Why is one Bacillus alpha-amylase more resistant against irreversible thermoinactivation than another?

Half-lives of Bacillus alpha-amylases at 90 degrees C and pH 6.5 greatly increase in the series from Bacillus amyloliquefaciens to Bacillus stearothermophilus to Bacillus licheniformis, e.g. the difference in thermostability between the first and the third enzymes exceeds 2 orders of magnitude. This stabilization is achieved by lowering the rate constant of monomolecular conformational scrambling, which is the cause of irreversible thermoinactivation of B. amyloliquefaciens and B. stearothermophilus alpha-amylases, so that for B. licheniformis alpha-amylase, another process, deamidation of Asn/Gln residues, emerges as the cause of inactivation. The extra thermostability of the thermophilic enzyme was found to be mainly due to additional salt bridges involving a few specific lysine residues (Lys-385 and Lys-88 and/or Lys-253). These stabilizing electrostatic interactions reduce the extent of unfolding of the enzyme molecule at high temperatures, consequently making it less prone to forming incorrect (scrambled) structures and thus decreasing the overall rate of irreversible thermoinactivation. The implications of these findings for protein engineering are discussed.     

Photoinactivation of photosystem II: is there more than one way to skin a cat?

We briefly review the main mechanisms proposed for photodamage to photosystem II (PSII), at the donor and acceptor sides, and then discuss the mechanism whereby filamentous cyanobacteria inhabiting biological sand crusts such as Microcoleus sp. are able to avoid serious damage to their photosynthetic machinery. We show that the decline in fluorescence following exposure to excess light does not reflect a reduction in PSII activity but rather the activation of a non-radiative charge recombination in PSII. Furthermore, we show that the difference in the thermoluminescent peak temperature intensities in these organisms, in the presence and absence of inhibitors such as dichlorophenyl-dimethylurea (DCMU), is smaller than observed in model organisms suggesting that the redox gap between Q(A)? and P???+ is smaller. On the basis of these data, we propose that this could enable an alternative, pheophytin-independent recombination, thereby minimizing the damaging 1O? production associated with radiative recombination.     

Why is the choice of future climate scenarios for species distribution modelling important?

Species distribution models (SDMs) are common tools for assessing the potential impact of climate change on species ranges. Uncertainty in SDM output occurs due to differences among alternate models, species characteristics and scenarios of future climate. While considerable effort is being devoted to identifying and quantifying the first two sources of variation, a greater understanding of climate scenarios and how they affect SDM output is also needed. Climate models are complex tools: variability occurs among alternate simulations, and no single 'best' model exists. The selection of climate scenarios for impacts assessments should not be undertaken arbitrarily - strengths and weakness of different climate models should be considered. In this paper, we provide bioclimatic modellers with an overview of emissions scenarios and climate models, discuss uncertainty surrounding projections of future climate and suggest steps that can be taken to reduce and communicate climate scenario-related uncertainty in assessments of future species responses to climate change.     

Why is it getting more difficult to successfully artificially inseminate dairy cows?

Successfully using artificial insemination (AI) is defined as getting cows pregnant when the farmer wants them in-calf and making the best use of appropriate genetic potential. Over the past 30 to 50 years, the percentage of animals in oestrus that stand-to-be-mounted (STBM) has declined from 80% to 50%, and the duration of STBM from 15 h to 5 h; both in parallel with a reduction in first-service-pregnancy-rate from 70% to 40%. Meanwhile, the incidence of lameness and mastitis has not decreased; and it takes more than an extra 40 and 18 days, respectively, to get a lame or mastitic cow in-calf compared to healthy herd-mates. The intensity of oestrus is 50% lower in severely lame cows, and fewer lame cows ovulate. Luteal phase milk progesterone concentrations are also 50% lower in lame cows, and follicular phase oestradiol is also lower in non-ovulating lame cows compared to ovulating animals. Furthermore, lame cows that do not ovulate do not have an LH surge, and the LH pulse frequency in their late follicular phase is lower (0.53 v. 0.76 pulses/h). Thus, we suggest that the stress of lameness reduces LH pulsatility required to drive oestradiol production by the dominant follicle. The consequent low oestradiol results in less-intense oestrus behaviour and failure to initiate an LH surge; hence there is no ovulation. A series of experimental studies substantiate our hypothesis that events activating the hypothalamus–pituitary–adrenal axis interfere at both the hypothalamus and the pituitary level to disrupt LH and oestradiol secretion, and thus the expression of oestrus behaviour. Our inability to keep stress at a minimum by appropriately feeding and housing high-production cows is leading to a failure to meet genetic potential for yield and fertility. We must provide realistic solutions soon, if we want to successfully use AI to maintain a sustainable dairy industry for the future.     

Historical background: Why is it important to improve automated particle selection methods?

A current trend in single-particle electron microscopy is to compute three-dimensional reconstructions with ever-increasing numbers of particles in the data sets. Since manual--or even semi-automated--selection of particles represents a major bottleneck when the data set exceeds several thousand particles, there is growing interest in developing automatic methods for selecting images of individual particles. Except in special cases, however, it has proven difficult to achieve the degree of efficiency and reliability that would make fully automated particle selection a useful tool. The simplest methods such as cross correlation (i.e., matched filtering) do not perform well enough to be used for fully automated particle selection. Geometric properties (area, perimeter-to-area ratio, etc.) and the integrated "mass" of candidate particles are additional factors that could improve automated particle selection if suitable methods of contouring particles could be developed. Another suggestion is that data be always collected as pairs of images, the first taken at low defocus (to capture information at the highest possible resolution) and the second at very high defocus (to improve the visibility of the particle). Finally, it is emphasized that well-annotated, open-access data sets need to be established in order to encourage the further development and validation of methods for automated particle selection.     

Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?

The recognition of transmembrane helices by the translocon is primarily guided by the average hydrophobicity of the potential transmembrane helix. However, the exact hydrophobicity of each amino acid can be identified in several different ways. The free energy of transfer for amino acid analogues between a hydrophobic media, for example, octanol and water can be measured or obtained from simulations, the hydrophobicity can also be estimated by statistical properties from known transmembrane segments and finally the contribution of each amino acid type for the probability of translocon recognition has recently been measured directly. Although these scales correlate quite well, there are clear differences between them and it is not well understood which scale represents neither the biology best nor what the differences are. Here, we try to provide some answers to this by studying the ability of different scales to recognize transmembrane helices and predict the topology of transmembrane proteins. From this analysis it is clear that the biological hydrophobicity scale as well scales created from statistical analysis of membrane helices perform better than earlier experimental scales that are mainly based on measurements of amino acid analogs and not directly on transmembrane helix recognition. Using these results we identified the properties of the scales that perform better than other scales. We find, for instance, that the better performing scales consider proline more hydrophilic. This shows that transmembrane recognition is not only governed by pure hydrophobicity but also by the helix preferences for amino acids, as proline is a strong helix breaker. Proteins 2014; 82:2190–2198. © 2014 Wiley Periodicals, Inc.     

Why is the subendocardium more vulnerable to ischemia? A new paradigm

Myocardial ischemia is transmurally heterogeneous where the subendocardium is at higher risk. Stenosis induces reduced perfusion pressure, blood flow redistribution away from the subendocardium, and consequent subendocardial vulnerability. We propose that the flow redistribution stems from the higher compliance of the subendocardial vasculature. This new paradigm was tested using network flow simulation based on measured coronary anatomy, vessel flow and mechanics, and myocardium-vessel interactions. Flow redistribution was quantified by the relative change in the subendocardial-to-subepicardial perfusion ratio under a 60-mmHg perfusion pressure reduction. Myocardial contraction was found to induce the following: 1) more compressive loading and subsequent lower transvascular pressure in deeper vessels, 2) consequent higher compliance of the subendocardial vasculature, and 3) substantial flow redistribution, i.e., a 20% drop in the subendocardial-to-subepicardial flow ratio under the prescribed reduction in perfusion pressure. This flow redistribution was found to occur primarily because the vessel compliance is nonlinear (pressure dependent). The observed thinner subendocardial vessel walls were predicted to induce a higher compliance of the subendocardial vasculature and greater flow redistribution. Subendocardial perfusion was predicted to improve with a reduction of either heart rate or left ventricular pressure under low perfusion pressure. In conclusion, subendocardial vulnerability to a acute reduction in perfusion pressure stems primarily from differences in vascular compliance induced by transmural differences in both extravascular loading and vessel wall thickness. Subendocardial ischemia can be improved by a reduction of heart rate and left ventricular pressure.     

Why is glycated LDL more sensitive to oxidation than native LDL? A comparative study

It is well established that oxidative modification of low-density lipoprotein (LDL) plays a causal role in human atherogenesis and the risk of atherosclerosis is increased in patients with diabetes mellitus. To examine the influence of different agents which may influence LDL-glycation and oxidation, experiments including glycation with glucose, glucose 6-phosphate, metal chelators (EDTA) and antioxidants (BHT) were performed. The influence of time dependence on the glycation process and the alteration of the electrophoretic mobility of LDL under diverse glycation and/or oxidation conditions was also investigated. The formation of conjugated dienes and levels of lipid peroxides in these different LDL-modifications were estimated. The copper-induced oxidation of LDL in vitro was determined by measurement of thiobarbituric acid reactive substances (TBARS) and expressed as nmol MDA/mg of LDL protein. We found that glycated LDL is more prone to oxidation than native LDL. Using native LDL, the maximal oxidation effect was found to reach a value of 49.72 nmol MDA/mg protein after 8 h. The maximum oxidation of the 31 days, glycated LDL with glucose was 71.76 nmol MDA/mg protein amounting to 144.33% of the value found for native LDL. In the case of glucose 6-phosphate glycation, the maximum oxidation under the same conditions amounted to 173.77% of the value found for native LDL. To measure the extent of glycation, fluorescence of advanced glycation end products (AGEs) was determined (370 nm excitation and 440 nm emission). The most potent glycation agent was glucose 6-phosphate leading to the formation of very high amounts of AGEs. This process was promoted in the absence of EDTA, which prevents the oxidative cleavage of modified Amadori products (ketoamines) to AGEs. We therefore conclude that both processes, glycation and oxidation, result in the modification of LDL. The lower the glycation-rate (+/- EDTA) as measured by relative fluorescence units RFU (generation of AGEs), the lower the additional oxidation rate after glycation as measured by TBARS (generation of MDA equivalents). Glycation and/or oxidation change the electrophoretic mobility of LDL.     

Why is the Pathology of Falciparum Worse than that of Vivax Malaria?

Here, Ian Clark and Bill Cowden summarize new evidence suggesting that nitric oxide (NO) generated by inducible NO synthase (iNOS) provides a functional link between the previously competing approaches to malarial disease pathogenesis: ischaemic hypoxia and NO. When combined with the newly recognized roles of iNOS in renal and pulmonary function and glucose metabolism, synergy between inflammatory cytokines and hypoxia in iNOS induction provides a framework to help explain, at a molecular level, the differences in the pathology seen in falciparum and vivax malaria. Thus sequestration, through localized hypoxia, might contribute to pathology by enhancing cytokine-induced iNOS. Generalized hypoxia might have the same effect.     

Maintainence of parasitaemia - is it to die for?

One of the major differences between protozoan differentiation and metazoan differentiation is that protozoan cells normally retain potency during differentiation, which need not, therefore, be considered altruistic. Altruism does, however, arise at the level of the organism and consequently, protozoons have the potential to evolve altruistic traits. This is particularly true when, as with Trypanosoma brucei parasitaemias, populations are genetically homogeneous. This essay argues that whilst reports of altruistic phenomena during the trypanosome life cycle remain controversial, the prospect of reagents able to instigate pathways of cell death or differentiation bears further investigation.     

Why is epigenetics important in understanding the pathogenesis of inflammatory musculoskeletal diseases?

In its widest sense, the term epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. These mechanisms comprise DNA and chromatin modifications and their associated systems, as well as the noncoding RNA machinery. The epigenetic apparatus is essential for controlling normal development and homeostasis, and also provides a means for the organism to integrate and react upon environmental cues. A multitude of functional studies as well as systematic genome-wide mapping of epigenetic marks and chromatin modifiers reveal the importance of epigenomic mechanisms in human pathologies, including inflammatory conditions and musculoskeletal disease such as rheumatoid arthritis. Collectively, these studies pave the way to identify possible novel therapeutic intervention points and to investigate the utility of drugs that interfere with epigenetic signalling not only in cancer, but possibly also in inflammatory and autoimmune diseases.     

Metapopulation dynamics: Does it help to have more of the same?

With the interest in conservation biology shifting towards processes from patterns, and to populations from communities, the theory of metapopulation dynamics is replacing the equilibrium theory of island biogeography as the population ecology paradigm in conservation biology. The simplest models of metapopulation dynamics make predictions about the effects of habitat fragmentation - size and isolation of habitat patches - on metapopulation persistence. The simple models may be enriched by considerations of the effects of demographic and environmental stochasticity on the size and extinction probability of local populations. Environmental stochasticity affects populations at two levels: it makes local extinctions more probable, and it also decreases metapopulation persistence time by increasing the correlation of extinction events across populations. Some controversy has arisen over the significance of correlated extinctions, and how they may affect the optimal subdivision of metapopulations to maximize their persistence time.     

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non‐existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km² area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait‐based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait‐based predictions of the biogeographical patterns exhibited by microbes.