Novel Cultivation-Based Approach To Understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from Sedimentary Ecosystems

The uncultured miscellaneous crenarchaeotic group (MCG) archaea comprise one of the most abundant microbial groups in the Earth''s subsurface environment. However, very little information is available regarding the lifestyle, physiology, and factors controlling the distribution of members of this group. We established a novel method using both cultivation and molecular techniques, including a pre-PCR propidium monoazide treatment, to investigate viable members of the MCG in vitro. Enrichment cultures prepared from estuarine sediment were provided with one of a variety of carbon substrates or cultivation conditions and incubated for 3 weeks. Compared with the samples from time zero, there was an order-of-magnitude increase in the number of MCG 16S rRNA genes in almost all cultures, indicating that MCG archaea are amenable to in vitro cultivation. None of the tested substrates or conditions significantly stimulated growth of MCG archaea more than the basal medium alone; however, glycerol (0.02%) had a significantly inhibitory effect (P < 0.05). Diversity analysis of populations resulting from four culture treatments (basal medium, addition of amino acids, H₂-CO₂ as the gas phase, or initial aerobic conditions) revealed that the majority of viable MCG archaea were affiliated with the MCG-8 and MCG-4 clusters. There were no significant differences in MCG diversity between these treatments, also indicating that some members of MCG-4 and MCG-8 are tolerant of initially oxic conditions. The methods outlined here will be useful for further investigation of MCG archaea and comparison of substrates and cultivation conditions that influence their growth in vitro.     

Selecting subsets of genotyped experimental populations for phenotyping to maximize genetic diversity

Selective phenotyping is a way of capturing the benefits of large population sizes without the need to carry out large-scale phenotyping and hence is a cost-effective means of capturing information about gene–trait relationships within a population. The diversity within the sample gives an indication of the efficiency of this information capture; less diversity implies greater redundancy of the genetic information. Here, we propose a method to maximize genetic diversity within the selected samples. Our method is applicable to general experimental designs and robust to common problems such as missing data and dominant markers. In particular, we discuss its application to multi-parent advanced generation intercross (MAGIC) populations, where, although thousands of lines may be genotyped as a large population resource, only hundreds may need to be phenotyped for individual studies. Through simulation, we compare our method to simple random sampling and the minimum moment aberration method. While the gain in power over simple random sampling for all tested methods is not large, our method results in a much more diverse sample of genotypes. This diversity can be applied to improve fine mapping resolution once a QTL region has been detected. Further, when applied to two wheat datasets from doubled haploid and MAGIC progeny, our method detects known QTL for small sample sizes where other methods fail.     

Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers

In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization.     

Current methods for molecular typing of Campylobacter species

Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection.     

CONVERGENT EVOLUTION OF SEXUAL DIMORPHISM IN SKULL SHAPE USING DISTINCT DEVELOPMENTAL STRATEGIES

Studies integrating evolutionary and developmental analyses of morphological variation are of growing interest to biologists as they promise to shed fresh light on the mechanisms of morphological diversification. Sexually dimorphic traits tend to be incredibly divergent across taxa. Such diversification must arise through evolutionary modifications to sex differences during development. Nevertheless, few studies of dimorphism have attempted to synthesize evolutionary and developmental perspectives. Using geometric morphometric analysis of head shape for 50 Anolis species, we show that two clades have converged on extreme levels of sexual dimorphism through similar, male‐specific changes in facial morphology. In both clades, males have evolved highly elongate faces whereas females retain faces of more moderate proportion. This convergence is accomplished using distinct developmental mechanisms; one clade evolved extreme dimorphism through the exaggeration of a widely shared, potentially ancestral, developmental strategy whereas the other clade evolved a novel developmental strategy not observed elsewhere in the genus. Together, our analyses indicate that both shared and derived features of development contribute to macroevolutionary patterns of morphological diversity among Anolis lizards.     

Synthesis and evaluation of quinazoline derivatives as phosphodiesterase 7 inhibitors

The latest scientific findings concerning PDE7 and PDE4 inhibition suggest that selective small-molecule inhibitors of both enzymes could provide a novel approach to treat a variety of immunological diseases. In this context, we describe a new series of quinazoline derivatives from quinazolin-4-thiones which include a substituted biphenyl fragment. Some of these compounds show inhibitory potencies at sub-micromolar levels against the catalytic domain of PDE7.     

Golgi tubules: their structure, formation and role in intra-Golgi transport

Tubules are common Golgi elements that can form extensive networks associated with the cis-, lateral and trans-Golgi sides, but despite this, they have almost been forgotten for decades. The molecular mechanisms involved in their formation, elongation and fission are only just beginning to be understood. However, the role of these membranes is not well understood. In the present review, we analyze the mechanisms that induce Golgi tubulation or, conversely, disrupt tubules in order to throw some lights on the nature of these elements. The putative role of these elements in the framework of current models for intra-Golgi transport is also discussed.     

Do foods imported into the UK have a greater environmental impact than the same foods produced within the UK?

Purpose

This study of seven foods assessed whether there are modes or locations of production that require significantly fewer inputs, and hence cause less pollution, than others. For example, would increasing imports of field-grown tomatoes from the Mediterranean reduce greenhouse gas (GHG) emissions by reducing the need for production in heated greenhouses in the UK, taking account of the additional transport emissions? Is meat production in the UK less polluting than the import of red meat from the southern hemisphere?

Methods

We carried out a life-cycle inventory for each commodity, which quantified flows relating to life-cycle assessment (LCA) impact categories: primary energy use, acidification, eutrophication, abiotic resource use, pesticide use, land occupation and ozone depletion. The system boundary included all production inputs up to arrival at the retail distribution centre (RDC). The allocation of production burdens for meat products was on the basis of economic value. We evaluated indicator foods from which it is possible to draw parallels for foods whose production follows a similar chain: tomatoes (greenhouse crops), strawberries (field-grown soft fruit), apples (stored for year-round supply or imported during spring and summer), potatoes (early season imports or long-stored UK produce), poultry and beef (imported from countries such as Brazil) and lamb (imported to balance domestic spring–autumn supply).

Results and discussion

Total pre-farm gate global warming potential (GWP) of potatoes and beef were less for UK production than for production in the alternative country. Up to delivery to the RDC, total GWP were less for UK potatoes, beef and apples than for production elsewhere. Production of tomatoes and strawberries in Spain, poultry in Brazil and lamb in New Zealand produced less GWP than in the UK despite emissions that took place during transport. For foods produced with only small burdens of GWP, such as apples and strawberries, the burden from transport may be a large proportion of the total. For foods with inherently large GWP per tonne, such as meat products, burdens arising from transport may only be a small proportion of the total.

Conclusions

When considering the GWP of food production, imports from countries where productivity is greater and/or where refrigerated storage requirement is less will lead to less total GWP than axiomatic preference for local produce. However, prioritising GWP may lead to increases in other environmental burdens, in particular leading to both greater demands on and decreasing quality of water resources.