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Chapter 5 - Ecophysiology Of Development, Janice M. Glime

Bryophyte Ecology Volume 1: Physiological Ecology

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Ebook sponsored by Michigan Technological University and the International Association of Bryologists.

Integrative Genomic And Transcriptomic Analysis For Pinpointing Recurrent Alterations Of Plant Homeodomain Genes And Their Clinical Significance In Breast Cancer, Huimei Yu, Yuanyuan Jiang, Lanxin Liu, Wenqi Shan, Xiaofang Chu, Zhe Yang, Zeng-Quan Yang

Oncology Faculty Publications

A wide range of the epigenetic effectors that regulate chromatin modification, gene expression, genomic stability, and DNA repair contain structurally conserved domains called plant homeodomain (PHD) fingers. Alternations of several PHD finger-containing proteins (PHFs) due to genomic amplification, mutations, deletions, and translocations have been linked directly to various types of cancer. However, little is known about the genomic landscape and the clinical significance of PHFs in breast cancer. Hence, we performed a large-scale genomic and transcriptomic analysis of 98 PHF genes in breast cancer using TCGA and METABRIC datasets and correlated the recurrent alterations with clinicopathological features and survival of ...

Minibrain And Wings Apart Control Organ Growth And Tissue Patterning Through Downregulation Of Capicua, Liu Yang

Graduate Doctoral Dissertations

The regulation of organ growth is a fundamental aspect of developmental biology. My work uses Drosophila as a model system to understand how the various growth regulators are coordinated. The transcriptional repressor Capicua (Cic) controls tissue patterning and restricts organ growth, and has been recently implicated in several cancers and neurodegenerative diseases. Cic has emerged as a primary sensor of signaling downstream of the receptor tyrosine kinase (RTK)/extracellular signal-regulated kinase (ERK) pathway, but how Cic activity is regulated in different cellular contexts remains poorly understood. In order to identify Cic regulators, I have used affinity purification/mass spectrometry (AP-MS ...

Boone River Watershed Stream Fish And Habitat Monitoring, Ia, Nicholas T. Simpson, Clay L. Pierce, Kevin J. Roe, Michael J. Weber

Natural Resources Ecology and Management Reports

Historically, Iowa’s landscape consisted of prairies, forests, and wetlands with meandering streams integrated throughout (Hewes 1950). The arrival and subsequent settlement of European immigrants began a long process of altering the landscape to help meet human needs. Cultivating row crops in Iowa became a popular and successful venture for many as the flat, fertile ground of the Midwestern United States provided a great opportunity for farmers (Easterlin 1976). Early Iowa farmers began to drain wetlands, cut down forests, remove prairies, and replace them with crop fields (Gallant et al. 2011). As the technology of farming practices improved and operations ...

Anticonvulsive Effects Of Licofelone On Status Epilepticus Induced By Lithium-Pilocarpine In Wistar Rats: A Role For Inducible Nitric Oxide Synthase, Seyyed Majid Eslami, Mohammad Mobin Moradi, Mehdi Ghasemi, Ahmad Reza Dehpour

Open Access Articles

BACKGROUND AND PURPOSE: Status epilepticus (SE) is a neurological disorder with high prevalence and mortality rates, requiring immediate intervention. Licofelone is a cyclooxygenase (COX) and 5-lipoxygenase (5-LOX) inhibitor, which its effectiveness to treat osteoarthritis has been approved. Increasing evidence suggests an involvement of COX and LOX enzymes in epileptic disorders. Thus, in the present study we investigate possible effects of licofelone on prevention and termination of SE. We also evaluated whether the nitrergic system could participate in this effect of licofelone.

METHODS: We have utilized lithium-pilocarpine model of SE in adult Wistar rats to assess the potential effect of licofelone ...

Evolution In The Deep Sea: Scales And Mechanisms Of Population Divergence, Amanda E. Glazier

Graduate Doctoral Dissertations

The deep sea is the Earth’s largest ecosystem and harbors a unique and largely endemic fauna. Although most research has focused on the ecological mechanisms that allow coexistence, recent studies have begun to investigate how this remarkable fauna evolved.. My work quantifies geographic patterns of genetic variation and investigates potential mechanisms that shape evolution in the deep ocean.

Bathymetric genetic divergence is common in the deep sea with population structure typically decreasing with depth. The evolutionary mechanisms that underlie these patterns are poorly understood. Geographic patterns of genetic variation indicated that the protobranch bivalve Neilonella salicensis was composed of ...

Variants In Wfs1 And Other Mendelian Deafness Genes Are Associated With Cisplatin-Associated Ototoxicity, Heather E. Wheeler, Eric R. Gamazon, Robert Frisina, Carlos Perez-Cervantes, Omar El Charif, Brandon Mapes, Sophie D. Fossa, Darren Feldman, Robert Hamilton, David J. Vaughn, Clair Beard, Chunkit Fung, Chiristian Kollmannsberger, Jeri Kim, Taisei Mushiroda, Michiaki Kubo, Shirin Ardeshir-Rouhani-Fard, Lawrence H. Einhorn, Nancy Cox, M. Eileen Dolan, Lois Travis

Bioinformatics Faculty Publications

Cisplatin is one of the most commonly used chemotherapy drugs worldwide and one of the most ototoxic. We sought to identify genetic variants that modulate cisplatin-associated ototoxicity (CAO). Experimental Design: We performed a genome-wide association study (GWAS) of CAO using quantitative audiometry (4-12 kHz) in 511 testicular cancer survivors of European genetic ancestry. We performed polygenic modeling and functional analyses using a variety of publicly available databases. We used an electronic health record cohort to replicate our top mechanistic finding. Results: One SNP, rs62283056, in the first intron of Mendelian deafness gene WFS1 (wolframin ER transmembrane glycoprotein) and an expression ...

Influence Of Maternal Breast Milk Ingestion On Acquisition Of The Intestinal Microbiome In Preterm Infants., Katherine E Gregory, Buck S Samuel, Pearl Houghteling, Guru Shan, Frederick M Ausubel, Ruslan I Sadreyev, W Allan Walker

BCM Faculty Publications

BACKGROUND: The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and nutrition have all been shown to play a role in the assembly of the intestinal microbiome during early life. For preterm infants, who are disproportionately at risk of inflammatory intestinal disease (i.e., necrotizing enterocolitis), a unique set of clinical factors influence the establishment of the microbiome. The purpose of this study was to establish the influence of nutritional exposures on the intestinal microbiome in a cohort of preterm infants ...

Kenaf Productivity And Morphology, When Grown In Iowa And In Kentucky, Marie Bourguignon, Kenneth Moore, Andrew Lenssen, Sotirios Archontoulis, Ben Goff, Brian Baldwin

Agronomy Publications

Kenaf (Hibiscus cannabinus L.), mostly produced in China and India, is grown to a limited extent in the U.S., although this natural fiber can be a promising alternative to synthetic fibers for reinforcing plastic or other composite materials, or fuel purposes. Producing kenaf in the Midwestern U.S. could provide a local source of this fiber for use in a number of manufactured products and potentially for use as a biofuel feedstock. The objectives of this study were to: 1) compare the productivity and the morphology of kenaf cultivars ‘Tainung 2’ and ‘Whitten’ when grown in Iowa and Kentucky ...

The Effects Of Interleukin-10 On Skeletal Muscle Insulin Resistance And Myogenesis, Sezin Dagdeviren

GSBS Dissertations and Theses

Skeletal muscle insulin resistance is a major characteristic of obesity and type 2 diabetes. Although obesity-mediated inflammation is causally associated with insulin resistance, the underlying mechanism is unclear. Our lab and others have shown that a chronic low-grade inflammation takes place in skeletal muscles during diet-induced obesity, as evidenced by increased macrophage markers and pro-inflammatory cytokine levels. Interleukin (IL)-10 is a Th₂-type cytokine that inhibits the synthesis and activity of pro-inflammatory cytokines and counteracts the Toll-like receptor-mediated inflammation. Our lab has previously demonstrated the preventive role of IL-10 against insulin resistance. Here, I have analyzed the effects ...

Analyzing And Modeling The Dysfunction Of Inhibitory Neurons In Alzheimer’S Disease, Carlos Perez, Jokubas Ziburkus, Ghamim Ullah

Physics Faculty Publications

Alzheimer’s disease (AD) is characterized by the abnormal proteolytic processing of amyloid precursor protein, resulting in increased production of a self-aggregating form of beta amyloid (Aβ). Several lines of work on AD patients and transgenic mice with high Aβ levels exhibit altered rhythmicity, aberrant neuronal network activity and hyperexcitability reflected in clusters of hyperactive neurons, and spontaneous epileptic activity. Recent studies highlight that abnormal accumulation of Aβ changes intrinsic properties of inhibitory neurons, which is one of the main reasons underlying the impaired network activity. However, specific cellular mechanisms leading to interneuronal dysfunction are not completely ...

Winner's Curse Correction And Variable Thresholding Improve Performance Of Polygenic Risk Modeling Based On Genome-Wide Association Study Summary-Level Data, Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja T. Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D. Figueroa, Victoria K. Cortessis, Nuria Malats, Margaret R. Karagas

Open Dartmouth: Peer-reviewed articles by Dartmouth faculty

Recent heritability analyses have indicated that genome-wide association studies (GWAS) have the potential to improve genetic risk prediction for complex diseases based on polygenic risk score (PRS), a simple modelling technique that can be implemented using summary-level data from the discovery samples. We herein propose modifications to improve the performance of PRS. We introduce threshold-dependent winner’s-curse adjustments for marginal association coefficients that are used to weight the single-nucleotide polymorphisms (SNPs) in PRS. Further, as a way to incorporate external functional/annotation knowledge that could identify subsets of SNPs highly enriched for associations, we propose variable thresholds for SNPs selection ...

Cullin-4 Regulates Wingless And Jnk Signaling-Mediated Cell Death In The Drosophila Eye., Meghana Tare, Ankita Sarkar, Shimpi Bedi, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

In all multicellular organisms, the fundamental processes of cell proliferation and cell death are crucial for growth regulation during organogenesis. Strict regulation of cell death is important to maintain tissue homeostasis by affecting processes like regulation of cell number, and elimination of unwanted/unfit cells. The developing Drosophila eye is a versatile model to study patterning and growth, where complex signaling pathways regulate growth and cell survival. However, the molecular mechanisms underlying regulation of these processes is not fully understood. In a gain-of-function screen, we found that misexpression of cullin-4 (cul-4), an ubiquitin ligase, can rescue reduced eye mutant phenotypes ...

Wide-Spectrum Biomimetic Antimicrobial Systems, Heidi A. Wright, Byron F. Brehm-Stecher

Food Science and Human Nutrition Publications

Antimicrobial peptides (AMPs) are effective components of the host immune response and are widely distributed throughout nature. Recently, nontoxic antimicrobial polymers that mimic the structures of naturally occurring AMPs have been designed and are under development commercially as novel therapeutics. These compounds have several potential advantages over natural AMPs, including greater stability and reduced immunogenicity compared to natural peptides, relatively simple and scalable syntheses and the ability to tailor or “fine tune” their activities through combinatorial approaches. In previous work, we demonstrated the utility of certain generally regarded as safe (GRAS) flavorant and aroma compounds as enhancers of uptake and ...

Exploring Knowledge, Beliefs And Practices Of Radon Gas Exposure Among Public Health Workers, Paschal Nwako

Seton Hall University Dissertations and Theses (ETDs)

Radon gas exposure is the highest cause of lung cancer among people that never smoked in the United States. People exposed to elevated levels of radon had a higher risk of developing lung cancer. Achieving the long term goal of the Indoor Radon Abatement Act (IRAA) of 1988 require a combined efforts of government agencies. Public health workers are change agents and their role in protecting and improving the health of their communities are well documented. This study created and utilized a multi question survey, the Public Health Workers Radon Assessment Instrument (PHWRAI) to explore knowledge, beliefs, personal and professional ...

Regulatory T Cells In Endemic Burkitt Lymphoma Patients Are Associated With Poor Outcomes: A Prospective, Longitudinal Study, Emily Parsons, Juliana A. Otieno, John Michael Ong'echa, Christina E. Nixon, John Vulule, Christian Munz, V. Ann Stewart, Ann M. Moormann

Open Access Articles

Deficiencies in Epstein-Barr virus (EBV)-specific T cell immunosurveillance appear to precede the development of endemic Burkitt lymphoma (eBL), a malaria-associated pediatric cancer common in sub-Saharan Africa. However, T cell contributions to eBL disease progression and survival have not been characterized. Our objective was to investigate regulatory and inflammatory T cell responses in eBL patients associated with clinical outcomes. By multi-parameter flow cytometry, we examined peripheral blood mononuclear cells from 38 eBL patients enrolled in a prospective cohort study in Kisumu, Kenya from 2008-2010, and 14 healthy age-matched Kenyan controls. Children diagnosed with eBL were prospectively followed and outcomes categorized ...

Connecting Culturally And Spiritually To Healthy Eating: A Community Assessment With Native Hawaiians, Mary Frances Oneha, Joan Dodgson, Mabel Ho`Oipo Decambra, Carol Titcomb, Rachelle Enos, Sandie Morimoto-Ching

Asian/Pacific Island Nursing Journal

Many of the chronic illnesses disproportionately experienced by Native Hawaiians are directly related to poor diets and long-standing obesity beginning in childhood. We report on the findings of in-depth key informant interviews (N = 14) that took place in two Native Hawaiian communities as part of a larger, community-based participatory research study that included a community assessment through individual interviews and focused group discussions, and a pilot intervention targeting pregnant women, their infants, and families. Four categories emerged from the qualitative analysis of interview transcripts that described an understanding of “healthy eating”: family roles and responsibilities, aspects of community and physical ...

Recent Diatoms Reported From The Central United States: Register Of Taxa And Synonyms, Mark E. Eberle

Biology Faculty Publications

This list of diatoms summarizes information for more than 1000 taxa and synonyms reported in published accounts of collections made in the central United States, principally within the states of Kansas, Nebraska, and Oklahoma, but also including adjacent areas in eastern Colorado and western Missouri. The objective was to provide people working on diatom projects in this region with a base reference to help them assess the results of their research. Records from Master’s theses and references focused on fossil diatoms were not incorporated into this list. Specimens were not examined, so taxa presented here are those reported in ...

Advancing Nasa’S Airmoss P-Band Radar Root Zone Soil Moisture Retrieval Algorithm Via Incorporation Of Richards’ Equation, Morteza Sadeghi, Alireza Tabatabaeenejad, Markus Tuller, Mahta Moghaddam, Scott B. Jones

Plants, Soils, and Climate Faculty Publications

P-band radar remote sensing applied during the Airborne Microwave Observatory of Subcanopy and Subsurface (AirMOSS) mission has shown great potential for estimation of root zone soil moisture. When retrieving the soil moisture profile (SMP) from P-band radar observations, a mathematical function describing the vertical moisture distribution is required. Because only a limited number of observations are available, the number of free parameters of the mathematical model must not exceed the number of observed data. For this reason, an empirical quadratic function (second order polynomial) is currently applied in the AirMOSS inversion algorithm to retrieve the SMP. The three free parameters ...

Tree Circumference Dynamics In Four Forests Characterized Using Automated Dendrometer Bands, Valentine Herrmann, Sean M. Mcmahon, Matteo Detto, James A. Lutz, Chia-Hao Chang-Yang, Kristina J. Anderson-Teixeira

Wildland Resources Faculty Publications

Stem diameter is one of the most commonly measured attributes of trees, forming the foundation of forest censuses and monitoring. Changes in tree stem circumference include both irreversible woody stem growth and reversible circumference changes related to water status, yet these fine-scale dynamics are rarely leveraged to understand forest ecophysiology and typically ignored in plot- or stand-scale estimates of tree growth and forest productivity. Here, we deployed automated dendrometer bands on 12–40 trees at four different forested sites—two temperate broadleaf deciduous, one temperate conifer, and one tropical broad-leaf semi-deciduous—to understand how tree circumference varies on time scales ...

The Replication Initiator Of The Cholera Pathogen’S Second Chromosome Shows Structural Similarity To Plasmid Initiators, Natalia Orlova, Matthew Gerding, Olha Ivashkiv, Paul Dominic B. Olinares, Brian T. Chait, Matthew K. Waldor, David Jeruzalmi

Publications and Research

The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a headto- head dimeric configuration ...

Generation Of Germ-Free /Ciona Intestinalis For Studies Of Gut-Microbe Interactions, Brittany A Leigh, Assunta Liberti, Larry J Dishaw

Marine Science Faculty Publications

Microbes associate with animal hosts, often providing shelter in a nutrient-rich environment. The gut, however, can be a harsh environment with members of the microbiome settling in distinct niches resulting in more stable, adherent biofilms. These diverse communities can provide orders of magnitude more gene products than the host genome; selection and maintenance of a functionally relevant and useful microbiome is now recognized to be an essential component of homeostasis. Germ-free (GF) model systems allow dissection of host-microbe interactions in a simple and direct way where each member of the symbiosis can be studied in isolation. In addition, because immune ...

Macroinvertebrate Community Composition, Food Web Structure, And Emergence Rate In Neotropical Cloud-Forest Streams In Mindo, Ecuador, Anna M. Harris

Masters Theses

Tropical cloud forest streams are one of the most threatened and understudied ecosystems in the world. Understanding how these ecosystems function is essential for effective conservation. In this study, macroinvertebrate community composition, functional feeding group analysis, ecosystem attributes, and physicochemical parameters were used to evaluate biophysical stream conditions of 3 low-order Neotropical cloud forest streams at Reserva Las Gralarias in Mindo, Ecuador. Additionally, food web structure was analyzed via stable isotope analysis and aquatic insect emergence rate was also examined. As stream size increased from 1st to 3rd order, the macroinvertebrate communities shifted from being collector-gatherer dominated (65.2 to ...

U.S. Drought Monitor, December 27, 2016, Brad Rippey

US Ag in Drought Archive

Drought map of U.S. for December 27, 2016 (12/27/16) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

2016, Sep. 22 -- Bulletin 118, Interim Update 2016, California's Groundwater Working Toward Sustainability, Dwr

State and Federal Documents Relating to Monterey and San Luis Obispo Counties

The purpose of the interim update to Bulletin 118 is to provide up-to-date information on California groundwater basins subject to critical conditions of overdraft, groundwater basin boundaries, and basin prioritization. The information is essential to the successful implementation of the Sustainable Groundwater Management Act passed in 2014 (SGMA), including the timely formation of groundwater sustainability agencies and the development of groundwater sustainability plans.

Novel Models Of Visual Topographic Map Alignment In The Superior Colliculus., Ruben A Tikidji-Hamburyan, Tarek A El-Ghazawi, Jason W. Triplett

Pediatrics Faculty Publications

The establishment of precise neuronal connectivity during development is critical for sensing the external environment and informing appropriate behavioral responses. In the visual system, many connections are organized topographically, which preserves the spatial order of the visual scene. The superior colliculus (SC) is a midbrain nucleus that integrates visual inputs from the retina and primary visual cortex (V1) to regulate goal-directed eye movements. In the SC, topographically organized inputs from the retina and V1 must be aligned to facilitate integration. Previously, we showed that retinal input instructs the alignment of V1 inputs in the SC in a manner dependent on ...

Can Sub-Saharan Africa Feed Itself?, Martin K. Van Ittersum, Lenny G. J. Van Bussel, Joost Wolf, Patricio Grassini, Justin Van Wart, Nicolas Guilpart, Lieven Claessens, Hugo De Groot, Keith Wiebe, Daniel Mason-D'Croz, Haishun Yang, Hendrik Boogard, Pepijn A. J. Van Oort, Marloes P. Van Loon, Kazuki Saito, Ochieng Adimo, Samuel Adjei-Nsiah, Alhassane Agali, Abdullahi Bala, Regis Chikowo, Kayuki Kaizzi, Mamoutou Kouressy, Joachim H. J. R. Makoi, Korodjouma Ouattara, Kindie Tesfaye, Kenneth G. Cassman

Agronomy & Horticulture -- Faculty Publications

Although global food demand is expected to increase 60% by 2050 compared with 2005/2007, the rise will be much greater in sub- Saharan Africa (SSA). Indeed, SSA is the region at greatest food security risk because by 2050 its population will increase 2.5-fold and demand for cereals approximately triple, whereas current levels of cereal consumption already depend on substantial imports. At issue is whether SSA can meet this vast increase in cereal demand without greater reliance on cereal imports or major expansion of agricultural area and associated biodiversity loss and greenhouse gas emissions. Recent studies indicate that the ...

Phosphorylation Of The Mdm2 Oncoprotein By The C-Abl Tyrosine Kinase Regulates P53 Tumor Suppression And The Radiosensitivity Of Mice, Michael I. Carr, Justine E. Roderick, Hong Zhang, Bruce A. Woda, Michelle A. Kelliher, Stephen N. Jones

UMass Metabolic Network Publications

The p53 tumor suppressor acts as a guardian of the genome by preventing the propagation of DNA damage-induced breaks and mutations to subsequent generations of cells. We have previously shown that phosphorylation of the Mdm2 oncoprotein at Ser394 by the ATM kinase is required for robust p53 stabilization and activation in cells treated with ionizing radiation, and that loss of Mdm2 Ser394 phosphorylation leads to spontaneous tumorigenesis and radioresistance in Mdm2S394A mice. Previous in vitro data indicate that the c-Abl kinase phosphorylates Mdm2 at the neighboring residue (Tyr393) in response to DNA damage to regulate p53-dependent apoptosis. In this present ...

Reef Society And The Tyranny Of Data, Robert Wintner

Animal Sentience

Modern science now approaches divergent processes in many areas, including health assessments of marine eco-systems and social aspects of marine species. Scientific data have long enjoyed a reputation for objectivity but incidents of science-for-hire, data spinning/skewing and political jading are more frequent than ever. In the field of reef creature sensitivity, technical treatises can “logically” explain away what a person of average education can clearly observe on any given reef. Western medicine discounted anecdotal evidence of any cure outside the 4% margin of error until those cures demanded attention and in some cases application. Modern science must now enter ...

Still Wondering How Flesh Can Feel, Gwen J. Broude

Animal Sentience

Reber believes he has simplified Chalmers’s “hard problem” of consciousness by arguing that subjectivity is an inherent feature of biological forms. His argument rests on the related notions of continuity of mind and gradual accretion of capacities across evolutionary time. These notions need to be defended, not just asserted. Because Reber minimizes the differences in mental faculties among species across evolutionary time, it becomes easier to assert, and perhaps believe, that sentience is already present in early biological forms. The more explicit we are about the differences among these mental faculties and the differences across species, the less persuasive ...