Biology Commons^™

Resource Partitioning Along Multiple Niche Axes Drives Functional Diversity In Parrotfishes On Caribbean Coral Reefs, Thomas C. Adam, Megan Kelley, Benjamin I. Ruttenberg, Deron E. Burkepile

Biological Sciences

The recent loss of key consumers to exploitation and habitat degradation has significantly altered community dynamics and ecosystem function across many ecosystems worldwide. Predicting the impacts of consumer losses requires knowing the level of functional diversity that exists within a consumer assemblage. In this study, we document functional diversity among nine species of parrotfishes on Caribbean coral reefs. Parrotfishes are key herbivores that facilitate the maintenance and recovery of coral-dominated reefs by controlling algae and provisioning space for the recruitment of corals. We observed large functional differences among two genera of parrotfishes that were driven by differences in diet. Fishes …

Complete Mitochondrial Genome Of The Speckled Dace Rhinichthys Osculus, A Widely Distributed Cyprinid Minnow Of Western North America, Samantha J. Bock, Morgan M. Malley, Sean Lema

Biological Sciences

The speckled dace Rhinichthys osculus (order Cypriniformes), also known as the carpita pinta, is a small cyprinid minnow native to western North America. Here, we report the sequencing of the full mitochondrial genome (mitogenome) of R. osculus from a male fish collected from the Amargosa River Canyon in eastern California, USA. The assembled mitogenome is 16 658 base pair (bp) nucleotides, and encodes 13 protein-coding genes, and includes both a 12S and a 16S rRNA, 22 tRNAs, and a 985 bp D-loop control region. Mitogenome synteny reflects that of other Ostariophysian fishes with the majority of genes and RNAs encoded …

Temperatures Experienced By Fresh-Cut Leafy Greens During Retail Storage And Display, W. Brown, E. Ryser, L. Gorman, Scott J. Steinmaus, Keith Vorst

Biological Sciences

There has been limited published work in the United States on temperature profiling of fresh-cut, bagged leafy greens during their transport, retail storage, and retail display. This study utilized temperature monitors placed in backrooms and display cases at nine supermarkets located in southern California: the Central Coast (Santa Barbara to Los Osos), Greater Los Angeles (Burbank area), and Greater Palm Desert. Sensors were installed midway along each 8-foot display case section containing fresh-cut leafy greens. Monitors were placed at the front and back of shelves and in the lower bin. In storage rooms, sensors were placed 4 feet from the …

Introduction Next Contents Vol 63(4) Global Research On Ultramafic (Serpentine) Ecosystems (8th International Conference On Serpentine Ecology In Sabah, Malaysia), Antony Van Der Ent, Nishanta Rajakaruna, Robert Boyd, Guillaume Echevarria, Rimi Repin, Dick Williams

Biological Sciences

Since 1991, researchers from approximately 45 nations have participated in eight International Conferences on Serpentine Ecology (ICSE). The ICSE conferences are coordinated by the International Serpentine Ecology Society (ISES), a formal research society whose members study geological, pedological, biological and applied aspects of ultramafic ecosystems worldwide. These conferences have provided an international forum to discuss and synthesise multidisciplinary research, and have provided opportunities for scientists in distinct fields and from different regions of the world to conduct collaborative and interdisciplinary research. The 8th ICSE was hosted by Sabah Parks in Malaysia, on the island of Borneo, and attracted the largest …

Structure-Activity Relationship Studies Of Small Molecules Directed Against The T-Box Specifier Loop, Spencer Weintraub

Biological Sciences

High rates of antibiotic use have resulted in the pervasiveness of multi-drug resistant organisms. With rising drug-resistance the development of antibiotics with new targets against these pathogens is imperative. The T-box regulatory mechanism is a process specific to Grampositive bacteria and controls many essential genes including aaRS genes, which are code for the aminoacyl-tRNA synthetases required to charge tRNA. The T-box Specifier Loop is a novel target for antibacterial drug discovery as we hypothesize that a small compound bound to the Specifier Loop will inhibit transcription of essential bacterial genes resulting in bacterial cell death or growth arrest. We used …

Use Of A Ph-Sensitive Probe To Study The Role Of Pkc-Epsilon In Phagocytosis Of Pathogens, Rebekah Marie Pierce

Biological Sciences

The main force behind innate immunity, our primary defense against infection, is the clearance of pathogens, or phagocytosis. Protein Kinase C-epsilon (PKC-ε) is necessary for efficient phagocytosis of antibody (IgG)-coated particles. Previous studies used IgG-coated glass beads, which are larger and more rigid than bacteria and lack their complex surface protein expression. To test the hypothesis that PKC-ε is necessary for phagocytosis of pathogens, we compared the rate of uptake of common pathogens by macrophages from wild type and PKC- ε knock out mice. We tested two targets, a bacteria (E. coli) and a yeast (zymosan), both physiologically relevant phagocytic …

The Rck/P54 Prion-Related Domain And Its Influence On The Localization And Function Of Rck/P54 During Hcv Infection, Lindsey Oltz

Biological Sciences

Currently over 180 million people are infected with Hepatitis C virus (HCV) worldwide. HCV infection is a major cause of hepatocellular carcinoma (HCC), liver cirrhosis, and chronic hepatitis. The available antiviral treatment of interferon and ribavirin has limited success, is costly and toxic. Furthermore, there is no vaccine. An increased understanding of how HCV exploits the many cellular pathways and host factors during infection will provide information necessary for the development of novel anti-HCV therapies, which target host proteins rather than the rapidly evolving viral proteins. During infection, HCV interacts with and manipulates many host mRNA pathways. The Pager lab …

Developing A Novel Means Of Observing The Intracellular Activities Of Heterogeneous Nuclear Ribonucleoprotein K Within Xenopus Laevis, Janeah A. Alexis

Biological Sciences

Research into the regeneration of optic nerves in Xenopus laevis has determined that heterogeneous nuclear ribonucleoprotein K (hnRNP K) plays a crucial role in regulating the trafficking and translation of mRNAs essential for the organization of the axonal cytoskeleton. To further explore this role, our lab has turned to tools that can definitively elucidate hnRNP K’s translocation in-and-out of the nucleus, as well as directly quantitate its degradation rate, in vivo. An appropriate tool for such experiments is the monomeric Eos fluorescent protein (mEosFP), which can be stably and irreversibly photo-converted. This fluorescent protein naturally emits green light (~516nm) and …

Identifying Genes That Affect Lactococcus Lactis Intron Mobility, Mary Njie

Biological Sciences

A gene consists of coding segments, exons, which are maintained and contribute to the final mRNA product, while non-coding segments, introns, are spliced out through RNA splicing mechanisms to code a functional gene. The mobility of the spliced introns and factors that affect mobility are an important field of study evolutionarily whereas splicing defects have medical implications. For this study, the genome of the Lactococcus lactis bacterial strain, IL1403 and the group II intron of interest, L1.LtrB were utilized. This intron moves into new sites on DNA by a process termed retrotransposition (RTP). Our goal is to identify genes that …

The Differential Splicing Of The Socs2 5’Utr, A Gene Involved In Successful Central Nervous System Axon Regeneration In Xenopus Laevis, Megan Gura

Biological Sciences

The amphibian Xenopus laevis has the ability to regenerate axons of its optic nerve even after metamorphosis. From previous studies done in our lab, we found that Suppressor of Cytokine Signaling 2 (SOCS2) could be involved in the complex pathway of genes regulating nervous system development and regeneration. 3’ and 5’ Rapid Amplification of cDNA Ends (RACE) revealed that the 5’ untranslated region (UTR) of SOCS2 contains two splice forms. One splice form contained a previously unidentified 68 base pair exon, which will be referred to as ‘Exon 2’, which we hypothesized is involved in post-transcriptional regulation of SOCS2. I …

Chronic Resveratrol Treatment Ameliorates Cognitive Deficits Associated With A High Fat Diet, Kelsey E. O'Leary

Biological Sciences

Resveratrol is a polyphenol antioxidant found in red wine known to have anti-aging, anti-cancer, and anti-obesity effects in both humans and animals. Resveratrol's primary biological action is as an antioxidant, causing a reduction in reactive oxygen species (ROS). ROS are produced as byproducts of normal metabolic functions, but become abnormally elevated in individuals who consume a high fat diet (HFD) or who have metabolic conditions like Type II Diabetes Mellitus (T2DM); in these circumstances, abnormal elevation in ROS leads to cellular damage and cell death. Another common effect of a diet high in fat and calories is cognitive impairment: specifically, …

Global Research On Ultramafic (Serpentine) Ecosystems (8th International Conference On Serpentine Ecology In Sabah, Malaysia): A Summary And Synthesis, Antony Van Der Ent, Nishanta Rajakaruna, Robert Boyd, Guillaume Echevarria, Rimi Repin, Dick Williams

Biological Sciences

Since 1991, researchers from approximately 45 nations have participated in eight International Conferences on Serpentine Ecology (ICSE). The Conferences are coordinated by the International Serpentine Ecology Society (ISES), a formal research society whose members study geological, pedological, biological and applied aspects of ultramafic (serpentine) ecosystems worldwide. These conferences have provided an international forum to discuss and synthesise multidisciplinary research, and have provided opportunities for scientists in distinct fields and from different regions of the world to conduct collaborative and interdisciplinary research. The 8th ICSE was hosted by Sabah Parks in Malaysia, on the island of Borneo, and attracted the largest …

Role Of Bacterial-Fungal Interactions On Heavy Metal Phytotoxicity In Serpentine Soil, Mihiri Seneviratne, Gamini Seneviratne, H. M. S. P. Madawala, M.C.M. Iqbal, Nishanta Rajakaruna, Tharanga Bandara, Meththika Vithanage

Biological Sciences

This study was conducted to understand the role of bacterial–fungal interactions on heavy metal uptake by Zea mays plants. A pot experiment was conducted for 90 days with Z. mays in serpentine soil inoculated with a Gram-negative bacterium, fungus (Aspergilllus sp.) and both microbes to determine the effects of inoculation on nickel, manganese, chromium and cobalt concentrations in plant tissue and soil. Soil nutrients and soil enzyme activities were measured to determine the effect of inoculations on soil quality. Inoculation of microorganisms increased shoot and root biomass, and the maximum biomass was in the bacterial–fungal inoculation. This could be …

Transfer Of Heavy Metals Through Terrestrial Food Webs: A Review, Jillian E. Gall, Robert Boyd, Nishanta Rajakaruna

Biological Sciences

Heavy metals are released into the environment by both anthropogenic and natural sources. Highly reactive and often toxic at low concentrations, they may enter soils and groundwater, bioaccumulate in food webs, and adversely affect biota. Heavy metals also may remain in the environment for years, posing long-term risks to life well after point sources of heavy metal pollution have been removed. In this review, we compile studies of the community-level effects of heavy metal pollution, including heavy metal transfer from soils to plants, microbes, invertebrates, and to both small and large mammals (including humans). Many factors contribute to heavy metal …

A Preliminary Survey Of The Diversity Of Soil Algae And Cyanoprokaryotes On Mafic And Ultramafic Substrates In South Africa, Arthurita Venter, Anatoliy Levanets, Stefan Siebert, Nishanta Rajakaruna

Biological Sciences

Despite a large body of work on the serpentine-substrate effect on vascular plants, little work has been undertaken to describe algal communities found on serpentine soils derived from peridotite and other ultramafic rocks. We report a preliminary study describing the occurrence of algae and cyanoprokaryotes on mafic and ultramafic substrates from South Africa. Results suggest that slope and aspect play a key role in species diversity and community composition and, although low pH, nutrients and metal content do not reduce species richness, these edaphic features also influence species composition. Further, typical soil genera such as Leptolyngbya, Microcoleus, Phormidium …

Growth And Nickel Uptake By Serpentine And Non-Serpentine Populations Of Fimbristylis Ovata (Cyperaceae) From Sri Lanka, P. K. D. Chathuranga, S. K. A. T. Dharmasena, Nishanta Rajakaruna, M.C.M. Iqbal

Biological Sciences

Compared with serpentine floras of Southeast Asia, the serpentine vegetation of Sri Lanka is impoverished in regard to serpentine endemics and nickel hyperaccumulators. All species so far documented from the serpentine outcrops of Sri Lanka also have non-serpentine populations; it is unclear whether the serpentine populations are physiologically distinct and deserve ecotypic recognition. We conducted a preliminary study to examine whether serpentine and non-serpentine populations of Fimbristylis ovata represent locally adapted ecotypes by investigating their growth and potential for nickel uptake and tolerance under greenhouse conditions. Although both populations of F. ovata showed a similar growth pattern in serpentine soil …

Calcium : Magnesium Ratio Affects Environmental Stress Sensitivity In The Serpentine-Endemic Alyssum Inflatum (Brassicaceae), Rasoul Ghasemi, Zohreh Zare Chavoshi, Robert S. Boyd, Nishanta Rajakaruna

Biological Sciences

Plants endemic to serpentine soils are adapted to harsh environmental conditions typical of those soils, particularly, low (<1) calcium (Ca) : magnesium (Mg) ratios. We compared survival of two perennial Alyssum species native to Iran under experimental manipulations of Ca : Mg ratio, including when Ca : Mg ratio was varied under conditions of high ammonium concentration and heat stress. Alyssum inflatum is a serpentine endemic capable of nickel (Ni) hyperaccumulation, whereas A. lanceolatum is found on non-serpentine soils and is not known to hyperaccumulate Ni. We grew plants of both species under four Ca : Mg ratios (0.4, 2, 20, 40) and tested survival when plants were exposed to elevated ammonium …

Vegetation Dynamics And Mesophication In Response To Conifer Encroachment Within An Ultramafic System, J. Burgess, K. Szlavecz, N. Rajakaruna, S. Lev, C. Swan

Biological Sciences

The biological, ecological, and evolutionary significance of serpentine habitats has long been recognised. We used an integrated physiochemical dataset combining plot spatial data with temporal data from tree cores to evaluate changes in soils and vegetation. Data suggest that this unique habitat is undergoing a transition, endangering local biodiversity and endemic plant species. The objective of this work was to analyse the vegetation dynamics of a xeric serpentine savanna located in the Mid-Atlantic, USA. We employed vegetation surveys of 32 10 × 15 m quadrats to obtain woody species composition, density, basal area, and developed a spatial physiochemical dataset of …

A Preliminary Report On Escherichia Coli Strain Diversity In Cows, Alison T. Stivers

Biological Sciences

Pyroprinting is a strain typing method that relies on the simultaneous pyrosequencing of the multi-copy rRNA intergenic transcribed spacer regions of E. coli (Black, et al., 2014). These pyroprints can be used to identify the source of E. coli in the environment. Currently, Cal Poly’s Center for Applications in Biotechnology (CAB) is augmenting the existing E. coli pyroprint library. By pyroprinting the intestinal E. coli of cows, we can quantify the strain diversity present, evaluate persistence, and determine the minimum sample size required for a complete overview of the cow intestinal E. coli population. These pyroprints can then be added …

Ecotypic Differentiation Of Mid-Atlantic Quercus Species In Response To Ultramafic Soils, Jerry Burgess, Katalin Szlavecz, Nishanta Rajakaruna, Christopher Swan

Biological Sciences

Spatial heterogeneity of soil conditions combined with intraspecific variation confer site-specific edaphic tolerance, resulting in local adaptation and speciation. To understand the geoecological processes controlling community assembly of woodland tree species on serpentine and mafic soils, we investigated resource gradients and provenance (geographic area of propagule collection) as variables affecting typical representative upland oak (Quercus) species distribution. Accordingly, we conducted a year-long reciprocal transplant experiment in the greenhouse with serpentine and mafic soils, using seedlings of five oak species (Quercus marilandica, Q. stellata, Q. montana, Q. michauxii and Q. alba). All seedlings, regardless …

Herbivory And The Resilience Of Caribbean Coral Reefs: Knowledge Gaps And Implications For Management, Thomas C. Adam, Deron E. Burkepile, Benjamin I. Ruttenberg, Michelle J. Paddack

Biological Sciences

Herbivory is a key process on coral reefs that can facilitate reef-building corals by excluding algae that otherwise negatively impact coral settlement, growth, and survivorship. Over the last several decades, coral cover on Caribbean reefs has declined precipitously. On many reefs, large structurally complex corals have been replaced by algae and other non-reef-building organisms, resulting in the collapse of physical structure and the loss of critical ecosystem services. The drivers of coral decline on Caribbean reefs are complex and vary among locations. On many reefs, populations of key herbivores have been greatly reduced by disease and overfishing, and this has …

Protemic Identification Of Germline Proteins In Caenorhabditis Elegans, B Elizabeth Turner, Sophia M. Basecke, Grace E. Bazan, Eric S. Dodge, Cassy M. Haire, Dylan J. Heussman, Chelsey L. Johnson, Chelsea K. Mukai, Adrianna M. Naccarati, Sunny-June Norton, Jennifer R. Sato, Chihara O. Talavera, Michael V. Wade, Kenneth J. Hillers

Biological Sciences

Sexual reproduction involves fusion of 2 haploid gametes to form diploid offspring with genetic contributions from both parents. Gamete formation represents a unique developmental program involving the action of numerous germline-specific proteins. In an attempt to identify novel proteins involved in reproduction and embryonic development, we have carried out a proteomic characterization of the process in Caenorhabditis elegans. To identify candidate proteins, we used 2D gel electrophoresis (2DGE) to compare protein abundance in nucleus-enriched extracts from wild-type C. elegans, and in extracts from mutant worms with greatly reduced gonads (glp-4(bn2) worms reared at 25°C); 84 proteins whose …

Immobilization And Phytotoxicity Reduction Of Heavy Metals In Serpentine Soil Using Biochar, I. Herath, P. Kumarathilaka, A. Navarantne, N. Rajakaruna, M. Vithanage

Biological Sciences

Purpose

Serpentine soils derived from ultramafic rocks release elevated concentrations of toxic heavy metals into the environment. Hence, crop plants cultivated in or adjacent to serpentine soil may experience reduced growth due to phytotoxicity as well as accumulate toxic heavy metals in edible tissues. We investigated the potential of biochar (BC), a waste byproduct of bioenergy industry in Sri Lanka, as a soil amendment to immobilize Ni, Cr, and Mn in serpentine soil and minimize their phytotoxicity.

Materials and methods

The BC used in this study was a waste byproduct obtained from a Dendro bioenergy industry in Sri Lanka. This …