Tracking the contribution of inductive bias to individualised internal models

Internal models capture the regularities of the environment and are central to understanding how humans adapt to environmental statistics. In general, the correct internal model is unknown to observers, instead they rely on an approximate model that is continually adapted throughout learning. However, experimenters assume an ideal observer model, which captures stimulus structure but ignores the diverging hypotheses that humans form during learning. We combine non-parametric Bayesian methods and probabilistic programming to infer rich and dynamic individualised internal models from response times. We demonstrate that the approach is capable of characterizing the discrepancy between the internal model maintained by individuals and the ideal observer model and to track the evolution of the contribution of the ideal observer model to the internal model throughout training. In particular, in an implicit visuomotor sequence learning task the identified discrepancy revealed an inductive bias that was consistent across individuals but varied in strength and persistence.     

A small molecule that disrupts S. Typhimurium membrane voltage without cell lysis reduces bacterial colonization of mice

As pathogenic bacteria become increasingly resistant to antibiotics, antimicrobials with mechanisms of action distinct from current clinical antibiotics are needed. Gram-negative bacteria pose a particular problem because they defend themselves against chemicals with a minimally permeable outer membrane and with efflux pumps. During infection, innate immune defense molecules increase bacterial vulnerability to chemicals by permeabilizing the outer membrane and occupying efflux pumps. Therefore, screens for compounds that reduce bacterial colonization of mammalian cells have the potential to reveal unexplored therapeutic avenues. Here we describe a new small molecule, D66, that prevents the survival of a human Gram-negative pathogen in macrophages. D66 inhibits bacterial growth under conditions wherein the bacterial outer membrane or efflux pumps are compromised, but not in standard microbiological media. The compound disrupts voltage across the bacterial inner membrane at concentrations that do not permeabilize the inner membrane or lyse cells. Selection for bacterial clones resistant to D66 activity suggested that outer membrane integrity and efflux are the two major bacterial defense mechanisms against this compound. Treatment of mammalian cells with D66 does not permeabilize the mammalian cell membrane but does cause stress, as revealed by hyperpolarization of mitochondrial membranes. Nevertheless, the compound is tolerated in mice and reduces bacterial tissue load. These data suggest that the inner membrane could be a viable target for anti-Gram-negative antimicrobials, and that disruption of bacterial membrane voltage without lysis is sufficient to enable clearance from the host.     

Between‐male variation in sperm size,velocity and longevity in sand martins Riparia riparia

Sperm mobility is known to be an important determinant of a male's sperm competitive ability. Although more debated, sperm length and its relation to sperm swimming ability has also been proposed to determine a male's fertilisation potential. Furthermore, both mobility and length may covary with a male's phenotype, either positively (the phenotype‐linked fertility hypothesis) or negatively if, for instance, low‐quality males have less access to females but invest more in sperm production. Using dummy females, we collected sperm samples from wild sand martins Riparia raparia males. We investigated the relationship between sperm length and sperm swimming speed as measured by sperm straight line velocity (VSL), and determined whether sperm traits are correlated with male body size and condition. We found that total sperm length is repeatable within‐ejaculate and shows substantial inter‐male variation. Sperm length was associated with sperm velocity: males with short sperm have sperm that swim initially faster but die sooner, whereas males with longer sperm have sperm that swim more slowly but for a longer time. Smaller males produced sperm with higher overall velocity. This correlation between male size and sperm behaviour may reflect alternative fertilisation strategies where small males having less mating opportunities invest more in sperm competitive ability. The existence of such alternative strategies would participate in maintaining variation in sperm length and velocity in this species.     

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.     

Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system

The microbial degradation of lignocellulose biomass is not only an important biological process but is of increasing industrial significance in the bioenergy sector. The mechanism by which the plant cell wall, an insoluble composite structure, activates the extensive repertoire of microbial hydrolytic enzymes required to catalyze its degradation is poorly understood. Here we have used a transposon mutagenesis strategy to identify a genetic locus, consisting of two genes that modulate the expression of xylan side chain-degrading enzymes in the saprophytic bacterium Cellvibrio japonicus. Significantly, the locus encodes a two-component signaling system, designated AbfS (sensor histidine kinase) and AbfR (response regulator). The AbfR/S two-component system is required to activate the expression of the suite of enzymes that remove the numerous side chains from xylan, but not the xylanases that hydrolyze the beta1,4-linked xylose polymeric backbone of this polysaccharide. Studies on the recombinant sensor domain of AbfS (AbfS(SD)) showed that it bound to decorated xylans and arabinoxylo-oligosaccharides, but not to undecorated xylo-oligosaccharides or other plant structural polysaccharides/oligosaccharides. The crystal structure of AbfS(SD) was determined to a resolution of 2.6A(.) The overall fold of AbfS(SD) is that of a classical Per Arndt Sim domain with a central antiparallel four-stranded beta-sheet flanked by alpha-helices. Our data expand the number of molecules known to bind to the sensor domain of two-component histidine kinases to include complex carbohydrates. The biological rationale for a regulatory system that induces enzymes that remove the side chains of xylan, but not the hydrolases that cleave the backbone of the polysaccharide, is discussed.     

Insulation and wiring specificity of BceR‐like response regulators and their target promoters in Bacillus subtilis

BceRS and PsdRS are paralogous two‐component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, P_bceA or P_psdA, resulting in a strong up‐regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross‐regulation has been observed between them. We therefore investigated the specificity determinants of P_bceA and P_psdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high‐affinity, low‐specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low‐affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.     

Glucose concentration gradient through the cerebral cortex in normoglycaemic anaesthetized rabbits

In this pilot study, the relationships between glucose and lactate concentrations of plasma, cerebrospinal fluid (CSF), cerebral cortex and subjacent white matter were investigated in one hyperglycaemic and three normoglycaemic anaesthetized rabbits. After a 90 min stabilization period, CSF was sampled and the brain frozen in situ. Triplet samples (n = 3 X 21) were obtained from the outer and inner halves of cortex and from the white substance and analysed for their water content as well as for glucose and lactate by enzymatic fluorescence methods. Preservation of the ATP content was demonstrated in brain slices by a bioluminescence method. The glucose and lactate levels of CSF seemed to reflect those of the outer half of the cortex. In the normoglycaemic animals, the tissue glucose and tissue lactate levels correlated inversely (r = 0.477: p less than 0.01). While the glucose concentrations were nearly identical in the inner cortex and white substance, there was a concentration difference of 0.54 mmol/kg tissue water between the outer half of the cortex and the white matter (p much less than 0.02). This might correspond to a steep intra-cortical glucose gradient starting from the CSF-facing surface and approximating the general cerebral glucose level in a depth of about 4-500 microns. The possible significance of this gradient in regulating CSF glucose is discussed.     

Sharing the moment: the duration of embraces in humans

Moments of some gestures may stand out from our constantly flowing life-time as memorable experiences. We feel subjective moments as our psychological present. Few behavioral acts can express a shared subjective experience so easily observable than people’s embraces after a significant life-event. Spontaneous embraces from the 2008 Summer Olympics Games were analysed, and were found to last for about 3 s, comparable to previously described perceptual and motor units in humans and also in other primate species. These 3-s segments of time are suggested to be the basic temporal building blocks of our behaviourally expressed subjective experiences.     

A microcomputer method for recording and analysing behavioural elements

The trend in ethology, psychopharmacology and behaviour genetics is to get increasingly higher resolution of the behaviour of animals, since it increases the sensitivity of the tests used. Consequently the higher resolution requires an increased data-logging efficiency, and a decreased time-investment for data handling. In this paper a method for inexpensive microcomputers is presented, which enables an individual experimenter to obtain frequency, relative duration and its variance from as many behavioural elements as desired.     

Condensation of heptaminol hydrochloride for its spectrofluorimetric determination in pure form and tablets: application in human plasma

A sensitive, simple, accurate and less expensive fluorimetric method was designed and validated for analysis of heptaminol HCl in both its pure and dosage forms, as well as in human plasma. The main principle used in the proposed approach was the condensation reaction between heptaminol's primary amino moiety and ethyl acetoacetate/formaldehyde reagents, giving a derivative that was highly fluorescent at 416 nm after excitation at 350 nm. Various experimental parameters that affected either the product's development or its stability were evaluated and optimized. The constructed calibration curve was linear over the range 0.2–2 μg/ml, with a good correlation coefficient (0.9996). Both the calculated limit of detection and limit of quantitation were 0.06 and 0.18 μg/ml, respectively. The presented approach was a success when used to determine Corasore® tablets and was validated according to International Council for Harmonisation guidelines.