Fleas of fleas: The potential role of bacteriophages in Salmonella diversity and pathogenicity.

Non-typhoidal salmonellosis is an important foodborne and zoonotic infection, that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators, however, little is known on the role prophages play in driving these characteristics. Here, we extracted prophages from 75 Salmonella genomes, which represent the 15 most important serovars in the United Kingdom. We analysed the genomes of the intact prophages for the presence of virulence factors which were associated with; diversity, evolution and pathogenicity of Salmonella and to establish their genomic relationships. We identified 615 prophage elements from the Salmonella genomes, from which 195 prophages are intact, 332 being incomplete while 88 are questionable. The average prophage carriage was found to be more prevalent in S. Heidelberg, S. Inverness and S. Newport (10.2-11.6 prophages/strain), compared to S. Infantis, S. Stanley, S. Typhimurium and S. Virchow (8.2-9 prophages/strain) and S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6-7.8 prophages/strain), and S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 2760 virulence factors were detected from the intact prophages and associated with cellular functionality being linked to effector delivery/secretion system (73%), adherence (22%), magnesium uptake (2.7%), resistance to antimicrobial peptides (0.94%), stress/survival (0.4%), exotoxins (0.32%) and antivirulence (0.18%). Close and distant clusters were formed among the prophage genomes suggesting different lineages and associations with bacteriophages of other Enterobacteriaceae. We show that diverse repertoire of Salmonella prophages are associated with numerous virulence factors, and may contribute to diversity, pathogenicity and success of specific serovars

Elucidation of structural and functional characteristics of the gut microbiome of beef cattle under water stress

The current trends in climate change and global warming are expected to have a profound effect on the cattle industry. Availability of good quality water in sufficient amounts is one aspect in cattle operations that can be adversely affected by such climate phenomenon. Water is an essential nutrient playing a pivotal role in maintaining critical physiological functions in cattle. The gastrointestinal microbial community of ruminants such as cattle are central to the digestion of plant material, production of volatile fatty acids, and the production of microbial crude protein essential in replenishing the nutrient requirement of the animal. Factors such as dietary composition, host genetics, production environment, age, sex etc. have been associated with significant changes in the gut microbiome of cattle. However, the effect of water restriction on the gut microbial dynamics of cattle is yet to be extensively studied. Hence, we used rumen and fecal samples from feedlot cattle collected during ad libitum water intake and at 50% water restriction) to reconstruct rumen and fecal microbial communities using 16S rRNA V4 gene amplicon sequencing and whole metagenome sequencing. The amplicon sequencing data summarized at genus level revealed significant differences (p<0.05) in the overall species composition of rumen and fecal microbiomes during water restriction. Genera such as Methanobrevibacter, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG_003 showed significant differences in their relative abundance when subjected to water restriction. The fecal microbiome exhibited the most prominent changes due to water restriction where genera such as Turicibacter, Clostridium_sensu_stricto_1, Christensenellaceae_R_7_group, Romboutsia, and Paeniclostridium showed significant differences (p<0.05) in their relative abundance in comparison to ad libitum water intake. Christensenellaceae_R_7_group, Paenoclostridum, Rombutsia, Clostridoides, Akkermansia and Lactobacillus were identified as biomarkers in animals that performed significantly better (p<0.05) under water restricted conditions. Metagenome sequencing data summarized at species level showed a significant decrease (p<0.05) in the abundance Ruminococcaceae bacterium P7, Methanosphaera sp BMS, and Methanobrevibacter millerae in the fecal microbiome during water restriction. A multitude of biologically significant metabolic pathways in the rumen/fecal microbiome, pertaining to amino acid biosynthesis, methanogenesis, pyruvate fermentation etc. differed significantly (p<0.05) in pathway abundance during water restriction

Biology of <em>Trypanosoma cruzi</em>

Trypanosoma cruzi, an important zoonotic protozoan that causes Chagas disease, affects at least 8 million people in Latin America. Chagas disease is an important life-long infection in humans that can be divided into distinct clinical stages: the acute phase, where patient symptoms can vary from asymptomatic to severe; the indeterminate form, which is usually asymptomatic; and the chronic phase, where cardiomyopathy and/or digestive megasyndromes appear. In addition to its medical importance, T. cruzi is an interesting biological model for studying processes such as: (1) cell differentiation, where a non-infective stage transforms into an infective one; (2) cell invasion, where the infective stages are able to penetrate into a mammalian host cell, where they multiply several times and thus amplify the infection; and (3) evasion from the immune system, using several mechanisms. This book, with 13 chapters, has been organized in four major sections: 1. "Basic Biology," 2. "Biochemistry and Molecular Biology," 3. "Parasite"Host Cell Interaction," and 4 "Chemotherapy." The chapters include basic biological information on the protozoan lifecycle, including new information on parasite genomics and proteomics. In addition, they analyze the interaction with host cells as well the immune response and evasion, ending with information on experimental chemotherapy against Chagas disease

Generating Reliable Genome Assemblies of Intestinal Protozoans from Clinical Samples for the Purpose of Biomarker Discovery

Protozoan parasites that cause diarrhoeal diseases in humans take a massive toll on global public health annually, with over 200,000 deaths in children of less than two years old in Asia and Sub-Saharan Africa being attributed to Cryptosporidium alone. They can, in particular, be a serious health risk for immuno-incompetent individuals. Genomics can be a valuable asset in helping combat these parasites, but there are still problems associated with performing whole genome sequencing from human stool samples. In particular there are issues associated with highly uneven sequence coverage of these parasite genomes, which may result in critical errors in the genome assemblies produced using a number of popular assemblers. We have developed an approach using the Gini statistic to better characterise depth of sequencing coverage. Furthermore, we have explored the sequencing biases resulting from Whole Genome Amplification approaches, and have attempted to relate those to the Gini statistic. We discuss these issues in two parasite genera: Cryptosporidium and Cyclospora, and perform an analysis of the sequencing coverage depth over these genomes. Finally we present our strategy to generate reliable genome assemblies of sufficient quality to facilitate discovery of new Variable Number Tandem Repeat (VNTR) biomarkers

Proceedings of International Virtual Seminar on Recent Trends in Life Sciences and Biotechnology: Strategies to Combat COVID-19, Zoonoses and Other Communicable Diseases

Proceedings of International Virtual Seminar on Recent Trends in Life Sciences and Biotechnology: Strategies to Combat COVID-19, Zoonoses and Other Communicable Diseases. Rakesh Book Service, New Delhi. 460p (ISBN: 978-93-84998-83-7)

Removal of antagonistic spindle forces can rescue metaphase spindle length and reduce chromosome segregation defects

Regular Abstracts - Tuesday Poster Presentations: no. 1925Metaphase describes a phase of mitosis where chromosomes are attached and oriented on the bipolar spindle for subsequent segregation at anaphase. In diverse cell types, the metaphase spindle is maintained at a relatively constant length. Metaphase spindle length is proposed to be regulated by a balance of pushing and pulling forces generated by distinct sets of spindle microtubules and their interactions with motors and microtubule-associated proteins (MAPs). Spindle length appears important for chromosome segregation fidelity, as cells with shorter or longer than normal metaphase spindles, generated through deletion or inhibition of individual mitotic motors or MAPs, showed chromosome segregation defects. To test the force balance model of spindle length control and its effect on chromosome segregation, we applied fast microfluidic temperature-control with live-cell imaging to monitor the effect of switching off different combinations of antagonistic forces in the fission yeast metaphase spindle. We show that spindle midzone proteins kinesin-5 cut7p and microtubule bundler ase1p contribute to outward pushing forces, and spindle kinetochore proteins kinesin-8 klp5/6p and dam1p contribute to inward pulling forces. Removing these proteins individually led to aberrant metaphase spindle length and chromosome segregation defects. Removing these proteins in antagonistic combination rescued the defective spindle length and, in some combinations, also partially rescued chromosome segregation defects. Our results stress the importance of proper chromosome-to-microtubule attachment over spindle length regulation for proper chromosome segregation.postprin

Psr1p interacts with SUN/sad1p and EB1/mal3p to establish the bipolar spindle

Regular Abstracts - Sunday Poster Presentations: no. 382During mitosis, interpolar microtubules from two spindle pole bodies (SPBs) interdigitate to create an antiparallel microtubule array for accommodating numerous regulatory proteins. Among these proteins, the kinesin-5 cut7p/Eg5 is the key player responsible for sliding apart antiparallel microtubules and thus helps in establishing the bipolar spindle. At the onset of mitosis, two SPBs are adjacent to one another with most microtubules running nearly parallel toward the nuclear envelope, creating an unfavorable microtubule configuration for the kinesin-5 kinesins. Therefore, how the cell organizes the antiparallel microtubule array in the first place at mitotic onset remains enigmatic. Here, we show that a novel protein psrp1p localizes to the SPB and plays a key role in organizing the antiparallel microtubule array. The absence of psr1+ leads to a transient monopolar spindle and massive chromosome loss. Further functional characterization demonstrates that psr1p is recruited to the SPB through interaction with the conserved SUN protein sad1p and that psr1p physically interacts with the conserved microtubule plus tip protein mal3p/EB1. These results suggest a model that psr1p serves as a linking protein between sad1p/SUN and mal3p/EB1 to allow microtubule plus ends to be coupled to the SPBs for organization of an antiparallel microtubule array. Thus, we conclude that psr1p is involved in organizing the antiparallel microtubule array in the first place at mitosis onset by interaction with SUN/sad1p and EB1/mal3p, thereby establishing the bipolar spindle.postprin