Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella

Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident genome. Mutations in hns are lethal in Salmonella unless accompanied by compensatory mutations in other regulatory loci. Thus, H-NS provides a previously unrecognized mechanism of bacterial defense against foreign DNA, enabling the acquisition of DNA from exogenous sources while avoiding detrimental consequences from unregulated expression of newly acquired genes. Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA.     

Extinction and ecosystem function in the marine benthos

Rapid changes in biodiversity are occurring globally, yet the ecological impacts of diversity loss are poorly understood. Here we use data from marine invertebrate communities to parameterize models that predict how extinctions will affect sediment bioturbation, a process vital to the persistence of aquatic communities. We show that species extinction is generally expected to reduce bioturbation, but the magnitude of reduction depends on how the functional traits of individual species covary with their risk of extinction. As a result, the particular cause of extinction and the order in which species are lost ultimately govern the ecosystem-level consequences of biodiversity loss.     

Characterization of starch morphology,composition, physicochemi-cal properties and gene expressions in oat

Starch is the major carbohydrate in oat(Avena sativa L.) and starch formation requires the coordinated actions of several synthesis enzymes. In this study, the granule morphology, composition and physicochemical properties of oat starch, as well as the expressions of starch synthesis genes were investigated during oat endosperm development. Under the scanning electron microscopy(SEM), we observed that the unique compound granules were developed in oat endosperms at 10 days post anthesis(DPA) and then fragmented into irregular or polygonal simple granules from 12 DPA until seed maturity. The amylose content, branch chain length of degree of polymerization(DP=13–24), gelatinization temperature and percentage of retrogradation were gradually increased during the endosperm development; whereas the distribution of short chains(DP=6–12) were gradually decreased. The relative expressions of 4 classes of 13 starch synthesis genes characterized in this study indicated that three expression pattern groups were significantly different among gene classes as well as among varied isoforms, in which the first group of starch synthesis genes may play a key role on the initiation of starch synthesis in oat endosperms.     

Pigeonpea improvement: An amalgam of breeding and genomic research

In the past five decades, constant research has been directed towards yield improvement in pigeonpea resulting in the deployment of several commercially acceptable cultivars in India. Though, the genesis of hybrid technology, the biggest breakthrough, enigma of stagnant productivity still remains unsolved. To sort this productivity disparity, genomic research along with conventional breeding was successfully initiated at ICRISAT. It endowed ample genomic resource providing insight in the pigeonpea genome combating production constraints in a precise and speedy manner. The availability of the draft genome sequence with a large‐scale marker resource, oriented the research towards trait mapping for flowering time, determinacy, fertility restoration, yield attributing traits and photo‐insensitivity. Defined core and mini‐core collection, still eased the pigeonpea breeding being accessible for existing genetic diversity and developing stress resistance. Modern genomic tools like next‐generation sequencing, genome‐wide selection helping in the appraisal of selection efficiency is leading towards next‐generation breeding, an awaited milestone in pigeonpea genetic enhancement. This paper emphasizes the ongoing genetic improvement in pigeonpea with an amalgam of conventional breeding as well as genomic research.     

Commuting distances to local non‐farm workplaces and out‐migration: The case of Northeast Thailand

The relationship between commuting distances and where people work has been studied for urban contexts in both developed countries and developing countries. However, few studies have examined the situation in rural areas, and none look at commuting distances to non‐farm workplaces in rural areas of developing countries. This paper investigates how commuting distance, and thus accessibility, to local non‐farm work influences non‐farm employment and out‐migration from rural villages in Northeast Thailand. The main issues examined are: (i) the distance that rural residents travel to work in local non‐farm jobs; and (ii) the influence that local non‐farm employment has on the number of outmigrants from rural villages. The study finds: (i) distance between villages and non‐farm work sites impact the number of villagers who are employed in regular wage work; (ii) beyond 20 km villagers are less likely to travel to non‐farm employment using their own means of transportation; and (iii) employment in regular wage work decreases outmigration. The findings from this study contribute to the debates over the drivers of rural out‐migration, rural livelihood changes, and agrarian changes that are taking place in Southeast Asia.     

Carbonate mineral filtrants with new surfaces reduce alkalinity in seawater and artificial seawater: Preliminary findings

Silica sand (silica), coral (aragonite), and oyster shell (calcite) were ground to similar particle sizes and placed in seawater and artificial seawater (GP2 Medium). Alkalinity and pH values of the artificial seawater decreased substantially over 24 h when in contact with coral and oyster shell; the effects in seawater were minor. Once alkalinity has been reduced, the maintenance of stable pH at values typical of seawater is made more difficult. The data, which are preliminary, have practical application.     

Thirty years of change and the future of Alaskan fisheries: Shifts in fishing participation and diversification in response to environmental,regulatory and economic pressures

Heterogeneity in human responses and decision‐making can contribute to the resilience of social–ecological systems in the face of environmental, political and economic pressures. In fishery systems worldwide, the ability of harvesters to maintain a diverse portfolio of fishing strategies is important for building adaptive capacity. We used a case‐study approach to examine the complexity of factors that inhibit or promote diversification in fisheries of Alaska, one of the major fishing regions of the world. Through a combination of harvest records and literature review, we explored shifts in participation and portfolio diversity in Alaskan fisheries over three decades. The four case‐studies examined the responses of fishers, fleets and communities to multiple, intersecting pressures, including biological declines, market and price dynamics, fishery privatization and the 1989 Exxon Valdez oil spill. These cases illustrate how stressors acting at multiple scales can encourage or constrain opportunities for diversification, and that these opportunities may be spread inequitably across participants. Overall, we found evidence for reduced participation and increasing specialization in Alaskan commercial fisheries. While numerous factors explain these trends, policies like individual quota systems and the increasing cost of entry into fisheries are forcing consolidation at local to regional scales. A portfolio approach to managing fisheries that reduces barriers to diversification and includes broad representation of resource users and communities in management may help to maintain opportunity and choice for fishers.     

Brown shrimp (Farfantepenaeus aztecus) density distribution in the Northern Gulf of Mexico: an approach using boosted regression trees

The estuarine‐dependent brown shrimp, Farfantepenaeus aztecus, is a significant commercial fishery and important species in the Gulf of Mexico (GOM) ecosystem as well as being a key component in energy transfer between benthic and pelagic food web systems. Because of the economical and ecological importance of brown shrimp, we developed a spatial population model to identify places of high shrimp density under a set of spatial, environmental and temporal variables in the Northern Gulf of Mexico (NGOM). We used fisheries‐independent data collected by the Southeast Area Monitoring and Assessment Program (SEAMAP) from 1992 to 2007 (summer and fall seasons). The relationship between the predictor variables and shrimp density was modeled using Boosted Regression Trees (BRT). Within the environmental variables included in the model, bottom type and depth of the water column were the most important predictors of shrimp density in the NGOM. Spatial predictions performed using the trained BRT model for summer and fall seasons showed a spatial segregation of shrimp density. During the summer, higher densities were predicted near the Texas and Louisiana coast and during the fall, higher densities were predicted further offshore. The model performed well and allowed successful prediction of brown shrimp hot spots in the NGOM. Model results allow fisheries managers to evaluate the potential impact from fisheries on the resource and to develop future fisheries management strategies, understand the biology of brown shrimp as well as assess the potential impacts of oil spills or climate change.