Genome-guided screening of bacterial isolates to identify potential antibiotic producers.

The urgent need for new antibiotics cannot be overemphasized. Bacterial secondary metabolites remain a relatively untapped source of new therapies. The ability to produce these bioactive compounds is however not universal to all bacterial species. Two key indicators are bacterial genome size (>3 Mb), and the presence of antibiotic-encoding biosynthetic gene cluster (BGCs) within the genomes. BGC distribution is largely determined by phylogeny. Another attribute of some antibiotic producers is the ability to withstand nutritional stress. We exploited these attributes to isolate and identify potential antibiotic producers. A minimal substrate medium was used to isolate nutritionally versatile bacterial strains from topsoil collected from the rhizosphere. The genera of isolates were identified by 16S rRNA gene sequence comparison as Pseudomonas, Hafnia and Obesumbacterium. The typical genome size of species in these genera are 6.2 Mb, 4.7 Mb and 5.0 Mb respectively. The antiSMASH database was browsed by phylogeny to determine the distribution pattern of BGCs in these genera. Pseudomonas strains have an average of 7 BGCs within their genomes that may encode antibiotics, whilst Hafnia and Obesumbacterium strains have 2 and 0 respectively. Therefore, the isolated Pseudomonas strain has the greatest potential to biosynthesis antibiotics. However, the biosynthetic potential of other isolates may be understated given the typical genome size of species in their genera, and their ecological origin. Consequently, all isolates are prime candidates for the next stage of the project which involves genome mining for cryptic or silent genes that may encode novel compounds with antibiotic properties. More isolates are also being recovered

Subjective assessment of listening environments in university classrooms: Perceptions of students,"

A questionnaire is developed to evaluate perception of the listening environment by university students. The objectives were to develop a questionnaire-based measurement tool, derive a measure of perceived classroom-listening quality, use the questionnaire to investigate factors that enhance, impair, or do not affect perceived listening quality, and consider the implications for classroom design. The questionnaire was administered to over 5700 students in 30 classrooms at one university. Physical and acoustical measurements were also performed in each classroom. The questionnaire included items that recorded aspects of student perception, as well as individual, course-, and instructor-specific factors. Responses to 19 perception items generated a perception of listening ease ͑PLE͒ score for each student and a classroom-average score. Decreased PLE was associated with women, English-second-language students, those with hearing impairment, students not interested in the course material, and those who found the material difficult. Increased PLE was associated with higher speech transmission index, acceptable lighting, temperature and seating, better instructor voice, increased visual-aid use, and easier course material. Results indicate that PLE is a useful measure of student perception of the classroom-listening environment, and that optimal classroom acoustical design must take into consideration "in-use" conditions, as well as classroom physical characteristics

Investigation into the antimicrobial activity of cationic antibacterials

The topic addressed by the 2011 WHO‘s World Health Day was antibacterial resistance. This action served to highlight the serious problem bacterial resistance now presents to healthcare professionals globally. This investigation focussed on the action of four cationic antimicrobial agents against E. coli, S. aureus and P. aeruginosa. Triclosan is widely used clinically and as an ingredient of personal care products that has come under renewed scrutiny by the FDA last year. Colistin is used clinically as salvage therapy against multi-drug resistant bacteria, particularly P. aeruginosa and A. baumanii. NP101 and NP108 are novel antimicrobial peptides, considered as a class with huge future potential in the treatment of not only bacterial but also viral and fungal infections in humans. The action of triclosan on all three test bacteria, including P. aeruginosa, historically considered resistant to triclosan, revealed concentration dependent bacteriostatic/bactericidal effects; reduction in bacterial growth; inhibition of second-phase logarithmic growth in S. aureus; induction of minimal K+ loss in all bacterial species; non-septation and aggregation in all test species. Colistin use was abandoned clinically between 1970-2000 and is not used clinically against Gram-positive species. Colistin exposure induced a common response from test bacteria including the Gram-positive S. aureus; concentration dependent retardation in onset of bacterial growth, without reduction in final bacterial density; significant K+ loss from S. aureus and E. coli but not P. aeruginosa; the development of resistance to the inhibitory colistin concentration by P. aeruginosa and S. aureus but not E. coli; production of small colony variants by P. aeruginosa; formation of spherical aggregates; membrane blebbing and inhibition of normal bacterial septation. Similar responses to NP101 and NP108 were observed to the test bacteria; an all or nothing effect on bacterial growth; prevention of second phase logarithmic growth in S. aureus; induction of significant K+ loss in all bacteria; size and shape alterations; extrusion of intracellular material, membrane blebbing; inhibition of bacterial septation and interruption of binary fission. Each of these peptides was incorporated into lyophilised wafers and tested for in vitro topical antibacterial efficacy and shown to have antibacterial activity against all test species.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Data_Sheet_1_The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps.xlsx

The gastrointestinal (GI) impact of fibers including resistant starch (RS) consumption depends on various types and amounts of fibers, the initial microbiome states, and accurate intake measurements. A randomized clinical trial evaluated the GI impact of varying doses of a novel resistant starch blend (RSB) with smart cap monitoring. RSB contained at least 50% RS and was a proprietary mixture of a potato starch, green banana flour, and apple fiber powder (a source of apple pectin, not resistant starch). The study design randomized participants to one of four arms: 10 g/day of potato starch (0 RSB), 10 g/day of RSB, 10 to 20 to 20 g/day of RSB or 10 to 20 to 30 g/day RSB for two-week intervals over 6 weeks. Results confirmed that while resistant starch of approximately 5 g per day improves GI symptoms at 2, 4, and 6 weeks, it did not demonstrate a detectable effect on short chain fatty acids. Increasing doses of the blend (RSB) led to a decrease in the diarrhea score. Using an estimate of total consumption of RSB based on smart cap recordings of container openings and protocol-specified doses of RSB, a reduction in the sleep disturbance score was associated with higher RSB dose. The exploratory microbiome evaluation demonstrated that among the 16S rRNA gene sequences most associated with the consumption of the novel blend RSB, two belong to taxa of notable interest to human health: Faecalibacterium and Akkermansia.</p

Presentation_1_The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps.zip

The gastrointestinal (GI) impact of fibers including resistant starch (RS) consumption depends on various types and amounts of fibers, the initial microbiome states, and accurate intake measurements. A randomized clinical trial evaluated the GI impact of varying doses of a novel resistant starch blend (RSB) with smart cap monitoring. RSB contained at least 50% RS and was a proprietary mixture of a potato starch, green banana flour, and apple fiber powder (a source of apple pectin, not resistant starch). The study design randomized participants to one of four arms: 10 g/day of potato starch (0 RSB), 10 g/day of RSB, 10 to 20 to 20 g/day of RSB or 10 to 20 to 30 g/day RSB for two-week intervals over 6 weeks. Results confirmed that while resistant starch of approximately 5 g per day improves GI symptoms at 2, 4, and 6 weeks, it did not demonstrate a detectable effect on short chain fatty acids. Increasing doses of the blend (RSB) led to a decrease in the diarrhea score. Using an estimate of total consumption of RSB based on smart cap recordings of container openings and protocol-specified doses of RSB, a reduction in the sleep disturbance score was associated with higher RSB dose. The exploratory microbiome evaluation demonstrated that among the 16S rRNA gene sequences most associated with the consumption of the novel blend RSB, two belong to taxa of notable interest to human health: Faecalibacterium and Akkermansia.</p

KCTD7 deficiency defines a distinct neurodegenerative disorder with a conserved autophagy-lysosome defect

International audienceOBJECTIVE:Several small case series identified KCTD7 mutations in patients with a rare autosomal recessive disorder designated progressive myoclonic epilepsy (EPM3) and neuronal ceroid lipofuscinosis (CLN14). Despite the name KCTD (potassium channel tetramerization domain), KCTD protein family members lack predicted channel domains. We sought to translate insight gained from yeast studies to uncover disease mechanisms associated with deficiencies in KCTD7 of unknown function.METHODS:Novel KCTD7 variants in new and published patients were assessed for disease causality using genetic analyses, cell-based functional assays of patient fibroblasts and knockout yeast, and electron microscopy of patient samples.RESULTS:Patients with KCTD7 mutations can exhibit movement disorders or developmental regression before seizure onset, and are distinguished from similar disorders by an earlier age of onset. Although most published KCTD7 patient variants were excluded from a genome sequence database of normal human variations, most newly identified patient variants are present in this database, potentially challenging disease causality. However, genetic analysis and impaired biochemical interactions with cullin 3 support a causal role for patient KCTD7 variants, suggesting deleterious alleles of KCTD7 and other rare disease variants may be underestimated. Both patient-derived fibroblasts and yeast lacking Whi2 with sequence similarity to KCTD7 have impaired autophagy consistent with brain pathology.INTERPRETATION:Biallelic KCTD7 mutations define a neurodegenerative disorder with lipofuscin and lipid droplet accumulation but without defining features of neuronal ceroid lipofuscinosis or lysosomal storage disorders. KCTD7 deficiency appears to cause an underlying autophagy-lysosome defect conserved in yeast, thereby assigning a biological role for KCTD7