Isolation of bovine follicular dendritic cells allows the demonstration of a particular cellular prion protein

As interaction of cellular prion protein (PrPc) and the infectious agent (PrPres) appears to be a crucial pathogenic step promoted by homology, variation in PrPc isoforms on bovine immune cells may explain the absence of infectivity in most bovine lymph organs. In this study, we examined PrPc expression in bovine lymph organs (tonsils and lymph nodes) and on isolated follicular dendritic cells (FDCs). We used a panel of different monoclonal antibodies (MoAbs) raised against different epitopes of prion protein. Two MoAbs recognise amino acids 79-92 (SAF 34 and SAF 32 Mo-Abs); the 6H4 antibody reacts with a specific peptide comprising the 144-152 amino acids, and the 12F10 MoAb recognises the sequence 142-160. After immunolabelling of frozen sections of lymph organs with 6H4 or 12F10 MoAbs, we detected cellular prion protein in germinal centres. However, using the SAF 34 or SAF 32 antibodies, PrPc was revealed outside the lymphoid tissues. No PrPc was observed in the germinal centres. Therefore, we adapted the method of FDC isolation, making it suitable for the study of PrPc expression on their surface. Using electron microscopy, the presence of PrPc on the surface of FDCs was demonstrated only with 6H4 MoAb. These results suggest that bovine follicular dendritic cells express a particular form of prion protein. Either the N-terminal part of PrPc is cleaved or the accessibility of the specific epitope (79-92) of SAF 34 MoAb is abolished by interaction with other molecules. This particular isoform of PrPc on bovine FDCs might be related to the apparent absence of infectivity in lymph organs in cattle affected by bovine spongiform encephalopathy.     

Seroepidemiologic evidence of Q fever and associated factors among workers in veterinary service laboratory in South Korea

The incidence of Q fever has rapidly increased in South Korea since 2015. This study was undertaken to investigate the seroprevalence and seroreactivity of Q fever and the risk factors associated with its seroprevalence among workers in the veterinary service laboratory (VSL) in South Korea. This seroepidemiologic study was conducted in a total of 661 human subjects out of 1,328 subjects working in 50 VSL existing in South Korea between July 15 and July 29, 2019. Data were collected by administering survey questionnaires and by analyzing collected blood samples to determine the presence of antibodies against Coxiella burnetii. The seroprevalence and seroreactivity of C. burnetii infection were determined based on serum titers as (phase II IgG ≥1:256 and/or IgM ≥1:16) and (phase II IgG ≥1:16 and/or IgM ≥1:16) as determined by indirect immunofluorescent assay. Work, work environment, behavioral risk and protective factors associated with seroprevalence of Q fever were assessed by employing multivariable logistic regression analysis. Among the 661, the seroprevalence and seroreactivity of C. burnetii infection were 7.9% and 16.0%, respectively. Multivariate logistic regression analysis showed the risk factors significantly associated with seroprevalence were the antemortem inspection of cattle, goats, or sheep (APR (adjusted prevalence ratio), 2.52; 95% CI, 1.23–4.70)), animal blood splashed into or around eyes (APR, 2.24; 95% CI, 1.04–4.41), and contact with animals having Q fever (APR, 6.58; 95% CI, 3.39–10.85) during the previous year. This study suggests the need for precautions when contact with cattle, goats, or sheep is expected, especially during the antemortem inspection, when dealing with C. burnetii infected animals, or when there is a risk of ocular contact with animal derivatives. Therefore, we recommend the consistent use of appropriate personal protective equipment and other protective measures including PPE treatment and washing of body surfaces after work to prevent C. burnetii infections among VSL staff in South Korea.     

Interpretation of network-based integration from multi-omics longitudinal data

Multi-omics integration is key to fully understand complex biological processes in an holistic manner. Furthermore, multi-omics combined with new longitudinal experimental design can unreveal dynamic relationships between omics layers and identify key players or interactions in system development or complex phenotypes. However, integration methods have to address various experimental designs and do not guarantee interpretable biological results. The new challenge of multi-omics integration is to solve interpretation and unlock the hidden knowledge within the multi-omics data. In this paper, we go beyond integration and propose a generic approach to face the interpretation problem. From multi-omics longitudinal data, this approach builds and explores hybrid multi-omics networks composed of both inferred and known relationships within and between omics layers. With smart node labelling and propagation analysis, this approach predicts regulation mechanisms and multi-omics functional modules. We applied the method on 3 case studies with various multi-omics designs and identified new multi-layer interactions involved in key biological functions that could not be revealed with single omics analysis. Moreover, we highlighted interplay in the kinetics that could help identify novel biological mechanisms. This method is available as an R package netOmics to readily suit any application.     

Limnological Studies on the River Tigris,Iraq. I. Environmental Characteristics

Regional and seasonal variations of some environmental characteristics in the 630 km stretch of the lower Tigris were studied and discussed. The lowest air and average water temperatures were recorded in January. The highest average pH values, generally found in October and July, are due mainly to the abundance of phytoplankton. The remarkably low average chlorosity values found in the periods of high water were correlated with the high discharge. The highest average values for dissolved oxygen concentration were generally recorded in January and April, and the lowest ones were observed in October and July.     

Identification of the target and mode of action for the prokaryotic nucleotide excision repair inhibitor ATBC

In bacteria, nucleotide excision repair (NER) plays a major role in repairing DNA damage from a wide variety of sources. Therefore, its inhibition offers potential to develop a new antibacterial in combination with adjuvants, such as UV light. To date, only one known chemical inhibitor of NER is 2-(5-amino-1,3,4-thiadiazol-2-yl)benzo(f)chromen-3-one (ATBC) exists and targets Mycobacterium tuberculosis NER. To enable the design of future drugs, we need to understand its mechanism of action. To determine the mechanism of action, we used in silico structure-based prediction, which identified the ATP-binding pocket of Escherichia coli UvrA as a probable target. Growth studies in E. coli showed it was nontoxic alone, but able to impair growth when combined with DNA-damaging agents, and as we predicted, it reduced by an approximately 70% UvrA’s ATPase rate. Since UvrA’s ATPase activity is necessary for effective DNA binding, we used single-molecule microscopy to directly observe DNA association. We measured an approximately sevenfold reduction in UvrA molecules binding to a single molecule of dsDNA suspended between optically trapped beads. These data provide a clear mechanism of action for ATBC, and show that targeting UvrA’s ATPase pocket is effective and ATBC provides an excellent framework for the derivation of more soluble inhibitors that can be tested for activity.     

Prediction of Soil Organic Carbon at the European Scale by Visible and Near InfraRed Reflectance Spectroscopy

Soil organic carbon is a key soil property related to soil fertility, aggregate stability and the exchange of CO₂ with the atmosphere. Existing soil maps and inventories can rarely be used to monitor the state and evolution in soil organic carbon content due to their poor spatial resolution, lack of consistency and high updating costs. Visible and Near Infrared diffuse reflectance spectroscopy is an alternative method to provide cheap and high-density soil data. However, there are still some uncertainties on its capacity to produce reliable predictions for areas characterized by large soil diversity. Using a large-scale EU soil survey of about 20,000 samples and covering 23 countries, we assessed the performance of reflectance spectroscopy for the prediction of soil organic carbon content. The best calibrations achieved a root mean square error ranging from 4 to 15 g C kg⁻¹ for mineral soils and a root mean square error of 50 g C kg⁻¹ for organic soil materials. Model errors are shown to be related to the levels of soil organic carbon and variations in other soil properties such as sand and clay content. Although errors are ∼5 times larger than the reproducibility error of the laboratory method, reflectance spectroscopy provides unbiased predictions of the soil organic carbon content. Such estimates could be used for assessing the mean soil organic carbon content of large geographical entities or countries. This study is a first step towards providing uniform continental-scale spectroscopic estimations of soil organic carbon, meeting an increasing demand for information on the state of the soil that can be used in biogeochemical models and the monitoring of soil degradation.     

Resequencing Microarray Technology for Genotyping Human Papillomavirus in Cervical Smears

There are more than 40 human papillomaviruses (HPVs) belonging to the alpha genus that cause sexually transmitted infections; these infections are among the most frequent and can lead to condylomas and anogenital intra-epithelial neoplasia. At least 18 of these viruses are causative agents of anogenital carcinomas. We evaluated the performance of a resequencing microarray for the detection and genotyping of alpha HPV of clinical significance using cloned HPV DNA. To reduce the number of HPV genotypes tiled on microarray, we used reconstructed ancestral sequences (RASs) as they are more closely related to the various genotypes than the current genotypes are among themselves. The performance of this approach was tested by genotyping with a set of 40 cervical smears already genotyped using the commercial PapilloCheck kit. The results of the two tests were concordant for 70% (28/40) of the samples and compatible for 30% (12/40). Our findings indicate that RASs were able to detect and identify one or several HPV in clinical samples. Associating RASs with homonym sequences improved the genotyping of HPV present in cases of multiple infection. In conclusion, we demonstrate the diagnostic potential of resequencing technology for genotyping of HPV, and illustrate its value both for epidemiological studies and for monitoring the distribution of HPV in the post-vaccination era.     

Correlation between the serine sensitivity and the derepressibility of the ilv genes in Escherichia coli relA- mutants.

Summary Upon addition of excess one carbon metabolites (including serine) bacteria stop growing because of isoleucine starvation. After such treatment stringent bacteria rapidly resume normal growth whereas relaxed mutants remain unable for some time to grow. We show here that this is due to a lack of derepressibility of ilv genes after the starvation period. Results are also presented which show that RNA polymerase structural mutants may be selected among the clones resistant to a mixture of serine, methionine and glycine, in relA ^-strains. Finally circumstancial evidence suggests that the one carbon metabolism may be involved in a process controlling isoleucine metabolism.Abbreviations: Throughout this work we have represented the mixture of amino acids serine, methionine and glycine (1 mM each) by the letters SMG. Para amino benzoic acid represented by the letters PABA