Human gut microbiota – its diversity and impact on our health

The human digestive tract is the living environment for billions of cells of various microorganisms that are part of the human microflora. The use of modern molecular biology techniques, such as NGS (Next Generation Sequencing), made it possible to study the microorganisms inhabiting the intestines and to understand their impact on human health. The gut microbiota plays a significant role in the synthesis and metabolism of many nutrients and metabolites, including short-chain fatty acids (SCFA), amino acids, lipids, bile acids and vitamins. Many factors such as diet, age, climate, and socioeconomic conditions influence the diversity of the microbiota. Rapid changes in the composition of the microbiota (disturbance of homeostasis) can lead to dysbiosis - a condition associated not only with intestinal disorders, but also with numerous extraintestinal diseases. The present work is a review of current reports on: research techniques used to analyze microbiota, the impact of various factors on its diversity and the impact of microbiota on our health.

Non-Coding RNAs in Kidney Diseases: The Long and Short of Them

Recent progress in genomic research has highlighted the genome to be much more transcribed than expected. The formerly so-called junk DNA encodes a miscellaneous group of largely unknown RNA transcripts, which contain the long non-coding RNAs (lncRNAs) family. lncRNAs are instrumental in gene regulation. Moreover, understanding their biological roles in the physiopathology of many diseases, including renal, is a new challenge. lncRNAs regulate the effects of microRNAs (miRNA) on mRNA expression. Understanding the complex crosstalk between lncRNA–miRNA–mRNA is one of the main challenges of modern molecular biology. This review aims to summarize the role of lncRNA on kidney diseases, the molecular mechanisms involved, and their function as emerging prognostic biomarkers for both acute and chronic kidney diseases. Finally, we will also outline new therapeutic opportunities to diminish renal injury by targeting lncRNA with antisense oligonucleotides.

Portable low-cost optical density meter

Measuring optical density (OD) is a very common technique in biological laboratories to determine the concentration of a substance in solution or of bacteria (or microscopic particles) in suspension. For example, bacterial cultures engineered to produce (express) a protein or compound of interest are a workhorse of modern molecular biology laboratories. Commonly, the expression of the product is triggered (induced) by a chemical signal added to the culture at the proper time in the growth curve of the culture (typically in the middle of the exponential growth phase, at an OD value of ~0.6). The most common tool for measuring OD is a spectrophotometer. However, most spectrophotometers are sophisticated, non-portable and expensive laboratory instruments, costing tens of thousands of dollars. Even a very low cost spectrophotometer for educational use costs at least US$1,000. Because of the cost, even well resourced labs have only one instrument, which becomes a bottleneck when multiple bacterial cultures need to be monitored simultaneously. The problem is more acute in developing countries, where multiple labs have to share a single spectrophotometer, or there's no such instrument at all. Having a cheap and simple device to measure OD would enable multiple people in a laboratory to monitor their bacterial cultures independently, even in resource-limited settings. At the same time, a portable OD meter could be useful for field work. Here we present the detailed build instructions and characterization of a very simple OD meter that costs only US$60, and can measure OD values from ~0.05 to 2.0.

Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data

Accurate reference genome sequences provide the foundation for modern molecular biology and genomics as the interpretation of sequence data to study evolution, gene expression, and epigenetics depends heavily on the quality of the genome assembly used for its alignment. Correctly organising sequenced fragments such as contigs and scaffolds in relation to each other is a critical and often challenging step in the construction of robust genome references. We previously identified misoriented regions in the mouse and human reference assemblies using Strand-seq, a single cell sequencing technique that preserves DNA directionality Here we demonstrate the ability of Strand-seq to build and correct full-length chromosomes by identifying which scaffolds belong to the same chromosome and determining their correct order and orientation, without the need for overlapping sequences. We demonstrate that Strand-seq exquisitely maps assembly fragments into large related groups and chromosome-sized clusters without using new assembly data. Using template strand inheritance as a bi-allelic marker, we employ genetic mapping principles to cluster scaffolds that are derived from the same chromosome and order them within the chromosome based solely on directionality of DNA strand inheritance. We prove the utility of our approach by generating improved genome assemblies for several model organisms including the ferret, pig, Xenopus, zebrafish, Tasmanian devil and the Guinea pig.

Viruses in Extreme Environments, Current Overview, and Biotechnological Potential

Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.

Autoimmune enteropathy

Autoimmune enteropathy (AIE) is a rare disease characterised by severe diarrhoea and immune-mediated damage of the intestinal mucosa. The objective: based on analysis of modern literature to describe the diagnostic criteria, etiology, pathogenesis, epidemiology, clinical features and treatment of AIE in children. Results. The diagnostic criteria of AIE include chronic diarrhoea (lasting more than 6 weeks), malabsorption syndrome, specific histological findings of small intestine biopsy when other causes of villous atrophy are excluded. An additional criterion is the presence of antibodies against enterocytes or goblet cells. The following types are singled out: (1) AIE associated with such syndromes as IPEX and APECED; (2) an isolated form of GI AIE with the presence of anti-enterocyte antibodies without diseases of the digestive system; and (3) any form of AIE in girls associated with any other autoimmune phenomena. At present, not less than five subtypes of AIE are known: Primary AIE (paediatric); Syndromal AIE (paediatric); Primary (sporadic) adult ОВОС AIE; Secondary (iatrogenic) adult AIE; Paraneoplastic AIE. Patients with AIE might have associated autoimmune diseases, including diabetes mellitus, autoimmune hepatitis, alopecia, hypothyroidism, and interstitial nephritis. AIE is a complex and potentially life-threatening disease, with the mortality rates reaching 30% in paediatric practice. The prognosis depends on the age of the disease onset, the severity of symptoms and histological lesions of the gastrointestinal tract. The use of therapy based on modern molecular biology technologies, along with nutritive support, immunosuppressive therapy, can help control the disease. Key words: autoimmune enteropathy, IPEX syndrome

Protein Structural Alignments From Sequence

Computing sequence similarity is a fundamental task in biology, with alignment forming the basis for the annotation of genes and genomes and providing the core data structures for evolutionary analysis. Standard approaches are a mainstay of modern molecular biology and rely on variations of edit distance to obtain explicit alignments between pairs of biological sequences. However, sequence alignment algorithms struggle with remote homology tasks and cannot identify similarities between many pairs of proteins with similar structures and likely homology. Recent work suggests that using machine learning language models can improve remote homology detection. To this end, we introduce DeepBLAST, that obtains explicit alignments from residue embeddings learned from a protein language model integrated into an end-to-end differentiable alignment framework. This approach can be accelerated on the GPU architectures and outperforms conventional sequence alignment techniques in terms of both speed and accuracy when identifying structurally similar proteins.

Fast gap-affine pairwise alignment using the wavefront algorithm

Motivation Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields. Results In this paper, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s2) memory. Furthermore, our algorithm exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code. We evaluate the performance of our algorithm, together with other state-of-the-art implementations. As a result, we demonstrate that the WFA runs 20-300x faster than other methods aligning short Illumina-like sequences, and 10-100x faster using long noisy reads like those produced by Oxford Nanopore Technologies. Availability The WFA algorithm is implemented within the wavefront-aligner library, and it is publicly available at https://github.com/smarco/WFA

Turner syndrome with rapidly progressive puberty: a case report and literature review

This report describes a clinically rare and atypical case of 46,X,idic(X)(q21.32)/45,X-type Turner syndrome with rapidly progressive puberty development. After 11 months of treatment with recombinant human growth hormone (rhGH), the child’s height increased. After 18 months of treatment with rhGH, the child showed secondary sex characteristics. The child was followed up for 1 year after the appearance of the secondary sex characteristics, and regular menses were still present. This case indicates that modern molecular biology techniques should be used rationally to further investigate the existence of X-chromosome translocations and occult chimeras to prevent misdiagnosis.