Aggregation Patterns in Stressed Bacteria

We study the formation of spot patterns seen in a variety of bacterial species when the bacteria are subjected to oxidative stress due to hazardous byproducts of respiration. Our approach consists of coupling the cell density field to a chemoattractant concentration as well as to nutrient and waste fields. The latter serves as a triggering field for emission of chemoattractant. Important elements in the proposed model include the propagation of a front of motile bacteria radially outward form an initial site, a Turing instability of the uniformly dense state and a reduction of motility for cells sufficiently far behind the front. The wide variety of patterns seen in the experiments is explained as being due the variation of the details of the initiation of the chemoattractant emission as well as the transition to a non-motile phase.Comment: 4 pages, REVTeX with 4 postscript figures (uuencoded) Figures 1a and 1b are available from the authors; paper submitted to PRL

Modern Michelson-Morley experiment using cryogenic optical resonators

We report on a new test of Lorentz invariance performed by comparing the resonance frequencies of two orthogonal cryogenic optical resonators subject to Earth's rotation over 1 year. For a possible anisotropy of the speed of light c, we obtain 2.6 +/- 1.7 parts in 10^15. Within the Robertson-Mansouri-Sexl test theory, this implies an isotropy violation parameter beta - delta - 1/2 of -2.2 +/- 1.5 parts in 10^9, about three times lower than the best previous result. Within the general extension of the standard model of particle physics, we extract limits on 7 parameters at accuracies down to a part in 10^15, improving the best previous result by about two orders of magnitude

Expression and Purification of Recombinant Hemoglobin in Escherichia coli

Recombinant DNA technologies have played a pivotal role in the elucidation of structure-function relationships in hemoglobin (Hb) and other globin proteins. Here we describe the development of a plasmid expression system to synthesize recombinant Hbs in Escherichia coli, and we describe a protocol for expressing Hbs with low intrinsic solubilities. Since the α- and β-chain Hbs of different species span a broad range of solubilities, experimental protocols that have been optimized for expressing recombinant human HbA may often prove unsuitable for the recombinant expression of wildtype and mutant Hbs of other species.As a test case for our expression system, we produced recombinant Hbs of the deer mouse (Peromyscus maniculatus), a species that has been the subject of research on mechanisms of Hb adaptation to hypoxia. By experimentally assessing the combined effects of induction temperature, induction time and E. coli expression strain on the solubility of recombinant deer mouse Hbs, we identified combinations of expression conditions that greatly enhanced the yield of recombinant protein and which also increased the efficiency of post-translational modifications.Our protocol should prove useful for the experimental study of recombinant Hbs in many non-human animals. One of the chief advantages of our protocol is that we can express soluble recombinant Hb without co-expressing molecular chaperones, and without the need for additional reconstitution or heme-incorporation steps. Moreover, our plasmid construct contains a combination of unique restriction sites that allows us to produce recombinant Hbs with different α- and β-chain subunit combinations by means of cassette mutagenesis

Clinal variation in body size and sexual dimorphism in an Indian fruit bat, \u3ci\u3eCynopterus sphinx \u3c/i\u3e (Chiroptera: Pteropodidae)

Geographic variation in body size and sexual dimorphism of the short-nosed fruit bat (Cynopterus sphinx ) was investigated in peninsular India. Bats were sampled at 12 localities along a 1,200 km latitudinal transect that paralleled the eastern flanks of the Western Ghats. The geographic pattern of variation in external morphology of C. sphinx conforms to the predictions of Bergmann’s Rule, as indicated by a steep, monotonic cline of increasing body size from south to north. This study represents one of the first conclusively documented examples of Bergmann’s Rule in a tropical mammal and confirms that latitudinal clines in body size are not exclusively restricted to temperate zone homeotherms. Body size was indexed by a multivariate axis derived from principal components analysis of linear measurements that summarize body and wing dimensions. Additionally, length of forearm was used as a univariate index of structural size to examine geographic variation in a more inclusive sample of bats across the latitudinal transect. Multivariate and univariate size metrics were strongly and positively correlated with body mass, and exhibited highly concordant patterns of clinal variation. Stepwise multiple regression on climatological variables revealed that increasing size of male and female C. sphinx was associated with decreasing minimum temperature, increasing relative humidity, and increasing seasonality. Although patterns of geographic size variation were highly concordant between the sexes, C. sphinx also exhibited a latitudinal cline in the magnitude and direction of sexual size dimorphism. The size differential reversed direction across the latitudinal gradient, as males averaged larger in the north, and females averaged larger in the south. The degree of female-biased size dimorphism across the transect was negatively correlated with body size of both sexes. Canonical discriminant analysis revealed that male- and female-biased size dimorphism were based on contrasting sets of external characters. Available data on geographic variation in the degree of polygyny in C. sphinx suggests that sexual selection on male size may play a role in determining the geographic pattern of sexual size dimorphism

Discovery of Fur binding site clusters in Escherichia coli by information theory models

Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence walkers, which are visual depictions of predicted binding sites, frequently appeared in clusters that fit the footprints (∼83% coverage). This indicated that the model can accurately predict Fur binding. Within the clusters, individual walkers were separated from their neighbors by exactly 3 or 6 bases, consistent with models in which Fur dimers bind on different faces of the DNA helix. When the E. coli genome was scanned, we found 363 unique clusters, which includes all known Fur-repressed genes that are involved in iron metabolism. In contrast, only a few of the known Fur-activated genes have predicted Fur binding sites at their promoters. These observations suggest that Fur is either a direct repressor or an indirect activator. The Pseudomonas aeruginosa and Bacillus subtilis Fur models are highly similar to the E. coli Fur model, suggesting that the Fur–DNA recognition mechanism may be conserved for even distantly related bacteria

Influence of Nutritional Status and Physical Exercise on Immune Response in Metabolic Syndrome

Metabolic Syndrome (MetS) is a cluster of metabolic alterations mostly related to visceral adiposity, which in turn promotes glucose intolerance and a chronic systemic inflammatory state, characterized by immune cell infiltration. Such immune system activation increases the risk of severe disease subsequent to viral infections. Strong correlations between elevated body mass index (BMI), type-2-diabetes and increased risk of hospitalization after pandemic influenza H1N1 infection have been described. Similarly, a correlation between elevated blood glucose level and SARS-CoV-2 infection severity and mortality has been described, indicating MetS as an important predictor of clinical outcomes in patients with COVID-19. Adipose secretome, including two of the most abundant and well-studied adipokines, leptin and interleukin-6, is involved in the regulation of energy metabolism and obesity-related low-grade inflammation. Similarly, skeletal muscle hormones—called myokines—released in response to physical exercise affect both metabolic homeostasis and immune system function. Of note, several circulating hormones originate from both adipose tissue and skeletal muscle and display different functions, depending on the metabolic context. This review aims to summarize recent data in the field of exercise immunology, investigating the acute and chronic effects of exercise on myokines release and immune system function

Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli

RNA thermometers are thermosensors that regulate gene expression by temperature-induced changes in RNA conformation. Naturally occurring RNA thermometers exhibit complex secondary structures which are believed to undergo a series of gradual structural changes in response to temperature shifts. Here, we report the de novo design of considerably simpler RNA thermometers that provide useful RNA-only tools to regulate bacterial gene expression by a shift in the growth temperature. We show that a single small stem-loop structure containing the ribosome binding site is sufficient to construct synthetic RNA thermometers that work efficiently at physiological temperatures. Our data suggest that the thermometers function by a simple melting mechanism and thus provide minimum size on/off switches to experimentally induce or repress gene expression by temperature

Genetically based low oxygen affinities of felid hemoglobins: Lack of biochemical adaptation to high-altitude hypoxia in the snow leopard

Genetically based modifications of hemoglobin (Hb) function that increase blood–O2 affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O2 affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, we characterized structural and functional variation of big cat Hbs and investigated molecular mechanisms of Hb adaptation and allosteric regulation thatmay contribute to the extreme hypoxia tolerance of the snow leopard. Experiments revealed that purified Hbs from snow leopard and African lion exhibited equally low O2 affinities and DPG sensitivities. Both properties are primarily attributable to a single amino acid substitution, β2His→Phe, which occurred in the common ancestor of Felidae. Given the low O2 affinity and reduced regulatory capacity of feline Hbs, the extreme hypoxia tolerance of snow leopards must be attributable to compensatory modifications of other steps in the O2-transport pathway

Optical cavity tests of Lorentz invariance for the electron

A hypothetical violation of Lorentz invariance in the electrons' equation of motion (expressed within the Lorentz-violating extension of the standard model) leads to a change of the geometry of crystals and thus shifts the resonance frequency of an electromagnetic cavity. This allows experimental tests of Lorentz invariance of the electron sector of the standard model. The material dependence of the effect allows to separate it from an additional shift caused by Lorentz violation in electrodynamics, and to place independent limits on both effects. From present experiments, upper limits on Lorentz violation in the electrons' kinetic energy term are deduced.Comment: 17 pages revte

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

We have designed an experimental/computational framework for studying complex phenotypes in bacteria.Our framework relies on whole-genome fitness profiling coupled with a module-level analysis to discover pathways that directly affect fitness.As a proof-of-principle, we studied ethanol tolerance in Escherichia coli and we identified key pathways that contribute to this phenotype.We then validated our findings through genetic manipulations, gene-expression profiling, metabolite-level measurements, and stable-isotope labeling