Life Sciences Commons^™

Development Of Multiplex Pcr Assay As A Basis For Predicting Pigment Related Features, Stephanie A. Rodriguez

Student Theses

Currently, short tandem repeats are used in forensic DNA typing to identify the DNA profiles recovered from evidence samples and deceased individuals. Recently, SNPs that are related to pigmentation have been researched for their use in the identification of phenotypic traits. The development of a SNP panel that could successful identify the eye and skin color of an individual, would be immensely useful in missing person cases or mass disaster victim identification. Eight SNPs were selected into a SNaPshot assay that could accurately predict eye and skin color, five for eye color and six for skin color. Development of the …

Venom Diversity And Evolution In The Most Divergent Cone Snail Genus Profundiconus, Guilia Fassio, Maria Vittoria Modica, Lou Mary, Paul Zaharias, Alexander E. Fedosov, Juliette Gorson, Yuri I. Kantor, Mandë E. Holford, Nicolas Puillandre

Publications and Research

Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also …

Invertebrate Retinal Progenitors As Regenerative Models In A Microfluidic System, Caroline D. Pena, Stephanie Zhang, Robert Majeska, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

Regenerative retinal therapies have introduced progenitor cells to replace dysfunctional or injured neurons and regain visual function. While contemporary cell replacement therapies have delivered retinal progenitor cells (RPCs) within customized biomaterials to promote viability and enable transplantation, outcomes have been severely limited by the misdirected and/or insuffcient migration of transplanted cells. RPCs must achieve appropriate spatial and functional positioning in host retina, collectively, to restore vision, whereas movement of clustered cells differs substantially from the single cell migration studied in classical chemotaxis models. Defining how RPCs interact with each other, neighboring cell types and surrounding extracellular matrixes are critical to …

An Amyloid Core Sequence In The Major Candida Albicans Adhesin Als1p Mediates Cell-Cell Adhesion, Vida Ho, Philippe Herman-Bausier, Christopher Shaw, Karen A. Conrad, Melissa C. Garcia-Sherman, Jeremy Draghi, Yves F. Dufrene, Peter N. Lipke, Jason M. Rauceo

Publications and Research

ABSTRACT The human fungal commensal Candida albicans can become a serious opportunistic pathogen in immunocompromised hosts. The C. albicans cell adhesion protein Als1p is a highly expressed member of a large family of paralogous adhesins. Als1p can mediate binding to epithelial and endothelial cells, is upregulated in infections, and is important for biofilm formation. Als1p includes an amyloidforming sequence at amino acids 325 to 331, identical to the sequence in the paralogs Als5p and Als3p. Therefore, we mutated Val326 to test whether this sequence is important for activity. Wild-type Als1p (Als1pWT) and Als1p with the V326N mutation (Als1pV326N) were expressed …

Microwave Solventless Synthesis Of Meso-Tetrakis (Pentafluorophenyl)Poprphyrin (Tppf20) And Tris(Pentafluorophenyl))Corrole [Chemistry], Sunaina Singh

Open Educational Resources

Organic chemistry is a two-semester course (Organic Chemistry I, SCC 251 and Organic Chemistry II, SCC 252) required for majors in Biology. The SCC 251 course has been designated for the Integrative Learning Core Competency as well the Digital Communication Ability. This course emphasizes the synthesis, structure, reactivity, and mechanisms of reaction of organic compounds. Laboratory stresses various organic synthetic and analytic techniques (distillation, extraction, chromatography and spectroscopy).

This lab provided an opportunity for students to go deeper with the chemistry content by correlating to the concepts they learned in General Chemistry courses such as Valence shell electron pair repulsion …

Titration Of A Newtown Creek Environmental Water Sample To Determine The Amount Of Chloride Ions [Chemistry], Kevin Mark

Open Educational Resources

Main Course Learning Objectives:

The General Chemistry 1 (SCC 201) course has multiple course learning objectives, which articulate key introductory chemistry concepts that all STEM students should possess. In particular, the Newtown Creek titration experiment aligns with SCC 201 learning objectives of:

1. Demonstrate an appreciation of the role of chemistry in various aspects of life
2. Perform basic laboratory skills such as the proper execution of titration techniques
3. Describe and explain the fundamental chemistry concept of solution concentration
4. Analyze and represent experimental data in tables and graphs, interpret experimental results and write laboratory reports

In the SCC 201 laboratory, students are …

Human Biology Oer, Bio 1100, Course Outline, Tatiana Voza

Open Educational Resources

This course will include selected biological concepts, including the chemical basis of life, cell structure and division, a broad survey of the major systems of the human body with a special emphasis on human health disease, human evolution and ecology. This course should provide students who do not plan to continue in the sciences or pre-health programs with a working knowledge of life science that will be useful in making informed decisions on health and the environment

Multi-Scale Predictors Of Parasite Risk In Wild Male Savanna Baboons (Papio Cynocephalus), Bobby Habig, David A.W.A.M. Jansen, Mercy Y. Akinyi, Laurence R. Gesquiere, Susan C. Alberts, Elizabeth A. Archie

Publications and Research

Several factors are thought to shape male parasite risk in polygynous and polygynandrous mammals, including male-male competition, investment in potentially immunosuppressive hormones, and dispersal. Parasitism is also driven by processes occurring at larger scales, including host social groups and populations. To date, studies that test parasite-related costs of male behavior at all three scales—individual hosts, social groups, and the host population—remain rare. To fill this gap, we investigated multi-scale predictors of helminth parasitism in 97 male savanna baboons (Papio cynocephalus) living in the Amboseli ecosystem in Kenya over a 5-year span. Controlling for multi-scale processes, we found that many of …

Systematics Of Carex Section Laxiflorae (Cyperaceae), Jenna Dorey

Dissertations, Theses, and Capstone Projects

Carex, with more than 2100 species, is the most species-rich genus of flowering plants in temperate regions of the world. Members of the family Cyperaceae are colloquially known as sedges, and members of the genus Carex are called “true sedges.” Carex occur on every continent except for Antarctica, they thrive in a panoply of habitats, and are ecologically important as a forage source for wildlife, carbon sequestration, prevention of soil erosion, and providing habitat for fresh water invertebrates. Despite their importance many sedges are still poorly known, such as the woodland sedges in Carex section Laxiflorae, which is …

Fetal Pig Dissection Manual (Biol 105), Nathalia G. Holtzman, Daniel J. Yakubov

Open Educational Resources

This book is a guide to the basic fetal pig dissection conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a three- 3-hour lab periods which focus on the relationship of form and function of the pig anatomy and physiology. Step by step instructions for the dissection are provided along with some microscopy tasks to look at the histology of key organs.

In addition to the full text of the …

Histology Atlas: Basic Mammalian Tissue Types (Biol 105), Joshua Barnes, Daniel J. Yakubov, Corinna Singleman, Nathalia G. Holtzman

Open Educational Resources

This book is a guide to the basic histology lab conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a single 3-hour lab periods which focus on the relationship of form and function of the cellular and organ level anatomy and physiology. Step by step instructions for each slide set are provided for all the key organs.

In addition to the full text of the book, we also provide a …

Green Infrastructure Design Influences Communities Of Urban Soil Bacteria, Jessica Lee Joyner, Jordan Kerwin, Maha Deeb, George Lozefski, Bharath Prithiviraj, Anna Paitseva, John Mclaughin, Peter M. Groffman, Zhongqi Cheng, Theodore R. Muth

Publications and Research

The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree …

Microdamage As A Bone Quality Component: Practical Guidelines For The Two‐Dimensional Analysis Of Linear Microcracks In Human Cortical Bone, Victoria M. Dominguez, Amanda M. Agnew

Publications and Research

Microdamage is a component of bone quality believed to play an integral role in bone health. However, comparability between existing studies is fraught with issues due to highly variable methods of sample preparation and poorly defined quantification criteria. To address these issues, this article has two aims. First, detailed methods for preparation and analysis of linear microcracks in human ribs, specifically addressing troubleshooting issues cited in previous studies, are laid out. Second, new, partially validated criteria are proposed in an effort to reduce subjective differences in microcrack counts and measures, ensuring more comparable results between studies. Revised definitions based on …

Human Anatomy And Physiology I: Course Map With Expected Learning Outcomes, Carlos Liachovitzky

Open Educational Resources

This document contains a list with all the Anatomy and Physiology I expected learning outcomes organized by topics, and grouped into ten units: 1. Introduction to A&P: body plan & organization; 2. Introduction to A&P: homeostasis; 3. The chemical level of organization; 4. Levels of organization: the cellular level of organization; 5. Levels of organization: the tissue level of organization; 6. Support and movement: integumentary system; 7. Support and movement: skeletal system & articulations; 8. Support and movement: muscular system; 9. Regulation, integration, and control: nervous system; 10. Regulation, integration, and control: special senses

Each learning outcome is referred to …

The Molecular Mechanisms Underlying The Cancer Killing Effect Of Interleukin-24, Leah Eshanie Persaud

Dissertations, Theses, and Capstone Projects

Interleukin-24 (IL-24) is an immunomodulatory cytokine that also displays specific anti-tumor effects across many cancer cell types. The tumor suppressor activities of IL-24 include inhibition of angiogenesis, metastasis, toxic autophagy, cancer-specific apoptosis, and sensitization to traditional cancer treatments like chemotherapy and radiation. Overexpression of IL-24 can selectively induce apoptosis in various cancer cells while having no adverse effects on normal cells. Due to this favorable killing effect, IL-24 is currently in phase II clinical trials. There is accumulating evidence that IL-24’s anti-cancer activity is primarily through the endoplasmic reticulum (ER) stress pathway but other pathways leading to cell death are …

The 5-Ht1a-R Knockout Mouse As A Model Of Later Life Anxiety Disorders: Implications For Sex Differences, Tatyana Budylin

Dissertations, Theses, and Capstone Projects

Anxiety affects nearly twice as many women as it affects men across all cultures and economic groups. Importantly, girls have a higher chance of inheriting anxiety disorders than boys, and many anxiety disorders appear at a very young age. However, little is known about sex differences in brain and behavioral development and how they relate to anxiety in adulthood. Serotonin 1A receptor (5-HT_1A-R) mediated signaling has been implicated in depression and anxiety, however most studies that focus on the involvement of the 5-HT_1A-R have been conducted in adults. Little is known about how the 5-HT_{1A …}

Getting At The Surface: A Promoter And Coding Sequence Characterization Of An Odorant Receptor, Irena G. Parvanova

Dissertations, Theses, and Capstone Projects

Odorant receptors (ORs) are expressed by mature olfactory sensory neurons (OSNs), in a monogenic and monoallelic fashion (singular gene choice). It has been repeatedly published that the singular expression of ORs is a consequence of epigenetic regulation. The model invokes the depositing of epigenetic marks (off marks) that reflect transcriptional inactivity on all OR genes in immature neurons followed by the activation of one OR allele in maturing neurons. OR expression has been exclusively studied via transgenic animal models, due to the lack of cell line system that can undergo singular gene choice. Here, we used chromatin immunoprecipitation-quantitative polymerase chain …

The Role And Regulation Of Alternative Polyadenylation In The Dna Damage Response, Michael R. Murphy

Dissertations, Theses, and Capstone Projects

Cellular homeostasis is achieved by the dynamic flux in gene expression. Post-transcriptional regulation of coding and non-coding RNA offers a fast method of adapting to a changing cellular environment, including deadenylation, microRNA (miRNA) pathway, and alternative polyadenylation (APA). In this dissertation, I explored some of the mechanisms involved in the post-transcriptional regulation of gene expression. The main hypothesis in these studies is that a single APA event after DNA damage is governed by specific conditions and factors outside of current known regulators of APA, and that the resultant transcript has a role in the DNA damage response (DDR). My aims …

Context Dependent Roles Of Mdmx (Mdm4) And Mdm2 In Breast Cancer Proliferation And Circulating Tumor Cells, Chong Gao

Dissertations, Theses, and Capstone Projects

Many human breast cancers overexpress the E3 ubiquitin ligase MDM2 and its homolog MDMX. Expression of MDM2 and MDMX occurs in both estrogen receptor α positive (ER+) and triple negative breast cancer (TNBC). We and others have reported that estrogen activated MDM2 strongly promotes proliferation in ER+ T47D breast cancer cells in a p53-independent manner. Whether MDM2 elicits in vivo p53-independent proliferative functions in T47D breast cancer cells has not been determined. Furthermore it has been shown that ectopic expression of MDM2 targets E-Cadherin for degradation thus leading to increased cell migration and invasion. Therefore we assessed the in vivo …

Zero Textbook Cost Syllabus For Env 3009/4900 (Conservation Biology And Sustainable Development), Stephen Gosnell

Open Educational Resources

Conservation biology is an interdisciplinary topic that explores how we can protect and maintain natural areas. Due to the resources we take and impacts we have on natural environments, this field is directly related to restoration ecology (restoring natural areas) and sustainable development/natural resource management. We will explore the basis for these related fields from an ecological, social, legal, and cultural perspective, as all conservation and management projects take place in the larger human landscape. We will consider how we measure biodiversity, why it matters, why is it is threatened, and how we can manage (protect, restore, maintain, use) it …

Spinal Matrix Metalloproteinase 8 Regulates Painafter Peripheral Trauma, Maral Tajerian, J. David Clark

Publications and Research

It is well documented that pain chronification requires a host of plastic mechanisms at the spinal cord (SC) level, including alterations in neuronal and glial structure and function. Such cellular plasticity necessitates the existence of a plastic extracellular matrix(ECM). Here, we describe a key role for ECM remodeling in the regulation of chronic pain following peripheral injury. Three weeks following tibia fracture in mice, we show increased levels of MMP8 in the SC. Furthermore, we show that the pharmacological or genetic down regulation of MMP8 ameliorates the pain phenotype observed after injury. These results delineate an extracellular mechanism for pain …

The Living Archive In The Anthropocene, Nora Almeida, Jen Hoyer

Publications and Research

This paper presents the concept of the living archive as a system which reflects how social behavior and cultural production are part of the Anthropocene. The authors explore how dominant narratives of both the Anthropocene and the archive work to consolidate power and maintain cultural and disciplinary divisions. The authors refute conceptions of the Anthropocene as a purely biophysical phenomenon that is alienated from cultural practice and of the archive as a comprehensive and nostalgic space. They then introduce the living archive as an alternative representational, creative, and reactive space and illustrate how the living archive can intervene in ecological …

Interfacial Stress In The Development Of Biologics: Fundamental Understanding, Current Practice, And Future Perspective, Jinjiang Li, Mary E. Krause, Xiaodong Cheng, Yuan Cheng, Weiguo Dai, John J. Hill, Min Huang, Susan Jordan, Daniel Lacasse, Linda Narhi, Evgenyi Shalaev, Ian C. Shieh, Justin C. Thomas, Raymond Tu, Songyan Zheng, Lily Zhu

Publications and Research

Biologic products encounter various types of interfacial stress during development, manufacturing, and clinical administration. When proteins come in contact with vapor–liquid, solid–liquid, and liquid–liquid surfaces, these interfaces can significantly impact the protein drug product quality attributes, including formation of visible particles, subvisible particles, or soluble aggregates, or changes in target protein concentration due to adsorption of the molecule to various interfaces. Protein aggregation at interfaces is often accompanied by changes in conformation, as proteins modify their higher order structure in response to interfacial stresses such as hydrophobicity, charge, and mechanical stress. Formation of aggregates may elicit immunogenicity concerns; therefore, it …

Identification And Characterization Of Barrier Insulator Activity In The T-Cell Receptor Alpha Locus Control Region, Gayathri Devi Raghupathy

Dissertations, Theses, and Capstone Projects

Genes of different spatiotemporal expression profiles are often juxtaposed in the genome. This organization raises risks of cross-regulatory influences from neighboring genes; for instance heterochromatin can spread over euchromatin or long-range acting enhancers can inappropriately activate genes. Gene regulatory elements such as Locus Control Regions (LCR) and Insulators prevent such cross-communications and allow for normal gene expression patterns. In transgenic systems, LCRs limit influences from surrounding chromatin by providing site-of-integration independent and specific spatiotemporal expression upon a linked transgene. The field’s understanding of the ability of an LCR to overcome chromatin influences and allow site-of-integration independent expression is minimal. Interestingly, …

Molecular Analysis Of Cone Photoreceptor Genesis From A Specific Retinal Progenitor Population, Diego F. Buenaventura

Dissertations, Theses, and Capstone Projects

There are two types of photosensitive cells of the retina that contribute to image formation: Cone photoreceptors that mediate color discrimination and rods that provide photosensitivity in low-light conditions. Given the importance of cones in high acuity and color vision, deficiencies in this cell type that result from ailments such as retinitis pigmentosa and macular degeneration can lead to a debilitating loss of vision. Currently, one of the most pressing goals in the field of retinal development is the elucidation of the gene regulatory networks (GRN) involved in inducing an undifferentiated cell into becoming a functional cone photoreceptor.

Recently, an …

Preclinical Evaluation Of Gold-Based Chemotherapeutic Candidates For The Treatment Of Metastatic Renal Cancer, Benelita Elie

Dissertations, Theses, and Capstone Projects

Renal cell carcinomas (RCCs) remain a significant health concern in the United States because of a lack of effective treatment. To date, RCCs account for 2.4% of all cancer deaths in the United States, and about 14,970 people will die from the disease in 2018, mostly of advanced or metastasized RCCs1,2. Mutations in metabolic pathways are characteristics of RCCs, including changes in redox metabolism, deregulation of proteolytic factor expression, and inflammation. These molecular events promote tumor vascularization, growth, invasion, and metastasis, which often correlate with a poor prognosis. Many pharmaceutical avenues have been explored, including cytotoxic chemotherapeutics, biologics targeting cellular …

A Study Of The Impact Of The Physical Properties Of Blood On The Interpretation Of Bloodstain Patterns In Forensic Investigations, Ira S. Dubey

Dissertations, Theses, and Capstone Projects

There are many situations when the value of the physical characteristics of blood far outweighs the information gained from DNA analysis of the bloodstain (Brodbeck, 2012; Raymond, Smith and Liesegang, 1996). Analysis of bloodstain patterns at crime scenes or on clothing often provides significant information and serves both as investigate aids and as evidence presented in court. There has been limited work done to evaluate the potential impact of variation in the physical properties of blood on the interpretation of blood spatter patterns. This dissertation will expand on previous work and investigate how changes in the physical properties of blood, …

Distribution And Population Structure Of The Invasive Nitellopsis Obtusa (Desv. In Loisel.) J. Groves And Native Species Of Characeae In The Northeast U.S.A., Robin Sleith

Dissertations, Theses, and Capstone Projects

Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and …

Putative Cellular And Molecular Roles Of Zika Virus In Fetal And Pediatric Neuropathologies, Rajendra Ghardbaran, Rajendra Ghardbaran, Latchman Somenarain

Publications and Research

Although the World Health Organization declared an end to the recent Zika virus (ZIKV) outbreak and its association with adverse fetal and pediatric outcome, on November 18, 2016, the virus still remains a severe public health threat. Laboratory experiments thus far supported the suspicions that ZIKV is a teratogenic agent. Evidence indicated that ZIKV infection cripples the host cells' innate immune responses, allowing productive replication and potential dissemination of the virus. In addition, studies suggest potential transplacental passage of the virus and subsequent selective targeting of neural progenitor cells (NPCs). Depletion of NPCs by ZIKV is associated with restricted brain …

Microrna-4719 And Microrna-6756-5p Correlate With Castration-Resistant Prostate Cancer Progression Through Interleukin-24 Regulation, Dibash K. Das, Leah Persaud, Moira Sauane

Publications and Research

Prostate cancer (PCa) is the second leading cause of cancer death in the United States. The five-year survival rate for men diagnosed with localized PCa is nearly 100%, yet for those diagnosed with aggressive PCa, it is less than 30%. The pleiotropic cytokine Interleukin-24 (IL-24) has been shown to specifically kill PCa cells compared to normal cells when overexpressed in both in vitro and in vivo studies. Despite this, the mechanisms regulating IL-24 in PCa are not well understood. Since specific microRNAs (miRNAs) are dysregulated in PCa, we used miRNA target prediction algorithm tools to identify miR-4719 and miR-6556-5p as …