Extremo-phage: In vitro selection of tolerance to a hostile environment

Extremophiles are microorganisms that thrive under extreme conditions such as temperatures above 65°C, pHs below 4 or above 10, salt concentrations above 0.5 m, or pressures of 600 atm. While studies of enzymes either isolated from extremophiles, or generated using site-specific mutagenesis, or adapted by in vivo or in vitro selection have established a precedent for the engineering and application of proteins at extreme conditions, generalization of the approaches to more complex multimolecular or multitask systems has remained elusive. Here we demonstrate that a significantly more complex system—a bacteriophage—can over a number of generations be adapted to tolerate a hostile and unnatural environment. An in vitro selection strategy was used to adapt phage to urea, a protein denaturing agent. As the concentration of urea employed in selections over 20 generations was gradually increased from 5 to 9 m, the surviving phages steadily improved their tolerance, finally achieving a greater than 350-fold stability enhancement over the original population.Correspondence to: J. Yin     

The microbial threat: Can rare earths help?

Despite an ever increasing demand for reliable and cheap methods in the detection and quantification of microbes, surprisingly few investigations have explored or utilized the luminescence of rare earths in the microbial context, neither in conventional, that is, plating and microscopic imaging techniques, nor in advanced methods like fluorescence flow cytometry. We have thus investigated the potential of some rare earth complexes and hybrid materials for microbiological analysis. We found fairly simple procedures for internal staining (dyes inside the bacterial cell) and external staining (dyes on the cell surface). The present paper is predominantly relying on microscopic imaging and luminescence spectroscopies (excitation, emission, decay times), but also evaluates model rare earth microspheres to estimate an eventual rare earth based stain for a fast and sensitive bacteria enumeration with luminescence flow cytometry.     

HIV-1 accessory proteins--ensuring viral survival in a hostile environment

One of the features of primate immunodeficiency viruses (HIVs and SIVs) that distinguishes them from other retroviruses is the array of "accessory" proteins they encode. Here, we discuss recent advances in understanding the interactions of the HIV-1 Nef, Vif, Vpu, and Vpr proteins with factors and pathways expressed in cells of the immune system. In at least three instances, the principal activity of the accessory proteins appears to be evasion from various forms of cell-mediated (or intrinsic), antiviral resistance. Broadly speaking, the HIV-1 accessory proteins modify the local environment within infected cells to ensure viral persistence, replication, dissemination, and transmission.     

Cepaea nemoralis in a hostile environment: continuity, colonizations and morph-frequencies over time

In the 1930s Cyril Diver sampled and scored populations of the polymorphic snail Cepaea nemoralis on the South Haven Peninsula, Dorset. His recording methods make it possible to be confident about the absence of the species from parts of the peninsula, which has acid soils and changing habitats, and is generally unfavourable for the species. A resurvey in 1999 revealed a pattern of retreats and extensions of distribution related to local environmental change. Where populations have persisted over the period, the pattern of morph-frequency distributions has remained the same; there is equivocal evidence for a small increase in the frequency of midbanded shells. While most wetland populations have disappeared, new populations have become established along a roadside, and on newly-stabilized foredune ridges. Morph-frequencies in these new populations relate to those of the nearest established populations, and are sometimes monomorphic. The results are discussed in relation to the history of the peninsula, and to the role of migration in determining observed morph-frequency distributions.     

Episymbiotic microbes as food and defence for marine isopods: unique symbioses in a hostile environment

Symbioses profoundly affect the diversity of life, often through novel biochemical services that symbionts provide to their hosts. These biochemical services are typically nutritional enhancements and less commonly defensive, but rarely both simultaneously. On the coral reefs of Papua New Guinea, we discovered unique associations between marine isopod crustaceans (Santia spp.) and episymbiotic microbes. Transmission electron microscopy and pigment analyses show that episymbiont biomass is dominated by large (20-30 microm) cyanobacterial cells. The isopods consume these photosymbionts and "cultivate" them by inhabiting exposed sunlit substrates, a behaviour made possible by symbionts' production of a chemical defence that is repulsive to fishes. Molecular phylogenetic analyses demonstrated that the symbiotic microbial communities are diverse and probably dominated in terms of population size by bacteria and small unicellular Synechococcus-type cyanobacteria. Although largely unknown in the oceans, defensive symbioses probably promote marine biodiversity by allowing niche expansions into otherwise hostile environments.     

The tables are turned: an invasive species under potential threat

This study reviews the current distribution of the native Asian common walking catfish (Clarias batrachus) within Singapore, and compares the present distribution to its historical distribution in the last 90 years based on literature records and museum material. We record a severe decline in the distribution of C. batrachus in Singapore concomitant with a sharp increase in the distribution of the invasive African sharptooth catfish (Clarias gariepinus). We review evidence suggesting that the introduction and the establishment of the African sharptooth catfish in Singapore have adversely affected the Asian common walking catfish. The potential displacement by the African sharptooth catfish of the Asian common walking catfish—itself a widespread invader in other parts of Asia and North America—is particularly interesting as an example of a notorious invasive species becoming threatened by an exotic within its own native range.     

不同生态环境中中国猪种的遗传多样性研究

采用最小二乘法研究了中国部分地方猪种血液蛋白质Tf、Am、Pa和Cp位点基因频率与生态环境之间的关系及其变化规律。结果表明,Tf、Am和Cp位点分别被检测出存在3个等位基因,而Pa位点存在2个等位基因。4个位点的各种基因频率在不同猪种类型和生态区域之间均表现出显着差异(P<0.05),显示出地理区域和生态类型对4个位点的基因频率和杂合度有明显的影响。洞庭-洪湖区-新安江-鄱阳湖区-太湖流域是各位点基因频率高低变化的起点.     

Genotype by environment interaction in response to cold stress in a composite beef cattle breed

Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than −5°C (TCL5), −15°C (TCL15) and −25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class; however, this heritability remained consistent across the cold load of TCL25 class. In contrast, the maternal heritability of BW was constant with cold load increase in all TCL classes, although a slight increase of maternal heritability was observed for TCL5 and TCL15. The direct and maternal genetic correlation for BW and maternal genetic correlation for WW across different cold loads between all TCL classes were high (r > 0.99), whereas the lowest direct genetic correlations observed for WW were 0.88 for TCL5 and 0.85 for TCL15. The Spearman rank correlation between the estimated breeding value of top bulls (n = 79) using univariate and reaction norm models across TCL classes showed some re-ranking in direct and maternal effects for both BW and WW particularly for TCL5 and TCL15. In general, cold stress did not have a big impact on direct and maternal genetic effects of BW and WW.     

To breed or not to breed: a model of partial migration

Migration is used by a number of species as a strategy for dealing with a seasonally variable environment. In many migratory species, only some individuals migrate within a given season (migrants) while the rest remain in the same location (residents), a phenomenon called ‘partial migration’. Most examples of partial migration considered in the literature (both empirically and theoretically) fall into one of two categories: either species where residents and migrants share a breeding ground and winter apart, or species where residents and migrants share an overwintering ground and breed apart. However, a third form of partial migration can occur when non‐migrating individuals actually forgo reproduction, essentially a special form of low‐frequency reproduction. While this type of partial migration is well documented in many taxa, it is not often included in the partial migration literature, and has not been considered theoretically to date. In this paper we present a model for this partial migration scenario and determine under what conditions an individual should skip a breeding opportunity (resulting in partial migration), and under what conditions individuals should breed every chance they get (resulting in complete migration). In a constant environment, we find that partial migration is expected to occur when the mortality cost of migration is high, and when individuals can greatly increase their fecundity by skipping a year before breeding. In a stochastic environment, we find that an individual should skip migration more frequently with increased risk of a bad year (higher probability and severity), with higher mortality cost of migration, and with lower mortality cost of skipping. We discuss these results in the context of empirical data and existing life history theory.     

What Hydra can teach us about chemical ecology -how a simple, soft organism survives in a hostile aqueous environment

Hydra and its fellow cnidarians - sea anemones, corals and jellyfish - are simple, mostly sessile animals that depend on bioactive chemicals for survival. In this review, we briefly describe what is known about the chemical armament of Hydra, and detail future research directions where Hydra can help illuminate major questions in chemical ecology, pharmacology, developmental biology and evolution. Focusing on two groups of putative toxins from Hydra - phospholipase A2s and proteins containing ShK and zinc metalloprotease domains, we ask: how do different venom components act together during prey paralysis? How is a venom arsenal created and how does it evolve? How is the chemical arsenal delivered to its target? To what extent does a chemical and biotic coupling exist between an organism and its environment? We propose a model whereby in Hydra and other cnidarians, bioactive compounds are secreted both as localized point sources (nematocyte discharges) and across extensive body surfaces, likely combining to create complex "chemical landscapes". We speculate that these cnidarian-derived chemical landscapes may affect the surrounding community on scales from microns to, in the case of coral reefs, hundreds of kilometers.     

Soil salinization and waterlogging: A threat to environment and agricultural sustainability

The development of irrigated agriculture is necessary for fulfilling the rising food requirements of the burgeoning global population. However, the intensification of irrigated agriculture causes the twin menace of waterlogging and soil salinization in arid and semiarid regions where more than 75% of the world's population lives. Waterlogging and salinization have direct and indirect effects on plant growth and yield. The damage to plant growth and yield is much serious when these processes occur simultaneously and generally yield reduction is linearly correlated with the salinity level. The control of shallow watertable with irrigation management and installation of drainage systems are suggestible to control the waterlogging and salinization problems of irrigated agriculture. This paper presents an overview of the different aspects of waterlogging and soil salinization and its impact on the food production and sustainability of irrigated agriculture. Conclusions are provided which could be useful for all the stakeholders.     

Tryptophan hydroxylase 1 gene haplotypes modify the effect of a hostile childhood environment on adulthood harm avoidance

We conducted a series of tests to determine whether there is any association between tryptophan hydroxylase 1 (TPH1) and temperament in adulthood. In addition to testing for main effects, we investigated whether TPH1 gene variation modifies the influence of childhood environment on temperament in adulthood. The subjects were 341 healthy adults whose childhood environment was assessed by their mothers in 1980 and who self-rated their temperaments twice, in 1997 and 2001. We found no association between the TPH1 gene and temperament; however, among women, the TPH1 gene modified a relationship between adverse childhood environment and harm avoidance in adulthood. This finding was confirmed in the same sample in another test setting 4 years later. The presence of the A/A haplotype of the TPH1 intron 7 A218A and A779C polymorphism predicted a high level of adulthood harm avoidance in the presence of a hostile childhood environment as defined in terms of emotional rejection, maternal neglect and harsh and inconsistent discipline. In addition, the findings suggest a gene-environment correlation for novelty seeking in men.