Why is PTPN22 a good candidate susceptibility gene for autoimmune disease?

The PTPN22 locus is one of the strongest risk factors outside of the major histocompatability complex that associates with autoimmune diseases. PTPN22 encodes lymphoid protein tyrosine phosphatase (Lyp) which is expressed exclusively in immune cells. A single base change in the coding region of this gene resulting in an arginine to tryptophan amino acid substitution within a polyproline binding motif associates with type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosis, Hashimotos thyroiditis, Graves disease, Addison's disease, Myasthenia Gravis, vitiligo, systemic sclerosis juvenile idiopathic arthritis and psoriatic arthritis. Here, we review the current understanding of the PTPN22 locus from a genetic, geographical, biochemical and functional perspective.     

Too much of a good thing? Variety is confusing in mate choice

Choice variety is supposed to increase the likelihood that a chooser's preferences are satisfied. To assess the effects of variety on real-world mate choice, we analysed human dating decisions across 84 speed-dating events (events in which people go on a series of sequential 'mini-dates'). Results showed that choosers made fewer proposals (positive dating decisions) at events in which the available dates showed greater variety across such attributes as age, height, occupation and education, and this effect was particularly strong when choosers were confronted with a larger number of opposite-sex speed daters. Additionally, participants attending events in which the available options showed greater variety across these attributes were less likely to choose the consensually preferred mate option and more likely to choose no one at all. In contexts in which time is a limited resource, choice variety-rather than facilitating choice quality or increasing choosiness-is confusing and potentially detrimental to choice quality.     

What is mzXML good for?

mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. Due to its dynamic history, its structure, purpose and applicability have all changed with time, meaning that groups that have looked at the standard at different points during its evolution have differing impressions of the usefulness of mzXML. In discussing mzXML, it is important to understand what mzXML is not. First, mzXML does not capture the raw data. Second, mzXML is not sufficient for regulatory submission. Third, mzXML is not optimized for computation and, finally, mzXML does not capture the experiment design. In general, it is the authors' opinion that XML is not a panacea for bioinformatics or a substitute for good data representation, and groups that want to use mzXML (or other XML-based representations) directly for data storage or computation will encounter performance and scalability problems. With these limitations in mind, the authors conclude that mzXML is, nonetheless, an indispensable data exchange format for proteomics.     

What is mzXML good for?

mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. Due to its dynamic history, its structure, purpose and applicability have all changed with time, meaning that groups that have looked at the standard at different points during its evolution have differing impressions of the usefulness of mzXML. In discussing mzXML, it is important to understand what mzXML is not. First, mzXML does not capture the raw data. Second, mzXML is not sufficient for regulatory submission. Third, mzXML is not optimized for computation and, finally, mzXML does not capture the experiment design. In general, it is the authors’ opinion that XML is not a panacea for bioinformatics or a substitute for good data representation, and groups that want to use mzXML (or other XML-based representations) directly for data storage or computation will encounter performance and scalability problems. With these limitations in mind, the authors conclude that mzXML is, nonetheless, an indispensable data exchange format for proteomics.     

Why is HIV a pathogen?

The pathogenesis of HIV begins with a profound depletion of CD4+ T cells in the gut followed by a long period of clinically silent but dynamic virus replication and diversification with high host cell turnover before the onset of AIDS. The AIDS-defining opportunistic infections and tumors mark the end-point of a long balancing act between virus and host that occurs when CD4+ T cell numbers fall below a level that can sustain immunity. Comparative studies of lentivirus infections in other species show that AIDS is not an inevitable outcome of infection because simian immunodeficiency virus in natural hosts seldom causes disease. What distinguishes pathogenic from 'passenger' infection is a systemic activation of immune responses followed by destruction of the integrity of lymphoid follicles. Macrophage and dendritic cell infection also contribute to pathogenesis. Maedi-Visna virus infection in sheep, which targets these cells but not T lymphocytes, also leads to progressive disease and death that resembles the wasting and brain diseases of HIV without the T cell immunodeficiency. Thus, lessons from pathogenic and nonpathogenic lentivirus infections provide insight into the complex syndrome called AIDS.     

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.     

Wrist dosimeter in nuclear medicine – An alternative for the ring dosimeter?

PurposeIndividual dosimetry is undoubtedly one of the best methods of assessing the exposure of personnel to ionizing radiation, however in case of nuclear medicine, the method applied to measure the dose does not always present a picture of the worker’s actual exposure. The highly non-homogeneous dose distribution on the hand means that the ring dosimeter, routinely used to measure the Hp(0.07), provides only approximate dose values received by fingertips, the body part most exposed to ionizing radiation. This paper is an attempt to answer the question whether the wrist dosimeter used as a replacement for the ring dosimeter is able to provide information on doses for the most exposed fragments of the hand of an employee during handling procedures with the use of radiopharmaceuticals.MaterialsThroughout measurements performed in five nuclear medicine facilities, high-sensitivity thermoluminescent detectors were used.ResultsCorrection coefficients have been determined, which constitute an amendment to be made to move from the dose recorded by the wrist dosimeter to the doses received by the most exposed hand fragments. The fingertips received on average 25 times higher doses, compared to the values recorded by the wrist dosimeter.ConclusionsA wrist dosimeter can be used to measure the Hp(0.07) in nuclear medicine, including as a gauge of the most exposed parts of the hand – the fingertips. However, the applicability of correction coefficients makes it necessary to ensure a stable position of the wrist dosimeter during routine procedures.     

Why are small males aggressive?

Aggression is ubiquitous in the animal kingdom, whenever the interests of individuals conflict. In contests between animals, the larger opponent is often victorious. However, counter intuitively, an individual that has little chance of winning (generally smaller individuals) sometimes initiates contests. A number of hypotheses have been put forward to explain this behaviour, including the "desperado effect" according to which, the likely losers initiate aggression due to lack of alternative options. An alternative explanation suggested recently is that likely losers attack due to an error in perception: they mistakenly perceive their chances of winning as being greater than they are. We show that explaining the apparently maladaptive aggression initiated by the likely loser can be explained on purely economic grounds, without requiring either the desperado effect or perception errors. Using a game-theoretical model, we show that if smaller individuals can accurately assess their chance of winning, if this chance is less than, but close to, a half, and if resources are scarce (or the contested resource is of relatively low value), they are predicted to be as aggressive as their larger opponents. In addition, when resources are abundant, and small individuals have some chance of winning, they may be more aggressive than their larger opponents, as it may benefit larger individuals to avoid the costs of fighting and seek alternative uncontested resources.     

Why is creatine kinase a dimer? Evidence for cooperativity between the two subunits

The dimeric chicken brain type isoenzyme of creatine kinase (BB-CK) was mutated by a C283S amino acid exchange in the catalytic site to produce a basically inactive dimer (B*B*-CK). The mutated enzyme showed a residual activity of about 4% compared to the wild-type, whereas substrate binding parameters were not altered. The inactivated dimer was hybridized with native dimeric muscle enzyme (MM-CK) to produce a partially inactivated MB*-CK heterodimeric hybrid and also to a his-tagged BB-CK (hBhB-CK) resulting in a partially inactive hBB*-CK homodimer. The generated hybrids were purified by chromatography. The V(max) and substrate binding parameters K(m) and K(d) were determined for both directions of the CK reaction and compared to the parameters of the wild-type enzymes (MM-, BB-, hBhB-, MB-CK). In the direction of ATP synthesis (reverse reaction), the MB*- and hBB*-CK hybrids showed a decrease of V(max) to 34% and 32%, respectively, compared to the unmodified wild-type isoform. The inactivation of a single subunit in MB*-CK led to an increase in the K(d) value resulting in an significant substrate synergism, not seen with the MB-CK wild-type enzyme. In the direction of phosphocreatine synthesis (forward reaction), the modified hybrids showed a decrease of V(max) to 50% of the wild-type enzymes and no significant alterations of the K(m) and K(d) parameters. These results strongly suggest an enzymatic cooperativity of the two subunits in the reverse reaction but independent catalytic function in the forward reaction.     

The burning question: Why is smoking a risk factor for pancreatic cancer?

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease. The prognosis is poor; less than 5% of those diagnosed are still alive five years after diagnosis, and complete remission is still rare. Tobacco smoking is a major risk factor of pancreatic cancer. However, the mechanism(s) through which it causes the disease remains unknown. Accumulating evidence indicates that carcinogenic compounds in cigarette smoke stimulate pancreatic cancer progression through induction of inflammation and fibrosis which act in concert with genetic factors leading to the inhibition of cell death and stimulation of proliferation resulting in the promotion of the PDAC.     

Why is joint attention a pivotal skill in autism?

Joint attention abilities play a crucial role in the development of autism. Impairments in joint attention are among the earliest signs of the disorder and joint attention skills relate to outcome, both in the 'natural course' of autism and through being targeted in early intervention programmes. In the current study, concurrent and longitudinal associations between joint attention and other social communication abilities measured in a sample of infants with autism and related pervasive developmental disorders at age 20 months, and language and symptom severity at age 42 months, were examined. Extending the findings from previous studies, joint attention ability was positively associated with language gains and (lower) social and communication symptoms, and imitation ability was also positively associated with later language. Some specificity in the association between different aspects of joint attention behaviours and outcome was found: declarative, triadic gaze switching predicted language and symptom severity but imperative, dyadic eye contact behaviours did not. Further, although joint attention was associated with later social and language symptoms it was unrelated to repetitive and stereotyped symptoms, suggesting the latter may have a separate developmental trajectory. Possible deficits in psychological and neurological processes that might underlie the impaired development of joint attention in autism are discussed.     

Why is chitosan mucoadhesive?

Chitosan is a biocompatible and biodegradable amino polysaccharide, which is soluble in aqueous solutions at pH < 6.5. It has been widely used for developing drug delivery systems because of its excellent mucoadhesive properties. Although many studies report on chitosan being mucoadhesive, the nature of interactions between chitosan and mucin remains poorly defined. Here, we have examined the role of primary amino groups and the role of electrostatic attraction, hydrogen bonding, and hydrophobic effects on aggregation of gastric mucin in the presence of chitosan. Reducing the number of amino groups through their half acetylation results in expansion of chitosan's pH-solubility window up to pH 7.4 but also reduces its capacity to aggregate mucin. We demonstrated that electrostatic attraction forces between chitosan and gastric mucin can be suppressed in the presence of 0.2 mol/L sodium chloride; however, this does not prevent the aggregation of mucin particles in the presence of this biopolymer. The presence of 8 mol/L urea or 10% v/v ethanol in solutions also affects mucin aggregation in the presence of chitosan, demonstrating the role of hydrogen bonding and hydrophobic effects, respectively, in mucoadhesion.     

How good is our genome?

Our genome has evolved to perpetuate itself through the maintenance of the species via an uninterrupted chain of reproductive somas. Accordingly, evolution is not concerned with diseases occurring after the soma's reproductive stage. Following Richard Dawkins, we would like to reassert that we indeed live as disposable somas, slaves of our germline genome, but could soon start rebelling against such slavery. Cancer and its relation to the TP53 gene may offer a paradigmatic example. The observation that the latency period in cancer can be prolonged in mice by increasing the number of TP53 genes in their genome, suggests that sooner or later we will have to address the question of heritable disease avoidance via the manipulation of the human germline.     

Thermal denaturation: is solid-state fermentation really a good technology for the production of enzymes?

The potential for thermal denaturation to cause enzyme losses during solid-state fermentation processes for the production of enzymes was examined, using the protease of Penicillium fellutanum as a model system. The frequency factor and activation energies for the first-order denaturation of this enzyme were determined as 3.447 x 10(59) h(-1) and 364,070 Jmol(-1), respectively. These values were incorporated into a mathematical model of enzyme deactivation, which was used to investigate the consequences of subjecting this protease to temporal temperature profiles reported in the literature for mid-height in a 34 cm high packed-bed bioreactor of 150 mm diameter. In this literature source, temperature profiles were measured for 5, 15 and 25 liters per minute of air and enzyme activities were measured as a function of time. The enzyme activity profiles predicted by the model were distributed similarly, one relative to the other, as had been found in the experimental study, with substantial amounts of denaturation being predicted when the substrate temperature exceeded 40 degrees C, which occurred at the lower two airflow rates. A mathematical model of a well-mixed bioreactor was used to explore the difficulties that would be faced at large scale. It suggests that even with airflows as high as one volume per volume per minute, up to 85% of the enzyme produced by the microorganism can be denatured by the end of the fermentation. This work highlights the extra care that must be taken in scaling up solid-state fermentation processes for the production of thermolabile products.