DNA fingerprinting of spore-forming bacterial isolates, using Bacillus cereus repetitive polymerase chain reaction analysis (Bc-Rep-PCR)

Bc-repetitive extragenic palindromic polymerase chain reaction (Bc-Rep PCR) analysis was conducted on seven Bacillus thuringiensis isolates accessed from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) culture collection and on five local isolates of entomopathogenic spore-forming bacteria. The five isolates were three strains of B. thuringiensis, one strain of B. cereus and one strain of Brevibacillus laterosporus. All five isolates were distinguished from each other using Bc-Rep PCR analysis. The three B. thuringiensis isolates were closely related. The isolate of B. laterosporus was not related to any of the B. cereus group isolates. Serotyping was also conducted on the five local isolates. However, only one of these isolates could be identified with serotyping and was identified as B. thuringiensis subsp. kenyae.Keywords: Bc-repetitive extragenic palindromic polymerase chain reaction, Bacillus sp., serotypingAfrican Journal of Biotechnology Vol. 12(14), pp. 1598-160

Perception of gluten-free bread as influenced by information and health and taste attitudes of millennials

Information on what drives consumers to like or dislike bread is needed to provide insight on developing gluten-free (GF) bread, using indigenous and sustainable crops in Africa, such as sorghum and millet. Consumer attitudes toward the health and taste aspects of food are major drivers of food choices. The objectives of this work were (1) to determine the health and taste attitudes (HTAs) and general perceptions of a group of millennial consumers in South Africa (n = 354), concerning GF breads; and (2) to determine whether HTAs affect the acceptability of sensory properties of commercial GF breads, as assessed by consumers (n = 173), under informed and uninformed conditions. Mean scores of the taste factors were higher compared to health factors, indicating a greater taste orientation. The sensory properties of standard wheat breads were preferred over two commercial GF breads, irrespective of the health/taste interests of consumers, or if they were informed/uninformed about the nature of the bread (GF or wheat). Knowledge that bread samples were GF reduced only the acceptability of the aroma of GF bread. GF bread was perceived as healthier, but less tasty. For this group of millennials, the sensory properties of bread was the main driver of choice.The National Research Foundation of South Africahttp://www.mdpi.com/journal/foodsdm2022Consumer ScienceFood Scienc

How should performance in EBUS mediastinal staging in lung cancer be measured?

There has been a paradigm shift in mediastinal staging algorithms in non-small cell lung cancer over the last decade in the United Kingdom (UK). This has seen endoscopic nodal staging (predominantly endobronchial ultrasound, EBUS) almost replace surgical staging (predominantly mediastinoscopy) as the pathological staging procedure of first choic

Information Theoretic Criteria for Community Detection

Many algorithms for finding community structure in graphs search for a partition that maximizes modularity. However, recent work has identified two important limitations of modularity as a community quality criterion: are solution limit; and a bias towards finding equal-sized communities. Information-theoretic approaches that search for partitions that minimize description length are a recent alternative to modularity. This paper shows that two information-theoretic algorithms are themselves subject to a resolution limit, identifies the component of each approach that is responsible for the resolution limit, proposes a variant, SGE (Sparse Graph Encoding), that addresses this limitation, and demonstrates on three artificial data sets that (1) SGE does not exhibit a resolution limit on sparse graphs in which other approaches do, and that (2) modularity and the compression-based algorithms, including SGE, behave similarly on graphs not subject to the resolution limit

siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect

<p>Abstract</p> <p>Background</p> <p>RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring perfect complementarity between the siRNA guide strand and the target mRNA, was believed to be extremely specific. However, a recent growing body of evidence has suggested that siRNA could down-regulate unintended genes whose transcripts possess complementarity to the 7-nt siRNA seed region. This off-target gene silencing may often provide incongruous results obtained from knockdown experiments, leading to misinterpretation. Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value.</p> <p>Results</p> <p>We present siDirect 2.0, an update of our web-based software siDirect, which provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5°C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects.</p> <p>Conclusion</p> <p>siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5°C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in RefSeq. siDirect 2.0 is available at <url>http://siDirect2.RNAi.jp/</url>.</p

New urbanism, crime and the suburbs: a review of the evidence

Sustainability now influences government policy in the UK, Australia and USA and planning policy currently advocates high density, mixed-use residential developments in 'walkable', permeable neighbourhoods, close to public transport, employment and amenities. This clearly demonstrates the growing popularity, influence and application of New Urbanist ideas.This paper reviews the criminological research relating to New Urbanism associated with the three key issues of permeability, rear laneway car parking and mixed-use development. These key issues are discussed from an environmental criminology perspective and challenge New Urbanist assumptions concerning crime. The paper proposes that crime prevention through environmental design (CPTED) and its crime risk assessment model represents a valuable tool for New Urbanists to utilise to reduce opportunities for crime and tackle fear of crime in the community. Recommendations for future research and collaboration are discussed

Life-History Evolution on Tropidurinae Lizards: Influence of Lineage, Body Size and Climate

The study of life history variation is central to the evolutionary theory. In many ectothermic lineages, including lizards, life history traits are plastic and relate to several sources of variation including body size, which is both a factor and a life history trait likely to modulate reproductive parameters. Larger species within a lineage, for example tend to be more fecund and have larger clutch size, but clutch size may also be influenced by climate, independently of body size. Thus, the study of climatic effects on lizard fecundity is mandatory on the current scenario of global climatic change. We asked how body and clutch size have responded to climate through time in a group of tropical lizards, the Tropidurinae, and how these two variables relate to each other. We used both traditional and phylogenetic comparative methods. Body and clutch size are variable within Tropidurinae, and both traits are influenced by phylogenetic position. Across the lineage, species which evolved larger size produce more eggs and neither trait is influenced by temperature components. A climatic component of precipitation, however, relates to larger female body size, and therefore seems to exert an indirect relationship on clutch size. This effect of precipitation on body size is likely a correlate of primary production. A decrease in fecundity is expected for Tropidurinae species on continental landmasses, which are predicted to undergo a decrease in summer rainfall

Sex Differences in the Brain: A Whole Body Perspective

Most writing on sexual differentiation of the mammalian brain (including our own) considers just two organs: the gonads and the brain. This perspective, which leaves out all other body parts, misleads us in several ways. First, there is accumulating evidence that all organs are sexually differentiated, and that sex differences in peripheral organs affect the brain. We demonstrate this by reviewing examples involving sex differences in muscles, adipose tissue, the liver, immune system, gut, kidneys, bladder, and placenta that affect the nervous system and behavior. The second consequence of ignoring other organs when considering neural sex differences is that we are likely to miss the fact that some brain sex differences develop to compensate for differences in the internal environment (i.e., because male and female brains operate in different bodies, sex differences are required to make output/function more similar in the two sexes). We also consider evidence that sex differences in sensory systems cause male and female brains to perceive different information about the world; the two sexes are also perceived by the world differently and therefore exposed to differences in experience via treatment by others. Although the topic of sex differences in the brain is often seen as much more emotionally charged than studies of sex differences in other organs, the dichotomy is largely false. By putting the brain firmly back in the body, sex differences in the brain are predictable and can be more completely understood