Biology Faculty Publications

Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysis

Sonja Hansen — Mon, 14 Jan 2013 07:05:21 PST

Bacterial populations produce antibiotic-tolerant persister cells. A number of recent studies point to the involvement of toxin/antitoxin (TA) modules in persister formation. hipBA is a type II TA module that codes for the HipB antitoxin and the HipA toxin. HipA is an EF-Tu kinase, which causes protein synthesis inhibition and dormancy upon phosphorylation of its substrate. Antitoxins are labile proteins that are degraded by one of the cytosolic ATP-dependent proteases. We followed the rate of HipB degradation in different protease deficient strains and found that HipB was stabilized in a lon^- background. These findings were confirmed in an in vitro...

Occurrence and distribution of diverse populations of magnetic protists in a chemically stratified coastal salt pond

Dennis A. Bazylinski — Fri, 25 May 2012 08:37:39 PDT

Chemical stratification occurs in the water columns and sediments of many aquatic habitats resulting in vertical chemical and redox gradients. Various types of microorganisms are often associated with specific depths and chemical parameters in these situations. For example, magnetite-producing magnetotactic bacteria are known to form horizontal "plates" of cells at the oxic/anoxic transition zone (OATZ) of such environments. Here, we report the presence of populations of diverse magnetic protists in a seasonally chemically stratified, coastal salt pond. The protistan types included several biflagellates, a dinoflagellate, and a ciliate that were each associated with specific depths and thus, specific chemical, microbiological...

Environmental rRNA inventories miss over half of protistan diversity

Sunok Jeon — Fri, 25 May 2012 07:36:10 PDT

Background

The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle. Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers.

Results

We show that each PCR primer set-specific clone...

New cultivation strategies bring more microbial plankton species into the laboratory

Stephen J. Giovannoni — Fri, 25 May 2012 07:36:08 PDT

Enumeration of sandy sediment bacteria: are the counts quantitative or relative?

Slava S. Epstein — Fri, 25 May 2012 07:36:06 PDT

Several tests were carried out to enable evaluation of the precision with which sandy sediment bacteria could be enumerated. This represented the first attempt to place direct epifluorescence counts of benthic bacteria on a quantitative, rather than relative, ground. The tests combined in situ radioisotope ([³H], [¹⁴C]) labeling of sediment bacteria, bacterial dislodgment by ultrasonic treatment, and bacterial enumeration via fluorescent staining. The results provided direct and indirect evidence that the employed protocol for bacterial enumeration accounted for 88 to 98% of all bacteria present in sediments. The identified approach thus allowed for a rather complete quantification of sediment bacteria....

Methodology of in situ grazing experiments: evaluation of a new vital dye for preparation of fluorescently labeled bacteria

Slava S. Epstein — Fri, 25 May 2012 07:36:04 PDT

A new fluorescent dye, cyanoditolyl tetrazolium chloride (CTC), is suggested for use in grazing studies to prepare fluorescently labeled bacteria (FLB). As food tracers, CTC-stained bacteria appeared to have advantages over FLBs prepared in accordance with previously published protocols. The CTC is a vital dye, non-toxic to the examined bacteria; in our study, the CTC-stained bacteria grew at the same rate as non-stained bacteria. This is an advantage over the commonly used DTAF-employing staining protocol, which results in heat-killed or immobilized prey particles. The CTC-stained bacteria were not toxic to the studied bacterial grazers; a test ciliate grew on FLBs...

Enumeration of sandy sediment bacteria: search for optimal protocol

Slava S. Epstein — Fri, 25 May 2012 07:36:03 PDT

We examined and compared a variety of existing protocols for enumeration of bacteria from marine sandy sediments. The focus was on how to dislodge bacteria from sediment particles; a commercial blender, an ultrasonic cleaner, and an ultrasonic cell disrupter were tested. The ultrasonic cell disrupter was found to be the most efficient device for bacterial dislodgment. With a 5 mm microtip vibrating at 109 μm amplitude and 20 kHz, the optimal sonication time of small (≤ 0.5 cm³) samples was 180 s. Having identified the optimal dislodgment treatment, we went through other steps of sediment bacteria enumeration (use of surfactants,...

Protistan diversity in the arctic: a case of paleoclimate shaping modern biodiversity?

Thorsten Stoeck — Fri, 25 May 2012 07:36:02 PDT

Background

The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes.

Methodology/Principal Findings

We investigate this hypothesis by analyzing an original dataset of 18S rRNA gene sequences from Western Greenland in the Arctic, and data from the existing literature on 18S rRNA gene diversity in hydrothermal vent, temperate sediments, and anoxic water column communities....

Nesting ecology and cuticular microbial loads in dampwood (Zootermopsis angusticollis) and drywood termites (Incisitermes minor, I. schwarzi, Cryptotermes cavifrons)

Rebeca B. Rosengaus — Mon, 07 May 2012 10:42:00 PDT

Termites form one-piece nests in wood that can vary in their moisture content and degree of decomposition, and thus microbial richness. To estimate the microbial load of nests and the potential risk they pose for colony members, we quantified the number of microbes in the nest and on the cuticle of the dampwood termite, Zootermopsis angusticollis, and three drywood termites, Incisitermes minor, I. schwarzi, and Cryptotermes cavifrons. The number of colony forming units (CFUs) cultured from nest material samples and washes of the cuticle of larvae and nymphs were determined. CFUs recorded from nest material was low (fewer than 60...

Disease resistance in the drywood termite, Incisitermes schwarzi: does nesting ecology affect immunocompetence?

Daniel V. Calleri II — Mon, 07 May 2012 10:41:59 PDT

Termites live in nests that can differ in microbial load and thus vary in degree of disease risk. It was hypothesized that termite investment in immune response would differ in species living in nest environments that vary in the richness and abundance of microbes. Using the drywood termite, Incisitermes schwarzi Banks (Isoptera: Kalotermitidae), as a model for species having low nest and cuticular microbial loads, the susceptibility of individuals and groups to conidia of the entomopathogenic fungus, Metarhizium anisopliae Sorokin (Hypocreales: Clavicipitaceae), was examined. The survivorship of I. schwarzi was compared to that of the dampwood termite, Zootermopsis angusticollis Hagen...

Neuromotor noise, error tolerance and velocity-dependent costs in skilled performance

Dagmar Sternad — Thu, 20 Oct 2011 12:47:09 PDT

In motor tasks with redundancy neuromotor noise can lead to variations in execution while achieving relative invariance in the result. The present study examined whether humans find solutions that are tolerant to intrinsic noise. Using a throwing task in a virtual set-up where an infinite set of angle and velocity combinations at ball release yield throwing accuracy, our computational approach permitted quantitative predictions about solution strategies that are tolerant to noise. Based on a mathematical model of the task expected results were computed and provided predictions about error-tolerant strategies (Hypothesis 1). As strategies can take on a large range of...

Cathepsin K deficiency in mice induces structural and metabolic changes in the central nervous system that are associated with learning and memory deficits

Stephanie Dauth — Tue, 20 Sep 2011 13:22:24 PDT

Background

Cathepsin K is a cysteine peptidase known for its importance in osteoclast-mediated bone resorption. Inhibitors of cathepsin K are in clinical trials for treatment of osteoporosis. However, side effects of first generation inhibitors included altered levels of related cathepsins in peripheral organs and in the central nervous system (CNS). Cathepsin K has been recently detected in brain parenchyma and it has been linked to neurobehavioral disorders such as schizophrenia. Thus, the study of the functions that cathepsin K fulfils in the brain becomes highly relevant.

Results

Cathepsin K messenger RNA was detectable in all brain regions of wild type...

Genetic diversity and connectivity in the threatened staghorn coral (Acropora cervicornis) in Florida

Elizabeth M. Hemond — Tue, 20 Sep 2011 11:37:40 PDT

Over the past three decades, populations of the dominant shallow water Caribbean corals, Acropora cervicornis and A. palmata, have been devastated by white-band disease (WBD), resulting in the listing of both species as threatened under the U.S. Endangered Species Act. A key to conserving these threatened corals is understanding how their populations are genetically interconnected throughout the greater Caribbean. Genetic research has demonstrated that gene flow is regionally restricted across the Caribbean in both species. Yet, despite being an important site of coral reef research, little genetic data has been available for the Florida Acropora, especially for the staghorn coral,...

Natural disease resistance in threatened staghorn corals

Steven V. Vollmer — Tue, 20 Sep 2011 11:37:38 PDT

Disease epidemics have caused extensive damage to tropical coral reefs and to the reef-building corals themselves, yet nothing is known about the abilities of the coral host to resist disease infection. Understanding the potential for natural disease resistance in corals is critically important, especially in the Caribbean where the two ecologically dominant shallow-water corals, Acropora cervicornis and A. palmata, have suffered an unprecedented mass die-off due to White Band Disease (WBD), and are now listed as threatened under the US Threatened Species Act and as critically endangered under the IUCN Red List criteria. Here we examine the potential for natural...

Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2

Christina R. DeMaso — Mon, 12 Sep 2011 12:30:32 PDT

Filamins are long, flexible, multi-domain proteins composed of an N-terminal actin-binding domain (ABD) followed by multiple immunoglobulin-like repeats (IgFLN). They function to organize and maintain the actin cytoskeleton, to provide scaffolds for signaling components, and to act as mechanical force sensors. In this study, we used transcript sequencing and homology modeling to characterize the gene and protein structures of the C. elegans filamin orthologs fln-1 and fln-2. Our results reveal that C. elegans FLN-1 is well conserved at the sequence level to vertebrate filamins, particularly in the ABD and several key IgFLN repeats. Both FLN-1 and the more divergent FLN-2...

Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific

David J. Combosch — Tue, 06 Sep 2011 12:55:59 PDT

Background

Coral reefs in the Tropical Eastern Pacific (TEP) are amongst the most peripheral and geographically isolated in the world. This isolation has shaped the biology of TEP organisms and lead to the formation of numerous endemic species. For example, the coral Pocillopora damicornis is a minor reef-builder elsewhere in the Indo-West Pacific, but is the dominant reef-building coral in the TEP, where it forms large, mono-specific stands, covering many hectares of reef. Moreover, TEP P. damicornis reproduces by broadcast spawning, while it broods mostly parthenogenetic larvae throughout the rest of the Indo-West Pacific. Population genetic surveys for P. damicornis...

SOS response induces persistence to fluoroquinolones in Escherichia coli

Tobias Dörr — Wed, 18 May 2011 10:29:08 PDT

Bacteria can survive antibiotic treatment without acquiring heritable antibiotic resistance. We investigated persistence to the fluoroquinolone ciprofloxacin in Escherichia coli. Our data show that a majority of persisters to ciprofloxacin were formed upon exposure to the antibiotic, in a manner dependent on the SOS gene network. These findings reveal an active and inducible mechanism of persister formation mediated by the SOS response, challenging the prevailing view that persisters are pre-existing and formed purely by stochastic means. SOS-induced persistence is a novel mechanism by which cells can counteract DNA damage and promote survival to fluoroquinolones. This unique survival mechanism may be...

Persisters: a distinct physiological state of E. coli

Devang Shah — Wed, 18 May 2011 10:14:57 PDT

Background
Bacterial populations contain persisters, phenotypic variants that constitute approximately 1% of cells in stationary phase and biofilm cultures. Multidrug tolerance of persisters is largely responsible for the inability of antibiotics to completely eradicate infections. Recent progress in understanding persisters is encouraging, but the main obstacle in understanding their nature was our inability to isolate these elusive cells from a wild-type population since their discovery in 1944.

Results
We hypothesized that persisters are dormant cells with a low level of translation, and used this to physically sort dim E. coli cells which do not contain sufficient amounts of unstable GFP expressed from...

Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli

Tobias Dörr — Wed, 18 May 2011 10:03:37 PDT

Bacteria induce stress responses that protect the cell from lethal factors such as DNA-damaging agents. Bacterial populations also form persisters, dormant cells that are highly tolerant to antibiotics and play an important role in recalcitrance of biofilm infections. Stress response and dormancy appear to represent alternative strategies of cell survival. The mechanism of persister formation is unknown, but isolated persisters show increased levels of toxin/antitoxin (TA) transcripts. We have found previously that one or more components of the SOS response induce persister formation after exposure to a DNA-damaging antibiotic. The SOS response induces several TA genes in Escherichia coli. Here,...

Adaptations of the gray catbird Dumetella carolinensis to long distance migration: energy stores and substrate concentrations in plasma

Richard L. Marsh — Wed, 22 Dec 2010 12:15:01 PST

The major body components (water, lean dry, and fat) were measured in the carcasses of Gray Catbirds from which the flight muscles had been removed. Birds were collected from May through October near Ann Arbor, Michigan and during September and October near Gainesville, Florida. Additionally, the glycogen content of muscle and liver and the concentrations of glucose and triglycerides in plasma were determined in catbirds sampled during fall migration in Florida. Catbirds attained maximum body masses of ∼50 g in Florida, largely due to the addition of fat. Relatively lean birds (∼3-4% body fat) in spring through fall weighed approximately...