Digital Commons Network^™

Stable Coexistence Or Competitive Exclusion? Fern Endophytes Demonstrate Rapid Turnover Favoring A Dominant Fungus, Brett Steven Younginger, Nathan U. Stewart, Mehmet Ali Balkan, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centred on seed-reproducing hosts, while spore-reproducing plants also host endophytes and may be colonized by unique community members. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we explored endophytes in a single population of ferns, Polystichum munitum, in the Pacific Northwest. Through metabarcoding, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in …

Genome Interpretation Using In Silico Predictors Of Variant Impact, Panagiotis Katsonis, Kevin Wilhelm, Amanda Williams, Olivier Lichtarge

Faculty, Staff and Students Publications

Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at …

Sources And Distribution Of Microplastics In The United Arab Emirates, Rana Zeeshan Habib

Dissertations

Microplastics (plastic pieces size) are an emerging environmental contaminant that is ubiquitously present in terrestrial, aquatic and aerial environments. United Arab Emirates (UAE) is categorized among the highest domestic waste producing countries (on per capita basis) in the world. A large portion of waste ends up in the environment and contains macro-, meso- and microplastics. No comprehensive study has been carried out in the UAE to investigate the abundance, sources, distribution and impact of microplastics on its environment. Therefore, a comprehensive study to analyze the sources and distribution of microplastics in the UAE was urgently needed. The objective of the …

A Review On Serum, Genetic And Mirna Associated Biomarkers For The Early Diagnosis Of Hepatocellular Carcinoma (Hcc)), Ambreen Kanwal, Asima Tayyeb

Journal of Bioresource Management

Hepatocellular carcinoma is the most devastating complication of liver cirrhosis and diagnosis in earlier stages could be useful in curative interventions. The main aim of this review was to analyze current diagnostic biomarkers which are available for the early diagnosis of hepatocellular carcinoma (HCC). For this purpose, we searched different web databases including Medline/Pubmed. We found multiple significant serum biomarkers for imperative diagnosis including α- Fetoprotein, Des- γ -carboxyprothrombin (DCP), Osteopontin (OPN), Glypican-3 (GPC3), Golgi protein-73 (GP73), Squamous cell carcinoma antigen (SCCA), Annexin A2 (ANXA2) and Heat shock protein 70 (HSP70) but all of these represent low sensitivity and low …

Knowledge, Attitudes And Practices Towards The Use Of Iron And Folic Acid Supplements Among Pregnant And Lactating Women In Dar Es Salaam, Cecilia N. Mshanga, Elina J. Maseta

Tanzania Journal of Science

The current study investigated knowledge, attitudes and practices (KAP) regarding the use of iron and folic acid (IFA) supplements among pregnant and lactating women living with Human Immunodeficiency Virus (HIV) in Dar es Salaam. A cross-sectional survey involved 294 pregnant and lactating women attending Prevention of Mother-To Child Transmission (PMTCT) clinics. A semi-structured questionnaire was used to collect data from the subjects. The data were analysed using SPSS. Multivariate regression analysis was carried out to determine factors associated with IFA supplement use among the study subjects. The findings indicated that knowledge of IFA supplement use among the subjects was good …

Effects Of Small-Scale Mining Activities On Fisheries And Livelihoods In The Birim River In Atiwa District, Eastern Region Of Ghana, Elliot Haruna Alhassan, Samuel Opoku Dandi, Sandra Akugpoka Atindana

Tanzania Journal of Science

The socioeconomic importance of small-scale mining in Ghana is of great interest to the country. It provides employment, supports the livelihood of poor rural areas, and also contributes to national income. Despite all these importance, it has a great influence on the surroundings, with surface and groundwater bodies being the most affected. The study was conducted to determine the effects of small-scale mining activities on fisheries and livelihoods along the Birim River in Atiwa District of Ghana, and also, to ascertain the nature of mining in the catchment and the current status of fisheries in the river. Data were collected …

Population Characteristics Of Selected Small Pelagic Fish Species Along The Tanzanian Coast, Godfrey Fabiani, Leonard J. Chauka, Christopher A. Muhando

Tanzania Journal of Science

Although small pelagic fishing in Tanzania is rising, lack of information on population structure has been a significant concern in its management. This study aimed to determine the species composition, length-weight relationship and length at first maturity of Amblygaster sirm, Encrasicholina heteroloba, Encrasicholina punctifer, Stolephorus commersonii, and Spratelloides gracilis landed at Kilwa Kivinje, Kipumbwi and Shangani along the Tanzanian coast. These landing sites were chosen because of their locations and importance in the small pelagic fishery. Sampling was done monthly from October 2018 to June 2020. The catch composition was site specific such that  E. heteroloba dominated at Kilwa Kivinje …

Bed Ii Phytolith Palaeolandscapes (1.5-1.1 Ma) At Oldupai Gorge, Tanzania, Makarius P. Itambu

Tanzania Journal of Science

The primary approach for reconstructing ancient plant landscapes is normally through the analysis of environmental proxy data and ultimately the application of the data from plant micro-remains to infer the vegetation patterns, distribution, and nature of past environments. Phytolith analyses serve as an important tool for identifying different micro-ecological niches in which human activities occurred. They are indicative of certain plant types and vegetation patterns, and the way in which plant landscapes respond to regional climate changes. Hence, in order to understand the ancient plant landscape of the Pleistocene Bed II sites of Oldupai Gorge 1.5 to 1.1 million years …

Generation Of Geochemical Exploration Targets From Regional Stream Sediment Data Using Principal Component And Factor Analysis: A Case Study Of Kibaya-Kiteto, Manyara-Tanzania, Yusto J. Shine, Charles D. Moye, Godfrey J. Mallya, Ambaliche L. Tamambele

Tanzania Journal of Science

A regional-scale stream sediment geochemical sampling was carried out with an average sampling density of one sample per nine square-kilometre in Kiteto District, Manyara Region. A total of 358 stream sediment samples were collected and analysed for major and trace elements by X-ray fluorescence (XRF) and fire assay with atomic absorption spectrometry (AAS) finish methods. In this study, Factor and Principal Component Multivariate (FPCM) analyses have been used to the stream geochemical data to delineate potential mineralization zones by plotting correlated factors as geochemical anomaly maps. Four factors that account for 73.7% of the total variance of the stream sediment …

Evaluation Of Natural Antifungal Compounds From Artemisia Afra And Its Effectiveness On Prevention Of Aflatoxins, Noela G. Kilenga, Daniel Maeda, Oscar Kibazohi, Lilian D. Kaale

Tanzania Journal of Science

Artemisia afra is a medicinal plant with antimicrobial activities, known to treat tuberculosis, measles, cough, and influenza. In consequence, its applications have increasingly become pivotal to control various microbes which cause different diseases. This study therefore, evaluated the chemical composition and the antifungal activity of A. afra essential oil. The extraction of essential oil was done using steam distillation. The essential oil chemical composition was analysed by GC-MS. The analysis revealed 19 compounds from A. afra. The main compounds were borneol (71.529%), terpinen-4-ol (8.582%), β-thujone (3.283%), β-terpineol (2.590%), α-terpineol (1.791%), chrysanthenone (1.507%), myrtenal (1.393%), eucalyptol (1,8-cineole) (1.263%), cis-sabinene hydrate (1.172%) …

Characterisation And Antimicrobial Potential Of Actinobacteria Isolated From Momela Soda Lakes, Tanzania, Witness S. Lema, Ally Mahadhy, Modester Damas, Joan J.E. Munissi, Thomas J. Lyimo

Tanzania Journal of Science

Extreme environments such as soda lakes are potential sources of microbes with biotechnological applications in different sectors. This study aimed at isolation, characterization and investigation of antibacterial potential of actinobacteria from Momela Soda Lakes, at Arusha National Park in Tanzania. One hundred and twenty (120) isolates were recovered from soil and water samples using the dilution plate technique. The isolates were morphologically and biochemically characterized, and further, screened for antimicrobial activity by disc diffusion method as well as the micro dilution technique. Cytotoxic effects were determined using the brine shrimp lethality test. Results showed that, all 120 isolates were Gram-positive …

Chemical Composition And Bioactive Potential Of Extracts From Diospyros Capricornuta F. White Against Aspergillus Flavus And Aspergillus Parasiticus, Princess W. Ngowi, Juma A. Mmongoyo, Lilian D. Kaale

Tanzania Journal of Science

Diospyros capricornuta is an endemic species widely distributed along the coast of Tanzania that is used as food condiments and traditional medicine. The chemical compositions of Diospyros capricornuta leaves, stem-bark, and root-bark extracts; and their bioactive potentials against Aspergillus flavus and Aspergillus parasiticus were investigated. The leaves, stem-bark, and root-bark samples of D. capricornuta were extracted using Soxhlet apparatus and the resultant extracts were analyzed using Gas Chromatography-Mass Spectrometry (GC-MS). A total of 14 compounds were identified from the extracts, whereby 2,4-di-tert-butylphenol was the most abundant compound in all extracts. The growth and aflatoxin production inhibitions against A. flavus and …

Pulse-Field Analysis Diversity Of Extended Spectrum Beta Lactamases Producing Gram Negative Bacteria Isolated From Periplaneta Americana (Cockroaches), Omolara D. Popoola, Moses O. Efuntoye, Georgia C. Agu, Benjamin T. Thomas

Tanzania Journal of Science

Extended spectrum beta lactamase (ESBL) producing bacteria are organisms of public health significance that have been implicated in prolonged hospital stay, treatment failures and higher fatalities. These organisms were originally thought to be widely distributed in hospital, but have since grown in terms of their epidemiological coverage. This study was therefore aimed at using pulse-field gel electrophoresis (PFGE) to understand the diversity of ESBL producing organisms originating from cockroaches in Ago-Iwoye, Nigeria. The diversity was determined by using a set of twenty six (26) ESBL producing bacterial strains isolated from cockroaches sampled in Ago-Iwoye community, Ogun State, Nigeria. PFGE analysis …

Access To Online Formative Assessments In Lower-Division Undergraduate Biology Courses: Investigating Barriers To Student Engagement, Allison M. Upchurch, Dana L. Kirkwood-Watts, Kathleen R. Brazeal, Lorey A. Wheeler, Brian A. Couch, Gabrielle B. Johnson, Sarah K. Spier

School of Biological Sciences: Faculty Publications

Instructors use a variety of online formative assessment (FA) activities to support learning outside class. Previous studies have revealed barriers for students in online courses, but little is known about the barriers students experience when completing online FA assignments. Understanding these barriers to access is critical to fostering more inclusive learning for all students. Using a framework from previous work in online learning, we examined student perceptions of online FA access with respect to five barrier categories: technical resources, instructor organization, social interactions, personal engagement, and learning environment. We developed and administered a survey to more than 1,200 undergraduate biology …

Editorial: C. Elegans Hostmicrobiome Interactions: From Medical To Ecological And Evolutionary Model, Michael A. Herman, Javier E. Irazoqui, Buck S. Samuel, Nic Vega

School of Biological Sciences: Faculty Publications

No abstract provided.

Editorial: C. Elegans Host-Microbiome Interactions: From Medical To Ecological And Evolutionary Model, Michael A. Herman, Javier E. Irazoqui, Buck S. Samuel, Nic Vega

School of Biological Sciences: Faculty Publications

Microbiomes often form specific functional associations with their hosts. Correlations between microbiome membership and states of host health and disease abound in many systems. However, there are few systems that allow for in depth functional studies that include precise manipulation and interrogation of both microbiome composition and host function. Recently the nematode Caenorhabditis elegans - an excellent genetic model organism for studying many fields of biology, including neurobiology and behavior, development, cell biology, and innate immunity - has proven to be a robust system to probe microbiome interactions and their effect on host physiology.

Not The Same Cure: Student Experiences In Course-Based Undergraduate Research Experiences Vary By Graduate Teaching Assistant, Emma C. Goodwin, Jessica R. Cary, Erin E. Shortlidge

Biology Faculty Publications and Presentations

To expose all undergraduate science students to the benefits of participating in research, many universities are integrating course-based undergraduate research experiences (CUREs) into their introductory biology laboratory curriculum. At large institutions, the bulk of introductory labs are instructed by graduate teaching assistants (GTAs). Graduate students, who are often teachers and researchers in training, may vary in their capacity to effectively teach undergraduates via the CURE model. To explore variation in GTA teaching and the subsequent outcomes for students, we used a case study research design at one institution where introductory biology students participate in GTA-taught CURE lab sections. We used …

Temperature Has A Unimodal Effect On The Functional Response Of Wolf Spiders, John Delong, Stella F. Uiterwaal, Alondra Magallanes

School of Biological Sciences: Faculty Publications

The response of biotic interactions to changes in temperature will play a large role in determining the impact of climate change on ecological communities. In particular, how warming alters predator-prey interactions will influence population stability, food web connectivity, and the movement of energy across trophic levels. The functional response relates predator foraging rates to prey availability, and it is often predicted to increase monotonically with temperature, at least within the limits of predator function. However, some studies suggest that functional responses peak and then decline, and such a difference has critical implications for the effect of warming on ecological communities. …

Forty Years Without Family: Three Novel Bacteriophages With High Similarity To Spp1 Reveal Decades Of Evolutionary Stasis Since The Isolation Of Their Famous Relative, Veronique A. Delesalle, Brianne E. Tomko, Albert C. Vill, Katherine B. Lichty, Gregory P. Krukonis

Biology Faculty Publications

SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage–host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more …

Development Of Phage Therapy Strategies Against Gram-Positive Bacterial Pathogens, Sara Arroyo Moreno

Theses

Bacterial resistance to conventional antibiotics has become an urgent healthcare issue worldwide. In this light, a renewed interest has emerged for therapy with bacteriophages (phages), which are viruses that can specifically infect bacteria. These viruses encode different proteins that degrade specific bonds within the bacterial cell wall, both to inject their genomic material into the bacterial cells and to release the viral progeny: virion-associated hydrolases and endolysins, respectively. Elimination of Gram-positive pathogens with recombinant versions of phage enzymes represents a promising alternative to classical antibiotics. In this thesis, different phage therapy strategies involving either whole phages or the use of …

Ecological Interactions Disrupted By Habitat Alteration In The Neotropics, Aniko Toth, Andrew Allen, S. Kathleen Lyons, John Alroy

School of Biological Sciences: Faculty Publications

Ecological interactions help determine the distribution of species across landscapes and play crucial roles in ecosystem services such as pollination, seed dispersal, and pest control1. Human disturbances, particularly habitat alteration, have the potential to modify or erase ecological interactions^2,3 and so jeopardise the processes they control. While examples of interactions becoming rewired under human influence have been recorded, studies of this process for speciose assemblages at regional to continental scales are uncommon⁴ and obstructed by logistical difficulties2. The consequences for ecological communities and people are therefore poorly understood. Here we show that human habitat alteration is associated with …

The Use Of Non-Model Drosophila Species To Study Natural Variation In Tor Pathway Signaling, Tessa Steenwinkel, Kailee K. Hamre, Thomas Werner

Michigan Tech Publications, Part 1

Nutrition and growth are strongly linked, but not much is known about how nutrition leads to growth. To understand the connection between nutrition through the diet, growth, and proliferation, we need to study the phenotypes resulting from the activation and inhibition of central metabolic pathways. One of the most highly conserved metabolic pathways across eukaryotes is the Target of Rapamycin (TOR) pathway, whose primary role is to detect the availability of nutrients and to either induce or halt cellular growth. Here we used the model organism Drosophila melanogaster (D. mel.) and three non-model Drosophila species with different dietary needs, Drosophila …

Mechanistic Insight Into Functionally Different Human Islet Polypeptide (Hiapp) Amyloid: The Intrinsic Role Of The C-Terminal Structural Motifs, Dibakar Sarkar, Narayan Chandra Maity, Gourav Shome, Kyriakos Gabriel Varnava, Vijayalekshmi Sarojini, Subramanian Vivekanandan, Nirakar Sahoo, Sourav Kumar, Atin Kumar Mandal, Ranjit Biswas, Anirban Bhunia

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet …

Multiple Generations Of Antibiotic Exposure And Isolation Influence Host Fitness And The Microbiome In A Model Zooplankton Species, Reilly O. Cooper, Sarah Tjards, Jessica Rischling, David T. Nguyen, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Background

Chronic antibiotic exposure impacts host health through changes to the microbiome, increasing disease risk and reducing the functional repertoire of community members. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied. However, much less is understood about the multigenerational effects of antibiotic exposure and how the microbiome may recover across host generations.

Results

In this study, we examined microbiome composition and host fitness across five generations of exposure to a suite of three antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where …

Seqcode: A Nomenclatural Code For Prokaryotes Described From Sequence Data, Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, William B. Whitman

Life Sciences Faculty Research

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and …

Targeting Of The Hedgehog Signaling Pathway In Cancer Treatment, Andrew J. Hawes

The Cardinal Edge

The Hedgehog (Hh) signaling pathway is a developmental pathway that is highly conserved evolutionarily. While typically only displaying high activity during embryogenesis, overactivation of the Hh pathway in adults has been linked to multiple forms of cancer including acute myeloid leukemia, myelofibrosis, basal-cell carcinoma, pancreatic ductal adrenal carcinoma, and triple negative breast cancer. The prevalence of Hh activation in many different cancers has made it a prime target for inhibition of these cancers through novel therapies. This literature review sought to assess the current state of cancer treatment through inhibition of Hh signaling. Most current clinical trials involving the pathway …

Pollutants Corrupt Resilience Pathways Of Aging In The Nematode C. Elegans, Andrea Scharf, Annette Limke, Karl Heinz Guehrs, Anna Von Mikecz

Biological Sciences Faculty Research & Creative Works

Delaying aging while prolonging health and lifespan is a major goal in aging research. One promising strategy is to focus on reducing negative interventions such as pollution and their accelerating effect on age-related degeneration and disease. Here, we used the short-lived model organism C. elegans to analyze whether two candidate pollutants corrupt general aging pathways. We show that the emergent pollutant silica nanoparticles (NPs) and the classic xenobiotic inorganic mercury reduce lifespan and cause a premature protein aggregation phenotype. Comparative mass spectrometry revealed that increased insolubility of proteins with important functions in proteostasis is a shared phenotype of intrinsic- and …

Species Distribution Models And Climatic Niche Comparisons Provide Clues On The Geographic Origin Of A Spider Invasion In The Americas, Laura Segura‑Hernandez, Gilbert Barrantes, Eduardo Chacon‑Madrigal, Adrián Garcia‑Rodriguez

School of Biological Sciences: Faculty Publications

Identifying the source population of alien species is important to assess the distribution and potential effects in the invaded area. The araneid spider Cyrtophora citricola is widely distributed in Europe, Asia, and Africa; however, in the last 26 years, it has been reported in several countries across the Americas. To date, the geographic origin of the populations established in the Americas remains unclear, but considering the successful colonization after its recent arrival, assessing climatic similarities between the invaded and native geographic ranges could be useful to address this question. In this study, we used a combination of Species Distribution Models …

Quantitative Assay For Farnesol And The Aromatic Fusel Alcohols From The Fungus Candida Albicans, Cory H. T. Boone, Daniel Gutzmann, Jaxon J. Kramer, Audrey L. Atkin, Kenneth Nickerson

School of Biological Sciences: Faculty Publications

The dimorphic fungus Candida albicans is a commensal and opportunistic fungal pathogen of humans. It secretes at least four small lipophilic molecules, farnesol and three aromatic fusel alcohols. Farnesol has been identified as both a quorum sensing molecule (QSM) and a virulence factor. Our gas chromatography (GC)-based assay for these molecules exhibits high throughput, prevention of analyte loss by avoiding filtration and rotary evaporation, simultaneous cell lysis and analyte extraction by ethyl acetate, and the ability to compare whole cultures with their cell pellets and supernatants. Farnesol synthesis and secretion were separable phenomena and pellet:supernatant ratios for farnesol were high, …

Visualizing Hormonal Effects On Cardiomyocyte Hypertrophic Growth Dynamics Using Digital Holographic Microscopy: Does Size Matter?, Jacquelyn Simmons

McNair Research Journal SJSU

Heart disease continues to be the leading cause of death in the United States. Humans are unable to regenerate their heart tissue following an injury. However, neonatal mice are able to regenerate their heart tissue when cardiomyocytes (CMs) proliferate. This regenerative ability is lost approximately one week after birth when proliferating mononucleated CMs become binucleated and can no longer complete the cell-cycle. Recent studies have shown the combined inhibition of thyroid hormone (T3) and norepinephrine (NE) increases CM proliferation, promotes heart regeneration, and reduces cell size in vivo. Using digital holographic microscopy, the aim of this study was to (1) …