A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria

Bacterial 16S ribosomal RNA (rRNA) genes contain nine "hypervariable regions" (V1-V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations. No single region can differentiate among all bacteria; therefore, systematic studies that compare the relative advantage of each region for specific diagnostic goals are needed. We characterized V1-V8 in 110 different bacterial species including common blood borne pathogens, CDC-defined select agents and environmental microflora. Sequence similarity dendrograms were created for hypervariable regions V1-V8, and for selected combinations of regions or short segments within individual hypervariable regions that might be appropriate for DNA probing and real-time PCR. We determined that V1 best differentiated among Staphylococcus aureus and coagulase negative Staphylococcus sp. V2 and V3 were most suitable for distinguishing all bacterial species to the genus level except for closely related enterobacteriaceae. V2 best distinguished among Mycobacterium species and V3 among Haemophilus species. The 58 nucleotides-long V6 could distinguish among most bacterial species except enterobacteriaceae. V6 was also noteworthy for being able to differentiate among all CDC-defined select agents including Bacillus anthracis, which differed from B. cereus by a single polymorphism. V4, V5, V7 and V8 were less useful targets for genus or species-specific probes. The hypervariable sequence-specific dendrograms and the "MEGALIGN" files provided online will be highly useful tools for designing specific probes and primers for molecular assays to detect pathogenic bacteria, including select agents.     

Fluorescent sensors of siderophores produced by bacterial pathogens

Siderophores are iron-chelating molecules that solubilize Fe³⁺ for microbial utilization and facilitate colonization or infection of eukaryotes by liberating host iron for bacterial uptake. By fluorescently labeling membrane receptors and binding proteins, we created 20 sensors that detect, discriminate, and quantify apo- and ferric siderophores. The sensor proteins originated from TonB-dependent ligand-gated porins (LGPs) of Escherichia coli (Fiu, FepA, Cir, FhuA, IutA, BtuB), Klebsiella pneumoniae (IroN, FepA, FyuA), Acinetobacter baumannii (PiuA, FepA, PirA, BauA), Pseudomonas aeruginosa (FepA, FpvA), and Caulobacter crescentus (HutA) from a periplasmic E. coli binding protein (FepB) and from a human serum binding protein (siderocalin). They detected ferric catecholates (enterobactin, degraded enterobactin, glucosylated enterobactin, dihydroxybenzoate, dihydroxybenzoyl serine, cefidericol, MB-1), ferric hydroxamates (ferrichromes, aerobactin), mixed iron complexes (yersiniabactin, acinetobactin, pyoverdine), and porphyrins (hemin, vitamin B12). The sensors defined the specificities and corresponding affinities of the LGPs and binding proteins and monitored ferric siderophore and porphyrin transport by microbial pathogens. We also quantified, for the first time, broad recognition of diverse ferric complexes by some LGPs, as well as monospecificity for a single metal chelate by others. In addition to their primary ferric siderophore ligands, most LGPs bound the corresponding aposiderophore with ∼100-fold lower affinity. These sensors provide insights into ferric siderophore biosynthesis and uptake pathways in free-living, commensal, and pathogenic Gram-negative bacteria.     

Participation of the host protein(s) in the morphogenesis of bacteriophage P22

Summary Spontaneous mutants of S. typhimurium resistant to thiolutin are conditionally non-permissive for phage P22 development (Joshi and Chakravorty 1979). At 40° C non-infective phage particles are produced. Phage development in two nonpermissive hosts (18/MC4 and 153/MC4) has been studied in detail. The steps at which the phage morphogenesis is interfered with differ in the two mutants. The electron micrograph of the particles produced in the mutant 18/MC4 reveals the presence of normal-looking particles; these particles contain phage DNA, adsorb to the permissive host but fail to inject their DNA. The particles produced in the mutant 153/MC4 which fail to adsorb to the host are found to be tail fibre-less. These observations indicate the involvement of host protein(s) in phage P22 morphogenesis.     

Labour-Efficient In Vitro Lymphocyte Population Tracking and Fate Prediction Using Automation and Manual Review

Interest in cell heterogeneity and differentiation has recently led to increased use of time-lapse microscopy. Previous studies have shown that cell fate may be determined well in advance of the event. We used a mixture of automation and manual review of time-lapse live cell imaging to track the positions, contours, divisions, deaths and lineage of 44 B-lymphocyte founders and their 631 progeny in vitro over a period of 108 hours. Using this data to train a Support Vector Machine classifier, we were retrospectively able to predict the fates of individual lymphocytes with more than 90% accuracy, using only time-lapse imaging captured prior to mitosis or death of 90% of all cells. The motivation for this paper is to explore the impact of labour-efficient assistive software tools that allow larger and more ambitious live-cell time-lapse microscopy studies. After training on this data, we show that machine learning methods can be used for realtime prediction of individual cell fates. These techniques could lead to realtime cell culture segregation for purposes such as phenotype screening. We were able to produce a large volume of data with less effort than previously reported, due to the image processing, computer vision, tracking and human-computer interaction tools used. We describe the workflow of the software-assisted experiments and the graphical interfaces that were needed. To validate our results we used our methods to reproduce a variety of published data about lymphocyte populations and behaviour. We also make all our data publicly available, including a large quantity of lymphocyte spatio-temporal dynamics and related lineage information.     

Superinfection exclusion and changes in cellular transport processes in phage infected Salmonella typhimurium.

Summary The changes induced by bacteriophage P22 in the cellular transport process(es) of the host Salmonella typhimurium (Taneja et al., 1975; Khandekar et al., 1975; Bandyopadhyay and Chakravorty, 1976) involve interactions between the superinfection exclusion system of the resident prophage and the C immunity region of the superinfecting phage. The sieA gene of the prophage interferes with the changes in the cellular transport process induced by the superinfecting phage. However, if the superinfecting phage carries active C ₁ and C ₂ genes of the superinfecting phage seem to be expressed in the sie A⁺ lysogen.     

Alteration of the C-Terminal Ligand Specificity of the Erbin PDZ Domain by Allosteric Mutational Effects

Modulation of protein binding specificity is important for basic biology and for applied science. Here we explore how binding specificity is conveyed in PDZ (postsynaptic density protein-95/discs large/zonula occludens-1) domains, small interaction modules that recognize various proteins by binding to an extended C terminus. Our goal was to engineer variants of the Erbin PDZ domain with altered specificity for the most C-terminal position (position 0) where a Val is strongly preferred by the wild-type domain. We constructed a library of PDZ domains by randomizing residues in direct contact with position 0 and in a loop that is close to but does not contact position 0. We used phage display to select for PDZ variants that bind to 19 peptide ligands differing only at position 0. To verify that each obtained PDZ domain exhibited the correct binding specificity, we selected peptide ligands for each domain. Despite intensive efforts, we were only able to evolve Erbin PDZ domain variants with selectivity for the aliphatic C-terminal side chains Val, Ile and Leu. Interestingly, many PDZ domains with these three distinct specificities contained identical amino acids at positions that directly contact position 0 but differed in the loop that does not contact position 0. Computational modeling of the selected PDZ domains shows how slight conformational changes in the loop region propagate to the binding site and result in different binding specificities. Our results demonstrate that second-sphere residues could be crucial in determining protein binding specificity.     

Response of rhizobacterial communities in watermelon to infection with cucumber green mottle mosaic virus as revealed by cultivation-dependent RISA

We investigated the rhizobacterial densities and community structure in watermelon rhizosphere under the infection of cucumber green mottle mosaic virus (CGMMV) by artificial inoculation. Rhizobacterial densities and communities were analysed from healthy and infected plants under aerobic and anaerobic culture techniques. The highest total number of aerobic rhizobacteria was counted to be 2.7 × 10⁸ colony forming units per gram (CFU · g^?1) and anaerobic rhizobacteria was to be 3.2 × 10⁶ CFU · g^?1, in healthy and infected plants, respectively. Cultivation-dependent ribosomal intergenic spacer analysis (RISA) was employed for further analysis on the rhizobacterial community structure. By incorporating the relative abundance of amplicons, the per cent similarity was determined by the similarity coefficients based only upon the absence or presence of DNA bands. The cluster analysis of RISA showed that the community structure of aerobic rhizobacteria exhibited 60% similarity between healthy and infected plant. The highest community structure similarity (50% similarity) of anaerobic rhizobacteria occurred between before planting and infected plant.     

β-Resorcylic Acid Derivatives,with Their Phytotoxic Activities,from the Endophytic Fungus Lasiodiplodia theobromae in the Mangrove Plant Xylocarpus granatum

Nine new β-resorcylic acid derivatives, (15S)-de-O-methyllasiodiplodin ( 1 ), (13S,15S)-13-hydroxy-de-O-methyllasiodiplodin ( 2 ), (14S,15S)-14-hydroxy-de-O-methyllasiodiplodin ( 3 ), (13R,14S,15S)-13,14-dihydroxy-de-O-methyllasiodiplodin ( 4 ), ethyl (S)-2,4-dihydroxy-6-(8-hydroxynonyl)benzoate ( 5 ), ethyl 2,4-dihydroxy-6-(8-hydroxyheptyl)benzoate ( 6 ), ethyl 2,4-dihydroxy-6-(4-methoxycarbonylbutyl)benzoate ( 7 ), 3-(2-ethoxycarbonyl-3,5-dihydroxyphenyl)propionic acid ( 8 ), and isobutyl (S)-2,4-dihydroxy-6-(8-hydroxynonyl)benzoate ( 9 ), together with a known ethyl 2,4-dihydroxy-6-(8-oxononyl)benzoate ( 10 ) were obtained from Lasiodiplodia theobromae GC-22. The structures of these compounds were elucidated by extensive spectroscopic analyses. Compounds 1 , 3 , and 6 showed growth inhibitory effects against Digitaria ciliaris. Conversely, treatment with compounds 5 , 6 , 7 , 9 , and 10 stimulated elongation activity toward the root of Lactuca sativa. These data expand the repertoire of new β-resorcylic acid derivatives that may function as lead compounds in the synthesis of new agrochemical agents.