Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies

BACKGROUND: The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of H. pylori require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene gdh (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene gtf (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations. RESULTS: Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes gdh and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene gtf had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the gdh and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for gtf the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly together and branched with American countries and South Africa, to the exclusion of Asian countries and the Congo. CONCLUSION: This study shows that saliva harbours protein-coding bacterial genes that are geographically structured, and which could potentially be used for addressing previously unresolved human migration events

MSM16/3 raw data of EM1002 multibeam echosounder (bathymetry & beam time series)

Bathymetry data based on the multibeam echosounders (MBES) KONGSBERG EM120 and EM1002 was conducted during R/V MARIA S. MERIAN cruise MSM16/3 between 13.10.2010 and 20.11.2010 in the Eastern Atlantic off Mauritania. The expedition aimed at a comprehensive understanding of the complex sedimentary system on the Mauritian Shelf as an atypical tropical eutrophic ecosystem and an archive of palaeoclimatic change in Africa during the Holocene. During the expedition, the chain of Mauritian coral reef mounds was mapped for the first time, carbonate-producing organisms successfully sampled and the flooding history of the Golfe d'Arguin investigated. Hydroacoustic surveys were conducted for a better understanding of the topography, and particularly for the identification of coral mounds and their morphological and structural patterns. In addition to bathymetric mapping, further instruments complemented the research programme, such as the sub-bottom profiler PARASOUND, a fast-rescue boat for shallow water surveys, various sediment sampling and coring devices, a CTD, an aerial dust collector and a remotely operated vehicle (ROV). CI Citation: Paul Wintersteller ([email protected]) as responsible party for bathymetry raw data ingest and approval. Description of the data source: During the MSM16/3 expedition, the KONGSBERG EM1002 multibeam ecosounder (MBES) was utilized for high-resolution bathymetric mapping in water depths from 30 to 800m. A semi-circular transducer array with a radius of 45 cm and 160° angular extent transmits a nominal sounding frequency of 95 kHz with a maximum angular coverage sector of 150°. During the reception, 111 beams with widths of 2° by 2.3° are formed. Depending on the reflectivity of the seafloor, the swath width can reach up to 7.4 times the water depth. During the cruise, the angular coverage sector and beam pointing angles were set to vary automatically with depth according to achievable coverage in order to maximize the number of usable beams. The depth of the water column is calculated through the two-way-travel time, beam angle and ray bending due to refraction in the water column by sound speed variations. Combining amplitude (for central beams) and phase (for slant beams) provides accuracy practically independent of the beam-pointing angle. For further information on the system, consult https://www.km.kongsberg.com/. Responsible persons during this cruise / PI: Andre Freiwald ([email protected]), Till Hanebuth ([email protected]) & Stephen Schilling Chief Scientist: Hildegard Westphal ([email protected]) CR: https://www.tib.eu/en/search/id/awi%3Adoi~10.2312%252Fcr_msm16_3/ CSR: https://www2.bsh.de/aktdat/dod/fahrtergebnis/2010/20100362.ht

MSM16/3 raw data of EM120 multibeam echosounder (bathymetry & beam time series)

Bathymetric data based on the multibeam echosounders (MBES) KONGSBERG EM120 and EM1002 was conducted during R/V MARIA S. MERIAN cruise MSM16/3 between 13.10.2010 and 20.11.2010 in the Eastern Atlantic off Mauritania. The expedition aimed at a comprehensive understanding of the complex sedimentary system on the Mauritian Shelf as an atypical tropical eutrophic ecosystem and an archive of palaeoclimatic change in Africa during the Holocene. During the expedition, the chain of Mauritian coral reef mounds was mapped for the first time, carbonate-producing organisms successfully sampled and the flooding history of the Golfe d'Arguin investigated. Hydroacoustic surveys were conducted for a better understanding of the topography, and particularly for the identification of coral mounds and their morphological and structural patterns. In addition to bathymetric mapping, further instruments complemented the research programme, such as the sub-bottom profiler PARASOUND, a fast-rescue boat for shallow water surveys, various sediment sampling and coring devices, a CTD, an aerial dust collector and a remotely operated vehicle (ROV). CI Citation: Paul Wintersteller ([email protected]) as responsible party for bathymetry raw data ingest and approval. Description of the data source: During the MSM16/3 expedition, the hull-mounted KONGSBERG EM120 multibeam ecosounder (MBES) was utilized for bathymetric mapping in water depth beyond 800 m as it allows accurate bathymetric mapping up to full ocean depth. Two linear transducer arrays in Mills Cross configuration transmit a nominal sonar frequency of 12 kHz with an emission beam of 150° across track and 1° along track, and receive 191 beams with widths of 2° across track and 20° along track. The actual footprint of a beam has a dimension of 1° by 2°. On flat bottom, the achievable swath width can reach up to six times the water depth. The angular coverage sector and beam pointing angles were set to vary automatically with depth according to achievable coverage. For further information on the system, consult https://www.km.kongsberg.com/. The depth of the water column is estimated through the two-way-travel time, beam angle and ray bending due to refraction in the water column by sound speed variations. Combining amplitude (for central beams) and phase (for slant beams) provides accuracy practically independent of the beam-pointing angle. Responsible persons during this cruise / PI: Andre Freiwald ([email protected]), Till Hanebuth ([email protected]) & Stephen Schilling Chief Scientist: Hildegard Westphal ([email protected]) CR: https://www.tib.eu/en/search/id/awi%3Adoi~10.2312%252Fcr_msm16_3/ CSR: https://www2.bsh.de/aktdat/dod/fahrtergebnis/2010/20100362.ht

Software-based detection of atrial fibrillation in long-term ECGs

Background Atrial fibrillation (AF) is common and may have severe consequences. Continuous long-term electrocardiogram (ECG) is widely used for AF screening. Recently, commercial ECG analysis software was launched, which automatically detects AF in long-term ECGs. It has been claimed that such tools offer reliable AF screening and save time for ECG analysis. However, this has not been investigated in a real-life patient cohort. Objective To investigate the performance of automatic software-based screening for AF in long-term ECGs. Methods Two independent physicians manually screened 22,601 hours of continuous long-term ECGs from 150 patients for AF. Presence, number, and duration of AF episodes were registered. Subsequently, the recordings were screened for AF by an established ECG analysis software (Pathfinder SL), and its performance was validated against the thorough manual analysis (gold standard). Results Sensitivity and specificity for AF detection was 98.5% (95% confidence interval 91.72%–99.96%) and 80.21% (95% confidence interval 70.83%–87.64%), respectively. Software-based AF detection was inferior to manual analysis by physicians (P < .0001). Median AF duration was underestimated (19.4 hours vs 22.1 hours; P < .001) and median number of AF episodes was overestimated (32 episodes vs 2 episodes; P < .001) by the software. In comparison to extensive quantitative manual ECG analysis, software-based analysis saved time (2 minutes vs 19 minutes; P < .001). Conclusion Owing to its high sensitivity and ability to save time, software-based ECG analysis may be used as a screening tool for AF. An additional manual confirmatory analysis may be required to reduce the number of false-positive findings

Is 7-day event triggered ECG recording equivalent to 7-day Holter ECG recording for atrial fibrillation screening?

Prolonged ECG monitoring is standard for atrial fibrillation (AF) screening. This study investigated whether 7-day event triggered (tECG) ECG recording is equivalent to 7-day continuous Holter (cECG) ECG recording for AF screening

Characterization of Endogenous SERINC5 Protein as Anti-HIV-1 Factor

We thank Oliver Dittrich-Breiholz for granting access to the StepOne Plus real-time PCR system. We thank the Flow Cytometry Core Facility at University Hospital Bonn for help with FACS analysis. We thank Heinrich Göttlinger for providing the SERINC5(iHA)-encoding pBJ5 plasmid. We are grateful to Thomas Pietschmann for constant support. We thank the NIH AIDS Reagent Program for providing essential reagents. TWINCORE is a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.International audienceSERINC5 is the long-searched-for antiviral factor that is counteracted by the HIV-1 accessory gene product Nef. Here, we engineered, via CRISPR/Cas9 technology, T-cell lines that express endogenous SERINC5 alleles tagged with a knocked-in HA epitope. This genetic modification enabled us to study basic properties of endogenous SERINC5 and to verify proposed mechanisms of HIV-1 Nef-mediated counteraction of SERINC5. Using this unique resource, we identified the susceptibility of endogenous SERINC5 protein to posttranslational modulation by type I IFNs and suggest uncoupling of Nef-mediated functional antagonism from SERINC5 exclusion from virions

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Das Lagemanagement des Robert Koch-Instituts während der COVID-19-Pandemie und der Austausch zwischen Bund und Ländern

The Robert Koch Institute (RKI) plays a central role in Germany in the management of health hazards of biological origin. The RKI's crisis management aims to contribute to protecting the health of the population in Germany in significant epidemic situations and to maintain the RKI's working ability over a long period of time even under high load. This article illustrates the crisis management of the RKI in general as well as during the COVID-19 pandemic. The generic RKI crisis management structures and the setup of the RKI emergency operations centre (EOC), their operationalisation in the context of the COVID-19 pandemic and the resulting challenges as of 31 October 2020 are described in this paper. The exchange between the federal and state governments during the pandemic is also described.The COVID-19 pandemic has led to extraordinary circumstances. During the epidemic situation, good communication and coordination has been essential, both within the RKI and with other federal or state authorities and expert groups. Under great pressure, the RKI produces and regularly updates recommendations, statements and assessments on various topics. To provide operational support for all COVID-19 related activities, an EOC was activated at the RKI. During the COVID-19 pandemic, there are various challenges regarding personnel and structures. It became apparent that good preparation (e.g. existing task descriptions and premises) has an important positive impact on crisis management