Structure, organization, and evolution of satellite DNAs in species of the genera Beta and Patellifolia

Genomes of higher plants comprise a large proportion of repetitive DNAs, where one major class is satellite DNA. Satellite DNA is organized in tandem arrays of basic repeating units, which often occurs in heterochromatin of centromeric/pericentromeric and intercalary as well as subtelomeric regions. Besides these typical satellite repeats, there are also non-typical satellite DNAs, which are organized in short tandem arrays and integrated into a transposable element. The chromosomal localization of non-typical satellites is not in large regions of heterochromatin, but tend to be dispersed along chromosomes. This thesis describes the identification of the major repeat classes including major satellite content in six beet and related species. The focus was on identification and characterization of new satellite families in the beet genomes. In this study, the information regarding repetitive DNA as well as satellite families fraction in six beet and related species was gained based on graph-based clustering of next generation sequenced short sequence reads. The repeat proportion of the six analyzed species ranges from 34.4% in C. quinoa to 65.6% in B. lomatogona, in which the portion of nearly 50% belongs to B. vulgaris, B. nana, P. procumbens, and P. patellaris. Among all classes of repetitive DNAs, LTR retrotransposons are the most abundant repeat type in all analyzed genomes, which is a common feature of higher plant genomes. The other repeat sequences are DNA transposons, rDNA, and satellite DNA with variable portions in different species. A set of satellite families in each species was analyzed in detail and reflects the relationship between six species. The closely related relationship between B. lomatogona and B. nana as well as between P. procumbens and P. patellaris is affirmed by seven and 13 satellite families shared between two species, respectively. Similarly, the closer relationship between B. vulgaris and two species B. lomatogona and B. nana than between B. vulgaris and two species P. procumbens and P. patellaris from the sister-genus Patellifolia is also confirmed. C. quinoa is a distantly related species and this is reflected by vastly different satellite content. Therefore, satellite DNA analysis might be a useful tool to trace species evolution. In the B. lomatogona genome, by the application of RepeatExplorer tool, six novel tandemly repeated DNA sequences were identified and designated BlSat1-BlSat6. The three typical satellite families BlSat1, BlSat5, and BlSat6 are organized in tandem arrays in large heterochromatic blocks. BlSat1 is mainly localized in the pericentric region of the chromosome 3, 5, 6, and 9, while BlSat5 is amplified in the pericentromeric region of the chromosome 3, 5, and 7. BlSat6 is a chromosome-specific satellite and is located in the subtelomeric region on the south arm of the chromosome 8. The other three satellite families BlSat2, BlSat3, and BlSat4 are characterized as non-typical satellite DNA because of their dispersed distribution along chromosomes. BlSat2 and BlSat3 are identified as a tandem repeat domain in Ogre/Tat retrotransposons. The occurrence of one or several short tandem arrays in a transposable element is a common phenomenon in both animals and plants. These short repeats are considered to be continuously evolving and eventually amplifying to new satellite families. Furthermore, the distribution of the six new satellite families in beet and related species was confirmed by comparative PCR, comparative Southern hybridization, and mapping of sequence reads from referent species against each satellite sequence. The BlSat1 and BlSat6 satellite families are specific for the genus Beta, while BlSat5 is only amplified in two sections Corollinae and Nanae of the genus Beta. BlSat4 is an ancient satellite family which exists in all tested species belonging to the genera Beta, Patellifolia, Chenopodium, and Spinacia, whereas BlSat2 and BlSat3 might have evolved before the separation of the genus Beta and Patellifolia but their sequences have been lost or heavily diverged during the species radiation. Comparison of two wild beet genomes P. procumbens and P. patellaris was performed aiming to address the open question whether P. patellaris is auto- or allotetraploid. The high similarity between these two genomes indicates their close relationship. However, the genetic difference between two genomes, in particular the molecular characteristics as well as the chromosomal localization of two satellite families PproSat1 and PpatSat1, might support a hypothesis that P. patellaris is allotetraploid species with a half of its chromosome set derived from P. procumbens. The results obtained in this work might provide comprehensive information of the repetitive classes as well as satellite families in the genomes of beets and related species. The results can be used as the species-specific and chromosome-specific markers in beet genome studies

The Commitment with FDI Firms of Accountants in Noi Bai Industrial Park - Creative Application in Economics Sociological Knowledge

This study was conducted to identify, evaluate and measure the attributes of accountants’ commitment with FDI firms in Noi Bai industrial park, Hanoi based on the organizational commitment theory of Meyer & Allen (1991) and Creative application in economics sociological knowledge.  Beside, we based on literature review and the results of some interviews, 150 questionnaires were sent directly to accountants in FDI firms in Noi Bai industrial park and were collected in 1 month. However, only 110 questionnaires were satisfactory and included in the analysis. The results of descriptive statistics, Cronbach’s Alpha analysis and Independent T-test have identified and measured 12 attributes of accountants’ commitment which effect on accountants in the FDI firms in Noi Bai industrial park. Based on the findings, some recommendations are given to improve the accountants’ commitment. Keywords: commitment, accountants, FDI firms, Noi Bai industrial park JED codes: M41, M40, O15 DOI: 10.7176/RJFA/10-22-15 Publication date: November 30th 201

Two new species of Dixonius from Vietnam and Laos with a discussion of the taxonomy of Dixonius (Squamata, Gekkonidae)

Integrated analyses using maximum likelihood (ML), Bayesian inference (BI), principal component analysis (PCA), discriminate analysis of principal components (DAPC), multiple factor analysis (MFA), and analysis of variance (ANOVA) recovered two new diagnosable species of gekkonid lizards in the genus Dixonius, one from the Central Highlands, Gia Lai Province, Vietnam and another from the Vientiane Province, Laos. Phylogenetic analyses based on the mitochondrial NADH dehydrogenase subunit 2 gene (ND2) and adjacent tRNAs showed that Dixonius gialaiensis sp. nov. is the sister species of D. minhlei from Dong Nai Province, Vietnam and is nested within a clade that also includes the sister species D. siamensis and D. somchanhae. Dixonius muangfuangensis sp. nov. is the sister species to D. lao from Khammouane Province, Laos and is embedded in a clade with D. vietnamensis, D. taoi, and undescribed species from Thailand. Multivariate (PCA, DAPC, and MFA) and univariate (ANOVA) analyses using combinations of 15 meristic (scale counts), six morphometric (measurements), and five categorical (color pattern and morphology) characters from 44 specimens encompassing all eight species of Dixonius from Vietnam and Laos clearly illustrate Dixonius gialaiensis sp. nov. and Dixonius muangfuangensis sp. nov. are statistically different and discretely diagnosable from all closely related species of Dixonius. These integrative analyses also highlight additional taxonomic issues that remain unresolved within Dixonius and the need for additional studies. The discovery of these new species further emphasizes the underappreciated herpetological diversity of the genus Dixonius and illustrates the continued need for field work in these regions

The Role of Serial NT-ProBNP Level in Prognosis and Follow-Up Treatment of Acute Heart Failure after Coronary Artery Bypass Graft Surgery

BACKGROUND: After coronary artery bypass graft (CABG) surgery, heart failure is still major problem. The valuable marker for it is needed. AIM: Evaluating the role of serial NT-proBNP level in prognosis and follow-up treatment of acute heart failure after CABG surgery. METHODS: The prospective, analytic study evaluated 107 patients undergoing CABG surgery at Ho Chi Minh Heart Institute from October 2012 to June 2014. Collecting data was done at pre- and post-operative days with measuring NT-proBNP levels on the day before operation, 2 hours after surgery, every next 24 h until the 5th day, and in case of acute heart failure occurred after surgery. RESULTS: On the first postoperative day (POD1), the NT-proBNP level demonstrated significant value for AHF with the cut-off point = 817.8 pg/mL and AUC = 0.806. On the second and third postoperative day, the AUC value of NT- was 0.753 and 0.751. It was statistically significant in acute heart failure group almost at POD 1 and POD 2 when analyzed by the doses of dobutamine, noradrenaline, and adrenaline (both low doses and normal doses). CONCLUSION: Serial measurement of NT-proBNP level provides useful prognostic and follow-up treatment information in acute heart failure after CABG surgery

The epidemiology and aetiology of diarrhoeal disease in infancy in southern Vietnam: a birth cohort study.

OBJECTIVES: Previous studies indicate a high burden of diarrhoeal disease in Vietnamese children, however longitudinal community-based data on burden and aetiology are limited. The findings from a large, prospective cohort study of diarrhoeal disease in infants in southern Vietnam are presented herein. METHODS: Infants were enrolled at birth in urban Ho Chi Minh City and a semi-rural district in southern Vietnam, and followed for 12 months (n=6706). Diarrhoeal illness episodes were identified through clinic-based passive surveillance, hospital admissions, and self-reports. RESULTS: The minimum incidence of diarrhoeal illness in the first year of life was 271/1000 infant-years of observation for the whole cohort. Rotavirus was the most commonly detected pathogen (50% of positive samples), followed by norovirus (24%), Campylobacter (20%), Salmonella (18%), and Shigella (16%). Repeat infections were identified in 9% of infants infected with rotavirus, norovirus, Shigella, or Campylobacter, and 13% of those with Salmonella infections. CONCLUSIONS: The minimum incidence of diarrhoeal disease in infants in both urban and semi-rural settings in southern Vietnam was quantified prospectively. A large proportion of laboratory-diagnosed disease was caused by rotavirus and norovirus. These data highlight the unmet need for a rotavirus vaccine in Vietnam and provide evidence of the previously unrecognized burden of norovirus in infants

Streptococcus suis, an Important Cause of Adult Bacterial Meningitis in Northern Vietnam

Streptococcus suis can cause severe systemic infection in adults exposed to infected pigs or after consumption of undercooked pig products. S. suis is often misdiagnosed, due to lack of awareness and improper testing. Here we report the first fifty cases diagnosed with S. suis infection in northern Viet Nam.In 2007, diagnostics for S. suis were set up at a national hospital in Hanoi. That year there were 43 S. suis positive cerebrospinal fluid samples, of which S. suis could be cultured in 32 cases and 11 cases were only positive by PCR. Seven patients were blood culture positive for S. suis but CSF culture and PCR negative; making a total of 50 patients with laboratory confirmed S. suis infection in 2007. The number of S. suis cases peaked during the warmer months.S. suis was commonly diagnosed as a cause of bacterial meningitis in adults in northern Viet Nam. In countries where there is intense and widespread exposure of humans to pigs, S. suis can be an important human pathogen

Microscopic Observation Drug Susceptibility Assay (MODS) for Early Diagnosis of Tuberculosis in Children

MODS is a novel liquid culture based technique that has been shown to be effective and rapid for early diagnosis of tuberculosis (TB). We evaluated the MODS assay for diagnosis of TB in children in Viet Nam. 217 consecutive samples including sputum (n = 132), gastric fluid (n = 50), CSF (n = 32) and pleural fluid (n = 3) collected from 96 children with suspected TB, were tested by smear, MODS and MGIT. When test results were aggregated by patient, the sensitivity and specificity of smear, MGIT and MODS against “clinical diagnosis” (confirmed and probable groups) as the gold standard were 28.2% and 100%, 42.3% and 100%, 39.7% and 94.4%, respectively. The sensitivity of MGIT and MODS was not significantly different in this analysis (P = 0.5), but MGIT was more sensitive than MODS when analysed on the sample level using a marginal model (P = 0.03). The median time to detection of MODS and MGIT were 8 days and 13 days, respectively, and the time to detection was significantly shorter for MODS in samples where both tests were positive (P<0.001). An analysis of time-dependent sensitivity showed that the detection rates were significantly higher for MODS than for MGIT by day 7 or day 14 (P<0.001 and P = 0.04), respectively. MODS is a rapid and sensitive alternative method for the isolation of M.tuberculosis from children

Experimental cultivation of Spirulina platensis using My An mineral water, Thua Thien Hue province

Spirulina platensis was experimentally cultivated by semi-continuous method at 20m2 scale pilot to effectively use the available bicarbonate and minerals of the My An mineral water, Phu Vang district, Thua Thien Hue province, and reduce production cost. Analyses of My An water quality showed that this mineral water source was suitable to cultivate Spirulina Platensis after removing H2S. The average algal yield reached to 10gDW/m2.day. The obtained algal biomass contained high nutrient compositions and was a suitable source for functional food (68.32 % protein, 7.32 % lipids containing Omega-3 and Omega-6, and low heavy metal concentration). The obtained results indicated that the My An mineral water source was indeed a suitable water source for producing Spirulina platensis biomass as a functional food

Evaluation of microscopic observation drug susceptibility assay for diagnosis of multidrug-resistant Tuberculosis in Viet Nam

<p>Abstract</p> <p>Background</p> <p>Early diagnosis of tuberculosis (TB) and multidrug resistant tuberculosis (MDR TB) is important for the elimination of TB. We evaluated the microscopic observation drug susceptibility (MODS) assay as a direct rapid drug susceptibility testing (DST) method for MDR-TB screening in sputum samples</p> <p>Methods</p> <p>All adult TB suspects, who were newly presenting to Pham Ngoc Thach Hospital from August to November 2008 were enrolled into the study. Processed sputum samples were used for DST by MODS (DST-MODS) (Rifampicin (RIF) 1 μg/ml and Isoniazid (INH) 0.4 μg/ml), MGIT culture (Mycobacterial Growth Indicator Tube) and Lowenstein Jensen (LJ) culture. Cultures positive by either MGIT or LJ were used for proportional DST (DST-LJ) (RIF 40 μg/ml and INH 0.2 μg/ml). DST profiles on MODS and LJ were compared. Discrepant results were resolved by multiplex allele specific PCR (MAS-PCR).</p> <p>Results</p> <p>Seven hundred and nine TB suspects/samples were enrolled into the study, of which 300 samples with DST profiles available from both MODS and DST-LJ were analyzed. Cording in MODS was unable to correctly identify 3 Mycobacteria Other Than Tuberculosis (MOTT) isolates, resulting in 3 false positive TB diagnoses. None of these isolates were identified as MDR-TB by MODS. The sensitivity and specificity of MODS were 72.6% (95%CI: 59.8, 83.1) and 97.9% (95%CI: 95.2, 99.3), respectively for detection of INH resistant isolates, 72.7% (95%CI: 30.9, 93.7) and 99.7% (95%CI: 98.1, 99.9), respectively for detecting RIF resistant isolates and 77.8% (95%CI: 39.9, 97.1) and 99.7% (95%CI: 98.1, 99.9), respectively for detecting MDR isolates. The positive and negative predictive values (PPV and NPV) of DST-MODS were 87.5% (95%CI: 47.3, 99.6) and 99.3% (95%CI: 97.5, 99.9) for detection of MDR isolates; and the agreement between MODS and DST-LJ was 99.0% (kappa: 0.8, <it>P </it>< 0.001) for MDR diagnosis. The low sensitivity of MODS for drug resistance detection was probably due to low bacterial load samples and the high INH concentration (0.4 μg/ml). The low PPV of DST-MODS may be due to the low MDR-TB rate in the study population (3.8%). The turnaround time of DST-MODS was 9 days and 53 days for DST-LJ.</p> <p>Conclusion</p> <p>The DST-MODS technique is rapid with low contamination rates. However, the sensitivity of DST-MODS for detection of INH and RIF resistance in this study was lower than reported from other settings.</p