Since 2005, anti-hepatitis B virus (anti-HBV) vaccine is part of the Expanded Program on Immunization (EPI) for infants born in Cameroon, with 99% anti-HBV coverage. In a context of generalized HIV epidemiology, we assessed paediatric anti-HBV vaccine response according to HIV status, feeding option and age in a tropical context.Prospective, observational and cross-sectional study conducted among 82 children , after complete anti-HBV vaccination (Zilbrix Hepta: 10μg AgHBs) at the Essos Health Centre in Yaounde, Cameroon, classified as group-A: HIV unexposed (28), group-B: HIV-exposed/uninfected (29), group-C: HIV-infected (25). Quantitative anti-HBs ELISA was interpreted as “no”, “low-” or “protective-response” with <1, 1–10, or ≥10 IU/L respectively; with p-value<0.05 considered significant.95% 0.933–7.500], p = 0.041. According to feeding option during first six months of life, 47.67% (21/45) developed a protective-response on exclusive breastfeeding vs. 43.24% (16/37) on mixed or formula feeding, OR: 1.148 [CI95% 0.437–3.026], p = 0.757. According to age, protective-response decreased significantly as children grow older: 58.33% (28/48) <24 months vs. 26.47% (9/34) ≥24 months, OR: 3.889 [CI95% 1.362–11.356], p = 0.004; and specifically 67.65% (23/34) ≤6 months vs. 0%, (0/5) 33–41 months, p = 0.008.Children were all HBV-unexposed (AcHBc-negative) and uninfected (HBsAg-negative). Response to anti-HBV vaccine was 80.49% (66/82), with only 45.12% (37/82) developed a protective-response (≥10IU/L). According to HIV status, 60.71% (17/28) developed a protective-response in group-A, vs. 51.72% (15/29) and 20% (5/25) in group-B and group-C respectively, Odds Ratio (OR): 2.627 [CIAnti-HBV vaccine provides low rate of protection (<50%) among children in general, and particularly if HIV-exposed, infected and/or older children. Implementing policies for early vaccination, specific immunization algorithm for HIV-exposed/infected children, and monitoring vaccine response would ensure effective protection in tropical settings, pending extensive/confirmatory investigations. Viral hepatitis B (HBV) and C are globally known as prevailing agents in hepatocellular carcinoma (HCC) and associated mortality . As the Out of 36.7 million of HIV-infected individuals (including 2.6 million children) worldwide, ~70% are living in SSA, with consistent risks of mother-to-child transmission ,5. FurthIn HBV-endemic settings like SSA, anti-HBV vaccination is strongly recommended to every newborn ,11. Of nIn contrast to the high vaccine-induced HBV-protection rate (90–95%) observed among children living in western countries , childreIn a tropical context with highly prevalent HIV/HBV coinfection and consistent MTCT like Cameroon ,7,14, inWe herein sought to ascertain the overall post-vaccination response against HBV in children, compare the degree of HBV protection according to HIV vertical exposure and infection, evaluate the impact of infant feeding option and age on vaccine response.th May– 04th August in 2014 among HBV-vaccinated children at the Essos Health Centre (EHC) in Yaounde, Cameroon; stratified according to HIV profile, feeding option and age range.A prospective, observational and cross-sectional study was conducted from 052 featuring a tropical wet and dry climate with constant temperature (22.9–25.7°C mean daily temperature); the population is over 2.5 million inhabitants, for a density of 14,000/km2. EHC currently has a large accommodation capacity of ~250 beds, innovative technical equipment and a very high-performance within a wide range of specialised services: general medicine, emergency, anaesthesiology, reanimation, surgery and sub-specialities, gynaecology, ophthalmology, dentistry, medical imaging, laboratories (including molecular biology), pharmacy, neonatology, paediatrics, etc. Specifically, EHC is a reference antiretroviral treatment (ART) centre for both adults and children since 2005, with ~450 HIV-infected children on ART to date. This performance ranked the EHC as the four national reference center for paediatric ART in Cameroon.EHC is a reference health facility based in the capital city of Cameroon, a township of 180 kmAt the EHC, PMTCT of HBV at the study site follows national guidelines, and starts with antenatal screening for HBV infection for all pregnant women during antenatal care. For positive-HBsAg mothers, early neonatal administration of anti-HBV immunoglobulin is strongly recommended within 48 hours after birth. Both for HBV vertically exposed and unexposed infants, anti-HBV vaccine (Zilbrix Hepta) is administered  at a series of three monthly doses. Assessing antibody response consists of anti-HBs serological testing recommended at least 1–4 months after the final (third) vaccine dose.Based on a convenient sampling, the sample size was calculated using the following formula: (42.9%) , and “D”3) for HIV-infected children. Four children had received the third vaccine dose ≥4 months ago prior to enrolment, while two others had insufficient samples for laboratory analysis. Final sampling therefore had 82 study participants. The HIV status of the 82 participants, as well as the CD4 count of HIV-infected children, was confirmed from their medical records at EHC.At the vaccination unit of the EHC paediatric service, mothers and their children attending the routine immunization program were provided with information on the study objectives. Then, 200 mothers of potentially eligible children received the written information sheet and the study informed consent form. Of these 200 women, 34% (88) mothers returned with a signed informed consent form, and their children were enrolled. Vaccination charts of the 88 children were then checked by retrieving information to confirm eligibility to study criteria, mainly based on age (6–59 months), on complete anti-HBV vaccination , and on the absence of advanced stage of immunodeficiency , HIV-exposed but uninfected (group-B), and HIV-exposed and infected (group-C).As per the study secondary outcomes, participants were furthered stratified according to feeding option and age in the frame of anti-HBV vaccine response.Evaluation of post-vaccination response was based on a component of three different HBV-specific biomarkers, among which anti-HBs, anti-HBc and HBsAg tests.0.10 for the mean negative control and of ≥0.80 for the mean positive control. Cut-off value was calculated using the mean negative control x 2.1. Samples were considered Anti HBS positive if D.O ≥1.00, Anti HBS negative or “no vaccine response” if D.O <1.00. “Protective response” was defined as Anti HBS titer >10 UI/ml; “low response” as Anti HBS titer: 1–9 UI/ml; and “no response” Anti HBS titer <1 UI/ml.Levels of anti-HBs antibody titer was measured to determine the threshold of effective protection in HBV vaccinated children, using the quantitative anti-HBs Sandwich enzyme-linked immunosorbent assay (ELISA) of CTK Biotech, USA (lot: E0604K3), as per the manufacturer’s instructions. Briefly, reagents were brought at room temperature (18–25°c), wash solutions were prepared with phosphate buffer saline (1/30), and 50 μl of controls (negative and positive) and samples were added in respective wells. 50 μl of conjugate was added in each well (except for the blank), followed by incubation at 37°c for 60 min. Wells were washed and 50 μl of substrates A and B added in every well (including the blank), then incubated for 30 min at room temperature in a back room. 100μl of stop solution was then added to each well and reading of optical densities performed at 450 nm wave length, with reference to 630–690 nm. Assay validation was performed with optical density of ≤ This anti-HBs ELISA kit is coupled to the systematic detection of anti-HBc marker, irrespective of anti-HBs present or absent in the analysed serum .®, USA), with 50μl of serum. Validated results were reported as Anti-HBc “response” or “no response”. Both Anti-HBc results were all concordant, confirming HBV unexposed status.Anti-HBc marker was used to qualitatively detect any child with past/on-going exposure with HBV. In addition to aforementioned testing of anti-HBc, anti-HBc was also tested using the lateral flow chromatographic immunoassay HBV-5 Rapid Test  of BioSino Biotechnology & Science Inc , with 100μl of serum. Validated results were reported as HBsAg reactive (HBV-positive) or non-reactive (HBV-negative).S) “low-response” (1–9 UI/ml anti-HBS), or “no response” (<1 UI/ml anti-HBS).Vaccine response was defined by a profile of anti-HBs positive, anti-HBc negative and HBsAg negative; further stratified as “protective-response”  were performed using Chi-square and Fisher Exact test where appropriate, with corresponding 95% CI. P-values, generated by SAS, SPSS, R software, were considered statistically significant if p<0.05.Administrative authorisation (Reference: N°005/14/DCHE/DA/CE/CHE/CNPS) was issued and ethical clearance for the study obtained from the Institutional Review Board (IRB) of the Essos Health Centre (Reference: N°2014/001/EC-CHE). Mothers of potential participating children received detailed information on the study (with provision of an information sheet). Compliant mothers then provided each a signed written proxy-informed consent; this consent procedure was approved by the IRB. Laboratory results were freely offered for participant clinical benefits, data management was under strict confidentiality by using specific identifiers and restricted access.Study dataset is provided as supporting information .In total, 82 eligible children were enrolled in the study, all being anti-HBc and HBsAg negative. Sex ratio was similar (F/M: 5/4), median  age was 27 [IQR: 9–47] months, min-max: 6–59 months. According to maternal HBV status, 22 children were born to HBV-negative mothers (of whom 7 were HBV-vaccinated), four from HBV-positive mothers, and 56 from mothers with unknown HBV-status.All HIV-infected children were normal clients  attending the routine immunization program; all were receiving antiretroviral therapy and the majority were asymptomatic without any event of advanced immunodeficiency .According to feeding option of the 82 children during the first six months of life, 54.87% experienced exclusive-breastfeeding, 26.83% formula feeding, and 18.30% mixed feeding. All these children were not exposed to HBV, reported by a negative result both to anti-HBc and HBsAg testing.Overall assessment of anti-HBV post-vaccine response showed that: 80.49% (66/82) of children responded to anti-HBs testing (positive anti-HBsAb), indicating an immune response following anti-HBs vaccination, while 19.51% (16/82) did not responded to vaccination (negative anti-HBsAb).Analysis on the level of protective vaccine response revealed that only 45.12% (37/82) developed a protective immune response against HBV (anti-HBsAb ≥10IU/L) against 35.37% (29/82) who developed a low post-vaccine response.95% 0.933–7.5], p = 0.041), as shown in In group-A (HIV unexposed children), 82.14% (23/28) responded to HBV-vaccination and 60.71% (17/28) had a protective response. In the group of HIV-vertically exposed children, 79.63% (43/54) responded to HBV-vaccination and only 37.03% (20/54) had a protective response. Compared to HIV-unexposed children, the level of anti-HBV protection dropped significantly (~two fold) in HIV-exposed children as compared to : 2.627 [CI95%1.099–17.602], p = 0.065).Among HIV-exposed/uninfected children, 82.76% (24/29) responded to HBV-vaccination and 51.72% (15/29) had a protective response. Among HIV-exposed/infected children, 76.00% (19/25) responded to HBV-vaccination and only 20.00% (5/25) developed a protective response. Compared to HIV-exposed/uninfected children, the level of anti-HBV protection dropped in HIV-exposed/infected children , as shown in Among HIV-infected children, 76.00% (19/25) responded to HBV-vaccination and only 20.00% (5/25) had a protective response. Among all HIV-uninfected children (exposed or unexposed), 82.46% (47/57) responded to HBV-vaccination and 56.14% (32/57) had a protective response. Compared to HIV-uninfected children, the level of anti-HBV protection dropped significantly (~three fold) in HIV-infected children  on exclusive breastfeeding, against 43.24% (16/37) on mixed (15) or formula feeding (22), OR: 1.079 [CI = 0.757 .95% 1.362–11.356], p = 0.004; with specifically 67.65% (23/34) ≤6 months vs. 0%, (0/5) 33–41 months, p = 0.008.Evaluation of vaccine efficacy according to the age ranges of children revealed that protective-response decreased from 67.65% (23/34) for age 6–14 months, 35.71% (5/14) for age 15–23 months, 20% (1/5) for age 24–32 months, 0% (0/5) for age 33–41 months . Most imFurthermore, among all HIV-exposed children (n = 54), age ≤12 vs. >12 months, respectively, confirmed the decreasing protection with higher age and HIV-infection: uninfected  and infected .In highly endemic HBV and HIV settings like Cameroon, considering paediatric HIV-exposure when monitoring paediatric anti-HBV vaccine response might be of great clinical and public health relevance, and supports optimal performance of the EPI ,7,10–12.Though the majority (80.49%) of children were showed a response to anti-HBs testing, a non-negligible rate 19.51%) failed completely, highlighting the necessity for routine evaluation of post-vaccination to either confirm efficacy or determine eligibility for re-vaccination .51% fail. This inHaemophilus influenzae type b, etc) as earlier addressed [et al. in Kenya [Levels of anti-HBV protection dropped significantly for HIV-vertically exposed and/or infected children. This reflects the potential impact of maternal immunodeficiency on the child protectiveness ,9, and cddressed ,20,24. Tddressed ,22,25. Tin Kenya ,22,26.Though feeding options, especially exclusive breastfeeding, had no significant impact on anti-HBV vaccine response (p = 0.757) in our dataset, further investigations with higher sample size are needed on the impact of feeding option on anti-HBV vaccine response. This is because breast-feeding is generally known to positively modulate response to vaccines  through significant developmental changes in Th-1 pipeline response , as compared to formula-fed infants . This isThe quality of response appears to be decreasing, as children grow older, thus supporting the fact that anti-HBV immunization stimulates higher production of Th2-type cytokines and higher levels of antigen-specific type 2 immunoglobulins in newborns than in adults . Though The high rate of non-consenting mothers is the major limitations to our study, as this is directly related to the statistical power in the three arms. Non-consenting were due to (a) believe that vaccination automatically provide the required protection, (b) fear that the child sample could be used for other purpose beside informed research goals, (c) fear of phlebotomy, (d) undisclosed or unknown motivations. These indicate needs for counselling parents on the importance of controlling vaccine efficacy, as well as sensitizing health staff on implementing such measures in routine care, for programmatic effectiveness .Higher sampling would have allowed closer age-match, gender-match, and wider immune status analysis  with respect to anti-HBV vaccine response . Lack ofDespite high response to anti-HBV vaccination among Cameroonian children, protectiveness is poor in general (<50%), worse with HIV-exposure, and even worst with HIV-infection; and a decreasing response as children grow older. Strategies supporting early-age vaccination as well as implementing policies to monitoring post-vaccination response and cost-effective analysis of specific immunization algorithms for HIV vertically exposed- or infected-children would be of high public health benefit in resource-limited settings. These observations therefore merit wider sampling for confirmation towards a stronger policy-implementation.S1 File(ZIP)Click here for additional data file.


Correction to:Leukemia (2017) 31, 2717–2725; doi:10.1038/leu.2017.143; published online 23 May 2017This article was originally published under a CC BY-NC-ND 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the paper have been modified accordingly.


SALL4 and ZNF217 have been widely acknowledged as pivotal effectors stimulating embryonic immortalization as well as oncogenicity. Nevertheless, their prognostic worthiness towards solid tumors remains obscure. Hence we performed this comprehensive meta-analysis aiming to unveil the survival significance of both aberrantly expressed proteins.Overall we included 22 eligible entries comprising of 3093 participants. Over-expression of SALL4 and ZNF217 were negatively correlated with clinical prognosis of 3-year, 5-year, 10-year and disease-free survival in solid malignancies, irrespective of cancer types, source regions, mean-age and sex predominance. Results of sensitivity analysis additionally verified the stability of the pooled outcomes. No publication bias was observed on the basis of Egger's test and Begg's test.Studies were eventually included via database searching and rigorous eligibility appraisal. Data extraction and methodological assessment were implemented under a standard manner. Review Manager 5.3 and STATA 12.0 were utilized as statistical platforms following the recommendations by Cochrane Collaboration protocols.Aberrant amplification of SALL4 and ZNF217 serve as unfavorable predictors of survival expectancy among cancer sufferers, revealing great potential as targeted spots in future therapeutics. Over the past decade, the global healthcare system has been heavily burdened by soaring amount of solid malignancies . Includiin vivo and in vitro, SALL4 was first described as an oncoprotein in leukemia carcinogenesis [SALL4, expressively silenced in mature entities, is constitutively enriched in embryonic tissue and serves to maintain self-renewal capability , 4. Aberogenesis . Similarogenesis . NeverthAs a novel zinc finger transcription factor, ZNF217 was initially identified as a tumorigenic stimulator in breast carcinoma and was frequently amplified in diverse malignancies . HoweverTherefore, as representatives of zinc-finger transcriptional factors with independent performances, we performed this comprehensive meta-analysis aiming to clarify the prognostic roles of SALL4 and ZNF217 in solid malignancies and provide promising targeted spots.Deriving from 742 preliminarily retrieved entries, 22 observational cohorts were eventually selected (13 for SALL4 and 9 for ZNF217), with a total sample-size of 3093 participants (2111 for SALL4 and 982 for ZNF217). The selection flow chart was depicted in Figure n = 5) and liver cancer (n = 9) respectively. The wide spectrum of sample-size ranged from 38 to 337, with a median value of 144. Baseline parameters were statistically comparable between both contrastive groups. Additional details were demonstrated in Table Among the studies featuring SALL4 expression, the chief source region and cancer type were Japan (n = 4). Meanwhile, China (n = 3) became the major source region of literatures, followed by USA (n = 2) and France (n = 2). The median sample-size was 84, with a wide range from 44 to 319    . However, a poorer prognosis of cancer patients was observed concerning 5-year (P = 0.008) and 10-year disease free survival (P = 0.003)  (Other types: P = 0.01). Meanwhile, its unfavorable impact on overall survival was similarly observed among patients with 5-year follow-up duration (Liver cancer: P < 0.00001) (Other types: P = 0.0003)  .P = 0.004) (Mean-age < 60: P < 0.0001) and 5-year overall survival (Mean-age > 60: P = 0.04) (Mean-age < 60: P < 0.00001)  disclosed a prognostic disadvantage among solid cancer patients, irrespective of 3-year (Mean-age > 60: 0.00001) .P < 0.00001) and 5-year survival expectancy (P < 0.00001). Similar outcomes were obtained in non-Asian subgroup (3-year: P < 0.00001) (5-year: P < 0.00001)  .P < 0.0001)  and 5-year overall prognosis    .P = 0.0001)   , 5-year (P = 0.003) and 10-year disease frees survival (P = 0.006)  (Others types: P = 0.02) and 5-year prognosis respectively (Breast cancer: P = 0.01) (Others types: P = 0.0004)  .P = 0.04) and 5-year follow-up duration (P < 0.00001). Nevertheless, there was no significant correlation between ZNF217 overexpression and long-term prognosis among patients with mean-age < 50 (3-year:P = 0.06) (5-year: P = 0.06)  .P = 0.02) (Non-Asian: P = 0.005) and 5-year overall survival in solid malignancies (Asian: P = 0.002) (Non-Asian: P = 0.002)  .P = 0.03)  and 5-year overall survival in solid malignancies    .P < 0.0001) and 5-year (P < 0.00001) overall survival rate, despite that Han et al. [P = 0.0002) and 5-year (P < 0.00001) overall survival in solid malignancies.Firstly, we performed sensitivity analysis by elimination of low-quality trials (NOS = 6). Outcomes remained stable in terms of 3-year  or 5-year overall survival (P < 0.00001).Secondly, we implemented another sensitivity analysis by excluding studies with cytoplasmic staining. Nguyen et al.  and Li eP = 0.125; ZNF217: P = 0.790) and Begg's test  jointly confirmed that there was no publication bias among the included studies in both groups  expression and clinical prognosis in solid malignancies; 3. The expression of SALL4 or ZNF217 was detected by immunohistochemistry (IHC).Studies were ruled out due to the following reasons: 1. Inadequate survival data for further quantification or the follow-up duration was shorter than 3 years; 2. Overlapped or duplicated studies; 3. Inappropriate article types such as reviews and case-reports; 4. Studies involving less than 10 participants as its sample-size.Two investigators independently implemented the selection process and any disagreement was settled by mutual discussion.Standardized extraction forms were applied for data extraction. Concerning the classification standards of SALL4 and ZNF217 expression, we generally recognized low-expression as < 25% of cell positivity while high-expression as > 25% of cell positivity. However, this criterion was adaptively adjusted if necessary, mainly based on original subgroups within individual trials. Two authors collaboratively extracted prognostic materials from main texts or Kaplan-Meier curves.Owing to the observational properties of included studies, a Newcastle-Ottawa Scale (NOS) was employed for methodological evaluation. The scale consisted of three categories including selection, comparability and outcome, with a maximum score of nine. Studies graded with more than six scores were identified as high quality trials in methodology. Each study was appraised by two evaluators in an independent way. Any disapproval was resolved by mutual discussion.I2 as a heterogeneity indicator with its value < 25%, 25%–50% and > 50% defined as low, moderate and significant heterogeneity respectively. A moderate or significant heterogeneity was adjusted by a random-effects model, otherwise a fix-effects model was preferred. The statistical significance within all comparisons was mathematically signified as P < 0.05. Moreover, sensitivity analysis was applied to examine the stability of pooled outcomes. Publication bias was statistically analyzed via Egger's test and Begg's test, based on the results from STATA 12.0.Our quantitative calculation was performed on Review Manager 5.3 under Cochrane Collaboration protocols. Odds ratio (OR) along with Mantel-Haenszel model were adopted for dichotomous variables. We acknowledged


Visceral adiposity is associated with higher productions of C-reactive protein (CRP) and interleukin-6 (IL-6). Inflammation of obese adipose tissues could contribute to systemic metabolic dysregulation, especially thermogenic activity of white adipose tissues, namely, beige adipogenesis, characterized by altered irisin expression. Thus, we investigated the roles of inflammation and adipocyte beiging in Chinese centrally obese (CO) adults with metabolic syndrome (MetS).  This cross-sectional study was conducted on 54 CO and 58 non-CO subjects drawn from 1492 Chinese people with age and sex matched during November 2010 and August 2013. Twenty (37.0%) of the CO subjects fulfilled the IDF worldwide definition of MetS. Serum CRP, IL-6, and irisin levels were examined.  Higher CRP and IL-6, but lower irisin, levels were manifested in MetS versus non-MetS subjects with or without CO. Multiple linear regression identified high-density lipoprotein cholesterol level as the only independent risk factor for irisin level. Categorized by median of CRP and IL-6 levels, a lower irisin level was only observed in high CRP group.  Under the condition of central obesity, chronic inflammation and impaired beige adipogenesis are associated with MetS in Chinese adults. People with metabolic syndrome (MetS) are at a heightened risk for overt diabetes and cardiovascular events . RelativC-reactive protein (CRP), an established marker of inflammation, is an acute phase protein secreted from liver, playing a key role in the underlying causes of endothelial dysfunction as indicated by decreased nitric oxide and increased endothelin-1, as well as reduced plasminogen activator inhibitor-1 (PAI-1) levels . Moreoveγ coactivator-1 α/uncoupling protein-1 signaling cascades to elicit beige adipogenesis, muscular mitochondrial biogenesis, and fibre-type switching, resulting in loss of body weight Low level of HDL-C Raised blood glucose This case-matched, cross-sectional study was conducted on 112 subjects drawn from 1492 Hong Kong Chinese people aged from 24 to 86 years with age and sex matched during November 2010 and August 2013 , 28. AllWaist circumference and blood pressure were measured by a trained researcher (Yu AP) . Waist ct- or Mann–Whitney U tests. Univariate and stepwise multiple linear regressions were employed to estimate the correlations of each clinical characteristic with serum CRP, IL-6, and irisin levels. A two-tailed test with P ≤ 0.05 was considered significantly different. All statistical analyses were conducted using SPSS Statistics 24.0.Data were presented as mean ± SD (standard deviation) or median (25th and 75th percentiles) for continuous variables and assessed for normality by Shapiro-Wilk test. Either one-way analysis of variance or Kruskal-Wallis test was used for comparing differences across MetS, CO, and non-CO groups. Group differences were compared using either Student's P < 0.01 and P < 0.001), systolic BP (P < 0.001), diastolic BP (P < 0.001), plasma triglyceride (P < 0.001), and fasting blood glucose (P < 0.001), but lower HDL-C (P < 0.001) in MetS compared with non-MetS subjects with or without CO, respectively, whereas there was no significant difference between CO and non-CO, non-MetS subjects, except waist circumference (P < 0.001).The clinical characteristics of our subjects were categorized by the presence of CO in P < 0.01) and non-CO, non-MetS subjects (P < 0.01) (P < 0.05) and non-CO, non-MetS subjects (P < 0.01).There were significantly higher serum levels of CRP and IL-6 in MetS versus CO ( < 0.01) . On the P < 0.001), diastolic BP (P = 0.04), and triglycerides (P < 0.001), but negatively correlated with HDL-C levels (P < 0.001). Serum IL-6 levels were positively associated with waist circumference (P = 0.03), systolic BP (P = 0.008), diastolic BP (P = 0.04), triglycerides (P < 0.001), and fasting plasma glucose (P = 0.002) and also negatively correlated with HDL-C levels (P = 0.002). More importantly, serum irisin levels were negatively correlated with systolic BP (P = 0.04) and fasting plasma glucose (P = 0.03), but positively associated with HDL-C levels (P = 0.001) (P < 0.001) and irisin (P = 0.005) levels, respectively, whereas systolic BP was found to be the only independent risk factor for serum IL-6 levels (P = 0.006).The correlations of clinical characteristics with serum levels of CRP, IL-6, and irisin were analyzed using univariate and stepwise multiple linear regression models. Serum CRP levels were shown to be positively correlated with systolic BP (= 0.001) . StepwisP < 0.001] and IL-6  levels (Tables P < 0.001) and triglycerides (P = 0.01), but lower HDL-C (P = 0.001) and irisin (P = 0.05) levels in high versus low CRP groups (P = 0.003) and fasting plasma glucose (P = 0.009), but lower HDL-C (P = 0.02), were observed , serum irisin levels were also negatively correlated with waist circumference (R = −0.15). In addition, stepwise multiple linear regression determined HDL-C as the only independent predictor for serum irisin levels, substantiating circulating irisin as a surrogate marker of improved lipid profile as previously described [Adipose tissue is metabolically active in nature and a highly secretory endocrine organ that is capable of modulating signals in appetite, energy expenditure, immune responses, inflammation, insulin sensitivity, and so forth . In enerescribed –33.β levels [P = 0.28). This phenomenon could be attributed to dual functions of IL-6 in both pro- and anti-inflammation, and its conflicting roles are largely dependent on (1) its expression levels of which lower extent exerts anti-inflammatory actions and vice versa, (2) different cell contexts as exemplified by its varying roles in hepatocytes, endothelial cells, skeletal muscle, and macrophages, and (3) its selective involvement in either classic or alternative transsignaling, where components of the transsignaling were positively associated with MetS, endothelial dysfunction, and arterial stiffness in male subjects at high risk of cardiovascular disease, and effective blockade of this signaling has been experimentally proven to attenuate innate immunity-triggered inflammatory responses in phenotypically IL-6-transsignaling knockout-like mice [It is known that in obesity, inflamed adipose tissues could cause impaired beige adipogenesis and hence less efficient energy metabolism through complex interactions between macrophages and adipocytes , yet theβ levels . In contike mice . HoweverThe present study provides a novel insight on how chronic inflammation affects the thermogenic activity of adipose tissue possibly through altered circulating levels of irisin in Chinese adults. Future studies are warranted to further delineate the exact mechanism(s) underlying the interplay among a spectrum of inflammatory mediators and irisin.


Scientific Reports5: Article number: 16768; 10.1038/srep16768 published online: 11252015; updated: 10202017.This Article contains errors in the legend of Figure 5.A) Systemic zinc chloride  significantly inhibited NaHS-induced scratching. (B) Local application of ZnCl2 (i.d. 5 nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (C) ZnCl2 (i.d. 5 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (D) ZnCl2(i.pl. 5 nmol) significantly inhibited NaHS-induced flinching. (E) Systemic ascorbic acid  significantly inhibited NaHS-induced scratching. (F) Asc (i.d. 1 nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (G) Asc (i.d. 1 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (H) Asc (i.pl. 1 nmol) significantly inhibited NaHS-induced flinching. (I) Local application of mibefradil (Mib) (i.d. 5–25 nmol) dose-dependently inhibited NaHS-induced scratching in mice. (J) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced scratching in RTX-treated mice. (K) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (L) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced flinching. All data are expressed by means ± SEM. n = 6–8 mice per group. *P < 0.05; **P < 0.01, ***P < 0.001 vs. vehicle control, Student’s t test”.“(should read:A) Local application of mibefradil (Mib) (i.d. 5–25 nmol) dose-dependently inhibited NaHS-induced scratching in mice. (B) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced scratching in RTX-treated mice. (C) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (D) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced flinching. (E) Systemic zinc chloride  significantly inhibited NaHS-induced scratching. (F) Local application of ZnCl2 (i.d. 5 nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (G) ZnCl2 (i.d. 5 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (H) ZnCl2 (i.pl. 5 nmol) significantly inhibited NaHS-induced flinching. (I) Systemic ascorbic acid  significantly inhibited NaHS-induced scratching. (J) Asc (i.d. 1 nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (K) Asc (i.d. 1 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (L) Asc (i.pl. 1 nmol) significantly inhibited NaHS-induced flinching. All data are expressed by means ± SEM. n = 6–8 mice per group. *P < 0.05; **P < 0.01, ***P < 0.001 vs. vehicle control, Student’s t test”.“(


This E. coli is serotype O25b and sequence type 131, a pandemic clonal group, causing worldwide antimicrobial-resistant infections.The draft genome sequence has been determined for an extended-spectrum-β-lactamase (ESBL)-producing ( Escherichia coli sequence type 131 (ST131) has emerged as a globally dispersed pathogen, the predominant lineage causing extraintestinal infections, and is often resistant to antibiotic treatment . The ESBL-producing E. coli strain E10394 (= CCUG 62462) was isolated from a urinary tract infection (UTI) sample as part of an outbreak of ESBL-producing Enterobacteriaceae in a neonatal postsurgery ward at Sahlgrenska University Hospital, Gothenburg, Sweden, in 2008  with command line arguments “—stringency 3—retain_unpaired.” After quality filtering, 1,424,760 paired reads and 2,356/75 unpaired forward/reverse reads were retained for analysis. The high-quality reads were assembled de novo with SPAdes version 3.7.0  -IIa on contig LZET01000076, and aadA5, mph(A), sul1, and dfrA17 on contig LZET01000047. PlasmidFinder (IncFIA (nucleotide accession no. AP001918) on contig LZET01000040, IncFIB (accession no. AP001918) on contig LZET01000042, and IncFII (accession no. AY458016) on contigs LZET01000050, LZET01000068, and LZET01000072. In addition, genes involved in type IV secretion systems (T4SS) were identified, using CONJscan (F), relaxases , and type IV coupling proteins (T4CP). Three small plasmids were completely assembled. First, a 5,627-bp plasmid (contig LZET01000060), which was 99% identical to the pJJ1886_3 plasmid previously described in E. coli strain JJ1886 (accession no. CP006787.1), was found. Second, a 5,166-bp plasmid (contig LZET01000063), and last, a 1,718-bp plasmid (contig LZET01000087), which was 99% identical to plasmid pEC648 previously described in E. coli strain ST648 (accession no. CP008716.1), were found.The  = CCUG 6462 was iLZET00000000. The version described in this paper is version LZET00000000.1.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no.


Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Avena sect. Avena) were estimated to be in the early to middle Miocene, and the A. sativa lineages were dated to the late Miocene to Pliocene. These periods coincided with the mild seasonal climatic contrasts and the Mediterranean climate established in the Mediterranean Basin. Our results suggest that polyploidy, lineage divergence, and complex reticulate evolution have occurred in Avena, exemplifying the long-term persistence of tetraploids and the multiple origins of hexaploids related to paleoclimatic oscillations during the Miocene-Pliocene interval in the circum-Mediterranean region. This newly-resolved infrageneric phylogenetic framework represents a major step forward in understanding the origin of the cultivated oat.Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of  Genome duplication following hybridization  is common among flowering plants, and is found in nearly a quarter of Poaceae that provide crops and fuel worldwideAvena L. (Poaceae) contains ca. 29 species exhibiting considerable morphological and ecological diversity in the Mediterranean Basin, Eastern Africa, Europe, Asia, and the Americas4Avena: Avenotrichon (Holub) Baum, Ventricosa Baum ex Romero-Zarco, Agraria Baum, Tenuicarpa Baum, Ethiopica Baum, Pachycarpa Baum, and Avenax = 14), AB- and A’C (DC)-genome tetraploids (4x = 28), to ACD-genome hexaploids (6x = 42)9The genus ds 4x = 2, to ACD-A. clauda DurA. canariensis Baum & Raj. & SampA. insularis Ladiz., A. maroccana Grand., and A. murphyi Ladiz. may contain the D genome found in hexaploid oat11Avena.Molecular data support a close relationship between D and A genomes12A. strigosa Schreb. DNA was homologous to the A-genome sequences of the cultivated oatA. canariensisA. longiglumis DurA. weistii SteudA. damascena Rajah & Baum, A. hirtula Lag., and A. wiestii Steud. rather than from one particular species9812Cultivated oat offers a model for unraveling the dynamic evolutionary process of polyploid crops in the Mediterranean BasinA. sativa21A. clauda)Given chromosome structural differentiation, the C-genome origin of cultivated oat has been under intense scientific scrutiny. Eighteen chromosomes were involved in intergenomic translocations between C and A genomes of Avena with 28 (96.55%) species 3 polyploid cool-season grasses, e.g., fodder ryegrassesThe Mediterranean Basin, encompassing an area between 28°–48°N and 10°–39°E, is one of the 34 global biodiversity hotspots with c. 24,000  plant speciesth 28 96.5% specieAvena species  parsimony-informative characters. The maximum likelihood (ML) analyses and the Bayesian inference (BI) showed an identical topology for Avena . Three clades and two nodes were observed in the ppcB1 phylogram: A’C-PPI  , and A- and A’-type sequences hexaploids ]  and hexaploids ] (A. wiestii and A’(D)-type sequences of hexaploids (without A. fatua and A. nuda)] (PP = 0.80) , and A’ and C-type sequences of tetraploids  and hexaploids (without A. nuda)] (PP = 0.54) (Avena (The monophyly of  = 0.98) ; node A’erilis)] ; node ABntalis)] ; A-PPI -types of  = 1.00) . C-type ’C-PPIII . As for in Avena .GBSSI matrix had 1352 characters, including exons 9, 10, 11, 12, 13, and 14, and introns 8, 9, 10, 11, 12, 13, and 14, with the lengths of 53 bp, 81 bp, 194 bp, 88 bp, 129 bp, 22 bp, 47 bp, 148 bp, 153 bp, 127 bp, 154 bp, 152 bp, and 4 bp, respectively (GBSSI data provided 434 (32.1%) parsimony-informative characters. The ML and BI analyses generated different topologies for Avena  ] were observed in the GBSSI tree: A’C-GBI    and hexaploid A. fatua]  , A’-type sequences of A. maroccana and A. murphyi and hexaploids] (Avena (The monophyly of  = 1.00)  and 4. I = 1.00) ; AB-GBI  = 0.93) ; and AB&aploids] . The cla] ] were observed in the GBSS1 tree: A’C-GBI   , and A’-type sequences of A. maroccana and A. murphyi)] (PP = 0.50)  and hexaploids (without A. nuda and A. sterilis)] (PP = 0.66) (A. sterilis). Clade AB-GBI was sister to clade AB-GBII, and this group (PP = 0.66) plus clade A’C-GBII (PP = 0.50) was assigned to a single monophyletic lineage (PP = 0.98), which was sister to clade A’C-GBI. This large clade received strong support  in Avena -type sequences of tetraploids  = 1.00) ; A’C-GBI = 0.50) ; AB-GBI  = 0.50) ; and AB- = 0.66) . Clades in Avena .GBSSI sequences were identified in four accessions of A. sativa , consistent with its hexaploid origin. These sequences fell into three distinct groups. In clade A’C-GBI, C-type sequences of A. sativa clustered with C-genome diploids, C-type sequences of tetraploids  and hexaploids (without A. nuda)  , and C]-types of  = 1.00) . A-type  AB-GBII , respectanalysis , and conanalysis .gpa1 matrix had 1034 characters, including exons 10, 11, 12, introns 10, 11, and 12; with the lengths of 22 bp, 94 bp, 60 bp, 681 bp, 92 bp, and 85 bp, of which 137 (13.25%) were parsimony-informative. ML and BI analyses had an identical topology for Avena . Seven clades were observed for the gpa1 tree  and five hexaploids (without A. nuda)] ; A’C-GPII  ; A-GPI (A. canariensis and A-type sequence of A. hybrida) ; AB-GPI  ; A’C-GPIII (A. hirtula and A’-type sequences of A. maroccana) ; and AB-GPII  . Clades A-GPII, A-GPI, AB-GPI, A’C-GPIII, and A’C-GPII formed one monophyletic lineage , and this lineage in turn was sister to clade A’C-GPI with strong support , then the large group was sister to clade C-GPI with strong support  (The monophyly of pa1 tree : C-GPI ( = 1.00) .gpa1 sequences were identified in a single accession of A. sativa (Liu 310). These sequences fell into two distinct groups, with A’(D)-type sequence of A. sativa nested within clade AB-GPII, and C-type sequences of A. sativa nested within clade A’C-GPI (Two [A’(D)- and C-] types of  A’C-GPI .Avena ; A’C-NRR  + AB-NRR . Clade A’C-NRR + AB-NRR  was sister to clade C-NRR in Avena  were parsimony-informative. The BEAST analysis generated a well-supported tree, which was identical to the topologies obtained from ML and BI analyses of Avena . Two clain Avena . Here weAvena was 20.04 [95% highest posterior density (HPD) 3.56–35.06] mya (node 1). This was also the stem ages for clades C-NRR and A’C-NRR + AB-NRR, whose crown ages were 10.71 (HPD: 1.62–20.25) and 14.54 (HPD: 2.68–25.02) mya, respectively (nodes 2 and 3). The crown age of clade A’C-NRR + AB-NRR was also the divergence time for nodes A’C-NRR and AB-NRR (nodes 4 and 8). The crown ages of the A. sativa lineages were 2.43, 2.46, and 2.97 mya , respectively (The uncorrelated-rate relaxed molecular clock suggests that the crown age of ectively .Avena were identified by the plastid data: the C-genome diploid lineage (Avena sect. Ventricosa) containing A. clauda, A. eriantha, and A. ventricosa in clade C-NRR; and the A-genome diploid-polyploid lineage (Avena sect. Avena) containing other congeneric species in clade AB-NRR + A’C-NRR -genome tetraploids and hexaploids.Two strongly supported infrageneric lineages within  A’C-NRR . Members’C-PPIII  and A’C-’C-PPIII . In the Avena sect. Avena was proposed for the A-genome diploid-polyploid lineage including nodes with low support in the plastid tree , A. damascena (Ad-genome), and A. longiglumis (Al-genome) clustered with three A’C(DC)-genome tetraploids  in node A’C-PPII , A. canariensis (Ac-genome), A. damascena (Ad-genome), and A. prostrata (Ap-genome) clustered with AB-genome tetraploids in node AB-PPI , A. damascena (Ad-genome), and A. longiglumis (Al-genome) clustered with AB-genome tetraploids in clade AB-GBII -genome tetraploids originated from different A-genome diploid ancestors 5gpa1 tree  showed specific genetic divergence from A. hirtula and A. hispanica (group 3) in high-density GBS analysis6) and the genome size (9.08 ± 0.1112), A. hirtula can be easily differentiated from the two As-genome diploids, that have a similar genome size to the smallest Ad-genome diploid A. damasceneAvena lusitanica and A. hispanica might represent ecotypes of A. hirtula found in the circum-Mediterranean, western Asia, and EuropeWithin the As-genome diploids, tid tree . Howeverca group  showed sAvena sect. Ventricosa and the C-copy sequences of A’C-genome tetraploids plus hexaploids was a novel discovery which suggested their C-genome donor to be the ancestor of Avena sect. Ventricosa. This was consistent with the hypothesis that the paleotetraploidy events pre-dated and potentially triggered divergence of the extant A’C(DC)-genome tetraploids in narrow ranges of the Mediterranean Basingpa1 tree, A’C(DC)-genome tetraploids together with hexaploids comprised the clade A’C-GPI - and C-genome diploid ancestors to form A’C -genome tetraploids. The second step includes subsequent recent allohexaploidy events involving hybridization between DC-genome tetraploids and the more recent A-genome diploid progenitors to form the extant ACD-genome hexaploids A’C-GPI . TherefoppcB1 tree, i.e., A. atlantica, A. longiglumis, and A. wiestii were embedded within the A’C-PPII-A1, A’C-PPII-A2, and A-PPI subclades  located in node A’C-PPII and clade A-PPI (FL intron2 clones (CIav 9053)A. wiestii is certainly different from other As-genome diploids. Although the different genome forms of A. wiestii were close in genome sizeA wiestii deserves further investigation. Two plausible explanations can be proposed for the ploidy level of allelic variation found in A. wiestii. First, the three diploids may have arisen by allopolyploidy and subsequent unequal diploidization led to heterozygotes. Second, introgression may have brought about very subtle morphological and genetic changes in Avena  and 10.71 (HPD: 1.62–20.25) mya, respectively  seem to correlate with highly seasonal climatic oscillation. Geographic isolation might have contributed to genetic differentiation in the progenitor-derivative species pair, the presumed D(or A’)-genome progenitors having disjunct distributions in the Mediterranean region A. wiestii (eastern-most) from A. atlantica (western-most). Therefore, the independent hexaploidy events of cultivated oat were modulated by harsh climatic oscillation, thus A. sativa was able to adapt to new habitats.Cultivated oat may have arisen multiple times in response to selection pressure such as geographic isolation. The long-term aridity of the Mediterranean Basin summer became more severe along a south-eastern to north-western gradient during the late Miocene to PlioceneAvena represents a remarkable model to study because its history of polyploidy, lineage divergence, and complex reticulate evolution. The complex evolution of cultivated oat and its close relatives involved paleotetraploidy events between the ancient A(or A’)- and C-genome diploid ancestors and subsequent recent allohexaploidy events between A’C(DC)-genome tetraploids and the more recent A-genome diploid progenitors. The pattern of recurrent polyploidizations in Avena and their temporal relationships with paleoclimatic oscillations is unparalleled among polyploid crops occurring in the circum-Mediterranean region4AvenaSupplementary Table S1Eighty-nine accessions of 27 species were sampled to represent the morphological diversity and geographic range of six sections in phosphoenolpyruvate carboxylase B1 (ppcB1), granule-bound starch synthase I (GBSSI) and G protein alpha subunit 1 (gpa1), were used. The ppcB1 gene encodes PEPC enzyme for the oxaloacetate replenishment of the tricarboxylic acid cycle in C3 plantsGBSSI gene encodes GBSSI enzyme for the amylose synthesis in plantsgpa1 gene encodes a G-protein α subunit for signal transduction in flowering plants247448Three low-copy nuclear genes, et alppcB1, GBSSI, and gpa1) and plastid  fragments, which were amplified using designed or published primers and protocols listed in Table S2Escherichia coli TOP10 competent cells following the protocol of TOPO TA Cloning Kit . The resulting sequences were edited using Sequencher v.5.2.3  and aligned with MUSCLE v.3.8.31http://tree.bio.ed.ac.uk/software/seal/). All sequences were deposited in GenBank .Genomic DNA was extracted following Liu Phylogenetic analyses were performed using maximum likelihoodhttp://tree.bio.ed.ac.uk/software/tracer). All resulting trees were then combined with LogCombiner v.1.6.1 (http://beast.bio.ed.ac.uk/) with 25% burn-ins. The remaining trees  were used to calculate the Bayesian posterior probabilities (PP) for internal nodes. Data sets and phylogenetic trees are available at TreeBase   based on a likelihood ratio testAvena. Three plastid markers were partitioned using BEAUTI v.1.8.2 (within BEAST) with the best fit model determined by Modeltest v.3.7  of three runs was obtained using TreeAnnotator v.1.8.2 (within BEAST) with a PP limit of 0.5 and mean lineage heights. The convergence between two runs was checked using the “cumulative” and “compare” functions in AWTYHow to cite this article: Liu, Q. et al. Unraveling the evolutionary dynamics of ancient and recent polypoidization events in Avena (Poaceae). Sci. Rep.7, 41944; doi: 10.1038/srep41944 (2017).Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


The first author is listed incorrectly in the citation. Please view the correct citation here:https://doi.org/10.1371/journal.pone.0186602Guardo AC, Gómez CE, Díaz-Brito V, Pich J, Arnaiz JA, Perdiguero B, et al. (2017) Safety and vaccine-induced HIV-1 immune responses in healthy volunteers following a late MVA-B boost 4 years after the last immunization. PLoS ONE 12(10): e0186602.


Leishmania but not found in mammals, is considered a potentially useful target for chemotherapy against leishmaniasis. Leishmania (Viannia) braziliensis is endemic in Latin America and causes American tegumentary leishmaniasis. We demonstrated that IPCs are localized internally in parasites, using a specific monoclonal antibody. Treatment with 5 μM myriocin  rendered promastigotes 8-fold less infective than controls in experimental hamster infection, as determined by number of parasites per inguinal lymph node after 8 weeks infection, suggesting the importance of parasite IPC or sphingolipid derivatives in parasite infectivity or survival in the host. IPC was isolated from promastigotes of three L. (V.) braziliensis strains and analyzed by positive- and negative-ion ESI-MS. The major IPC ions were characterized as eicosasphinganine and eicosasphingosine. Negative-ion ESI-MS revealed IPC ion species at m/z 778.6 (d20:1/14:0), 780.6 (d20:0/14:0), 796.6 (t20:0/14:0), 806.6 (d20:1/16:0), and 808.6 (d20:0/16:0). IPCs isolated from L. (V.) braziliensis and L. (L.) major showed significant differences in IPC ceramide composition. The major IPC ion from L. (L.) major, detected in negative-ion ESI-MS at m/z 780.6, was composed of ceramide d16:1/18:0. Our results suggest that sphingosine synthase  in L. (V.) braziliensis is responsible for synthesis of a long-chain base of 20 carbons (d20), whereas SPT in L. (L.) major synthesizes a 16-carbon long-chain base (d16). A phylogenetic tree based on SPT proteins was constructed by analysis of sequence homologies in species of the Leishmania and Viannia subgenera. Results indicate that SPT gene position in L. (V.) braziliensis is completely separated from that of members of subgenus Leishmania, including L. (L.) major, L. (L.) infantum, and L. (L.) mexicana. Our findings clearly demonstrate sphingoid base differences between L. (V.) braziliensis and members of subgenus Leishmania, and are relevant to future development of more effective targeted anti-leishmaniasis drugs.Inositol phosphorylceramide (IPC), the major sphingolipid in the genus  Leishmania. The prevalence of leishmaniasis worldwide was recently estimated as 12 million cases, with ~1.5–2 million new cases per year  and Leishmania (Viannia), species of which are responsible for various clinical pathologies  and related biological, molecular, and biochemical features  has received considerable research attention during the past three decades because of their biological relevance as structural cell membrane components, and as bioactive compounds involved in cell-cell recognition, cell adhesion, cell growth, and signal transduction , with condensation by serine palmitoyltransferase (SPT) of L-serine and palmitoyl-CoA (16:0) to form 3-ketosphinganine, followed by reduction of this intermediate to produce sphinganine  in a reaction that involves NADPH  that contain two hydroxyl groups, and are denoted by the letter “d” (di) followed by the number of carbons in the chain. SLs in plants and fungi are derived from dihydroxylated or trihydroxylated sphingoid bases, and are denoted respectively by the letter “d” or “t.” Trihydroxylated sphingoid bases in plants and fungi are later acylated to form phytoceramide, a precursor of inositol phosphorylceramides (IPCs) and glycosyl inositol phosphorylceramides (GIPCs)  donovani promastigotes , sphingomyelin (SM), IPCs, and GIPCs  braziliensis promastigotes are present in fractions enriched in membrane microdomains resistant to non-ionic detergent at 4°C  mexicana  major  braziliensis contain mainly C14:0 fatty acid  braziliensis, one of the major etiologic agents of cutaneous and mucocutaneous leishmaniasis in South America. In cutaneous leishmaniasis, parasites spread from the skin to the naso-oropharyngeal mucosa. The causative factors for such mucosal dissemination and resulting mucosal disease are poorly understood. Effective systemic treatment of cutaneous leishmaniasis caused by L. (V.) braziliensis will presumably reduce the risk of mucosal disease development. We focused on characterization of IPCs from L. (V.) braziliensis mainly because these molecules, and enzymes involved in their specific biosynthetic pathways, are promising targets for anti-Leishmania drug development  tandem MS with electrospray ionization (ESI) in both negative-ion mode [M-H]Stock solutions of 2 mM myriocin (a SL synthesis inhibitor)  were prepared in dimethyl sulfoxide and stored at −70°C for a maximum of 1 month.L. (V.) braziliensis strains MHOM/BR/1987/M11272, MHOM/BR/2001/BA778  and MHOM/BR/1975/M2903 were cultured at 23°C by several passages of log-phase parasites in Medium 199 supplemented with 10% heat-inactivated fetal calf serum , 2 mM L-glutamine (Sigma-Aldrich), 0.02 mg ml−1 bovine hemin, 100 U ml−1 penicillin, 100 μg ml−1 streptomycin, and 2% sterile male human urine (complete medium). The starting inoculum (0.4 × 107 cells ml−1) consisted of parasites isolated from early stationary phase. Parasites were collected either in log-phase or after 48 h (stationary phase). L. (V.) major strain MRHO/SU/59/P (LV39) was also cultured at 23°C in complete Medium 199.Promastigotes of Leishmania (Viannia) braziliensis MHOM/BR/2001/BA778 promastigotes were cultured (starting inoculum 0.4 × 107 cells ml−1) in complete medium in the presence of myriocin (5 μM) or equivalent vehicle concentration for 6 days. Cell growth was estimated by counting cells with a hemocytometer (Improved Double Neubauer). Parasite viability was determined by SYTOX® Blue staining  as per the manufacturer's protocol, and shown to be >85% in control and myriocin-treated cultures. Parasite cultures were washed with PBS, cells were resuspended in PBS, and 1 × 106 parasites (0.05 ml) were inoculated subcutaneously in footpads of female golden hamsters (Mesocricetus auratus) (groups of four). Eight weeks after inoculation (infection), inguinal lymph nodes were removed and homogenized in 3 ml culture medium. Parasite suspension from each node was plated in complete Medium 199, and parasites were quantified by limiting dilution in 96-well plates containing 120 μl well−1. Plates were kept at 23°C for 7 days. Parasite number (PN) per lymph node was estimated based on the highest dilution at which parasites were detected after 7 days  × 3 . Experiments were performed in triplicate. All animal procedures were conducted in accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals of the Brazilian National Council of Animal Experimentation (www.cobea.org.br). The protocol was approved by the Research Ethical Committee of Federal University of São Paulo .Leishmania IPC; Godoy et al., MS in prep) and SST-1  .Parasites were fixed with 2% formaldehyde in 10 mM phosphate buffer, pH 7.2, containing 150 mM NaCl (PBS), for 10 min. Some fixed cells were permeabilized with 0.1% saponin. Cells were washed, resuspended in 1 ml PBS, and 100 μl of the solution was added to coverslips pretreated with 0.1% poly-L-lysine. Coverslips were blocked for 3 h with 0.1% gelatin in PBS and for 1 h with 10% skimmed milk and 1% bovine serum albumin (BSA) in PBS. Parasites were incubated sequentially with primary antibody LST-1   and with chloroform/methanol (CM)   20 psi, and nebulizing gas (N2) 40 psi. Each MS2 individual ion fragmentation was optimized with regard to capillary and collision energy to minimize variations in relative ion abundance resulting from differences in dissociation rates. The CID gas was argon at 2 mTorr. The inlet system consisted of a direct infusion pump (Harvard Apparatus), and methanol/ water  with 5 mM ammonium formate as mobile phase, flow rate 30 μl min−1. Precursor ion scan (PREIS) for detection of ion containing phosphoinositol derivative m/z 259 (inositol monophosphate anion) and m/z 241  was performed in negative ion mode with capillary energy -110 V and collision energy 40 V. Typically, 20 scans were used for accumulation of non-targeted scan range, and 30 scans for analysis of precursor ions. Ion characterization was performed by CID in negative and positive ion mode with collision energy 15, 30, or 45 V  with ESI source. Data acquisition was performed using the Varian MS Workstation program, V. 6.9. Sample analysis was conducted in positive-ion and negative-ion ESI modes with respective needle voltages 5.8 and 5 kV  infantum, L. (L.) donovani, L. (L.) mexicana, L. (L.) major, L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) panamensis, T. brucei, and T. cruzi CL Brener. Sequences were chosen by homology search using BLAST software with annotated yeast and/or human proteins as baits. Sequences were retrieved from GenBank or GeneDB (TriTrypDB) .Phylogenetic analysis was performed using gene data from SPT enzymes from many distinct species of the family Trypanosomatidae: B) Table . ID sequt-test, using GraphPad Prism software program V. 5.0 . Differences between means were considered statistically significant for p < 0.01. All experiments were performed in triplicate.Quantitative data were analyzed by Student's Leishmania surface, parasites were double-labeled with monoclonal antibodies (mAbs) directed to L. (V.) braziliensis glycolipids (mAb SST-1), and to Leishmania IPC (mAb LST-1). Representative images from a z-stack confocal series are shown in Figure To determine whether IPCs are expressed on the  mAb SST-, and to  mAb SST-, and to L. (V.) braziliensis IPC expression, growth rate, and cytokinesis , and at m/z 241, corresponding to inositol-1,2-cyclic phosphate anion (InsP-H2O). ESI-MS of [M-H]− ions of IPC fractions purified from three L. (V.) braziliensis strains  were performed, and similar spectral profiles were observed for all strains. In full scan of IPC fraction from negative-ion ESI-MS of L. (V.) braziliensis (M11272), major ions were detected at m/z 778.6 and 780.6, and minor components were detected at m/z 796.6, 806.6, and 808.6  major IPC fraction showed a distinctive profile: the major IPC ion was at m/z 778.6, relative abundance of m/z 780.6 was significantly reduced, and minor IPC ions were detected at m/z 796.6 and 806.6  braziliensis, and at m/z 780.6, 782.6, 798.6, and 808.6 for L. (L.) major  braziliensis and L. (L.) major  braziliensis and L. (L.) major  braziliensis  and 241 (InsP-H2O).CID was performed for major IPC ions detected in  Figures  and at ms Figure , phosphoL. (V.) braziliensis [M+H]+ ions at m/z 780.6, using collision energy of 15V, yielded expected fragments at m/z 762 (M-H2O), 520 (M-InsP), and 502 (M-InsP-H2O) . Application of higher collision energy (45 V) for the ion at m/z 780.6 , suggesting that this compound was d20:1/14:0-IPC. Figure L. (V.) braziliensis [M+H]+ ion at m/z 780.6.Ceramide moieties were characterized by CID in positive-ion mode using various collision energies. MS/MS product ion spectra of ) Figure . We also6 Figure , in addiL. (L.) major [M+H]+ ion at m/z 780.6, using collision energies 15 and 30V, gave rise as expected to ions at m/z 762 (M-H2O), 520 (M-InsP), and 502 (M-InsP-H2O)  braziliensis. The ion profile, in terms of LCB and fatty acid composition, was distinct from that of L. (V.) braziliensis. Ions were detected at m/z 236 (indicating the presence of d16:1 sphingoid base), and fragments at m/z 308 and 284 , identifying the 18:0-fatty acyl substituent, as described by Hsu et al.  braziliensis [M+H]+ ion at m/z 782.6 using collision energies 15 and 45 V , 522 (M-InsP), 504 (M-InsP-H2O), 294 , 252, and 228  , indicating that this compound is d20:0/14:0-IPC.ESI-MS/MS spectra of  Figures  generateL. (V.) braziliensis. ESI-MS/MS spectra of [M-H]− ions at m/z 796.6, 806.6, and 808.6 are shown in Figures m/z 259 (InsP) and 241 (InsP-H2O) were detected in all IPC ions.We also characterized minor IPC ions of + ion at m/z 798.6 allowed us to characterize the ceramide moiety. Using collision energy 45V , 520 (M-InsP-H2O), 328, 310, 292 (characteristic products of phytosphingosine t20:0), 252, and 228  . These findings suggest that this ion (m/z 798.6 in positive-ion mode) corresponds to t20:0/14:0-IPC.Analysis of ESI-MS/MS spectra of the [M+H]V Figure , the spe+ ion at m/z 808.6 using collision energy 45 V , 530 (M-InsP-H2O), 292 (characteristic of sphingoid base d20:1), 280, and 256 (corresponding to fatty acid 16:0 acyl substituent) , suggesting that this compound is d20:1/16:0-IPC.Analysis of ESI-MS/MS spectra of the [M+H]V Figure  generate+ ion at m/z 810.6 using collision energy 45 V , 532 (M-InsP-H2O), 294 (characteristic of d20:0), 280, and 256 (corresponding to fatty acid 16:0 acyl substituent) , suggesting that this compound is d20:0/16:0-IPC.Analysis of ESI-MS/MS spectra of the [M+H]V Figure  generateL. (V.) braziliensis are summarized in Table L. major  braziliensis display predominantly 20-carbon LCBs , and C14:0 and C16:0 fatty acids. Positive-ion ESI-CID-MS/MS of IPC ions from L. (V.) braziliensis did not detect product ions related to d16:0 (m/z 238) or d16:1(m/z 236). Positive-ion ESI-CID-MS/MS of L. (L.) major IPC ion at m/z 780.6 did not detect sphingoid base product related to d20:1 (m/z 292)  braziliensis strains M11272, BA778, and M2903.IPC proposed structures and positive- and negative-ion ESI-CID-MS/MS fragments of IPC ions from ) Figure , Table 2L. (V.) braziliensis is responsible for synthesis of 20-carbon LCB (d20), whereas L. (L.) major presents mainly 16-carbon LCB (d16), and T. brucei and T. cruzi SLs present mainly 18-carbon sphingoid bases (d18)  braziliensis, L. (V.) guyanensis and L. (V.) panamensis) were completely separated from those of the Leishmania subgenus (L. (L.) infantum, L. (L.) mexicana, and L. (L.) major), and comprised two distinct clades. SPTs of T. brucei and T. cruzi also represented different clades.SPT in Leishmania SPTs, we also analyzed N-terminal and catalytic portions of SPTs of L. (V.) braziliensis and L. (L.) major to determine whether sequence homologies refer specifically to the catalytic portion. Phylogenetic results were similar for sequences of SPT whole proteins, N-terminal regions, and catalytic regions  braziliensis  showed that IPCs and GIPLs are not co-localized in L. (V.) braziliensis promastigotes; GIPLs are found on the parasite surface whereas IPCs are localized internally. Labeling of IPCs was observed only when parasites were permeabilized with 0.1% saponin, confirming the internal localization of IPCs. Previous studies have demonstrated the involvement of Leishmania SLs in a variety of biological processes, including differentiation, replication, trafficking, and virulence  braziliensis promastigotes treated with the SPT inhibitor myriocin displayed reduced IPC accumulation and incomplete cytokinesis  braziliensis infectivity. Golden hamsters were infected by subcutaneous footpad injection of promastigotes treated (or not) with 5 μM myriocin for 6 days. After 8 weeks of infection, PN was counted in inguinal lymph nodes, and found to be ~8-fold lower for myriocin-treated parasites in comparison with controls. Our findings suggest that IPCs (and/or their intermediate SLs) are important for L. (V.) braziliensis infectivity, for their survival during the first few hours inside macrophages, for differentiation to amastigotes, and for amastigote proliferation. We obtained similar results in a previous study of L. (L.) amazonensis mouse experimental infection, in which parasite burden was reduced by infection of mouse footpads with promastigotes pretreated with a different SL inhibitor: the IPC synthase inhibitor aureobasidin A  major displayed defective membrane trafficking events in extracellular promastigotes, thus delaying promastigote infection in BALB/c mice  braziliensis contain mainly C14:0 fatty acid  major and L. (L.) donovani contain mainly C18:0 fatty acids  braziliensis strains, isolated from patients living in different regions of Brazil: reference strain MHOM/BR/1975/M2903 from a subject in Pará (Northern Brazil), strain MHOM/BR/01/BA788 from a cutaneous leishmaniasis patient in Bahia State (Northeastern Brazil), and strain MHOM/BR/1987/M11272 from a cutaneous leishmaniasis patient in Paraná State (Southern Brazil). IPC molecules were detected by negative-ion ESI-MS, as described by Hsu et al.  braziliensis, and to identify novel IPC structures. The major IPC ions detected by negative-ion ESI-MS were at m/z 778 and 780 for all three strains, regardless of whether ions were isolated at logarithmic or stationary growth phase. These two ions accounted for >70% of IPCs expressed in the parasites. In negative-ion mode, the full scan profile of IPC fractions isolated from the three strains showed ions at m/z 778.6, 780.6, 796.6, 806.6, and 808.6  major and L. (L.) donovani  major  donovani  braziliensis IPC [M+H]+ ions at m/z 780.6 and 782.6 displayed fragments at m/z 292 (20:1-LCB), 294 (20:0-LCB), and 228 (C14:0-fatty acyl substituent). IPC ions with the same mass in positive-ion mode (m/z 780 and 782) from L. (L.) major presented d16:1 and d16:0 LCBs, respectively, with C18:0-fatty acid. IPCs are the major SLs in Leishmania; these findings therefore suggest strongly that L. (V.) braziliensis preferentially synthesizes sphingoid bases through condensation of L-serine and stearoyl-CoA (18:0) to produce d20:0 in LCBs and ceramide, whereas L. (L.) major and L. (L.) donovani (subgenus Leishmania) preferentially synthesize d16:0 sphingoid base through condensation of L-serine and myristoyl-CoA (14:0)  braziliensis showed that the SPT protein sequence of L. (V.) braziliensis is completely separated from those of species in the Leishmania subgenus, suggesting that L. (V.) braziliensis and the Leishmania subgenus species represent different clades. The constructed trees suggest that genetic factors are involved in SPT separation. More precise studies are needed to clarify this issue. The two Leishmania subgenera may have differentiated at different times, as evidenced by the SPT protein data, and this separation may be responsible for observed differences in enzyme functions and specificities. The overall conclusion from the SPT phylogenetic tree is that neither L. major nor L. braziliensis is closer to T. cruzi or T. brucei. It appears that the common SPT ancestor of L. braziliensis and L. major separated from the Trypanosomatidae prior to the separation of Leishmania.In the present study, we investigated the role of SLs in u et al. , who dem6 Figure . PredomiL. (V.) braziliensis vs. L. major, in addition to differences in LCBs, show distinctive fatty acid compositions. In L. (V.) braziliensis IPCs, the major fatty acid is C14:0, and there are only trace amounts of fatty acid 16:0, as detected in positive-ion mode ESI-MS/MS at m/z 808.6 and 810.6. In contrast, the major fatty acid in L. (L.) major and L. (L.) donovani IPCs is stearic acid (C18:0)  braziliensis, preferentially use d20:0 and myristoyl-CoA (14:0) or palmitoyl-CoA (16:0), whereas members of the Leishmania subgenus, e.g., L. (L.) major and L. (L.) donovani, preferentially use d16:0 and stearoyl-CoA (18:0) amino)hexanoyl)sphingosine C6-ceramide.The existence of o et al.  reporteda et al.  showed tLeishmania enzyme specificities in LCB synthesis and concurrent ceramide synthesis will contribute to the development of more effective drugs having high ligand efficiency indices against L. (V.) braziliensis, L. (L.) major, or L. (L.) donovani, but low (or zero) ligand efficiency to mammalian host cells.Future studies on ED and AS conceived and designed the experiments, and wrote the manuscript. ED performed the experiments. ED and MT performed mass spectrometric analysis. RW and DB performed phylogenetic studies. ED and RM performed confocal microscopy and image analysis. HT critically reviewed and revised the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies. The ~4 Mb human leukocyte antigen (HLA) complex on chromosome 6 in humans is amongst the most polymorphic gene regions in the genome . SeventeBone Marrow Donors Worldwide (BMDW) is a centralized databank of HLA phenotypes and other relevant data of unrelated stem cell donors which aims to support HSCT programmes . The SouDonor registries continuously try to improve their recruitment strategies through increasing donor numbers , recruitIn this study, we describe HLA allele and haplotype frequency data from 237 donors registered with the SABMR, which serves as the source of unrelated marrow donors in South Africa. Frequencies of HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 alleles and haplotypes were analyzed with the aim of developing a resource for disease association, anthropology, and evolutionary studies. Furthermore, these data will support models for population-specific vaccine development  and willhttps://hml.nmdp.org/MacUI/.Two hundred and thirty-seven (237) SABMR-registered-consenting volunteer bone marrow donors HLA typed at varying resolutions were included in this study. This subset was accessed following an extensive reconsenting procedure of donors in the SAMBR. The self-reported ethnic grouping of the study population was Asian, Black, Chinese, Coloured, White, and some unknown. High-resolution typing has recently been adopted by SABMR, with most donors having low-resolution typing (two digit) , 21 whichttp://www.ebi.ac.uk/ipd/imgt/hla/) [Allele and haplotype  frequencies were estimated by resolving phase and allelic ambiguities using the expectation-maximization (EM) algorithm , 37 in Hgt/hla/) , 3 and rgt/hla/) . Global gt/hla/) . MAC codSelf-reported ethnicity was not considered for analysis in this study owing to redundancy and simplicity of this classification as previously discussed , 42. Onep < 0.05), with HLA-C and HLA-DQB1 having insignificant (p > 0.05) differences between expected and observed heterozygosity (p < 0.001), as summarized in In this donor subset, HLA-A, HLA-B, and HLA-DRB1 genotypes deviated from the expected HWE proportions (zygosity . No signzygosity . In addi∗02:01g (0.096), A∗03:01g (0.093), and A∗01:01g (0.057); B∗07:02g (0.082), B∗08:01g (0.049), and B∗58:02 (0.048); C∗07:02g (0.180), C∗07:01g (0.104), and C∗04:01g (0.091); DRB1∗15:01 (0.072), DRB1∗15:03 (0.065), and DRB1∗07:01 (0.057); and DQB1∗06:02 (0.157), DQB1∗03:01 (0.139), and DQB1∗05:01 (0.118).The full list of alleles including those derived from MACs and their frequencies are listed in ∗33:95~B∗07:231N (1.08725E-06), A∗03:01g~C∗07:02g~DQB1∗03:02 (1.03519E-06), and A∗11:01g~C∗01:02g~DRB1∗01:01~DQB1∗05:01 (2.8507E-06) were less frequent two, three, and four locus haplotypes, respectively (∗03:01g~B∗07:02g~C∗07:02g~DRB1∗15:01~DQB1∗06:02 being the most frequent (0.067).All two, three, four, and five (extended) haplotype frequencies are detailed in Supplementary ectively . The twehttps://hml.nmdp.org/MacUI) were analyzed using a robust Hapl-o-Mat [Although this study had a limited sample size of 237, we provide an in-depth analysis of HLA diversity in a subset of donors in the SABMR. Mixed resolution HLA typing data with multiple allele codes (pl-o-Mat  package pl-o-Mat . Althougp < 0.001 in p > 0.05), which contrasts to the significant deviation (p < 0.05) observed in the current study  encoded alleles [The main thrust of our study has been the ability to estimate, with high confidence, haplotype frequencies from mixed resolution typings including MAC , despitAlthough results reported here are from a small subset of SABMR registered donors, allele and haplotype frequencies generated by Hapl-o-Mat tool  could be


Bacillus velezensis YJ11-1-4 is a strain that exhibits broad-spectrum antimicrobial activity against various pathogens. It was isolated from doenjang, a traditional Korean fermented soybean paste. The genome comprises a single circular chromosome of 4,006,637 bp with 46.42% G+C content without plasmids. Bacillus velezensis was first proposed by Ruiz-García et al.  which has revealed good antimicrobial activities against various foodborne pathogens, including Bacillus cereus, Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Aspergillus flavus subsp. Flavus, was isolated from homemade doenjang, and its complete genome was sequenced.a et al.  as a surdization . Recentldization  suggesteB. velezensis YJ11-1-4 was sequenced using a Pacific Biosciences RS II platform with a 20-kb SMRTbell template library at Macrogen . It generated a total of 969,934,944 bp (about 198-fold coverage) with 112,837 reads. The sequencing reads were assembled using the Hierarchical Genome Assembly Process version 2.0 (HGAP2.0). The assembled genome of strain YJ11-1-4 comprises a single circular chromosome of 4,006,637 bp with a 46.42% G+C content without plasmids. The complete genome sequence was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The tRNA and rRNA genes were detected using tRNAscan-SE  encoded by bacABCDE (AAV30_01545 to AAV30_01565) (acnABCDEF (AAV30_04380 to AAV30_04405) (fenEDCBA (AAV30_10135 to AAV30_10160), bacillomycin D (targeting yeast) encoded by bmyDABC (AAV30_10275 to AAV30_10290), surfactin (targeting virus) encoded by srfABCD (AAV30_17390 to AAV30_17405), and an LCI gene (targeting some Gram-negative bacteria) (AAV30_17550)  . Strain B. velezensis YJ11-1-4 was deposited in NCBI under GenBank accession number CP011347.The genome information for


The genetic basis for biofilm formation among nontyphoidal salmonellae (NTS) remains poorly understood. This draft genome submission provides initial insights on the genetic differences between biofilm-forming and non-biofilm-forming clinical and environmental NTS serovars. Nontyphoidal salmonellae (NTS) are pathogens of global importance  with varSalmonella enterica serovars , which possess diametrically opposed biofilm phenotypes (biofilm formers and non-biofilm formers) as assessed by the crystal violet binding assay , and S. Dublin MN-12 (D15-051537) were isolated from a poultry barn, bovine lymph node, and porcine lung, respectively. The three non-biofilm-forming strains S. Heidelberg MN-618, S. Typhimurium variant 5 MN-62 (D15-043619), and S. Dublin MN-69 (D15-009047) were isolated from a poultry barn, bovine brain, and porcine lung, respectively.The NTS isolates sequenced in this study include pairs of strains from each of three ng assay . The thrde novo assembled by the A5-miseq pipeline (http://rast.nmpdr.org), and PGAP, of the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The occurrence of antibiotic resistance genes, clustered regularly interspaced short palindromic repeat (CRISPR) regions, prophages, Salmonella pathogenicity islands (SPIs), and number of plasmids on assembled sequences were predicted using ResFinder version 2.1 (http://crispr.i2bc.paris-saclay.fr/Server/), PHAST (https://cge.cbs.dtu.dk/services/SPIFinder), and PlasmidFinder version 1.3  and processed on the MiSeq platform . Paired-end reads were pipeline . The asssion 2.1 , CRISPRF), PHAST , SPI Finsion 1.3 , respectsion 1.3 .S. Heidelberg MN-714 , S. Typhimurium variant 5 MN-74 (D15-052810) , and S. Dublin MN-D12 (D15-051537)  possessed a higher number of plasmids than the non-biofilm-forming strains S. Heidelberg MN-618 (ColpVC and IncX1), S. Typhimurium variant 5 MN-62 (D15-043619) (no plasmid), and S. Dublin D MN-69 (D15-009047) (IncA/C2). Biofilms provide an ideal niche for plasmid exchange and also promotes plasmid stability  relative to non-biofilm formers. A larger genome size would favor increased functional gene content and could enhance the ability of organisms to form biofilms under stressful conditions. It is also noteworthy that the biofilm-forming strains D15-04361 , S. Dublin MN-12 (D15-051537), S. Heidelberg MN-618, S. Typhimurium variant 5 MN-62 (D15-043619), and S. Dublin MN-69 (D15-009047) have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Whole-genome sequences of the six NTS isolates


In the article titled “Chitosan Prevents Gentamicin-Induced Nephrotoxicity via a Carbonyl Stress-Dependent Pathway” , the namhttps://www.doi.org/10.1016/j.toxlet.2013.01.024. Additionally, the same picture of Figure 2(e) was presented as Figure 2(c). The corrected Also, there was an error in Figure 2. Figures 2(b) and 2(e) were inadvertently reused from Yi-Chieh Li, Yi-Min Shih, and Jen-Ai Lee, “Gentamicin caused renal injury deeply related to methylglyoxal and Nɛ-(carboxyethyl)lysine (CEL),” Toxicology Letters, Volume 219, Issue 1,


Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of A. alpinus strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes.The online version of this article (doi:10.1186/s40793-017-0264-0) contains supplementary material, which is available to authorized users. Antarctica. The optimum growth temperature range of this bacterium is 10–16 °C, which rendered it a promising source for discovery of novel cold-adapted enzymes. The complete genome sequence of 10.1601/nm.20084 strain R3.8 was generated using Single Molecule Real Time sequencing technology to provide a rapid and complete insight into its biotechnological potential. Here, we highlight various genome features that indicate the potential biotechnological value of 10.1601/nm.20084 strain R3.8 in the context of xenobiotic biodegradation and metabolism, chitin utilization, and as a potential component in bio-fertilizers.The production of cold-adapted enzymes by psychrotolerant bacteria has important scientific and industrial interest due to their highly specific activity and catalytic efficiency at low and moderate temperatures . The useArea No.129 . Strain R3.8 was isolated using basal medium supplied with C6-HSL as sole carbon source. An isolation temperature of 4 °C was used to select for psychrophilic or psychrotolerant bacteria maintained on Luria Bertani (LB) agar  and urease gamma subunit [AOC05_18490]). Urease is important in catalyzing one of the metabolic pathways involved in microbial-induced calcite precipitation. MICP is a promising approach in the containment of heavy metals such as lead and cadmium in contaminated soils , 24.Various other xenobiotic biodegradation genes and pathways of 10.1601/nm.20084 strain R3.8 are available from the PATRIC server.Chitinase is a biotechnologically-important enzyme widely used in waste management industries for the degradation of chitinous waste into simpler depolymerized substances , in agriN-acetylglucosamine utilization being identified, including beta-hexosaminidase (EC 3.2.1.52) , eukaryotic type N-acetylglucosamine kinase (EC 2.7.1.59) [AOC05_12050], PTS system, N-acetylglucosamine (EC 2.7.1.69) [AOC05_12345], N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) [AOC05_15120], eukaryotic type N-acetylglucosamine kinase (EC 2.7.1.59) [AOC05_15120], chitinase (EC 3.2.1.14) [AOC05_02965], N-acetyl-glucosamine kinase 2, ROK family (EC 2.7.1.59) [AOC05_03295], transcriptional regulator of N-acetylglucosamine utilization, GntR family [AOC05_07215] and glucosamine-6-phosphate deaminase (EC 3.5.99.6) [AOC05_10045].The full chitinolytic potential of 10.1601/nm.20084 strain R3.8 was also identified here, with various genes involved in chitin and N-(5′-phosphoribosyl) anthranilate isomerase [AOC05_12350] were identified. Production of bacterial IAA is important to assist plants to overcome abiotic stresses and inhibitory compounds, and thus contributes to plant growth stimulation [Application of psychrotrophic PGP bacteria to vegetation can promote growth and improve cold tolerance of crops . From thmulation . SeveralAntarctica. The strain was sequenced to explore its biotechnological potential. By analyzing the complete genome of 10.1601/nm.20084 strain R3, we identified genes involved in xenobiotic biodegradation and metabolism, and chitin utilization, as well as genes that potentially promote plant growth. Further comparative genomic studies with related isolates together with functional studies will provide better understanding of the potential biotechnological value of this strain.We report the complete genome sequence of 10.1601/nm.20084 strain R3.8 that was originally isolated from the soil collected from Rothera Point, Adelaide Island, maritime


Delineation of high-risk LTBI can, however, allow for chemoprophylaxis and curtail majority cases of active tuberculosis (ATB). There is epidemiological evidence to support the view that LTBI in context of HIV-1 co-infection is high-risk for progression to ATB relative to LTBI among HIV-ve persons. We recently showed that assays of M.tb thymidylate kinase (TMKmt) antigen and host specific IgG can differentiate ATB from LTBI and or no TB . In this study, we aimed to expose the differential levels of TMKmt Ag among HIV+ve co-infected LTBI relative to HIV-ve LTBI as a strategy to advance these assays for designating incipient LTBI.Precise designation of high risk forms of latent Mycobacterium TMKmt host specific IgM and IgG detection Enzyme Immuno-Assays (EIA) were conducted on 40 TB exposed house-hold contacts (22 LTBI vs. 18 no TB (NTB) by QunatiFERON-TB GOLD®); and TMKmt Ag detection EIA done on 82 LTBI (46 HIV+ve vs 36 HIV-ve) and 9 NTB (American donors). Purified recombinant TMKmt protein was used as positive control for the Ag assays.IgM levels were found to be equally low across QuantiFERON-TB GOLD® prequalified NTB and TB exposed house-hold contacts. Higher TMKmt host specific IgG trends were found among TB house-hold contacts relative to NTB controls. TMKmt Ag levels among HIV+ve LTBI were 0.2676 ± 0.0197 (95% CI: 0.2279 to 0.3073) relative to 0.1069 ± 0.01628 (95% CI: 0.07385 to 0.14) for HIV-ve LTBI (supporting incipient nature of LTBI in context of HIV-1 co-infection). NTB had TMKmt Ag levels of 0.1013 ± 0.02505 (5% CI: 0.0421 to 0.1606) (intimating that some were indeed LTBI).TMKmt Ag levels represent a novel surrogate biomarker for high-risk LTBI, while host-specific IgG can be used to designate NTB from LTBI.The online version of this article (10.1186/s12879-018-3007-y) contains supplementary material, which is available to authorized users. Mycobacterium tuberculosis (M. tb)  as per our prior work ) relative to HIV-ve LTBI (<0.14: 0.1069 ± 0.01628[95% CI: 0.07385 to 0.14]) (see Table On one hand:(a) for n=128 and prevalence of 80.0 , the sensitivity, specificity, PPV and NPV of pre-set TMKmt Ag capture-EIA-OD cut-off for differentiating ATB from NTB alone at 95% CI were respectively: 99.0 , 68.0 , 92.7 , and 94.4  [yielding a ROC-area of 83.5 ] compared to 96.6 , 21.1 , 78.9  and 66.7  [ROC-area 58.8 ] obtained using pre-set TMKmt host-specific IgG-EIA-OD cut-offs on n=154 participants and prevalence of 74.0 . On the other hand, (b) for n=220 and prevalence of 63.0 , the sensitivity, specificity, PPV and NPV of pre-set TMKmt Ag capture-EIA-OD cut-off for differentiating ATB from both LTBI & NTB at 95% CI were respectively: 73.9 , 90.2 , 92.7  and 67.3  [ ROC-area of 82.1 ] compared to 92.6 , 34.8 , 78.9  and 64.0  [ROC-area 63.7 ] obtained using pre-set TMKmt host-specific IgG-EIA-OD cut-offs for n=167 participants and prevalence of 72.0   as a surrogate for disease progression. Although several M.tb targets inclusive of lip-arabinomannose (LAM), IP-10, early secretory antigen 6(ESAT-6) and colony filtrate protein 10 (CFP-10) have previously been developed for the purpose of detecting TB, none meets the criteria for designating delineating high-risk LTBI [tb targets [A key limitation of our work—as is the case for all projects that aim to advance novel biomarkers for LTBI, is the absence of a gold standard for precisely designating LTBI and NTB –19. As nisk LTBI –7. On pa targets , 51. It  targets –19.In conclusion, TMKmt Ag and host specific IgG antibodies offer us novel surrogate biomarkers for LTBI in-context of HIV-1 co-infection. Precisely, Levels of TMKmt Ag represent a novel surrogate biomarker for high-risk LTBI, while host-specific IgG can be used to designate NTB from LTBI. TMKmt host specific IgM levels might be relevant towards evaluating TB exposure among residents of low TB endemic areas (NTB) who recently travelled to a high TB endemic area.Additional file 1:This file shows processing of the duplicate EIA readings for TMKmt Ag capture among the 46 HIV+ve LTBI and 36 HIV-ve LTBI relative to the 9 NTB controls and 2 rTMKmt positive controls. Overall, readings of blanks were subtracted from the average ODs of the test wells to obtain a corrected average ODs used to draw the graphs. (XLSX 29 kb)