Exploring a Transcriptional Regulatory Region in Mycobacteriophage JacoRen57

Mycobacteriophages are infectious particles that infect mycobacteria, and little is known about cis-regulatory elements that control their gene expression. In phage genomes, cis-regulatory elements commonly precede a series of genes that are expressed as an operon. JacoRen57 is a cluster AB mycobacteriophage that possesses forward and reverse genes with non-coding gaps interspersed throughout its genome. We assayed one of the gap regions of JacoRen57 (40644-40974 bps) for regulatory activity in the downstream direction when present in its host, Mycobacterium smegmatis, by cloning the region into pLO86, a vector containing the mCherry reporter gene. The putative regulatory region induced the expression of mCherry in vivo, indicating the presence of a promoter in this region of the JacoRen57 genome. Utilizing 5’ deletions analysis, we identified promoter and repressor elements within this regulatory region. We are conducting further experiments to understand the characteristics of the repressor region and which sigma factor/s binds to this promoter

Discovering Gene Functions in Mycobacteriophage Sbash Using a Genetic Screen

Sbash is a temperate bacteriophage, which was isolated on the host, Mycobacterium smegmatis mc2 155 from soil collected in South Africa. It is classified as cluster I and sub-cluster I2. Its genome consists of 55,832 base pairs and 89 protein-coding genes of which only 25 genes were assigned a function by bioinformatic analysis. We are using a genetic screen to uncover the functions of phage genes for which function is unknown. To begin to uncover the functions of the protein products of the genes in Sbash’s genome, we cloned each gene into the pExTra plasmid and assayed each phage gene for two phenotypes: cytotoxicity, the ability to interfere with host cell growth, and defense, the ability to protect the host cell from infection by other phages. In total, we successfully cloned approximately half of the genes in Sbash’s genome with sizes ranging from 90 bp to nearly 1500 bp. We identified two Sbash genes that defend host cells from infection by other mycobacteriophages. We identified six genes that reduced the growth of host cells when expressed. Here, we report our progress on this project. We have also analyzed genes in Mycobacteriophage Island3, a cluster I1 phage, for cytotoxicity and defense to complete the screen of this phage started by students in previous research groups

Exploring a Putative Promoter Region in Mycobacteriophage JacoRen57

Phages are abundant particles that infect bacteria. For the SEA-PHAGES program, students discover phages and annotate their genomes. Throughout the annotation process, genes are identified based on bioinformatics evidence; however, little is known about mycobacteriophage promoters as they are not annotated. Promoters are necessary for gene expression, and in mycobacteriophages, a promoter typically precedes a series of genes that are expressed as a single transcript from which multiple proteins are translated. JacoRen57 is a singleton mycobacteriophage with a siphoviridae morphotype that possesses forward and reverse genes with gaps located at the transitions from forward to reverse genes. We hypothesized that these gaps contain promoters. We used BPROM and PePPER, prokaryotic promoter predictor software, which yielded matches to promoter consensus sequences in one of the gap regions. We cloned the putative promoter region into pLO86, a vector containing the mCherry reporter gene, to determine if the cloned region functions as a promoter by inducing mCherryexpression in Mycobacterium smegmatis. The putative promoter region did not function as a promoter in vivo under standard M. smegmatisgrowth conditions

Preparatory Piano Students Recital

This is the program for the preparatory piano students. Many students performed, including Sara Scott, Guy T. Nelson, Jr., Louis Byron Cady, Esther Garrett, Bruce Watson, Carol Drummond, Cynthia Landers, Mary Gail Baber, Denise Watson, David Dahlstedt, Veda Smith, Charlotte Goodson, Roy Cagle, Margery Goodson, Nancy Goodson, Danny Taft, Carol Cantrell, and Jim McCarty. This recital took place on May 23, 1963, in Mitchell Hall

Annotation of Two Soil Mycobacteriophages: JacoRen57 and DrLupo

We discovered two novel Mycobacteriophagesfrom soil samples. JacoRen57 is a singleton, most closely related to cluster AB phages. DrLupois a member of the rare H2 sub-cluster containing only one other member. Both phages exhibit a siphoviridaemorphotype, double-stranded DNA genome, and a non-contractile tail. The genome of JacoRen57 is composed of 52,411 base pairs with a 56.7% GC content and includes genes and plaque morphology that suggest a lytic life cycle. The genome is organized according to the following order from the left to right arm: 33 forward genes followed by 16 reverse genes and 24 forward genes. We identified functions for 33 of the 73 protein coding genes using bioinformatics software. The 70,030 base-pairgenome of DrLupohas a 57.5% GC content and contains genes that support a lytic life cycle. We identified 110 forward genes and assigned functions to 25 of them

Historia del municipio de Chichigalpa, Departamento de Chinandega a partir de la segunda mitad del siglo XIX a la actualidad

La presente investigacion monográfica titulada “ Historia local del municipio de Chichigalpa, Departamento de Chinandega a partir de la segunda mitad del siglo XIX a la actualidad” se ubica en la línea de investigación de Historia Regional y Local, que permite plantear, descubrir, identificar y comparar los cambios, en el contexto sociocultural y en materia económica, ante el desarrollo del municipio. El municipio de Chichigalpa se vio inmerso en el factor dinamizador de la economía que influyó en el crecimiento agrícola a partir de la llegada de la caña de azúcar y la edificación de vías ferroviarias que permitieron la influencia del medio de transporte y cambios en el municipio, incidió consigo en el involucramiento de los habitantes de esta municipalidad trascendiendo en el entorno sociocultural y económico de una comunidad meramente agrícola, convirtiendose en uno de los lugares mas productivos de la región de Occidente. Para comprender el desarrollo historico del municipio,se aplicó y la metodología de análisis y síntesis de fuentes documentales, primarias y secundarias, la técnica a utilizar fue el fichaje de fuentes históricas para su respectivo análisis e interpretación, se utilizó el método deductivo e inductivo. El perfil de esta temática obedece al enfoque cualitativo para su plena asimilación y entendimiento, de manera comparativa se investigó el antes, y después de la introducción de la caña de azúcar para ir conociendo esos cambios que han tenido las actividades realizadas en esta localidad logrando aportar una nueva fuente de información que permita la iniciativa de nuevos estudios académico

Phun With Phages: Discovering Novel Bacteriophages in the Soil

We used three bacterial hosts: Mycobacterium smegmatis, Microbacterium foliorum, and Gordonia terrae, to isolate novel bacteriophages from soil samples. We named these phages, created high titer lysates, and purified their DNA genomes. We have archived the high titer lysates at Northwestern College and the University of Pittsburgh. The genomes of three of our phages were sequences at the University of Pittsburgh and we will be sequencing the remaining genomes this summer. Additionally, we are planning to image our phages with transmission electron microscopy at the University of Iowa or Nebraska yet this semester

Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas.

Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations

Enhanced Stress Wave Analysis of Scaled Monopiles in Glacial Till at Cowden

Conventional stress wave analysis for pile driving involves a subjective signal matching process using pile driving analyser (PDA) measurements. The PICASO (PIle Cyclic AnalySis: Oxford and Ørsted) research project provided an opportunity to collect high frequency strain measurements using optical fibre Bragg grating (FBG) sensors over the embedded length of the pile, in addition to conventional PDA data. This paper reports the application of a novel hybrid approach incorporating FBG data into the signal matching process, as developed by Buckley et al. (2020a), to an overconsolidated glacial till site in Cowden, Hull, UK. The additional information on stress wave propagation, obtained through FBG measurements, provides insights into the development of soil resistance to driving (SRD) in stiff clays. The results obtained using the new framework are compared to the resistance predicted using a widely-adopted empirical method

Genetic Annotation of Bacteriophages MScarn, Knocker, and Neos5

We annotated the genomes of three recently discovered bacteriophages to learn more about their genetic composition. MScarn is a lytic bacteriophage that infects Gordonia terrae 3612. It was discovered and purified from soil collected in Iroquois, SD. MScarn is a cluster CT phage, one of only 37 discovered to date. Its genome is 45,677 base pairs long and has 10-nucleotide 3’ sticky overhanging ends. Its GC content is 60.3% which is typical of CT cluster members. Knocker is a cluster B9 phage that was isolated on the host Mycobacterium smegmatis mc²155 from soil collected in Watertown, SD. Its circularly permuted genome contains 71,459 base pairs, and it has a high GC content of 69.7%. Similar to the other three members of the B9 cluster, it exhibits a lytic life cycle. Neos5, a lytic bacteriophage, was also isolated on Mycobacterium smegmatis mc²155 from soil collected in Baltimore, MD. It is a cluster B3 phage with a circularly permuted genome of 68,886 base-pairs and a 67.5% GC content, synonymous to the other 37 members of the cluster. All three phages were discovered, purified, and annotated by Northwestern College students