heterogeneous disorders related to developmental disabilities occurring in the uterus and prolongs during all stages of life, resulting in short stature, facial deformities and abnormal brain.

Objective: To determine the exact cause of the disease in two Vietnamese patients priory diagnosed with PD by severe pre-and postnatal growth retardation with marked microcephaly and some bone abnormalities.

Methods: Whole-exome sequencing was performed for the two patients and mutations in genes related to PD were screened. Sanger sequencing was applied to examine the mutations in the patients of their families.

Results: Three novel mutations in the PCNT gene which have not been reported previously were identified in the two patients. Of which, two frameshift mutations (p.Thr479Profs*6 and p.Glu2742Alafs*8) were detected in patient I and one stop-gained mutation (p.Gln1907*) was detected in the patient II. These mutations may result in a truncated PCNT protein, leading to an inactivated PACT domain corresponding to residue His3138-Trp3216 of PCNT protein. Therefore, the three mutations may cause a deficiency of protein functional activity and result in the phenotypes of primordial dwarfism in the two patients.

Conclusions: Clinical presentations in combination with genetic analyses supported an accurate diagnosis of the two patients with microcephalic osteodysplastic primordial dwarfism type II (MOPD II). In addition, these results have important implications for prenatal genetic screening and genetic counseling for the families.
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http://dx.doi.org/10.1007/s13258-020-01032-5DOI Listing
February 2021

Dynamics and Environmental Characteristics of Spin Labels in a KvAP Voltage Sensor by Molecular Dynamics Simulations.

J Phys Chem B 2021 01 18;125(3):748-756. Epub 2021 Jan 18.

Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.

The nitroxide spin label is the most widely used probe for electron paramagnetic resonance (EPR) spectroscopy studies of the structure and function of biomolecules. However, the role of surrounding environments in determining the dynamics of nitroxide spin labels in biological complex systems remains to be clarified. This study aims to characterize the dynamics and environmental structure of spin labels in the voltage-sensing domain (VSD) of a KvAP potassium channel by means of molecular dynamics (MD) studies. MD simulations for unlabeled and 132 spin-labeled KvAP-VSD models (spin labels introduced at positions 20-151) were carried out in a phospholipid bilayer to evaluate conformational dynamics of nitroxide spin-label side chains in the VSD. Structural flexibility, conformational freedom, and orientation of the spin-label side chains were investigated in relation to their dynamics in different microenvironments. The analysis of MD data showed that the attached spin-label probe did not severely perturb the protein dynamics. The conformational freedoms of the nitroxide side chain vary with the physical structure of the surrounding environments. The two terminal dihedral angles of the nitroxide side chain tend to cluster and adopt several preferred rotameric states. From the nearest-neighbor analysis, the spin label can be exposed to either a homogeneous or heterogeneous environment with various exposure scenarios. The dynamical movement of KvAP-VSD is high at a water-exposed site, moderate in the membrane, and low in the protein core. Understanding the structure and dynamics behaviors of spin labels helps to manage the experimental uncertainty and avoid misleading interpretation in relation to the protein structure.
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http://dx.doi.org/10.1021/acs.jpcb.0c08993DOI Listing
January 2021

Characterization of a thermophilic cytochrome P450 of the CYP203A subfamily from Binh Chau hot spring in Vietnam.

FEBS Open Bio 2021 01 30;11(1):124-132. Epub 2020 Nov 30.

Department of Biochemistry, Saarland University, Saarbrucken, Germany.

Cytochromes P450 (CYPs or P450s) comprise a superfamily of heme-containing monooxygenases that are involved in a variety of biological processes. CYPs have broad utilities in industry, but most exhibit low thermostability, limiting their use on an industrial scale. Highly thermostable enzymes can be obtained from thermophiles in geothermal areas, including hot springs, offshore oil-producing wells and volcanoes. Here, we report the identification of a gene encoding for a thermophilic CYP from the Binh Chau hot spring metagenomic database, which was designated as P450-T2. The deduced amino acid sequence showed the highest identity of 73.15% with CYP203A1 of Rhodopseudomonas palustris, supporting that P450-T2 is a member of the CYP203A subfamily. Recombinant protein expression yielded 541 nm. The optimal temperature and pH of P450-T2 were 50 °C and 8.0, respectively. The half-life of P450-T2 was 50.2 min at 50 °C, and its melting temperature was 56.80 ± 0.08 °C. It was found to accept electrons from all tested redox partners systems, with BmCPR-Fdx2 being the most effective partner. Screening for putative substrates revealed binding of phenolic compounds, such as l-mimosine and emodin, suggesting a potential application of this new thermophilic P450 in the production of the corresponding hydroxylated products.
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http://dx.doi.org/10.1002/2211-5463.13033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7780096PMC
January 2021

Whole Exome Sequencing as a Diagnostic Tool for Unidentified Muscular Dystrophy in a Vietnamese Family.

Diagnostics (Basel) 2020 Sep 24;10(10). Epub 2020 Sep 24.

Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam.

Muscular dystrophies are a group of heterogeneous clinical and genetic disorders. Two siblings presented with characteristics like muscular dystrophy, abnormal white matter, and elevated serum creatine kinase level. The high throughput of whole exome sequencing (WES) makes it an efficient tool for obtaining a precise diagnosis without the need for immunohistochemistry. WES was performed in the two siblings and their parents, followed by prioritization of variants and validation by Sanger sequencing. Very rare variants with moderate to high predicted impact in genes associated with neuromuscular disorders were selected. We identified two pathogenic missense variants, c.778C>T (p.H260Y) and c.2987G>A (p.C996Y), in the gene (NM_000426.3), in the homozygous state in two siblings, and in the heterozygous state in their unaffected parents, which were confirmed by Sanger sequencing. Variant c.2987G>A has not been reported previously. These variants may lead to a change in the structure and function of laminin-α2, a member of the family of laminin-211, which is an extracellular matrix protein that functions to stabilize the basement membrane of muscle fibers during contractions. Overall, WES enabled an accurate diagnosis of both patients with -related muscular dystrophy and expanded the spectrum of missense variants in .
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http://dx.doi.org/10.3390/diagnostics10100741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598670PMC
September 2020

Late-Onset Ornithine Transcarbamylase Deficiency and Variable Phenotypes in Vietnamese Females With Mutations.

Front Pediatr 2020 23;8:321. Epub 2020 Jul 23.

Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.

Ornithine transcarbamylase deficiency (OTCD) is an X- linked recessive disorder and the most common error of the urea cycle, caused by the mutations in the gene. Due to X-inactivation, 15-20% of female carriers present symptoms of OTCD at late onset. Early diagnosis of OTCD by molecular analysis in females is highly desirable. The aim of the study was to identify the mutations in two unrelated Vietnamese girls suspected with OTCD and the carriers in their families for definitive diagnosis and proper counseling. Two patients presented with an acute encephalopathy at the first admission. Biochemical tests revealed hyperammonemia, hyperlactatemia, elevated glutamine level, elevated transaminase, elevated urinary orotic and uracil acid levels, and disorder of prothrombin time. Brain magnetic resonance imaging indicated cerebral edema. Based on the clinical and laboratory results, the two patients were diagnosed with urea cycle disorders. Therefore, the two patients were managed by stopping feeding, with infused glucose, l-carnitine, l-arginine, and sodium benzoate, and with hemofiltration. The two patients were alert and recovered with normal blood ammonia levels after 72 h of treatment. The family history of patient 1 showed that her brother died at 4 days of age due to a coma and dyspnea, while her parents were asymptomatic. Variable phenotypes were observed in three generations of the patient 2's family, including asymptomatic (mother), affected female adults dying at the first symptom (grandmother and aunt), and affected males dying in the first week of life (uncle, cousin, and siblings). Whole-exome sequencing showed two mutations in the gene, including one novel missense mutation, c.365A>T, in the patient 1 and one previously reported splicing mutation, c.717+1G>A, in the patient 2. The two mutations are evaluated as likely pathogenic and pathogenic, respectively, according to the recommendations of the American College of Medical Genetics and Genomics (ACMG). Genetic analyses in the families indicated the mothers were heterozygous. Clinical, biochemical, and molecular findings accurately diagnosed the two patients with late-onset OTCD. Our results explained the genetic causes and proposed the risk in the patients' families, which could be useful for genetic counseling and monitoring in prenatal diagnosis.
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http://dx.doi.org/10.3389/fped.2020.00321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7390877PMC
July 2020

Cost-Effective Approaches Based on Machine Learning to Predict Dynamic Modulus of Warm Mix Asphalt with High Reclaimed Asphalt Pavement.

Materials (Basel) 2020 Jul 23;13(15). Epub 2020 Jul 23.

Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam.

Warm mix asphalt (WMA) technology, taking advantage of reclaimed asphalt pavements, has gained increasing attention from the scientific community. The determination of technical specifications of such a type of asphalt concrete is crucial for pavement design, in which the asphalt concrete dynamic modulus (E*) of elasticity is amongst the most critical parameters. However, the latter could only be determined by complicated, costly, and time-consuming experiments. This paper presents an alternative cost-effective approach to determine the dynamic elastic modulus (E*) of WMA based on various machine learning-based algorithms, namely the artificial neural network (ANN), support vector machine (SVM), Gaussian process regression (GPR), and ensemble boosted trees (Boosted). For this, a total of 300 samples were fabricated by warm mix asphalt technology. The mixtures were prepared with 0%, 20%, 30%, 40%, and 50% content of reclaimed asphalt pavement (RAP) and modified bitumen binder using Sasobit and Zycotherm additives. The dynamic elastic modulus tests were conducted by varying the temperature from 10 °C to 50 °C at different frequencies from 0.1 Hz to 25 Hz. Various common quantitative indications, such as root mean square error (RMSE), mean absolute error (MAE), and correlation coefficient (R) were used to validate and compare the prediction capability of different models. The results showed that machine learning models could accurately predict the dynamic elastic modulus of WMA using up to 50% RAP and fabricated by warm mix asphalt technology. Out of these models, the Boosted algorithm (R = 0.9956) was found as the best predictor compared with those obtained by ANN-LMN (R = 0.9954), SVM (R = 0.9654), and GPR (R= 0.9865). Thus, it could be concluded that Boosted is a promising cost-effective tool for the prediction of the dynamic elastic modulus (E*) of WMA. This study might help in reducing the cost of laboratory experiments for the determination of the dynamic modulus (E*).
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http://dx.doi.org/10.3390/ma13153272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7436179PMC
July 2020

A novel frameshift PHKA2 mutation in a family with glycogen storage disease type IXa: A first report in Vietnam and review of literature.

Clin Chim Acta 2020 Sep 7;508:9-15. Epub 2020 May 7.

Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Viet Nam; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Viet Nam. Electronic address:

Background: Glycogen storage diseases (GSDs) are clinically and genetically heterogeneous disorders. Overlapping features between liver GSDs are a major challenge in the clinical diagnosis of them. Genetic testing can provide an early and accurate diagnosis of patients suspected with GSDs.

Case Presentation: In this study, we report two siblings born to healthy, non-consanguineous Vietnamese parents with hepatomegaly. The proband presented with hepatomegaly, normal spleen, elevated transaminases, without hypoglycemia, normal lactate dehydrogenase and creatine kinase. Liver biopsy revealed degeneration and swollen hepatocytes, suggesting a diagnosis with GSDs.

Methods: Whole exome sequencing was applied to identify genetic variants in the proband. Variant validation and familial co-segregation analysis were examined using Sanger sequencing.

Results: A novel frameshift duplication mutation c.3308_3312dupATGTC (p.L1105Mfs*11) of the PHKA2 gene was identified in the proband and his elder brother at the hemizygous state. This mutation was inherited from their mother. Their father and younger brother were normal genotype.

Conclusions: The two siblings were accurately diagnosed with GSD type XIa. This is the first case report of GSD type IXa in Vietnamese patients with a mutation in the PHKA2 gene. This finding may support for genetics diagnosis of unknown cause of hepatomegaly.
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http://dx.doi.org/10.1016/j.cca.2020.05.010DOI Listing
September 2020

De novo Mutations in Vietnamese Patients with Cornelia de Lange Syndrome.

Medicina (Kaunas) 2020 Feb 14;56(2). Epub 2020 Feb 14.

Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam.

Cornelia de Lange Syndrome (CdLS) is a rare congenital genetic disease causing abnormal unique facial phenotypes, several defects in organs and body parts, and mental disorder or intellectual disorder traits. Main causes of CdLS have been reported as variants in cohesin complex genes, in which mutations in the gene have been estimated to account for up to 80%. Our study included three Vietnamese patients with typical CdLS phenotypes. Whole exome sequencing revealed two known heterozygous mutations c.6697G>A (p.Val2233Met) and c.2602C>T (p.Arg868X), and a novel heterozygous mutation c.4504delG (p.Val1502fsX87) in the gene of the three patients. In silico analyses of the identified mutations predicted possible damaging and truncating effects on the NIPBL protein. Inherited analyses in the patients' families showed that all of the mutations are de novo. Our results lead a definitive diagnosis of patients with CdLS and expand the spectrum of mutations in the gene. These findings also confirm whole exome sequencing is an efficient tool for genetic screening of CdLS.
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http://dx.doi.org/10.3390/medicina56020076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073647PMC
February 2020

A Novel Nonsense Mutation c.374C>G in CYP21A2 Gene of a Vietnamese Patient with Congenital Adrenal Hyperplasia.

Adv Exp Med Biol 2020 ;1292:27-35

Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam.

Inactivating mutations of the CYP21A2 gene, encoding for steroid synthesis, have been reported in patients with congenital adrenal hyperplasia (CAH). We report a case of an infant who were diagnosed with CAH and presented with the severe phenotype of CAH with symptoms such as increased testicular volume, elevated of 17-hydroxyprogesteron, testosterone and progesterone. In this study, we established an assay for the detection of unusual genetic in the CYP21A2 gene in the proband and his family. A novel nonsense mutation c.374C > G which caused a substitutions of Serine for a stop codon at codon 125 (p.S125) within exon 3 was found in the proband. Parental genotype studies confirmed carrier state in the father, but the mother showed a wild allele by PCR and sequencing. This inspired us to find deletions using multiplex ligation-dependent probe amplification (MLPA) technique. The probands were found to have a large deletion in exons 1 and 3, while the mother only had deletion in exon 1. Therefore, mutation c.374C > G (p.S125) in the proband is considered as a heterozygous deletion. This mutation caused a truncated protein which lead to the salt wasting CAH phenotype of the proband. This novel nonsense mutation expands the CYP21A2 mutation spectrum in CAH disorder. This case also highlights the need of caution when interpreting results of molecular genetic testing during genetic counseling.
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http://dx.doi.org/10.1007/5584_2018_300DOI Listing
January 2021

Transcriptome Sequencing and Analysis of Changes Associated with Insecticide Resistance in the Dengue Mosquito () in Vietnam.

Am J Trop Med Hyg 2019 05;100(5):1240-1248

National Institute of Malariology Parasitology and Entomology, Hanoi, Vietnam.

The mosquito is a transmission vector for dangerous epidemic diseases in humans. Insecticides have been used as the most general vector control method in the world. However, have developed many resistant mechanisms such as reduced neuronal sensitivity to insecticides (target-site resistance), enhanced insecticide metabolism (metabolic resistance), altered transport, sequestration, and other mechanisms. It has become a major problem for vector control programs. Transcriptome sequencing and bioinformatic analysis were used to compare transcription levels between a susceptible strain (Bora7) and a resistant strain (KhanhHoa7) collected from the field. A total of 161 million Illumina reads, including 66,076,678 reads from the Bora7 strain and 69,606,654 reads from the KhanhHoa7 strain, were generated and assembled into 11,174 genes. A comparison of the KhanhHoa7 transcriptome to that of Bora7 showed 672 upregulated genes and 488 downregulated genes. We identified the highly upregulated genes: cytochrome P450 , , , , isoform X2, , isoform X2, , , , , and ; Glutathione S transferase (GST1), UGT1-3, 1-7, 2B15, and 2B37; binding cassette transporter (ABC) transporter F family member 4 and ABC transporter G family member 20. Interestingly, there was a significant increase in the expression of the genes such as (8.3-fold), (5.9-fold), (5.4-fold), (5.4-fold), (5.2-fold), (3.5-fold), and ABC transporter 4 (2.1-fold). Our results suggested a potential relationship between the expression of the genes in metabolic processes and insecticide resistance in the studied strain. These results may contribute to the understanding of the mechanisms of insecticide resistance in .
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http://dx.doi.org/10.4269/ajtmh.18-0607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6493926PMC
May 2019

Isolation of Nontuberculous Mycobacteria in Southeast Asian and African Human Immunodeficiency Virus-infected Children With Suspected Tuberculosis.

Clin Infect Dis 2019 05;68(10):1750-1753

Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.

We enrolled 427 human immunodeficiency virus-infected children (median age, 7.3 years), 59.2% severely immunodeficient, with suspected tuberculosis in Southeast Asian and African settings. Nontuberculous mycobacteria were isolated in 46 children (10.8%); 45.7% of isolates were Mycobacterium avium complex. Southeast Asian origin, age 5-9 years, and severe immunodeficiency were independently associated with nontuberculous mycobacteria isolation.

Clinical Trials Registration: NCT01331811.
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http://dx.doi.org/10.1093/cid/ciy897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6495014PMC
May 2019

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam.

Nat Genet 2018 06 21;50(6):849-856. Epub 2018 May 21.

Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.

To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.
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http://dx.doi.org/10.1038/s41588-018-0117-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6143168PMC
June 2018

Bacterial risk factors for treatment failure and relapse among patients with isoniazid resistant tuberculosis.

BMC Infect Dis 2018 03 6;18(1):112. Epub 2018 Mar 6.

Oxford University Clinical Research Unit, 763 Vo Van Kiet, Ho Chi Minh City, Vietnam.

Background: Drug resistant tuberculosis (TB) is increasing in prevalence worldwide. Treatment failure and relapse is known to be high for patients with isoniazid resistant TB treated with standard first line regimens. However, risk factors for unfavourable outcomes and the optimal treatment regimen for isoniazid resistant TB are unknown. This cohort study was conducted when Vietnam used the eight month first line treatment regimen and examined risk factors for failure/relapse among patients with isoniazid resistant TB.

Methods: Between December 2008 and June 2011 2090 consecutive HIV-negative adults (≥18 years of age) with new smear positive pulmonary TB presenting at participating district TB units in Ho Chi Minh City were recruited. Participants with isoniazid resistant TB identified by Microscopic Observation Drug Susceptibility (MODS) had extended follow-up for 2 years with mycobacterial culture to test for relapse. MGIT drug susceptibility testing confirmed 239 participants with isoniazid resistant, rifampicin susceptible TB. Bacterial and demographic factors were analysed for association with treatment failure and relapse.

Results: Using only routine programmatic sputum smear microscopy for assessment, (months 2, 5 and 8) 30/239 (12.6%) had an unfavourable outcome by WHO criteria. Thirty-nine patients were additionally detected with unfavourable outcomes during 2 year follow up, giving a total of 69/239 (28.9%) of isoniazid (INH) resistant cases with unfavourable outcome by 2 years of follow-up. Beijing lineage was the only factor significantly associated with unfavourable outcome among INH-resistant TB cases during 2 years of follow-up. (adjusted OR = 3.16 [1.54-6.47], P = 0.002).

Conclusion: One third of isoniazid resistant TB cases suffered failure/relapse within 2 years under the old eight month regimen. Over half of these cases were not identified by standard WHO recommended treatment monitoring. Intensified research on early identification and optimal regimens for isoniazid resistant TB is needed. Infection with Beijing genotype of TB is a significant risk factor for bacterial persistence on treatment resulting in failure/relapse within 2 years. The underlying mechanism of increased tolerance for standard drug regimens in Beijing genotype strains remains unknown.
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http://dx.doi.org/10.1186/s12879-018-3033-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840777PMC
March 2018

Dramatic Influence of Ionic Liquid and Ultrasound Irradiation on the Electrophilic Sulfinylation of Aromatic Compounds by Sulfinic Esters.

Molecules 2017 Sep 4;22(9). Epub 2017 Sep 4.

Department of Organic Chemistry, VNUHCM-University of Science, 227 Nguyen Van Cu St., Dist. 5, 700000 Ho Chi Minh City, Vietnam.

The sulfinylation reaction of aromatic and hetero-aromatic compounds with sulfinic esters as electrophiles has been investigated in different ionic liquids and by means of different Lewis acid salts in order to get moderate to good yields of asymmetrical sulfoxides. Mixtures of 1-butyl-3-methylimidazolium chloride and aluminum chloride were found to be the most efficient and recyclable reaction framework. Ultrasound sonication appeared to be the most useful and green activation method to afford the sulfoxides in yields better than or equivalent to those obtained under the longer-lasting conventional stirring conditions.
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http://dx.doi.org/10.3390/molecules22091458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151476PMC
September 2017

Quadruple-first line drug resistance in Mycobacterium tuberculosis in Vietnam: What can we learn from genes?

Infect Genet Evol 2017 06 23;50:55-61. Epub 2017 Feb 23.

Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam.

In Vietnam, a country with high tuberculosis (137/100.000 population) and multidrug-resistant (MDR)-TB burdens (7.8/100.000 population), little is known about the molecular signatures of drug resistance in general and more particularly of second line drug (SLD) resistance. This study is specifically focused on Mycobacterium tuberculosis isolates resistant to four first-line drugs (FLDs) that make TB much more difficult to treat. The aim is to determine the proportion of SLD resistance in these quadruple drug resistant isolates and the genetic determinants linked to drug resistance to better understand the genetic processes leading to quadruple and extremely drug resistance (XDR). 91 quadruple (rifampicin, isoniazid, ethambutol and streptomycin) FLD resistant and 55 susceptible isolates were included. Spoligotyping and 24-locus MIRU-VNTR techniques were performed and 9 genes and promoters linked to FLD and SLD resistance were sequenced. SLD susceptibility testing was carried out on a subsample of isolates. High proportion of quadruple-FLD resistant isolates was resistant to fluoroquinolones (27%) and second-line injectable drugs (30.2%) by drug susceptibility testing. The sequencing revealed high mutation diversity with prevailing mutations at positions katG315, inhA-15, rpoB531, embB306, rrs1401, rpsL43 and gyrA94. The sensitivity and specificity were high for most drug resistances (>86%), but the sensitivity was lower for injectable drug resistances (<69%). The mutation patterns revealed 23.1% of pre-XDR and 7.7% of XDR isolates, mostly belonging to Beijing family. The genotypic diversity and the variety of mutations reflect the existence of various evolutionary paths leading to FLD and SLD resistance. Nevertheless, particular mutation patterns linked to high-level resistance and low fitness costs seem to be favored.
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http://dx.doi.org/10.1016/j.meegid.2017.02.012DOI Listing
June 2017

Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.

Int J Syst Evol Microbiol 2016 Dec 23;66(12):5320-5327. Epub 2016 Sep 23.

Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea.

Ginseng-cultivated soil is an excellent habitat for soil-borne bacteria to proliferate. A novel strain, DCY87T, was isolated from ginseng-cultivated soil in Gochang County, Republic of Korea, and subsequently characterized by polyphasic approach. Cells were rod shaped, non-motile, aerobic, Gram-reaction-positive, oxidase-negative and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY87T shared the highest similarity to 'Phycicoccus ochangensis' L1b-b9 (98.7 %). Closely phylogenetic relatives of strain DCY87T were identified: Phycicoccus ginsenosidimutans BXN5-13T (97.9 %), Phycicoccus soli THG-a14T (97.8 %), Phycicoccus bigeumensis MSL-03T (97.3 %), Phycicoccus cremeus V2M29T (97.3 %), Phycicoccus aerophilus 5516T-20T (97.3 %), Phycicoccus dokdonensis DS-8T (97.3 %) and Phycicoccus jejuensis KSW2-15T (97.1 %). The major polar lipids were classified as phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were composed of iso-C15 : 0, anteiso-C15:0, C17 : 0 and C17 : 1ω8c. The menaquinone was resolved as MK-8(H4). Strain DCY87T contained meso-diaminopimelic acid as diamino acid in the cell-wall peptidoglycan and glucose, xylose and rhamnose in the whole-cell sugar. The genomic DNA G+C content was calculated to be 72.7 mol%. DNA-DNA hybridization value between strain DCY87T and 'P. ochangensis' L1b-b9 was estimated to be 50 %. However, DNA-DNA hybridization value obtained between strain DCY87T and P. ginsenosidimutans BXN5-13T, P. soli THG-a14T and P. bigeumensis MSL-03T was well below 17 %. In general, polyphasic taxonomy demonstrated that DCY87T strain represented a novel species within the genus Phycicoccus. Accordingly, we propose the name Phycicoccus ginsengisoli sp. nov. The type strain is DCY87T (=KCTC 39635T=JCM 31016T).
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http://dx.doi.org/10.1099/ijsem.0.001515DOI Listing
December 2016

Mycobacterium tuberculosis lineages and anti-tuberculosis drug resistance in reference hospitals across Viet Nam.

BMC Microbiol 2016 07 28;16(1):167. Epub 2016 Jul 28.

MIVEGEC (IRD 224-CNRS 5290-Université de Montpellier), Centre IRD, Montpellier, France.

Background: Mycobacterium tuberculosis, the tuberculosis (TB) pathogen, despite a low level of genetic diversity, has revealed a high variety of biological and epidemiological characteristics linked to their lineages, such as transmissibility, fitness and propensity to acquire drug resistance. This has important implications for the epidemiology of TB. We conducted this first countrywide cross-sectional study to identify the prevalent M. tuberculosis lineages and to assess their epidemiological associations and their relation to drug resistance. The study was conducted among isolates acquired in reference hospitals across Vietnam. Isolates with drug susceptibility testing profiles were identified for their lineages by spoligotyping. Logistic regression was used to investigate the association of M. tuberculosis lineages with location, age and sex of the patients and drug resistance levels.

Results: Results showed that the most prevalent lineage was Beijing (55.4 %), followed by EAI (27.5 %), T (6.4 %), LAM (1.3 %), Haarlem (1 %) and Zero type (0.3 %). The proportion of Beijing isolates in the North (70.4 %) and the South (68 %) was higher than in the Centre (28 %) (OR = 1.7 [95 % CI: 1.4-2.0], p < 0.0001), whereas the proportion of EAI isolates in the North (7.1 %) and the South (17 %) was much lower compared with the Centre (59 %) (OR = 0.5 [95 % CI: 0.4-0.6], p < 0.0001). Overall, Beijing isolates were the most likely to be drug-resistant and EAI isolates were the least likely to be drug-resistant, except in the South of Vietnam where EAI is also highly drug-resistant. The proportion of Beijing isolates was significantly higher (p < 0.01), and the proportion of EAI isolates was significantly lower (p < 0.05) in younger patients. The proportion of drug-resistance was higher in isolates collected from male patients and from patients in the middle age groups.

Conclusions: The findings suggest ongoing replacement of EAI lineage, which is mainly more drug-susceptible with highly drug-resistant Beijing lineage in all studied regions of Vietnam. Male patients of working ages should be the focus for better control to prevent the emergence of drug-resistant TB.
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http://dx.doi.org/10.1186/s12866-016-0784-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4964266PMC
July 2016

Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.

Antonie Van Leeuwenhoek 2016 Sep 29;109(9):1199-208. Epub 2016 Jun 29.

Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea.

A novel bacterial strain, designated DCY106(T), was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY106(T) is Gram-negative, yellow-pigmented, non-flagellate, motile, non-spore-forming, rod-shaped, and strictly aerobic. The strain grows optimally at 25-30 °C and pH 6.5-7.5. Phylogenetically, strain DCY106(T) is closely related to Flavobacterium arsenitoxidans KCTC 22507(T) (98.41 %), followed by Flavobacterium cutihirudini LMG 26922(T) (97.67 %), Flavobacterium nitrogenifigens LMG 28694(T) (97.59 %), Flexibacter auranticus LMG 3987(T) (97.38 %), Flavobacterium defluvi KCTC 12612(T) (97.21 %) and Flavobacterium chilense LMG 26360(T) (97.05 %). The 16S rRNA gene sequence similarities to all other Flavobacterium species were below 97 %. The DNA G+C content of strain DCY106(T) is 34.2 mol% and the DNA-DNA relatedness between strain DCY106(T) and F. cutihirudini LMG 26922(T), F. auranticus LMG 3987(T), F. defluvi KCTC 12612(T) and F. chilense LMG 26360(T) were below 40.0 %. The menaquinone of the type MK-6 was found to be the predominant respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids (APL1, APL6) and one unidentified lipid L2. C15:0, iso-C15:0 and summed feature 3 (iso-C15:0 2OH/C16:1 ω7c) were identified as the major fatty acids present in DCY106(T). The results of physiological and biochemical tests allowed strain DCY106(T) to be differentiated phenotypically from other recognized species belonging to the genus Flavobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Flavobacterium panacis sp. nov. is proposed with the type strain designated as DCY106(T) (= JCM 31468(T)= KCTC 42747(T)).
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http://dx.doi.org/10.1007/s10482-016-0720-7DOI Listing
September 2016

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

PLoS One 2016 17;11(5):e0155055. Epub 2016 May 17.

Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea.

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155055PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871511PMC
July 2017

Flavobacterium panacisoli sp. nov., isolated from soil of a ginseng field.

Arch Microbiol 2016 Sep 27;198(7):645-51. Epub 2016 Apr 27.

Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University, 1 Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 449-701, Republic of Korea.

A novel bacterial strain, designated DCY70(T), was isolated from soil of a ginseng field in Republic of Korea and was characterized in order to determine its taxonomic position. The strain was Gram-reaction negative, yellow-pigmented, rod-shaped and catalase- and oxidase-positive. Based on the 16S rRNA gene sequence similarity, strain DCY70(T) was shown to belong to the genus Flavobacterium, most closely related to Flavobacterium oncorhynchi 631-08(T) (98.4 %), Flavobacterium plurextorum 1126-1H-08(T) (97.9 %), Flavobacterium chilense LM-09-Fp(T) (97.9 %) and Flavobacterium chungangense CJ(T) (97.7 %). The chemotaxonomic characteristics showed only menaquinone-6 (MK-6), iso-C15:0, iso-C15:0 3OH, iso-C17:0 3OH and summed feature 3 as major cellular fatty acids. Polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids, four unidentified polar lipids and one unidentified phospholipid. The DNA G+C content was 34.9 mol%. Based on the phylogenetic, phenotypic and genotypic data, a novel species, Flavobacterium panacisoli sp. nov., is proposed (=KCTC 32393(T) = JCM 19162(T)).
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http://dx.doi.org/10.1007/s00203-016-1216-6DOI Listing
September 2016

Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea.

Arch Microbiol 2016 Apr 31;198(3):211-7. Epub 2015 Dec 31.

Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea.

A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).
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http://dx.doi.org/10.1007/s00203-015-1180-6DOI Listing
April 2016

Labrys soli sp. nov., isolated from the rhizosphere of ginseng.

Int J Syst Evol Microbiol 2015 Nov;65(11):3913-3919

Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea.

In this study, we describe strain DCY64T that was isolated from the rhizosphere of three-year-old Korean ginseng root. Cells were Gram-reaction negative, oxidase- and catalase-positive, strictly aerobic, capsulated, non-motile, non-sporulating and spherical to short rod-shaped. Multiplicative budding cells were produced. Vesicles covered the surface of cells. Phylogenetic analysis placed strain DCY64T within the genus Labrys with the highest similarity to Labrys monachus VKM B-1479T (97.6 % 16S rRNA gene sequence similarity), followed by Labrys okinawensis MAFF 210191T (97.5 %), Labrys miyagiensis G24103T (97.4) and Labrys portucalensis F11T (97.0 %). The genomic DNA G+C content was 63 mol%. The presences of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 1 cyclo ω8c and C16 : 0 as major fatty acids; phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol as major polar lipids; ubiquinone Q-10 as the predominant quinone and sym-homospermidine as the dominant polyamine were found in strain DCY64T. These chemotaxonomic results were in accordance with those of members of the genus Labrys. However, the absence of C16 : 0 2-OH, C16 : 0 3-OH and C18 : 1 2-OH from the fatty acids profile and differences in minor polar lipids and phenotypic characteristics distinguished strain DCY64T from the closest type strains. The discrimination was also supported by unique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) fingerprints, as well as DNA-DNA hybridization values ( ≤ 48 %) between strain DCY64T and related type strains. Therefore, we propose that strain DCY64T represents a novel species of the genus Labrys. The name Labrys soli sp. nov. is proposed, with DCY64T ( = KCTC 32173T = JCM 19895T) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.000512DOI Listing
November 2015

Lactobacillus vespulae sp. nov., isolated from gut of a queen wasp (Vespula vulgaris).

Int J Syst Evol Microbiol 2015 Oct;65(10):3326-3332

Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University Giheung-gu Yongin-si, Gyeonggi-do, Republic of Korea.

A Gram-stain-positive, oxidase- and catalase-negative, rod-shaped, facultatively anaerobic bacterial strain, DCY75T, was isolated from a queen wasp (Vespula vulgaris). Growth occurred at 4–37 °C (optimum, 30 °C), at pH 3.5–8.0 (optimum, pH 5.0–6.0) and with ≤ 7.0 % (w/v) NaCl. Strain DCY75T produced gas during growth on glucose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DCY75T belonged to the genus Lactobacillus and was closely related to Lactobacillus sanfranciscensis ATCC 27651T and Lactobacillus lindneri DSM 20690T at sequence similarities of 96.7 and 96.4 %, respectively. A comparison of two housekeeping genes, pheS and rpoA, revealed that strain DCT75T was well separated from other species of the genus Lactobacillus. Strain DCY75T produced d- and l-lactic acid isomers in a ratio of 22.5 : 77.5 (v/v). The major fatty acids were summed feature 8 (comprising C18 :  1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω9c and C18 : 0.The peptidoglycan structure was of the A4α (l-Lys–d-Asp) type. Cell-wall sugars were glucose, galactose and ribose. The DNA G+C content was 35.5 ± 1.3 mol%. Based on phenotypic and genotypic properties, strain DCY75T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus vespulae sp. nov. is proposed. The type strain is DCY75T ( = KCTC 21023T = JCM 19742T).
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http://dx.doi.org/10.1099/ijsem.0.000420DOI Listing
October 2015

Microbacterium rhizomatis sp. nov., a β-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng.

Int J Syst Evol Microbiol 2015 Sep 25;65(9):3196-3202. Epub 2015 Jun 25.

Department of Oriental Medicinal Biotechnology, Kyung Hee University Giheung-gu Yongin-si, Gyeonggi-do, Republic of Korea.

A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100(T), was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100(T) belonged to the genus Microbacterium and was most closely related to Microbacterium ginsengisoli KCTC 19189(T) (97.9%), Microbacterium lacus JCM 15575(T) (97.2%) and Microbacterium invictum DSM 19600(T) (97.1%). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0%) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA-DNA hybridization relatedness values between strain DCY100(T) and Microbacterium ginsengisoli KCTC 19189(T), Microbacterium lacus JCM 15575(T) and Microbacterium invictum DSM 19600(T) were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8%, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus Microbacterium, for which the name Microbacterium rhizomatis DCY100(T) is proposed. The type strain is DCY100(T) ( = KCTC 39529(T) = JCM 30598(T)).
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http://dx.doi.org/10.1099/ijsem.0.000399DOI Listing
September 2015

Paenibacillus panaciterrae sp. nov., isolated from ginseng-cultivated soil.

Int J Syst Evol Microbiol 2015 Nov 20;65(11):4080-4086. Epub 2015 Aug 20.

Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea.

A novel bacterium, designated DCY95T, was isolated from ginseng-cultivated soil in Quang Nam province, Vietnam. On the basis of 16S rRNA and gyrB gene sequence analysis, this isolate was assigned to the genus Paenibacillus and found to be closely related to Paenibacillus sacheonensis SY01T (97.1 % 16S rRNA gene sequence similarity) and Paenibacillus taihuensis THMBG22T (96.4 %). The partial gyrB gene of DCY95T possessed 69.6-83.9 % sequence identity to those of other members of the genus Paenibacillus. Strain DCY95T was Gram-reaction-negative, catalase-negative, oxidase-positive, strictly aerobic, rod-shaped and motile by means of peritrichous flagella. Ellipsoidal free spores or subterminal endospores were produced in sporangia. MK-7 was the diagnostic menaquinone. The cell-wall peptidoglycan contained meso-diamonopimelic acid as the diamino acid. Whole-cell sugars comprised ribose, mannose and glucose. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, and two unidentified phospholipids. The genomic DNA G+C content was 60.7 ± 0.9 mol%. Phenotypic and chemotaxonomic results placed strain DCY95T within the genus Paenibacillus. However, DNA-DNA relatedness values between strain DCY95T and P. sacheonensis KACC 14895T or P. taihuensis NBRC 108766T were lower than 36 %. The low DNA relatedness data in combination with phylogenetic and (GTG)5-PCR analyses, as well as biochemical tests, indicated that strain DCY95T could not be assigned to any recognized species. In conclusion, the results in this study support the classification of strain DCY95T as a representative of a novel species within the genus Paenibacillus, for which the name Paenibacillus panaciterrae is proposed. The type strain is DCY95T ( = KCTC 33581T = DSM 29477T).
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http://dx.doi.org/10.1099/ijsem.0.000540DOI Listing
November 2015
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