Life Sciences Commons^™

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

Salicylic Acid And N-Hydroxypipecolic Acid At The Fulcrum Of The Plant Immunity-Growth Equilibrium, Alyssa Shields, Vanessa Shivnauth, Christian Danve M. Castroverde

Biology Faculty Publications

Salicylic acid (SA) and N-hydroxypipecolic acid (NHP) are two central plant immune signals involved in both resistance at local sites of pathogen infection (basal resistance) and at distal uninfected sites after primary infection (systemic acquired resistance). Major discoveries and advances have led to deeper understanding of their biosynthesis and signaling during plant defense responses. In addition to their well-defined roles in immunity, recent research is emerging on their direct mechanistic impacts on plant growth and development. In this review, we will first provide an overview of how SA and NHP regulate local and systemic immune responses in plants. We …

Salicylic Acid: A Key Regulator Of Redox Signalling 1 And Plant Immunity, Mohd Saleem, Qazi Fariddudin, Christian Castroverde

Biology Faculty Publications

In plants, the reactive oxygen species (ROS) formed during normal conditions are essential in regulating several processes, like stomatal physiology, pathogen immunity and developmental signaling. However, biotic and abiotic stresses can cause ROS over-accumulation leading to oxidative stress. Therefore, a suitable equilibrium is vital for redox homeostasis in plants, and there have been major advances in this research arena. Salicylic acid (SA) is known as a chief regulator of ROS; however, the underlying mechanisms remain largely unexplored. SA plays an important role in establishing the hypersensitive response (HR) and systemic acquired resistance (SAR). This is underpinned by a robust and …

Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina

Biology Faculty Publications

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview …

Diversity And Substrate-Specificity Of Green Algae And Other Micro-Eukaryotes Colonizing Amphibian Clutches In Germany, Revealed By Dna Metabarcoding, Sten Anslan, Maria Sachs, Lois Rancilhac, Henner Brinkmann, Jörn Petersen, Sven Künzel, Anja Schwarz, Hartmut Arndt, Ryan R. Kerney, Miguel Vences

Biology Faculty Publications

Amphibian clutches are colonized by diverse but poorly studied communities of micro-organisms. One of the most noted ones is the unicellular green alga, Oophila amblystomatis, but the occurrence and role of other micro-organisms in the capsular chamber surrounding amphibian clutches have remained largely unstudied. Here, we undertook a multi-marker DNA metabarcoding study to characterize the community of algae and other micro-eukaryotes associated with agile frog (Rana dalmatina) clutches. Samplings were performed at three small ponds in Germany, from four substrates: water, sediment, tree leaves from the bottom of the pond, and R. dalmatina clutches. Sampling substrate strongly …

Toward The Discovery Of Biological Functions Associated With The Mechanosensor Mtl1p Of Saccharomyces Cerevisiae Via Integrative Multi-Omics Analysis, Nelson Martínez-Matías, Nataliya Chorna, Sahily González-Crespo, Lilliam Villanueva, Ingrid Montes-Rodríguez, Loyda M. Melendez-Aponte, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ednalise Santiago-Cartagena, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina

Biology Faculty Publications

Functional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased …

The Importance Of Ile716 Toward The Mutagenicity Of 8-Oxo-2’-Deoxyguanosine With Bacillus Fragment Dna Polymerase, Michelle L. Hamm, Anarosa A. Garcia, Rachel Gilbert, Manavi Johri, Miranda Ricart, Samantha L. Sholes, Laura A. Murray-Nerger, Eugene Y. Wu

Biology Faculty Publications

8-oxo-2’-deoxyguanosine (OdG) is a prominent DNA lesion that can direct the incorporation of dCTP or dATP during replication. As the latter reaction can lead to mutation, the ratio of dCTP/dATP incorporation can significantly affect the mutagenic potential of OdG. Previous work with the A-family polymerase BF and seven analogues of OdG identified a major groove amino acid, Ile716, which likely influences the dCTP/dATP incorporation ratio opposite OdG. To further probe the importance of this amino acid, dCTP and dATP incorporations opposite the same seven analogues were tested with two BF mutants, I716M and I716A. Results from these studies support the …

Autophagy Protein Nrbf2 Has Reduced Expression In Alzheimer's Brains And Modulates Memory And Amyloid-Beta Homeostasis In Mice, Veronik Lachance, Qian Wang, Eric Sweet, Insup Choi, Cui-Zan Cai, Xu-Xu Zhuang, Jessica Li Jiang, Robert D. Blitzer, Ozlem Bozdagi-Gunal, Bin Zhang, Jia-Hong Lu, Zhenyu Yue

Biology Faculty Publications

Background Dysfunctional autophagy is implicated in Alzheimer's Disease (AD) pathogenesis. The alterations in the expression of many autophagy related genes (ATGs) have been reported in AD brains; however, the disparity of the changes confounds the role of autophagy in AD. Methods To further understand the autophagy alteration in AD brains, we analyzed transcriptomic (RNAseq) datasets of several brain regions (BA10, BA22, BA36 and BA44 in 223 patients compared to 59 healthy controls) and measured the expression of 130 ATGs. We used autophagy-deficient mouse models to assess the impact of the identified ATGs depletion on memory, autophagic activity and amyloid-beta (A …

Co-Cultures Of Oophila Amblystomatis Between Ambystoma Maculatum And Ambystoma Gracile Hosts Show Host-Symbiont Fidelity, Ryan R. Kerney, Jasper S. Leavitt, Elizabeth M. Hill, Huanjia Zhang, Eunsoo Kim, John Burns

Biology Faculty Publications

A unique symbiosis occurs between embryos of the spotted salamander (Ambystoma maculatum) and a green alga (Oophila amblystomatis). Unlike most vertebrate host-symbiont relationships, which are ectosymbiotic, A. maculatum exhibits both an ecto- and an endo-symbiosis, where some of the green algal cells living inside egg capsules enter embryonic tissues as well as individual salamander cells. Past research has consistently categorized this symbiosis as a mutualism, making this the first example of a “beneficial” microbe entering vertebrate cells. Another closely related species of salamander, Ambystoma gracile, also harbors beneficial Oophila algae in its egg capsules. However, our …

Some Current Trends And Challenges In Philippine Aquaculture, With An Emphasis On Synergies With Biodiversity Initiatives, Ronald Allan L. Cruz, Vikas Kumar, Janice A. Ragaza

Biology Faculty Publications

No abstract provided.

Differential Uptake Of Gold Nanoparticles By 2 Species Of Tadpole, The Wood Frog (Lithobates Sylvaticus) And The Bullfrog (Lithobates Catesbeianus), Lucas B. Thompson, Gerardo L.F. Carfagno, Kurt Andresen, Andrea J. Sitton, Taylor B. Bury, Laura L. Lee, Kevin T. Lerner, Peter P. Fong

Biology Faculty Publications

Engineered nanoparticles are aquatic contaminants of emerging concern that exert ecotoxicological effects on a wide variety of organisms. We exposed cetyltrimethylammonium bromide–capped spherical gold nanoparticles to wood frog and bullfrog tadpoles with conspecifics and in combination with the other species continuously for 21 d, then measured uptake and localization of gold. Wood frog tadpoles alone and in combination with bullfrog tadpoles took up significantly more gold than bullfrogs. Bullfrog tadpoles in combination with wood frogs took up significantly more gold than controls. The rank order of weight-normalized gold uptake was wood frogs in combination > wood frogs alone > bullfrogs in combination …

Transposon-Mediated Stable Suppression Of Gene Expression In The Developing Chick Retina, Masaru Nakamoto, Chizu Nakamoto

Biology Faculty Publications

The embryonic chick has long been a favorite model system for in vivo studies of vertebrate development. However, a major technical limitation of the chick embryo has been the lack of efficient loss-of-function approaches for analyses of gene functions. Here, we describe a methodology in which a transgene encoding artificial microRNA sequences is introduced into embryonic chick retinal cells by in ovo electroporation and integrated into the genome using the Tol2 transposon system. We show that this methodology can induce potent and stable suppression of gene expression. This technique therefore provides a rapid and robust loss-of-function approach for studies of …

Population Dynamics And Community Composition Of Ammonia Oxidizers In Salt Marshes After The Deepwater Horizon Oil Spill, Anne E. Bernhard, Roberta Sheffer, Anne E. Giblin, John M. Marton, Brian J. Roberts

Biology Faculty Publications

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment …

Analogous Cellular Contribution And Healing Mechanisms Following Digit Amputation And Phalangeal Fracture In Mice, Lindsay A. Dawson, Jennifer Simkin, Michelle Sauque, Maegan Pela, Teresa Palkowski, Ken Muneoka

Biology Faculty Publications

Regeneration of amputated structures is severely limited in humans and mice, with complete regeneration restricted to the distal portion of the terminal phalanx (P3). Here, we investigate the dynamic tissue repair response of the second phalangeal element (P2) post amputation in the adult mouse, and show that the repair response of the amputated bone is similar to the proximal P2 bone fragment in fracture healing. The regeneration-incompetent P2 amputation response is characterized by periosteal endochondral ossification resulting in the deposition of new trabecular bone, corresponding to a significant increase in bone volume; however, this response is not associated with bone …

Homeotic Gene Teashirt (Tsh) Has A Neuroprotective Function In Amyloid-Beta 42 Mediated Neurodegeneration, Michael T. Moran, Meghana Tare, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Background: Alzheimer's disease (AD) is a debilitating age related progressive neurodegenerative disorder characterized by the loss of cognition, and eventual death of the affected individual. One of the major causes of AD is the accumulation of Amyloid-beta 42 (Aβ42) polypeptides formed by the improper cleavage of amyloid precursor protein (APP) in the brain. These plaques disrupt normal cellular processes through oxidative stress and aberrant signaling resulting in the loss of synaptic activity and death of the neurons. However, the detailed genetic mechanism(s) responsible for this neurodegeneration still remain elusive.

Methodology/Principal Findings: We have generated a transgenic Drosophila eye model where …

Using Rnai In C. Elegans To Demonstrate Gene Knockdown Phenotypes In The Undergraduate Biology Lab Setting, Nicole M. Roy

Biology Faculty Publications

RNA interference (RNAi) is a powerful technology used to knock down genes in basic research and medicine. In 2006 RNAi technology using Caenorhabditis elegans (C. elegans) was awarded the Nobel Prize in medicine and thus students graduating in the biological sciences should have experience with this technology. However, students struggle conceptually with the molecular biology behind the RNAi technology and find the technology difficult to grasp. To this end, we have provided a simple, streamlined and inexpensive RNAi procedure using C. elegans that can be adopted in upper level biology classes. By using an unknown RNAi-producing bacteria, students perform novel …

Fret-Based Identification Of Mrnas Undergoing Translation, Benjamin Stevens, Chunlai Chen, Ian Farrell, Haibo Zhang, Jaskiran Kaur, Steven L. Broitman, Zeev Smilansky, Barry S. Cooperman, Yale E. Goldman

Biology Faculty Publications

No abstract provided.

Dynamic Glucoregulation And Mammalian-Like Responses To Metabolic And Developmental Disruption In Zebrafish, Agata Jurczyk, Nicole M. Roy, Rabia Bajwa, Philipp Gut, Kathryn Lipson, Chaoxing Yang, Laurence Covassin, Waldemar J. Racki, Aldo A. Rossini, Nancy Phillips, Didier Y. R. Stainier, Dale L. Greiner, Michael A. Brehm, Rita Bortell, Philip Diiorio

Biology Faculty Publications

Zebrafish embryos are emerging as models of glucose metabolism. However, patterns of endogenous glucose levels, and the role of the islet in glucoregulation, are unknown. We measured absolute glucose levels in zebrafish and mouse embryos, and demonstrate similar, dynamic glucose fluctuations in both species. Further, we show that chemical and genetic perturbations elicit mammalian-like glycemic responses in zebrafish embryos. We show that glucose is undetectable in early zebrafish and mouse embryos, but increases in parallel with pancreatic islet formation in both species. In zebrafish, increasing glucose is associated with activation of gluconeogenic phosphoenolpyruvate carboxykinase1 (pck1) transcription. Non-hepatic Pck1 protein is …

Choosing The Right Path: Enhancement Of Biologically Relevant Sets Of Genes Or Proteins Using Pathway Structure, Reuben Thomas, Julia M. Gohlke, Geffrey F. Stopper, Frederick M. Parham, Christopher J. Portier

Biology Faculty Publications

A method is proposed that finds enriched pathways relevant to a studied condition using the measured molecular data and also the structural information of the pathway viewed as a network of nodes and edges. Tests are performed using simulated data and genomic data sets and the method is compared to two existing approaches. The analysis provided demonstrates the method proposed is very competitive with the current approaches and also provides biologically relevant results.

Mutations Affecting A Putative Mutla Endonuclease Motif Impact Multiple Dna Mismatch Repair Functions, Naz Erdeniz, Megan Nguyen, Suzanne M. Deschênes, R. Michael Liskay

Biology Faculty Publications

Mutations in DNA mismatch repair (MMR) lead to increased mutation rates and higher recombination between similar, but not identical sequences, as well as resistance to certain DNA methylating agents. Recently, a component of human MMR machinery, MutLα, has been shown to display a latent endonuclease activity. The endonuclease active site appears to include a conserved motif, DQHA(X)₂E(X)₄E, within the COOH-terminus of human PMS2. Substitution of the glutamic acid residue (E705) abolished the endonuclease activity and mismatch-dependent excision in vitro. Previously, we showed that the PMS2-E705K mutation and the corresponding mutation in Saccharomyces cerevisiae were …

Myod Synergizes With The E-Protein Heb Beta To Induce Myogenic Differentiation, Maura H. Parker, Robert L.S. Perry, Melanie C. Fauteux, Charlotte A. Berkes, Michael A. Rudnicki

Biology Faculty Publications

The MyoD family of basic helix-loop-helix transcription factors function as heterodimers with members of the E-protein family to induce myogenic gene activation. The E-protein HEB is alternatively spliced to generate alpha and beta isoforms. While the function of these molecules has been studied in other cell types, questions persist regarding the molecular functions of HEB proteins in skeletal muscle. Our data demonstrate that HEB alpha expression remains unchanged in both myoblasts and myotubes, whereas HEB beta is upregulated during the early phases of terminal differentiation. Upon induction of differentiation, a MyoD-HEB beta complex bound the E1 E-box of the myogenin …

Myod Targets Chromatin Remodeling Complexes To The Myogenin Locus Prior To Forming A Stable Dna-Bound Complex, Ivana L. De La Serna, Yasuyuki Ohkawa, Charlotte A. Berkes, Donald A. Bergstrom, Caroline S. Dacwag, Stephen J. Tapscott, Anthony N. Imbalzano

Biology Faculty Publications

The activation of muscle-specific gene expression requires the coordinated action of muscle regulatory proteins and chromatin-remodeling enzymes. Microarray analysis performed in the presence or absence of a dominant-negative BRG1 ATPase demonstrated that approximately one-third of MyoD-induced genes were highly dependent on SWI/SNF enzymes. To understand the mechanism of activation, we performed chromatin immunoprecipitations analyzing the myogenin promoter. We found that H4 hyperacetylation preceded Brg1 binding in a MyoD-dependent manner but that MyoD binding occurred subsequent to H4 modification and Brg1 interaction. In the absence of functional SWI/SNF enzymes, muscle regulatory proteins did not bind to the myogenin promoter, thereby providing …

Intracellular Transport, Assembly, And Degradation Of Wild-Type And Disease-Linked Mutant Gap Junction Proteins, Judy K. Vanslyke, Suzanne M. Deschênes, Linda S. Musil

Biology Faculty Publications

More than 130 different mutations in the gap junction integral plasma membrane protein connexin32 (Cx32) have been linked to the human peripheral neuropathy X-linked Charcot–Marie–Tooth disease (CMTX). How these various mutants are processed by the cell and the mechanism(s) by which they cause CMTX are unknown. To address these issues, we have studied the intracellular transport, assembly, and degradation of three CMTX-linked Cx32 mutants stably expressed in PC12 cells. Each mutant had a distinct fate: E208K Cx32 appeared to be retained in the endoplasmic reticulum (ER), whereas both the E186K and R142W mutants were transported to perinuclear compartments from which …

Eph Receptors And Ephrins, Masaru Nakamoto

Biology Faculty Publications

The Eph receptors are the largest known family of receptor tyrosine kinases. The Eph receptors and theirmembrane-attached ligands, ephrins, show diverse expression patterns during development. Recent studies havedemonstrated that Eph receptors and ephrins play important roles in many developmental processes, includingneuronal network formation, the patterning of the neural tube and the paraxial mesoderm, the guidance of cellmigration, and vascular formation. In the nervous system, Eph receptors and ephrins have been shown to act aspositional labels to establish topographic projections. They also play a key role in pathway ®nding by axons andneural crest cells. The crucial roles of Eph receptors and …

Interactions Involving The Human Rna Polymerase Ii Transcription/Nucleotide Excision Repair Complex Tfiih, The Nucleotide Excision Repair Protein Xpg, And Cockayne Syndrome Group B (Csb) Protein, Narayan Iyer, Michael S. Reagan, Kou-Juey Wu, Bertram Canagarajah, Errol C. Friedberg

Biology Faculty Publications

The human basal transcription factor TFIIH plays a central role in two distinct processes. TFIIH is an obligatory component of the RNA polymerase II (RNAP II) transcription initiation complex. Additionally, it is believed to be the core structure around which some if not all the components of the nucleotide excision repair (NER) machinery assemble to constitute a nucleotide excision repairosome. At least two of the subunits of TFIIH (XPB and XPD proteins) are implicated in the disease xeroderma pigmentosum (XP). We have exploited the availability of the cloned XPB, XPD, p62, p44, and p34 genes (all …

Complementary Gradients In Expression And Binding Of Elf-1 And Mek4 In Development Of The Topographic Retinotectal Projection Map, Masaru Nakamoto

Biology Faculty Publications

Topographic maps with a defined spatial ordering of neuronal connections are a key feature of brain organization. Such maps are believed to develop in response to complementary position-specific labels in presynaptic and postsynaptic fields. However, the complementary labeling molecules are not known. In the well studied visual map of retinal axons projecting to the tectum, the labels are hypothesized to be in gradients, without needing large numbers of cell-specific molecules. We recently cloned ELF-1 as a ligand for Eph family receptors. Here, RNA hybridization shows matching expression gradients for ELF-1 in the tectum and its receptor Mek4 in the retina. …

Mouse Heparin Binding Protein-44 (Hbp-44) Associates With Brushin, A High-Molecular-Weight Glycoprotein Antigen Common To The Kidney And Teratocarcinomas, Masaru Nakamoto, Masayuki Ozawa, Sonia Jacinto, Tatsuhiko Furukawa, Yasuhiro Natori, Hiroshi Shirahama, Suguru Yonezawa, Tatsuo Nakayama, Takashi Muramatsu

Biology Faculty Publications

Heparin binding protein-44 (HBP-44) is a heparin binding protein of 44 kDa, found by cDNA cloning using antibodies against teratocarcinoma glycoproteins [Furukawa, T. et al. (1990) J. Biochem. 108, 297-302]. The N-terminal sequence analysis reported in this publication establishes the structure of its mature form. Immunohistochemical staining revealed that HBP-44 was located in the tubular brush border of the kidney. HBP-44 formed a complex with brushin, a high molecular weight (460 kDa) glycoprotein antigen common to the kidney and teratocarcinoma, but not with OR8 antigen, another antigen (350 kDa) of the same category. Brushin was shown to be the mouse …

Morfología Y Moléculas: Bases Complementarias De La Sistemática Moderna, Rafael O. De Sá, David M. Hillis

Biology Faculty Publications

RESUMEN

El auge de las técnicas moleculares en las últimas dos décadas ha traído nuevos enfoques en los estudios sistemáticos. Aquí presentaremos una revisión del uso, las aplicaciones, y los problemas de las principales metodologías de trabajo. Cada una de estas técnicas es aplicable a algunos problemas e inapropiada para otros, y es importante entender las suposiciones y limitaciones de cada técnica. Concluimos que el uso combinado de los enfoques morfológicos y moleculares otorga mejor resolución a los problemas sistemáticos.

ABSTRACT

The development of molecular techniques during the last two decades has brought new approaches to the analysis of systematic …

A Comparative 2-Dimensional Gel Protein Database Of The Intact And Regenerating Newt Limbs, Panagiotis A. Tsonis

Biology Faculty Publications

In this paper we describe a two-dimensional gel database of the regenerating newt limb. Protein synthesis was compared in the intact limb, in the 1-week regenerating limb, representing the dedifferentiation stage, and in the 2-week regenerating limb, representing the formation of the blastema. This comparative database provided data on differential expression of about 800 proteins during the process of limb regeneration. In addition, a map has been generated for these proteins for future guidance in characterizing further new, unknown proteins. The overall expression patterns of the proteins indicated that the dedifferentiation stage was marked by down-regulation of most proteins, while …

A New Family Of Heparin Binding Growth/Differentiation Factors: Differential Expression Of The Midkine (Mk) And Hb-Gam Genes During Mouse Development, Masaru Nakamoto, Shyuichiro Matsubara, Teruo Miyauchi, Hiroya Obama, Takashi Muramatsu

Biology Faculty Publications

MK (midkine) and HB-GAM (heparin-binding growth-associated molecule) constitute a new family of heparin-binding growth differentiation factors. The modes of expression of MK and HB-GAM during mouse development were quantitatively examined by mRNA hybridization. The following three distinct patterns of expression were observed in the brain/head region. On the 11th-13th days of gestation, MK was intensely, but HB-GAM relatively weakly expressed; on the 15th-19th days, both MK and HB-GAM expression became weaker; and in the neonatal period, HB-GAM was intensely expressed and MK expression increased slightly. The level of HB-GAM expression was lower than that of MK in the whole embryo …