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Background Stunting is a global health problem affecting hundreds of millions of children worldwide and contributing to 45% of deaths in children under the age of five. Current therapeutic interventions have limited efficacy. Understanding the epigenetic changes underlying stunting will elucidate molecular mechanisms and likely lead to new therapies. Results We profiled the repressive mark histone H3 lysine 9 trimethylation (H3K9me3) genome-wide in peripheral blood mononuclear cells (PBMCs) from 18-week-old infants (n = 15) and mothers (n = 14) enrolled in the PROVIDE study established in an urban slum in Bangladesh. We associated H3K9me3 levels within individual loci as well as genome-wide with anthropometric measurements and other biomarkers of stunting and performed functional annotation of differentially affected regions. Globally elevated H3K9me3 levels were associated with poor linear growth between birth and one year of age. A large proportion of the affected genes code for proteins targeting viral mRNA and highly significant regions were enriched in transposon elements with potential regulatory roles in immune system activation and cytokine production. Maternal data show a similar trend with child’s anthropometry, however, lack statistical significance to infer an intergenerational relationship. Conclusions We speculate that high H3K9me3 levels may result in poor linear growth by repressing genes involved in immune system activation. Importantly, changes to H3K9me3 were detectable before the overt manifestation of stunting and therefore may be valuable as new biomarkers of stunting.

Background Stunting is a condition in which a child does not reach their full growth potential due to chronic undernutrition. It arises during the first 2 years of a child’s life and is associated with developmental deficiencies and life-long health problems. Current interventions provide some benefit, but new approaches to prevention and treatment grounded in a molecular understanding of stunting are needed. Epigenetic analyses are critical as they can provide insight into how signals from a poor environment lead to changes in cell function. Results Here we profiled histone H3 acetylation on lysine 27 (H3K27ac) in peripheral blood mononuclear cells (PBMCs) of 18-week-old (n = 14) and 1-year-old children (n = 22) living in an urban slum in Dhaka, Bangladesh. We show that 18-week-old children destined to become stunted have elevated levels of H3K27ac overall, functional analysis of which indicates activation of the immune system and stress response pathways as a primary response to a poor environment with high pathogen load. Conversely, overt stunting at 1-year-of age is associated with globally reduced H3K27ac that is indicative of metabolic rewiring and downregulation of the immune system and DNA repair pathways that are likely secondary responses to chronic exposure to a poor environment with limited nutrients. Among processes altered in 1-year-old children, we identified one-carbon metabolism, the significance of which is supported by integrative analysis with results from histone H3 trimethylation on lysine 4 (H3K4me3). Together, these results suggest altered one-carbon metabolism in this population of stunted children. Conclusions The epigenomes of stunted children undergo two global changes in H3K27ac within their first year of life, which are associated with probable initial hyperactive immune responses followed by reduced metabolic capacity. Limitation of one-carbon metabolites may play a key role in the development of stunting. Trial registration ClinicalTrials.gov NCT01375647. Registered 17 June 2011, retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT01375647.

Introduction: The Renin-Angiotensin-System is essential to maintain blood pressure and fluid electrolyte homeostasis. Because precise regulation of expression and release of renin is critical for survival, understanding the molecular regulation of the renin cell identity is a vital area of study. Advances in epigenetics have enabled finer dissection of chromatin factors which maintain the identity of the renin cell. By studying genes with heightened accessibility profiles that are unique to the JG cell, we now have the capacity to unravel the determinants of the renin cell identity. Hypothesis: That transcription factors central to the governance of renin cell identity can be identified through the Assay for Transposase Accessible Chromatin (ATAC-seq) differential accessibility analysis. Methods: Native renin cell ATAC-seq was compared to existing ENCODE ATAC-seq datasets from 40 other cell types to define regions/peaks which characterize the JG program. Peaks with high intensity and ≥2-fold increase in signal were selected for Motif analysis to search for transcription factors (TFs) whose consensus sequence is enriched in those regions. Identified TFs were then selected for validation by in-situ hybridization and conditional deletion in renin cells. Results: 1) The Mef2c transcription factor was identified as having a consensus sequence in regulatory regions unique to the JG cell. It has clear expression in RNA-seq of renin cells (65 transcripts per million, n=3) and a predicted binding site in the renin gene. These results were validated by in-situ hybridization where signal localized at the JG area was detected in concordance with our in-silico results. 2) We generated Mef2c conditional knockout animals using our Ren1d-Cre mouse to study the effect in renin expression and identity. These mice displayed reduced renin immunostaining at the JG area and a 40% reduction in renin mRNA expression by qPCR from kidney cortices relative to wild-type (n=2, preliminary data). Conclusions: Our studies identified Mef2c as a TF target which likely has an essential role in maintaining and preserving renin cell identity. Experiments involving transcriptomics and epigenomics are ongoing to understand the changes wrought by Mef2c deletion in renin cells.

BackgroundStunting is a condition in which a child does not reach their full growth potential due to chronic undernutrition. It arises during the first two years of a child’s life and is associated with developmental deficiencies and life-long health problems. Current interventions provide some benefit, but new approaches to prevention and treatment grounded in a molecular understanding of stunting are needed. Epigenetic analyses are critical as they can provide insight into how signals from a poor environment lead to changes in cell function.ResultsHere we profiled histone H3 acetylation on lysine 27 (H3K27ac) in peripheral blood mononuclear cells (PBMCs) of 18-week-old and one-year-old children living in an urban slum in Dhaka, Bangladesh. We show that 18-week-old children destined to become stunted have elevated levels of H3K27ac overall, functional analysis of which indicates activation of the immune system and stress response pathways as a primary response to a poor environment with high pathogen load. Conversely, overt stunting at 1-year-of age is associated with globally reduced H3K27ac that is indicative of metabolic rewiring and downregulation of the immune system and DNA repair pathways that are likely secondary responses to chronic exposure to a poor environment with limited nutrients. The results from one-year-old children also point toward deficiency in one-carbon metabolism, which is further supported by integrative analysis with results from histone H3 trimethylation on lysine 4 (H3K4me3).ConclusionsThe epigenomes of stunted children undergo two global changes in H3K27ac within their first year of life, which are associated with probable initial hyperactive immune responses followed by reduced metabolic capacity. Limitation of one-carbon metabolites may play a key role in the development of stunting. Trial registration: ClinicalTrials.govNCT01375647. Registered 17 June 2011, retrospectively registered.

One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments. On the other hand, the output of whole metagenomic shotgun sequencing is mixture of short DNA fragments belonging to various genomes, therefore this approach requires more sophisticated computational algorithms for clustering of related sequences, commonly referred to as sequence binning. There are currently two types of binning methods: taxonomy dependent and taxonomy independent. The first type classifies the DNA fragments by performing a standard homology inference against a reference database, while the latter performs the reference-free binning by applying clustering techniques on features extracted from the sequences. In this review, we describe the strategies within the second approach. Although these strategies do not require prior knowledge, they have higher demands on the length of sequences. Besides their basic principle, an overview of particular methods and tools is provided. Furthermore, the review covers the utilization of the methods in context with the length of sequences and discusses the needs for metagenomic data preprocessing in form of initial assembly prior to binning. Keywords: Metagenomics, Taxonomy independent, Sequence binning, Genomic signature, Abundance, Visualization

Background Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. Results In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation. Conclusions We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering. Electronic supplementary material The online version of this article (10.1186/s12864-018-4805-8) contains supplementary material, which is available to authorized users.

Circular plots showing average coverage of the genome by RNA-Seq reads in all six time points. The outermost and the second outermost circles represent positions of genes on the forward (red) and reverse (blue) strands respectively. The third circle (green) stands for pseudogenes. The yellow peak and shading area represents transcription greater than the average and violet lower than average. Floating window of 10,000 bp with step of 200 bp was used to render the shading area. (PDF 701 kb)

Dotplot of C. beijerinckii NRRL B-598 and C. beijerinckii NCIMB 8052 genome. Dotplots showing that no major rearrangement between the two strains are present. (PDF 315 kb)

COG functional categories of differential expressed genes. Barplots showing the number of COG categories associated with differentially expressed genes between adjacent time points. (PDF 226 kb)

Snapshots from microscopic observation during cultivation. (PDF 628 kb)

Differential analysis of adjacent time points using MA plots. MA plots showing statistically differentially expressed genes in color. Color coding respect the color coding used in Venn diagrams in Fig. 4. (PDF 315 kb)

Silent pseudogenes. (PDF 195 kb)

Putative active genes misidentified as pseudogenes due to assembly errors. (PDF 210 kb)

Nanopore sequencing has become an invaluable aid in small sequencing projects. Thanks to its compact size, the Oxford Nanopore MinION platform is often used in crisis situations, such as outbreaks of microbial infections, to determine the causes of the problem. As a platform that produces data in real-time, it requires bioinformatics techniques designed for fast data processing. In this paper, we demonstrate the possibility of the direct processing of nanopore current signals, the so-called squiggles, for fast reference-free identification of phage DNA. The proposed technique is based on the computation of Hjorth parameters and is suitable for fast visualization of the data, as well as for proper classification by many machine learning algorithms. The classification of the data also raises the possibility of applying adapted base calling algorithms for both groups separately, as phage and host DNA have different features.

2016, was the 100 years anniversary from launching of the first industrial acetone-butanol-ethanol (ABE) microbial production process. Despite this long period and also revival of scientific interest in this fermentative process over the last 20 years, solventogenic clostridia, mainly Clostridium acetobutylicum, Clostridium beijerinckii, Clostridium saccharoperbutylacetonicum and Clostridium pasteurianum, still have most of their secrets. One such poorly understood mechanism is butanol tolerance, which seems to be one of the most significant bottlenecks obstructing industrial exploitation of the process because the maximum achievable butanol concentration is only about 21 g/L. This review describes all the known cellular responses elicited by butanol, such as modifications of cell membrane and cell wall, formation of stress proteins, extrusion of butanol by efflux pumps, response of regulatory pathways, and also maps both random and targeted mutations resulting in high butanol production phenotypes. As progress in the field is inseparably associated with emerging methods, enabling a deeper understanding of butanol tolerance and production, progress in these methods, including genome mining, RNA sequencing and constructing of genome scale models are also reviewed. In conclusion, a comparative analysis of both phenomena is presented and a theoretical relationship is described between butanol tolerance/high production and common features including efflux pump formation/activity, stress protein production, membrane modifications and biofilm growth.

Correlated mutation (CM) analysis has been proved to be an important tool used in protein contact map prediction from primary amino acid sequence. Over the last years CM methods have been refined and then often combined with methods of different nature in order to improve reached precision. However, since the methods are still relatively new, only precision and improvement have been reported without mentioning recall which is very low. In this paper, we combine previously described CM analysis methods with an outcome of four new techniques which significantly increase recall for the cost of minimal precision impairment. This study is the first of our knowledge with focus on recall improvement.