A novel IGHMBP2 variant and clinical diversity in Vietnamese SMARD1 and CMT2S patients.

Background: Pathogenic variants in the IGHMBP2 gene are associated with two distinct autosomal recessive neuromuscular disorders: spinal muscular atrophy with respiratory distress type 1 (SMARD1; OMIM #604320) and Charcot-Marie-Tooth type 2S (CMT2S; OMIM #616155). SMARD1 is a severe and fatal condition characterized by infantile-onset respiratory distress, diaphragmatic palsy, and distal muscular weakness, while CMT2S follows a milder clinical course, with slowly progressive distal muscle weakness and sensory loss, without manifestations of respiratory disorder. Methods: Whole-exome sequencing of the IGHMBP2 gene was performed for eight Vietnamese patients with IGHMBP2-related neuromuscular disorders including five patients with SMARD1 and the others with CMT2S. Results: We identified one novel IGHMBP2 variant c.1574T > C (p.Leu525Pro) in a SMARD1 patient. Besides that, two patients shared the same pathogenic variants (c.1235 + 3A > G/c.1334A > C) but presented completely different clinical courses: one with SMARD1 who deceased at 8 months of age, the other with CMT2S was alive at 3 years old without any respiratory distress. Conclusion: This study is the first to report IGHMBP-2-related neuromuscular disorders in Vietnam. A novel IGHMBP2 variant c.1574T > C (p.Leu525Pro) expressing SMARD1 phenotype was detected. The presence of three patients with the same genotype but distinct clinical outcomes suggested the interaction of variants and other factors including relating modified genes in the mechanism of various phenotypes.

Merosin-deficient congenital muscular dystrophy type 1a: detection of LAMA2 variants in Vietnamese patients.

Background: Merosin-deficient congenital muscular dystrophy type 1A (MDC1A), also known as laminin-α2 chain-deficient congenital muscular dystrophy (LAMA2-MD), is an autosomal recessive disease caused by biallelic variants in the LAMA2 gene. In MDC1A, laminin- α2 chain expression is absent or significantly reduced, leading to some early-onset clinical symptoms including severe hypotonia, muscle weakness, skeletal deformity, non-ambulation, and respiratory insufficiency. Methods: Six patients from five unrelated Vietnamese families presenting with congenital muscular dystrophy were investigated. Targeted sequencing was performed in the five probands. Sanger sequencing was carried out in their families. Multiplex ligation-dependent probe amplification was performed in one family to examine an exon deletion. Results: Seven variants of the LAMA2 (NM_000426) gene were identified and classified as pathogenic/likely pathogenic variants using American College of Medical Genetics and Genomics criteria. Two of these variants were not reported in the literature, including c.7156-5_7157delinsT and c.8974_8975insTGAT. Sanger sequencing indicated their parents as carriers. The mothers of family 4 and family 5 were pregnant and a prenatal testing was performed. The results showed that the fetus of the family 4 only carries c.4717 + 5G>A in the heterozygous form, while the fetus of the family 5 carries compound heterozygous variants, including a deletion of exon 3 and c.4644C>A. Conclusion: Our findings not only identified the underlying genetic etiology for the patients, but also provided genetic counseling for the parents whenever they have an offspring.

Anti-Aliasing Attention U-net Model for Skin Lesion Segmentation.

The need for a lightweight and reliable segmentation algorithm is critical in various biomedical image-prediction applications. However, the limited quantity of data presents a significant challenge for image segmentation. Additionally, low image quality negatively impacts the efficiency of segmentation, and previous deep learning models for image segmentation require large parameters with hundreds of millions of computations, resulting in high costs and processing times. In this study, we introduce a new lightweight segmentation model, the mobile anti-aliasing attention u-net model (MAAU), which features both encoder and decoder paths. The encoder incorporates an anti-aliasing layer and convolutional blocks to reduce the spatial resolution of input images while avoiding shift equivariance. The decoder uses an attention block and decoder module to capture prominent features in each channel. To address data-related problems, we implemented data augmentation methods such as flip, rotation, shear, translate, and color distortions, which enhanced segmentation efficiency in the international Skin Image Collaboration (ISIC) 2018 and PH2 datasets. Our experimental results demonstrated that our approach had fewer parameters, only 4.2 million, while it outperformed various state-of-the-art segmentation methods.

Electrocardiogram Heartbeat Classification for Arrhythmias and Myocardial Infarction.

An electrocardiogram (ECG) is a basic and quick test for evaluating cardiac disorders and is crucial for remote patient monitoring equipment. An accurate ECG signal classification is critical for real-time measurement, analysis, archiving, and transmission of clinical data. Numerous studies have focused on accurate heartbeat classification, and deep neural networks have been suggested for better accuracy and simplicity. We investigated a new model for ECG heartbeat classification and found that it surpasses state-of-the-art models, achieving remarkable accuracy scores of 98.5% on the Physionet MIT-BIH dataset and 98.28% on the PTB database. Furthermore, our model achieves an impressive F1-score of approximately 86.71%, outperforming other models, such as MINA, CRNN, and EXpertRF on the PhysioNet Challenge 2017 dataset.

The mitochondrial DNA HVI and HVII sequences and haplogroup distribution in a population sample from Vietnam.

BACKGROUND: Mitochondrial DNA (mtDNA) analysis has been used in forensics and requires well-established population databases for statistical interpretations. However, high-quality mtDNA data from Vietnamese population samples have been limited. AIM: To examine the mtDNA sequences and haplogroup compositions of a Vietnamese population to provide an mtDNA dataset that can further be used to construct a Vietnamese-specific reference database. SUBJECTS AND METHODS: A total of 173 Vietnamese individuals were analysed for two hypervariable regions (HVI and HVII) of mtDNA. Forensic parameters were calculated and haplogroup assignment was performed based on the resulting mtDNA haplotypes. Genetic relationships between the Vietnamese and other Asian populations were investigated through principal component analysis (PCA) and pairwise Fst. RESULTS: The Vietnamese population sample consisted of 145 different haplotypes with a random match probability of 0.96%, a power of discrimination of 0.9904, and a haplotype diversity of 0.9962. The samples were assigned to 83 haplogroups that were commonly reported in Asia. PCA and pairwise Fst revealed close relationships of the Vietnamese population with other Asian populations, especially with populations in proximity. CONCLUSION: The results from this study can contribute to the current genetic information content as a supplementary mtDNA reference dataset for forensic investigations and phylogenetic research.

Sex differences in frailty of geriatric outpatients with type 2 diabetes mellitus: a multicentre cross-sectional study.

Frailty and type 2 diabetes mellitus (T2DM) can occur concurrently and are increasingly prevalent in older populations. There is a marked variability in frailty progression between men and women. This study aimed to investigate sex differences in the prevalence and factors associated with frailty in older outpatients with T2DM. This multicentre cross-sectional study included 638 outpatients (aged ≥ 60 years; median age 71 years [interquartile range, 66-77]; male, 55.5%) and was conducted from January 2019 to July 2020. Frailty was assessed using the Fried frailty phenotype. Factors associated with frailty were assessed using a logistic regression analysis. The overall frailty prevalence was 28.2% (men, 26.8%; women, 29.9%; P = 0.388). In the adjusted model, the factors associated with greater odds of being frail were older age (odds ratio [OR], 1.08; 95% confidence interval [CI], 1.05-1.11; P < 0.001) and body mass index (BMI) less than 20 kg/m2 (OR, 1.96; 95% CI, 1.16-3.32; P = 0.012). Higher education (OR, 0.64; 95% CI, 0.42-0.98; P = 0.041) and productive work (OR, 0.11; 95% CI, 0.03-0.36; P < 0.001) were protective factors against frailty. Frailty was associated with all four factors in women, but only with older age and productive work in men. Our study found that the prevalence of frailty in older outpatients with T2DM was 28.2%, though not significantly different between men and women. While older age and BMI less than 20 kg/m2 can increase the odds of frailty, and higher education and productive work can decrease the odds of frailty in women, only age and productive work were associated with frailty in men with T2DM.

Detection of Neisseria gonorrhoeae or Chlamydia trachomatis from oral wash specimens using the Abbott RealTime CT/NG assay and the Cobas 4800 CT/NG assay: A prospective study.

INTRODUCTION: Isolating oropharyngeal Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) from oral wash specimens (OWSs) is uncommon. Therefore, we evaluated the performance of the Abbott RealTime CT/NG assay and the Cobas 4800 CT/NG assay in detecting NG and CT in OWSs. METHODS: This multicenter prospective study included 457 patients from 14 medical facilities suspected of having untreated male urethritis or female cervicitis from November 2014 to December 2015. OWSs were collected and tested using the Abbott and Cobas assays. Finally, the discordant results were confirmed using the APTIMA Combo 2 transcription-mediated amplification assay and retested using each assay. RESULTS: The sensitivity and specificity of the Abbott assay were 100% and 97.2% for NG and 87.5% and 100% for CT, respectively, and of the Cobas assay were 100% and 98.8% for NG and 93.8% and 99.8% for CT, respectively. Both assays had high negative but low positive predictive values for oropharyngeal NG (Abbott assay: 65.7%, Cobas assay: 82.1%). Based on the definition of "true positive," the prevalence of oropharyngeal NG and CT were 5.0% and 3.5%, respectively. CONCLUSIONS: The Abbott and Cobas assays using OWSs had high sensitivity and specificity, which can help diagnose oropharyngeal NG and CT. We consider that if a positive result is obtained, the patient should be treated because the negative predictive values were high. However, limited data are available on oropharyngeal NG and CT detection, and further studies are needed to clarify the role of oropharyngeal sexually transmitted infections.

Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system.

Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.

Characterization of envelope sequence of HIV virus in children infected with HIV in Vietnam.

BACKGROUND: HIV is characterized by high levels of genetic variability, including increased numbers of heterogeneous sequences of the envelope region. Therefore, studying genetic variability of HIV in relation to viral replication might facilitate prognosis of disease progression. METHODS: The study was designed as cross-sectional; data and samples of participants collected and analyzed env genes were obtained from 23 children enrolled by Vietnam National Children's Hospital. RESULTS: Substantial mutations in the C2 region were found in patients with high levels of viral replication while changes in the C3 region were mostly found in patients with low viral load. In the V1 region, we found profound amino acid modifications in patients with low HIV viral loads in contrast to the V2 sequence, where we identified single point mutations in patients with increased HIV viral load. The V3 region was relatively homogeneous, while profound deletions in the V4 region were detected in patients with increased viral replication. CONCLUSION: Our results suggest that genetic variations in different regions of the HIV envelope sequence, including both conserved C2 and C3 and variable V1/V2 and V4 regions, might be involved in increased viral infectivity and replication capacity. Such knowledge might help improve prediction of HIV progress and treatment in patients.

Assessment of 6 STR loci for prenatal diagnosis of Duchenne Muscular Dystrophy.

OBJECTIVE: Duchenne Muscular Dystrophy is an X-linked recessive disorder characterized by progressive muscular degeneration, patients often develop cardiac failure in the later stage and death occurs before 20 years of age. For a disease with poor postnatal prognosis such as Duchenne Muscular Dystrophy (DMD), providing the carrier mother with the option of prenatal diagnosis in a subsequent pregnancy is accepted practice in many places where termination of pregnancy is allowed. Though methods of direct sequencing such as Sanger's sequencing has been widely used, Next-Generation Sequencing is been increasingly replacing most of its application. For the DMD gene, being the longest gene in the human genome, methods of direct sequencing is often unpractical and time-consuming, instead, STR analysis for linkage analysis would be a cost-effective option and have been used routinely for prenatal diagnosis of DMD. The diagnostic significance of the STRs is based on several criteria, the most important one being the heterozygosity of the locus, power of discrimination (PD) and power of exclusion (PE). MATERIAL AND METHODS: In this study, we investigated the feasibility of application and diagnostic value of 6 STR loci (DSTR49, DSTR50, DXS1036, DXS1067, DXS890, DXS9907) in the proximity of the DMD gene, 66 healthy individuals were recruited for STR analysis and 5 cases of prenatal diagnosis for carrier mother were performed. RESULT: Allele frequency, heterozygosity, polymorphic information content, the power of discrimination and exclusion and Hardy-Weinberg equilibrium were analyzed and calculated for the 6 STR loci. 5 of these loci (DSTR49, DSTR50, DXS1067, DXS890, DXS9907) were found practical and useful for preimplantation Genetic diagnosis (PGD) and prenatal diagnosis. All 5 cases of prenatal diagnosis using the method had informative STR results and correct diagnosis. CONCLUSION: We concluded that our protocol of STR analysis can be applied for prenatal diagnosis and pre-implantation genetic diagnosis of DMD with high confidence and accuracy, especially in clinical settings where diagnostic resources are more limited.

Acromesomelic dysplasia Maroteaux-type in patients from Vietnam.

Acromesomelic dysplasias are rare skeletal disorders leading to severe short stature and abnormal skeletal morphology. Acromesomelic dysplasia Maroteaux-type is caused by homozygous or compound heterozygous pathogenic variants in NPR2 that encodes for natriuretic peptide receptor B. Here, we reported the first AMDM case in South East Asia and identified a novel pathogenic variant in NPR2 (c. 152T>C, p. (Leu51Pro)). Further analyses reveal the parents and two other family members were heterozygous for the variant. The clinical report highlights the importance of molecular genetic testing in diagnosing rare hereditable disease affecting skeletal abnormalities.

In Vitro Production of Cartilage Tissue from Rabbit Bone Marrow-Derived Mesenchymal Stem Cells and Polycaprolactone Scaffold.

In vitro production of tissues or tissue engineering is a promising approach to produce artificial tissues for regenerative medicine. There are at least three important components of tissue engineering, including stem cells, scaffolds and growth factors. This study aimed to produce cartilage tissues in vitro from culture and chondrogenic differentiation of rabbit bone marrow-derived mesenchymal stem cells (BMMSCs), induced by chondrogenesis medium, on biodegradable polycaprolactone (PCL) scaffolds. BMMSCs were isolated from rabbit bone marrow according to the standard protocol. The adherence, proliferation and differentiation of BMMSCs on scaffolds were investigated using two scaffold systems: PCL scaffolds and collagen-coated PCL (PCL/col) scaffolds. The results showed that BMMSCs could attach and grow on both PCL and PCL/col scaffolds. However, the adhesion efficacy of BMMSCs on the PCL/col scaffolds was significantly better than on PCL scaffolds. Under induced conditions, BMMSCs on PLC/col scaffolds showed increased aggrecan accumulation and upregulated expression of chondrogenesis-associated genes (e.g. collagen type II, collagen type I, aggrecan and collagen type X) after 3, 7, 21 and 28 days of induction. These in vitro cartilage tissues could form mature chondrocyte-like cells after they were grafted into rabbits. The results suggest that use of BMMSCs in combination with polycaprolactone scaffolds and chondrogenesis medium can be a way to form in vitro cartilage tissue.

Mosaicism in carrier of Duchenne muscular dystrophy mutation - Implication for prenatal diagnosis.

OBJECTIVE: Duchenne muscular dystrophy (DMD) is a severe disorder caused by mutation in the X-linked dystrophin gene, therefor carrier testing is required for all female family members. However, there are cases mutation analysis cannot detect any mutation due to a phenomenon called mosaicism. The case report describes a case of mosaicism in a DMD carrier and discusses the approach in diagnosis and counseling of familial disorder. CASE REPORT: The proband was diagnosed with DMD at age six. Sequencing of Dystrophin gene identified a 2-nucleotide deletion c.2032_2033delCA, p.Q678DfsX41. Family investigation suggested that the mother was an obligate carrier of Dystrophin mutation. Sequencing of DNA sample from the mother's peripheral blood did not reveal any mutation, there for we take sample from hair follicle for analysis. The result indicated that the mother was a carrier but was masked from initial analysis by mosaicsism. CONCLUSION: We suggested that more care need to be taken in identifying cases when no mutation was detected in probable or obligate carrier and prenatal diagnosis should remain an option.

Mutations in ParC and GyrA of moxifloxacin-resistant and susceptible Mycoplasma genitalium strains.

Macrolide or fluoroquinolone-resistant Mycoplasma genitalium is spreading worldwide. We aimed to determine the influence of single nucleotide polymorphisms (SNPs) in the quinolone resistance determining regions (QRDR) of parC and gyrA in cultured M. genitalium strains. In addition, we examined the prevalence of macrolide- and fluoroquinolone resistance mediating mutations in specimens collected from Japanese male patients with urethritis in two time-periods between 2005-2009 and 2010-2017, respectively, by sequencing the QRDR of parC and gyrA and domain V of the 23S rRNA gene. The minimum inhibitory concentrations (MIC) of moxifloxacin, sitafloxacin, ciprofloxacin, levofloxacin, doxycycline, minocycline, azithromycin and clarithromycin were determined in 23 M. genitalium strains. Three cultured strains had elevated MICs for moxifloxacin at 16, 4 and 2 mg/L and had SNPs with the amino-acid change Ser83→Ile in ParC (p<0.001) and 3 kinds of SNPs with amino-acid changes Asp99→Asn, Gly93→Cys and Met95→Ile in GyrA, respectively. Among a total of 148 M. genitalium positive urine specimens, the prevalence of A2058G and A2059G SNPs in the 23S rRNA gene and any SNPs in ParC increased from 4.8% and 22.6% in 2005-2009 to 42.2% and 53.1% in 2010-2017, respectively. If M. genitalium is considered multi-drug resistant in clinical specimens carrying SNPs in the 23S rRNA gene and Ser83→Ile in ParC, the prevalence of multi-drug resistance is 12.5% in 2010-2017 in Japan. In conclusion, the SNP resulting in Ser83→Ile in ParC is closely related to moxifloxacin resistance even though other factors may also affect treatment outcomes by moxifloxacin. The prevalence of circulating multi-drug resistant M. genitalium strains with macrolide- and fluoroquinolone-resistance is dramatically increasing in Japan.

The detection of microorganisms related to urethritis from the oral cavity of male patients with urethritis.

OBJECTIVES: To investigate the presence of microorganisms related to urethritis in the oral cavity of male patients with urethritis and the efficacies of antimicrobials for urethritis on microorganisms in the oral cavity. METHODS: Ninety-two male patients with urethritis and 17 male controls participated to this study at 12 urology clinics in Japan between March 2014 and March 2015. The first voided urine (FVU) and oral wash fluid (OWF) specimens were collected from the participants. The microorganisms in both FVU and OWF specimens were detected by nucleic acid amplification tests at the first and follow-up visit. The efficacies of antimicrobials were evaluated after 1-4 weeks treatment completion. RESULTS: In a total of 92 male patients with urethritis, Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, Ureaplasma parvum, Trichomonas vaginalis and Gardnerella vaginalis were detected from OWF specimens of 12%, 3%, 9%, 0%, 12%, 3%, 3% and 15% patients, respectively. From control males, no microorganism was detected from OWF specimens. Among 46 patients who could be evaluated for antimicrobial efficacies at the follow-up visit, 5 in FVU specimens failed by azithromycin (AZM), and 10 failed in OWF specimens (7 by AZM, 2 by tetracycline, 1 by spectinomycin; p = 0.002). Especially, a high prevalence of G. vaginalis remained positive after treatment for urethritis in the oral cavity. CONCLUSION: Microorganisms related to urethritis were detected in the oral cavity of male patients with urethritis. Antimicrobials that focused on urethritis, especially AZM regimen seem to be less effective for microorganisms in the oral cavity.

Comparative Clinical Observation of Arthroscopic Microfracture in the Presence and Absence of a Stromal Vascular Fraction Injection for Osteoarthritis.

Osteoarthritis (OA) is a degenerative cartilage disease that is characterized by a local inflammatory reaction. Consequently, many studies have been performed to identify suitable prevention and treatment interventions. In recent years, both arthroscopic microfracture (AM) and stem cell therapy have been used clinically to treat OA. This study aimed to evaluate the clinical effects of AM in the presence and absence of a stromal vascular fraction (SVF) injection in the management of patients with OA. Thirty patients with grade 2 or 3 (Lawrence scale) OA of the knee participated in this study. Placebo group patients (n = 15) received AM alone; treatment group patients (n = 15) received AM and an adipose tissue-derived SVF injection. The SVF was suspended in platelet-rich plasma (PRP) before injection into the joint. Patient groups were monitored and scored with the Western Ontario and McMaster Universities Arthritis Index (WOMAC), Lysholm, Visual Analog Pain Scale (VAS), and modified Outerbridge classifications before treatment and at 6, 12, and 18 months post-treatment. Bone marrow edema was also assessed at these time points. Patients were evaluated for knee activity (joint motion amplitude) and adverse effects relating to surgery and stem cell injection. Treatment efficacy was significantly different between placebo and treatment groups. All treatment group patients had significantly reduced pain and WOMAC scores, and increased Lysholm and VAS scores compared with the placebo group. These findings suggest that the SVF/PRP injection efficiently improved OA for 18 months after treatment. This study will be continuously monitored for additional 24 months. Stem Cells Translational Medicine 2017;6:187-195.

Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.

Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.

Isolation and proliferation of umbilical cord tissue derived mesenchymal stem cells for clinical applications.

Umbilical cord (UC) is a rich source of rapidly proliferating mesenchymal stem cells (MSCs) that are easily cultured on a large-scale. Clinical applications of UC-MSCs include graft-versus-host disease, and diabetes mellitus types 1 and 2. UC-MSCs should be isolated and proliferated according to good manufacturing practice (GMP) with animal component-free medium, quality assurance, and quality control for their use in clinical applications. This study developed a GMP standard protocol for UC-MSC isolation and culture. UC blood and UC were collected from the same donors. Blood vasculature was removed from UC. UC blood was used as a source of activated platelet rich plasma (aPRP). Small fragments (1-2 mm(2)) of UC membrane and Wharton's jelly were cut and cultured in DMEM/F12 medium containing 1 % antibiotic-antimycotic, aPRP (2.5, 5, 7.5 and 10 %) at 37 °C in 5 % CO2. The MSC properties of UC-MSCs at passage 5 such as osteoblast, chondroblast and adipocyte differentiation, and markers including CD13, CD14, CD29, CD34, CD44, CD45, CD73, CD90, CD105, and HLA-DR were confirmed. UC-MSCs also were analyzed for karyotype, expression of tumorigenesis related genes, cell cycle, doubling time as well as in vivo tumor formation in NOD/SCID mice. Control cells consisted of UC-MSCs cultured in DMEM/F12 plus 1 % antibiotic-antimycotic, and 10 % fetal bovine serum (FBS). All UC-MSC (n = 30) samples were successfully cultured in medium containing 7.5 and 10 % aPRP, 92 % of samples grew in 5.0 % aPRP, 86 % of samples in 2.5 % aPRP, and 72 % grew in 10 % FBS. UC-MSCs in these four groups exhibited similar marker profiles. Moreover, the proliferation rates in medium with PRP, especially 7.5 and 10 %, were significantly quicker compared with 2.5 and 5 % aPRP or 10 % FBS. These cells maintained a normal karyotype for 15 sub-cultures, and differentiated into osteoblasts, chondroblasts, and adipocytes. The analysis of pluripotent cell markers showed UC-MSCs maintained the expression of the oncogenes Nanog and Oct4 after long term culture but failed to transfer tumors in NOD/SCID mice. Replacing FBS with aPRP in the culture medium for UC tissues allowed the successful isolation of UC-MSCs that satisfy the minimum standards for clinical applications.

Alphaproteobacteria species as a source and target of lateral sequence transfers.

Alphaproteobacterial genomes show a remarkable genome plasticity linked with different lifestyles (intracellular, facultative, and free-living). They represent the major source of the genome repertoire of mitochondria, and their genes (specifically those of Wolbachia) have been massively transferred into their modern eukaryotic hosts, such as arthropods and nematodes. Conversely, other organisms (bacteria, viruses, archaea, and eukaryotes) and selfish DNA have contributed to their genomes. This bidirectional lateral sequence transfer explains the mosaic nature of their genomes. In contrast to those living in allopatry, alphaproteobacteria living in sympatry (in protist cells such as in the environment) favor lateral sequence transfer. Evidence shows that intracellular transfer of the type IV secretion system might have played a critical role in the evolution of these alphaproteobacteria.

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.

BACKGROUND: Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species. RESULTS: We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like". CONCLUSIONS: Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.