Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform

Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three - encoding tape-measure proteins, lysins, and minor tail proteins - are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education. © 2006 Hatfull et al

Variability in the Effect of 5-HTTLPR on Depression in a Large European Population: The Role of Age, Symptom Profile, Type and Intensity of Life Stressors.

BACKGROUND: Although 5-HTTLPR has been shown to influence the risk of life stress-induced depression in the majority of studies, others have produced contradictory results, possibly due to weak effects and/or sample heterogeneity. METHODS: In the present study we investigated how age, type and intensity of life-stressors modulate the effect of 5-HTTLPR on depression and anxiety in a European population cohort of over 2300 subjects. Recent negative life events (RLE), childhood adversity (CHA), lifetime depression, Brief Symptoms Inventory (BSI) depression and anxiety scores were determined in each subject. Besides traditional statistical analysis we calculated Bayesian effect strength and relevance of 5-HTTLPR genotypes in specified models. RESULTS: The short (s) low expressing allele showed association with increased risk of depression related phenotypes, but all nominally significant effects would turn to non-significant after correction for multiple testing in the traditional analysis. Bayesian effect strength and relevance analysis, however, confirmed the role of 5-HTTLPR. Regarding current (BSI) and lifetime depression 5-HTTLPR-by-RLE interactions were confirmed. Main effect, with other words direct association, was supported with BSI anxiety. With more frequent RLE the prevalence or symptoms of depression increased in ss carriers. Although CHA failed to show an interaction with 5-HTTLPR, in young subjects CHA sensitized towards the depression promoting effect of even mild RLE. Furthermore, the direct association of anxiety with the s allele was driven by young (</=30) individuals. LIMITATIONS: Our study is cross-sectional and applies self-report questionnaires. CONCLUSIONS: Albeit 5-HTTLPR has only weak/moderate effects, the s allele is directly associated with anxiety and modulates development of depression in homogeneous subgroups

Student Perception and Affinity: Establishment of an Institutional Framework for the Examination of Underrepresented Programs Such as Agriculture in Honors

This (2019) study assesses student perceptions of an honors college relative to other colleges in an institutional framework. Disproportionately low enrollments in honors from specific majors (particularly those in the College of Agriculture, Food, and Environmental Sciences) prompt researchers to investigate the culture of honors, perceived curricular demands, and the relationship of honors to other colleges and the students they serve. Researchers survey honors and non-honors students (n = 259) across disciplines (n = 59) representing all academic colleges across campus. Data suggest that while a majority of students affirm their abilities to complete the honors curriculum and perceive honors study to be beneficial, fewer than half (.4) of respondents report actively pursuing honors distinction. Researchers identify three major reasons: perceived lack of time, misunderstanding of requirements, and aversion to independent study. Respondents also indicate that their interests in honors might increase if connections between honors and their majors/colleges were more apparent. The authors conclude that student-centered ideas for creating value in honors are essential for future efforts in programming and recruitment

Complex Relationships within Highly Abundant Mycobacteriophage Phamilies

<div><p>(A) Complex relationships among members of the Pham7 (Lysin A) phamily. The output of a BLAST comparison of Wildcat gp49 against other mycobacteriophage proteins shows that only 16 other mycobacteriophage proteins are matched and that these correspond to different parts of Wildcat gp49. Colored bars represent the strength of the matches, with red being the strongest, followed by purple, blue, and black.</p><p>(B) Phylogenetic relationships between members of mycobacteriophage Pham23 (tape-measure protein; Tmp). Amino acid sequences for each of the 30 constituent members of Pham23 were aligned using ClustalW and the unrooted phylogenetic relationships represented using NJTree. Bootstrap values from 1,000 reiterations are shown.</p><p>(C) Chimerism in Pham28 (minor tail) proteins. Llij gp18 is related to both gp18 and gp19 of phage Che8 at high levels of amino acid sequence identity, and these proteins are related in turn to other members of Pham28 as shown.</p></div

Nucleotide Sequence Comparison of 30 Mycobacteriophage Genomes as Illustrated in a Dotter Plot Using a Sliding Window of 25 bp [63]

<p>The lower triangle represents the relationships at an elevated level of gray-scale relative to the upper triangle, revealing weaker sequence relationships.</p

Estimating the Number of Mycobacteriophage Phams

<p>A subset of the 30 phages was randomly selected without replacement, and the total number of Phams was determined; this was repeated 10,000 times with the mean shown as a blue circle. For each subset, an additional phage was then randomly chosen, and the average number of new Phams found in that phage was determined; these data are shown as red squares. The total number of Phams was fit to a hyperbolic function, with the best-fit equation determined by least-squares regression.</p