Meeting review : ESF workshop on "Impact of nucleic acid chemistry on gene function analysis: antisense, aptamers, ribozymes and RNAi"

The shortage of functional information compared to the abundance of sequence information characterizes today’s situation in functional genomics. For many years the knock-down of a gene’s product has been the most powerful way of analysing its function. In addition to the complete knock-out by homologous recombination, several different techniques have been developed to temporarily knock down gene expression through methods based on specific sequence recognition, such as knockdown by antisense oligonucleotides, ribozymes, aptamers or RNAi. The ESF workshop on ‘Impact of Nucleic Acid Chemistry on Gene Function Analysis’ brought together researchers who use techniques that are different but highly related. It offered an opportunity for an in-depth discussion of recent progress and common problems. Antisense oligonucleotides aptamers and ribozymes are techniques that have been used successfully for many years to validate targets. However, recent developments, such as increased tightness of binding (e.g. locked nucleic acids) or the combination of different methods (e.g. using aptamers to design ribozymes), have continued to improve the existing techniques. RNA interference (RNAi) is a defence mechanism of the cell against viruses. Since the exact mechanism of action within the cell is still unclear, RNAi was a particularly exciting topic at the workshop and was addressed in the largest number of presentations. Predictability of positional effects (accessibility of RNA) is a problem shared by all techniques using sequence-specific recognition and was the subject of quite controversial debates. The meeting comprised over 50 people from 14 countries (13 European countries and the USA)

The intracellular proteome of the gut bacterium Bacteroides thetaiotaomicron is widely unaffected by a switch from glucose to sucrose as main carbohydrate source

Bacteroides thetaiotaomicron is a gram negative bacterium within the human gut microbiome that metabolizes a wide range of dietary and mucosal polysaccharides. Here, we analyze the proteome response of B. thetaiotaomicron cultivated on two different carbon sources, glucose and sucrose. Two quantitative LC-MS based proteomics approaches, encompassing label free quantification and isobaric labeling by tandem mass tags were applied. The results obtained by both workflows were compared with respect to the number of identified and quantified proteins, peptides supporting identification and quantification, sequence coverage, and reproducibility. A total of 1719 and 1696 proteins, respectively, were quantified, covering 35 % of the predicted B. thetaiotaomicron proteome. The data show that B. thetaiotaomicron widely maintains its intracellular proteome upon change of the carbohydrates and that major changes are observed solely in the machinery necessary to make use of the carbon sources provided. With respect to the central role of carbohydrates on gut health these data contribute to the understanding of how different carbohydrates contribute to shape bacterial community in the gut microbiome. All proteomics raw data have been uploaded to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD033704

Computational methods for metabolomic data analysis of ion mobility spectrometry data-reviewing the state of the art

Ion mobility spectrometry combined with multi-capillary columns (MCC/IMS) is a well known technology for detecting volatile organic compounds (VOCs). We may utilize MCC/IMS for scanning human exhaled air, bacterial colonies or cell lines, for example. Thereby we gain information about the human health status or infection threats. We may further study the metabolic response of living cells to external perturbations. The instrument is comparably cheap, robust and easy to use in every day practice. However, the potential of the MCC/IMS methodology depends on the successful application of computational approaches for analyzing the huge amount of emerging data sets. Here, we will review the state of the art and highlight existing challenges. First, we address methods for raw data handling, data storage and visualization. Afterwards we will introduce de-noising, peak picking and other pre-processing approaches. We will discuss statistical methods for analyzing correlations between peaks and diseases or medical treatment. Finally, we study up-to-date machine learning techniques for identifying robust biomarker molecules that allow classifying patients into healthy and diseased groups. We conclude that MCC/IMS coupled with sophisticated computational methods has the potential to successfully address a broad range of biomedical questions. While we can solve most of the data pre-processing steps satisfactorily, some computational challenges with statistical learning and model validation remain

Long-Term Oncological Efficacy of Retroperitoneoscopic Radical Nephrectomy of Localized Renal Cell Cancer pT1-3 (≤12 cm)

Investigation of oncological efficacy in retroperitoneoscopic radical nephrectomy (RRN) of patients with localized renal cell carcinoma (RCC). Consecutive patients undergoing RRN for localized stage pT1-3 RCC in 2 tertiary care centers in Switzerland were evaluated. Excellent long-term oncological efficacy was found. Our long-term follow-up validates the survival outcome from comparable literature after conventional open or laparoscopic radical nephrectomy

Lactobacillus Acidophilus/Bifidobacterium Infantis Probiotics Are Beneficial to Extremely Low Gestational Age Infants Fed Human Milk

To evaluate the nutrition-related effects of prophylactic Lactobacillus acidophilus/ Bifidobacterium infantis probiotics on the outcomes of preterm infants <29 weeks of gestation that receive human milk and/or formula nutrition. We hypothesize that human-milk-fed infants benefit from probiotics in terms of sepsis prevention and growth. Methods: We performed an observational study of the German Neonatal Network (GNN) over a period of six years, between 1 January, 2013 and 31 December, 2018. Prophylactic probiotic use of L. acidophilus/B. infantis was evaluated in preterm infants <29 weeks of gestation (n = 7516) in subgroups stratified to feeding type: (I) Exclusively human milk (HM) of own mother and/or donors (HM group, n = 1568), (II) HM of own mother and/or donor and formula (Mix group, n = 5221), and (III) exclusive exposure to formula (F group, n = 727). The effect of probiotics on general outcomes and growth was tested in univariate models and adjusted in linear/logistic regression models. Results: 5954 (76.5%) infants received L. acidophilus/B. infantisprophylactically for the prevention of necrotizing enterocolitis (NEC). Probiotic use was associated with improved growth measures in the HM group (e.g., weight gain velocity in g/day: effect size B = 0.224; 95% CI: 2.82–4.35; p < 0.001) but not in the F group (effect size B = −0.06; 95% CI: −3.05–0.28; p = 0.103). The HM group had the lowest incidence of clinical sepsis (34.0%) as compared to the Mix group (35.5%) and the F group (40.0%). Only in the Mix group, probiotic supplementation proved to be protective against clinical sepsis (OR 0.69; 95% CI: 0.59–0.79; p < 0.001). Conclusion: Our observational data indicate that the exposure to L. acidophilus/B. infantis probiotics may promote growth in exclusively HM-fed infants as compared to formula-fed infants. To exert a sepsis-preventive effect, probiotics seem to require human milk

The challenges for women's health in sub-Saharan Africa: Lessons learned from an integrative multistakeholder workshop in Gabon.

The sub-Saharan African (SSA) region is home to more than 230 million females of reproductive age who face multiple intersecting health, social, gender and economic challenges [1]. Neglected tropical diseases (NTDs) are a group of chronic disabling, almost exclusively communicable diseases affecting the poorest of the poor, especially in Africa, which alone bears about 40% of the global burden of NTDs [2- 4]. While both men and women are impacted, biological and sociocultural biases mean that NTDs disproportionately affect women and girls [5]. In recent decades, there has been a global shift from communicable toward non-communicable diseases (NCDs), which cause almost 32 million deaths in low-and lower- middle- income countries (LMIC) [6]. It is expected that by 2030, 85% of NCD-related deaths among women will occur in LMICs, including many countries of SSA region [7]. For women older than 50, NCDs are the leading cause of both death and disability-adjusted life years (DALYs) [8]. Important disparities persist in access to maternal and reproductive health services both within and between countries in SSA [9]; it is estimated that almost half of the women in SSA do not have access to essential health care during pregnancy and childbirth. In 2017, SSA accounted for roughly two-thirds of all maternal deaths in the world [10]. Hence, it is evident that many, if not most, women and girls in SSA carry a triple burden of vulnerability to NTDs, NCDs and poor reproductive health outcomes. Here, we report on the outcomes of an integrative, multistakeholder workshop held in Gabon, Central Africa, to help develop a framework for synergistic, sustainable and gender- and context-appropriate interventions to manage the NTD-NCD complex and additionally reproductive health