Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome

Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.     

Early ocean distribution of juvenile Chinook salmon in an upwelling ecosystem

Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California [37°30′N) to Newport, Oregon (44°00′N]) for a 2‐week period over three summers (2010–2012). At each station, we measured chlorophyll‐a as an indicator of primary productivity, acoustic‐based metrics of zooplankton density as an indicator of potential prey availability and physical characteristics such as bottom depth, temperature and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91–98%). We constructed generalized logistic‐linear negative binomial hurdle models and chose the best model(s) using Akaike's Information Criterion (AIC) to determine which covariates influenced the salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with a high chlorophyll‐a concentration and close to an individual's natal river. Catch abundance was primarily influenced by year, mean fork length and proximity to natal rivers. At the scale of sampling stations, presence and abundance were not related to acoustic indices of zooplankton density. In the weeks to months after ocean entry, California's juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets.     

Provenance of global seafood

Knowing where and how seafood is caught or farmed is central to empowering consumers, and the importers that supply them, with informed choices. Given the wide‐ranging, complex and at times commercially sensitive nature of global seafood trade, it can prove very challenging to link imported seafood with information about its provenance. The databases involved are incomplete, at times vague and not harmonized. Here, we present a first attempt to link all global seafood imports through a virtual marketplace to exports and map their origins. Considerable work remains to ground‐truth the specific origins of all seafood commodities. We illustrate the flow of seafood and its evolution since the 1970s when supporting records began. This work allows the impact of fishing or marine farming to be associated with seafood imports.     

Homonymy, synonymy and hybrid misassignments in butternut (Juglans cinerea) and Japanese walnut (Juglans ailantifolia) nut cultivars

Butternut (Juglans cinerea), a tree native to North America and Japanese walnut (J. ailantifolia), native to Japan, form the basis for a small but growing specialty nut crop industry in the eastern United States and Canada. Over the last century, Canadian and American nut tree growers, academic plant breeders and nursery owners have clonally propagated cultivars and freely exchanged scion wood, creating the possibility of misidentification. To detect homonymy, synonymy and hybrid misassignments, we used 12 highly polymorphic microsatellites to genotype most of the butternut and Japanese walnut cultivars grown in the United States and Canada. Bayesian clustering and identity analyses revealed high levels of homonymies (genetically different cultivars with the same name) and synonymies (genetically identical cultivars with different names). Over 41% of the butternut cultivars and 45% of the Japanese walnut cultivars tested had homonymies, and a majority of the cultivars in both species also had synonymies. Further, 43 entries (~15%) identified by the contributors as either J. cinerea or J. ailantifolia were interspecific hybrids. Given our results we recommend that any comparative studies on the cultivars of either species or their hybrids include reference genetic fingerprints as a part of the study.     

Anti-biofilm compounds derived from marine sponges

Bacterial biofilms are surface-attached communities of microorganisms that are protected by an extracellular matrix of biomolecules. In the biofilm state, bacteria are significantly more resistant to external assault, including attack by antibiotics. In their native environment, bacterial biofilms underpin costly biofouling that wreaks havoc on shipping, utilities, and offshore industry. Within a host environment, they are insensitive to antiseptics and basic host immune responses. It is estimated that up to 80% of all microbial infections are biofilm-based. Biofilm infections of indwelling medical devices are of particular concern, since once the device is colonized, infection is almost impossible to eliminate. Given the prominence of biofilms in infectious diseases, there is a notable effort towards developing small, synthetically available molecules that will modulate bacterial biofilm development and maintenance. Here, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms specifically through non-microbicidal mechanisms. Importantly, we discuss several sets of compounds derived from marine sponges that we are developing in our labs to address the persistent biofilm problem. We will discuss: discovery/synthesis of natural products and their analogues-including our marine sponge-derived compounds and initial adjuvant activity and toxicological screening of our novel anti-biofilm compounds.     

Marketing Locally Produced Organic Foods in Three Metropolitan Arkansas Farmers’ Markets: Consumer Opinions and Food Safety Concerns

Consumers embrace local food systems as an alternative to the global corporate model, and nearly 75% of consumers in the United States purchase organic foods occasionally. To assess consumers’ knowledge of locally grown organic foods, surveys were administered at three metropolitan farmers’ markets in Little Rock, Hot Springs, and Texarkana, Arkansas. Consumers with Bachelor's, Associate's, or technical degrees accounted for almost half of the people surveyed. Seventy-one percent believed organic foods were safer than conventional foods. Three times as many consumers were concerned about harmful bacteria in conventional foods than in organic. The number one reason for purchasing was to support local farmers.     

Mapping the Literature of Food Science Revisited: 2003–2005

ABSTRACT

After reviewing previously published literature in citation analysis and literature mapping, this study mapped the literature of food science and explored the relationships found within it. Using articles published in the Journal of Food Science from 2003 through 2005, a stratified random sample of citations was studied to yield a ranked list of the thirteen most frequently cited journals, which formed a core set for further analysis. Using the Science Citation Index and a standard statistical package (SPSS₁₃), a two-dimensional map was created, relationships between the journals were studied, and the discipline of food science was explored. The study is an extension of previously published research covering the years 2000–2002 and attempts to analyze and compare the results across time frames.