Sample storage conditions induce post-collection biases in microbiome profiles

Background

Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4?°C, ??20?°C, and???80?°C), and hypoxic conditions.

Results

Only storage in lysis buffer significantly reduced DNA content, yet without integrity loss. Storage in EDTA affected alpha diversity the most, which was also reflected in cluster separation. Distinct changes were also seen in the phyla and bacterial species abundance per storage strategy. Metabolic function analysis showed 22 pathways not significantly affected by storage conditions, whereas the tyrosine metabolism pathway was significantly changed in all strategies except by EDTA.

Conclusion

Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data.

     

High Reinfection Rate after Preventive Chemotherapy for Fishborne Zoonotic Trematodes in Vietnam

Background

The World Health Organization aims for complete morbidity control of fishborne zoonotic trematodes (FZT) in endemic areas by 2020. The main intervention tool for achieving this goal is regular use of preventive chemotherapy by offering praziquantel to those at risk in endemic areas. The purpose of this study was to investigate the effectiveness of preventive chemotherapy to control FZT in an endemic area in Northern Vietnam.

Methodology and principle findings

We followed a cohort of 396 people who fulfilled the criteria for receiving preventive chemotherapy. Stool samples were examined by Kato-Katz technique for the presence of trematode eggs before, and two, 16, 29 and 60 weeks after preventive chemotherapy. The prevalence of trematode eggs in stool was 40.2% before, 2.3% two weeks after and increased to a cumulative prevalence of 29.8% sixty weeks after preventive chemotherapy.

Conclusions

The effectiveness of preventive chemotherapy as a main component in control of FZT is not well documented in most endemic areas. We found a high reinfection rate within the first year after preventive chemotherapy. Since these trematodes are zoonoses, preventive chemotherapy may not have sufficient impact alone on the transmission to have a lasting effect on the prevalence. Animal reservoirs and farm management practices must be targeted to achieve sustainable control of fishborne zoonotic trematode infections, hence control programs should consider a One Health approach.     

Bartonella henselae Endocarditis in Laos – ‘The Unsought Will Go Undetected’

Background

Both endocarditis and Bartonella infections are neglected public health problems, especially in rural Asia. Bartonella endocarditis has been described from wealthier countries in Asia, Japan, Korea, Thailand and India but there are no reports from poorer countries, such as the Lao PDR (Laos), probably because people have neglected to look.

Methodology/Principal Findings

We conducted a retrospective (2006–2012), and subsequent prospective study (2012–2013), at Mahosot Hospital, Vientiane, Laos, through liaison between the microbiology laboratory and the wards. Patients aged >1 year admitted with definite or possible endocarditis according to modified Duke criteria were included. In view of the strong suspicion of infective endocarditis, acute and convalescent sera from 30 patients with culture negative endocarditis were tested for antibodies to Brucella melitensis, Mycoplasma pneumoniae, Bartonella quintana, B. henselae, Coxiella burnetii and Legionella pneumophila. Western blot analysis using Bartonella species antigens enabled us to describe the first two Lao patients with known Bartonella henselae endocarditis.

Conclusions/Significance

We argue that it is likely that Bartonella endocarditis is neglected and more widespread than appreciated, as there are few laboratories in Asia able to make the diagnosis. Considering the high prevalence of rheumatic heart disease in Asia, there is remarkably little evidence on the bacterial etiology of endocarditis. Most evidence is derived from wealthy countries and investigation of the aetiology and optimal management of endocarditis in low income countries has been neglected. Interest in Bartonella as neglected pathogens is emerging, and improved methods for the rapid diagnosis of Bartonella endocarditis are needed, as it is likely that proven Bartonella endocarditis can be treated with simpler and less expensive regimens than “conventional” endocarditis and multicenter trials to optimize treatment are required. More understanding is needed on the risk factors for Bartonella endocarditis and the importance of vectors and vector control.     

应用斑点酶免疫法检测狂犬病毒抗体的研究

本文通过特异性试验、重复性试验、稳定性试验,建立了斑点酶免疫试验(DEIA)检测狂犬病毒抗体的方法,其结果与间接免疫荧光(IFA)法进行了比较,符合率100％,实验结果表明本法不但简便、稳定而且敏感特异,不需要特殊仪器设备及昂贵的荧光显微镜,是一种值得推广的检测狂犬病毒抗体的方法。     

Combined removal of nitrate and carbon in granular sludge: Substrate competition and activities

Granular sludge from an upflow anaerobic sludge blanket reactor treating synthetic waste water containing a mixture of volatile fatty acids and nitrate showed a removal efficiency of nearly 100% for both nitrogen and carbon. This activity was achieved by a combined process of denitrification and methanogenesis under conditions of surplus carbon. Under batch conditions the two processes proceeded clearly separated in time with first denitrification dominating and excluding methanogenesis. However, as soon as nitrate was depleted, methane production was initiated, showing that the inhibition of methanogenesis by nitrate was reversible. Of the volatile fatty acids supplied to the reactor, i.e. acetate, propionate, and butyrate, the denitrifying population clearly preferred butyrate and propionate even though acetate could also be metabolized. Consequently, growth of syntrophic volatile fatty acid degraders was suppressed by the denitrifiers in cases of low C:N ratios in the medium, leaving acetate as the major substrate for methanogenesis.Abbreviations UASB upflow anaerobic sludge blanket - COD chemical oxygen demand - VFA volatile fatty     

3T3-L1 adipocyte glucose transporter (HepG2 class): sequence and regulation of protein and mRNA expression by insulin, differentiation, and glucose starvation

A glucose transporter cDNA (GLUT) clone was isolated from mouse 3T3-L1 adipocytes and sequenced. The nucleotide and deduced amino acid sequences were, respectively, 95 and 99% homologous to those of the rat brain transporter. The mouse cDNA and a polyclonal antibody recognizing the corresponding in vitro translation product were used to compare changes in transporter mRNA and protein levels during differentiation, glucose starvation, and chronic insulin exposure of 3T3-L1 preadipocytes. The respective cellular content of transporter mRNA and protein were increased 6.6- and 7.8-fold during differentiation, and 3.8- and 2.5-fold from chronic insulin exposure of differentiated adipocytes. Glucose starvation increased transporter mRNA and protein levels 2.2- and 3.5-fold in undifferentiated preadipocytes and 1.8- and 3.1-fold in differentiated adipocytes. Starvation of undifferentiated cells completely converted the native transporter to an incompletely glycosylated form, while increasing basal transport rates 4.5-fold. Either full glycosylation is not required to produce a functionally active transporter, or starvation causes a unique predifferentiation induction of the normally absent "responsive" transporter. The changes in transporter protein expression elicited by differentiation were attributed primarily to increased rates of transporter synthesis, while the disproportionate changes in mRNA and protein expression from chronic insulin treatment and starvation suggested these conditions increase synthesis and decrease turnover rates in regulating transporter protein expression. Although chronic insulin exposure and glucose starvation each raised the expression of transporter protein greater than 3-fold and basal transport rates 2.5- to 4.5-fold, no significant increase in the insulin responsiveness of 3T3-L1 preadipocytes or differentiated adipocytes was observed. Thus, the changes in the transporter mRNA and protein expression observed in this study were most consistent with their being associated with the regulated expression of a basal or low level insulin-responsive transporter.     

Phylogenetic relationships of the tribe Operophterini (Lepidoptera, Geometridae): a case study of the evolution of female flightlessness

A molecular phylogenetic analysis was conducted in order to reconstruct the evolution of female flightlessness in the geometrid tribe Operophterini (Lepidoptera, Geometridae, Larentiinae). DNA variation in four nuclear gene regions, segments D1 and D2 of 28S rRNA, elongation factor 1α , and wingless , was examined from 22 species representing seven tribes of Larentiinae and six outgroup species. Direct optimization was used to infer a phylogenetic hypothesis from the combined sequence data set. The results obtained confirmed that Operophterini (including Malacodea ) is a monophyletic group, and Perizomini is its sister group. Within Operophterini, the genus Malacodea is the sister group to the genera Operophtera and Epirrita , which form a monophyletic group. This relationship is also supported by morphological data. The results suggest that female flightlessness has evolved independently twice: first in the lineage of Malacodea and, for the second time, in the lineage of Operophtera after its separation from the lineage of Epirrita . An alternative reconstruction (i.e. recovery of flight ability in an ancestor of Epirrita ) appears unlikely for various reasons. The similarities shared by Epirrita with a basal representative of Perizomini, Perizoma didymatum , allow the proposal of a sequence of evolutionary events that has led to flightlessness. It is likely that the transition to female flightlessness in the two lineages of Operophterini occurred after the colonization of stable forest habitats, followed by the evolution of a specific set of permissive traits, including larval polyphagy, limited importance of adult feeding, and adult flight during the cold months of the season.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 241–252.