Life Sciences Commons^™

For The Birds, Milan Bull

Wrack Lines

A new column about shore birds, starting with piping plovers.

Smart Phone App Puts Rain Gardens Into Mobile Tech Mode, Margaret (Peg) A. Van_Patten Ms.

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A fun smart phone app can help you design the rain garden of your dreams.

The Sh2 Domain Interaction Landscape, Kazuya Machida, Christopher M. Thompson, Bruce J. Mayer

UCHC Articles - Research

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a new high-density peptide chip technology that allows probing the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique we have experimentally identified thousands of putative SH2- peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2 mediated …

There's A New Crop In Town, Margaret (Peg) A. Van_Patten Ms.

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This food is being grown and sold in Connecticut for the first time--maybe it's not what you think!

Partners In Spread Prevention, Nancy C. Balcom

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Working together to stop the spread of aquatic invasive species.

A New Planting Tool For Coastal Homeowners, Juliana Barrett

Wrack Lines

It's not a shovel--it's an online visualization aid.

Determination Of Dosage Compensation Of The Mammalian X Chromosome By Rna-Seq Is Dependent On Analytical Approach, Nathaniel K. Jue, Michael B. Murphy, Seth D. Kasowitz, Sohaib M. Qureshi, Craig J. Obergfell, Sahar Elsisi, Robert J. Foley, Rachel J. O’Neill, Michael J. O’Neill

Open Access Author Fund Awardees' Articles

Background

An enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation has been observed in a variety of organisms. Incongruence in the conclusions reached in some recent reports has been attributed to different high-throughput approaches to transcriptome analysis. However, recent reports each utilizing RNA-seq to gauge X-linked gene expression relative to autosomal gene expression also arrived at diametrically opposed conclusions regarding X chromosome dosage compensation in mammals.

Results

Here we analyze RNA-seq data from X-monosomic female human and mouse tissues, which are uncomplicated …

Computationally Designed Peptide Inhibitors Against The Ubiquitin E3 Ligase Scf Fbx4, Bing Hao

UCHC Articles - Research

Telomerase is a reverse transcriptase that maintains telomere length. Telomerase activity is suppressed in somatic cells such that telomere attrition triggers replicative senescence or apop-tosis. In cancer cells, telomerase is up-regulated or reactivated, effectively making the cell immortal. Previous studies have shown that telomerase activity positively correlates with unfavorable cancer prognosis. Since it was discovered that activation of telomerase is a rate-limiting step in carcinogenesis, telomerase has gained much interest as a drug target. Both screening and structure-based methods have been extensively employed to identify small molecule leads that can selectively disrupt telomerase activity. Strategies commonly used to target telomerase …

Resistive-Pulse Measurements With Nanopipettes: Detection Of Au Nanoparticles And Nanoparticle-Bound Anti-Peanut Igy†, Vigneshwaran Mani, Naimish Sardesai, James F. Rusling

UCHC Articles - Research

Solid-state nanopores have been widely employed in sensing applications from Coulter counters to DNA sequencing devices. The analytical signal in such experiments is the change in ionic current flowing through the orifice caused by the large molecule or nanoparticle translocation through the pore. Conceptually similar nanopipette-based sensors can offer several advantages including the ease of fabrication and small physical size essential for local measurements and experiments in small spaces. This paper describes the first evaluation of nanopipettes with well characterized geometry for resistive-pulse sensing of Au nanoparticles (AuNP), nanoparticles coated with an allergen epitope peptide layer, and AuNP–peptide particles with …

Coordination Of Peroxide To The Cum Center Of Peptidylglycine Α-Hydroxylating Monooxygenase (Phm): Structural And Computational Study, Betty A. Eipper, Richard E. Mains

UCHC Articles - Research

Many bioactive peptides, such as hormones and neuropeptides, require amidation at the C terminus for their full biological activity. Peptidylglycine α-hydroxylating monooxygenase (PHM) performs the first step of the amidation reaction—the hydroxylation of peptidylglycine substrates at the Cα position of the terminal glycine. The hydroxylation reaction is copper- and O₂-dependent and requires 2 equiv of exogenous reductant. The proposed mechanism suggests that O₂ is reduced by two electrons, each provided by one of two nonequivalent copper sites in PHM (Cu_H and Cu_M). The characteristics of the reduced oxygen species in the PHM reaction and …

Preconditioning Induces Sustained Neuroprotection By Down Regulation Of Ampk, Louise D. Mccullough, Venugopal Reddy Venna, Jun Li, Sharon E. Benashski, Sami Tarabishy

UCHC Articles - Research

Abstract Background and Purpose—Ischemic preconditioning (IPC) induces endogenous neuroprotection from a subsequent ischemic injury. IPC involves down-regulation of metabolic pathways. As Adenosine 5′-monophosphate-activated protein kinase (AMPK) is a critical sensor of energy balance and plays a major role in cellular metabolism, its role in IPC was investigated.

Methods—A brief 3 minute middle cerebral artery occlusion (MCAO) was employed to induce IPC in male mice 72 hours prior to 90 minute MCAO. Levels of AMPK and pAMPK, the active form of the kinase, were assessed after IPC. A pharmacological activator or inhibitor of AMPK was utilized to determine the …

Computational Analysis Of Rho Gtpase Cycling, Cibele Vieira Falkenberg, Leslie M. Loew

UCHC Articles - Research

The Rho family of GTPases control actin organization during diverse cellular responses (migration, cytokinesis and endocytosis). Although the primary members of this family (RhoA, Rac and Cdc42) have different downstream effects on actin remodeling, the basic mechanism involves targeting to the plasma membrane and activation by GTP binding. Our hypothesis is that the details of GTPase cycling between membrane and cytosol are key to the differential upstream regulation of these biochemical switches. Accordingly, we developed a modeling framework to analyze experimental data for these systems. This analysis can reveal details of GDI-mediated cycling and help distinguish between GDI-dependent and -independent …

Direct And Indirect Selection On Floral Pigmentation By Pollinators And Seed Predators In A Color Polymorphic South African Shrub, Jane E. Carlson, Kent E. Holsinger

EEB Articles

The coexistence of different color morphs is often attributed to variable selection pressures across space, time, morph frequencies or selection agents, but the routes by which each morph is favored are rarely identified. In this study we untangle the interactions and trait pleiotropisms that influence floral color polymorphisms on a local scale in Protea, within which ~40% of species are polymorphic. Previous work shows that seed predators and reproductive differences likely influence polymorphism maintenance in four Protea species. Here, we explore whether selection acts on floral color directly or indirectly in Protea aurea, using path analysis of pollinator …

Retrospective Study Of Microorganisms Associated With Vascular Access Infections In Hemodialysis Patients, Andre A. Kaplan, Richard S. Feinn, Rajesh V. Lalla

UCHC Articles - Research

Objective

To assess microorganisms associated with vascular access-associated infections (VAIs) in hemodialysis patients, with respect to possible origin from the mouth.

Study Design

A retrospective and comparative analysis of the microbes associated with VAI in hemodialysis patients treated during a 10-year period was performed using the Human Oral Microbiome Database (HOMD).

Results

Of 218 patient records identified, 65 patients collectively experienced 115 VAI episodes. The most common microorganisms involved were Staphylococcus aureus (49.6% of infections), Staphylococcus epidermidis (10.4%), Serratia marcescens (10.4%), Pseudomonas aeruginosa (9.6%), and Enterococcus faecalis / fecum (8.7%). None of these was found in 1% or more of …

Copper Signaling In The Mammalian Nervous System: Synaptic Effects, Eric D. Gaier, Betty A. Eipper, Richard E. Mains

UCHC Articles - Research

Copper (Cu) is an essential metal present at high levels in the CNS. Its role as a co-factor in mitochondrial ATP production and in other essential cuproenzymes is well defined. Menkes and Wilson’s diseases are severe neurodegenerative conditions that demonstrate the importance of Cu transport into the secretory pathway. Brain levels of Cu, which is almost entirely protein bound, exceed extracellular levels by more than a hundred-fold. Cu stored in the secretory pathway is released in a Ca²⁺-dependent manner and can transiently reach concentrations over 100 µM at synapses. The ability of low µM levels of Cu to …

Euryhalinity In An Evolutionary Context, Eric T. Schultz, Stephen D. Mccormick

EEB Articles

This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.