Active-site mutants of class B beta-lactamases: substrate binding and mechanistic study

Increased resistance to β-lactam antibiotics is mainly due to β-lactamases. X-ray structures of zinc β-lactamases unraveled the coordination of the metal ions, but their mode of action remains unclear. Recently, enzymes in which one of the zinc ligands was mutated have been characterized and their catalytic activity against several β-lactam antibiotics measured. A molecular modeling study of these enzymes was performed here to explain the catalytic activity of the mutants. Coordination around the zinc ions influences the way the tetrahedral intermediate is bound; any modification influences the first recognition of the substrate by the enzyme. For all the studied mutants, at least one of the interactions fails, inducing a loss of catalytic efficiency compared to the wild type. The present studies show that the enzyme cavity is a structure of high plasticity both structurally and mechanistically and that local modifications may propagate its effects far from the mutated amino acid. Received 28 August 2002; received after revision 22 October 2002; accepted 24 October 2002 RID="*" ID="*"Corresponding author.     

A peculiar fatty acid, (Z,Z)-9,12,17-octadecatrienoic acid,identified in the phospholipids of the pea aphid,Acyrthosiphon pisum (Harris) (homoptera: aphididae)

A peculiar fatty acid previously detected in the phospholipids of the pea aphid,Acyrthosiphon pisum, is identified as (Z,Z)-9,12,17-octadecatrienoic acid. It is the first report of this compound in the literature. Comparison of fatty acid profiles of phospholipids between normal and aposymbiotic pea aphids shows that aphid symbionts are not responsible for the biosynthesis of this unusual fatty acid.     

The distribution of α2β1, α3β1 and α6β4 integrins identifies distinct subpopulations of basal keratinocytes in the outer root sheath of the human anagen hair follicle

The human hair follicle is composed of different concentric compartments, which reflect different programmes of differentiation. Using monoclonal antibodies against α2β1 and α3β1 integrins we demonstrated a shift in their expression, from a basolateral distribution in the basal cells of the lower outer root sheath, to an apicolateral expression in the upper outer root sheath, as in epidermis. This shift takes place in a transition zone, localized to the midpart of the follicle. The distinct basolateral distribution of α2β1 and α3β1 integrins in the lower portion of the outer root sheath coincides with the presence of basal cell protrusions and is probably linked to the presence of the vitreous membrane which surrounds the bottom part of the anagen human hair follicle. Moreover, we showed that the expression of α6β4 integrin is discontinuous along the hair follicle and coincides with that of laminin 5. Together these results establish that within a given compartment – namely the outer root sheath – several domains can be clearly identified, which probably reflect the onset of successive differentiation pathways along the hair follicle. Received 17 January 1997; received after revision 18 February 1997; accepted 24 February 1997     

Role of glutamic acid decarboxylase in the pathogenesis of type 1 diabetes

Glutamic acid decarboxylase (GAD) is considered to be one of the strongest candidate autoantigens involved in triggering β-cell-specific autoimmunity. The majority of recent onset type 1 diabetes patients and prediabetic subjects have anti-GAD antibodies in their sera, as do nonobese diabetic (NOD) mice, one of the best animal models for human type 1 diabetes. Immunization of young NOD mice with GAD results in the prevention or delay of the disease as a result of tolerizing autoreactive T cells. Autoimmune diabetes can also be prevented by the suppression of GAD expression in antisense GAD trans genic mice backcrossed with NOD mice for seven generations. These results support the hypothesis that GAD plays an important role in the development of T-cell-mediated autoimmune diabetes. However, there is some controversy regarding the role of GAD in the pathogenesis of diabetes. Whether GAD truly plays a key role in the initiation of this disease remains to be determined. The examination of the development of insulitis and diabetes in β-cell-specific GAD knockout NOD mice will answer this remaining question. Received 12 April 2002; received after revision 24 May 2002; accepted 27 May 2002 RID="*" ID="*"Corresponding author.     

Computation in cognitive science: it is not all about Turing-equivalent computation

It is sometimes suggested that the history of computation in cognitive science is one in which the formal apparatus of Turing-equivalent computation, or effective computability, was exported from mathematical logic to ever wider areas of cognitive science and its environs. This paper, however, indicates some respects in which this suggestion is inaccurate. Computability theory has not been focused exclusively on Turing-equivalent computation. Many essential features of Turing-equivalent computation are not captured in definitions of computation as (digital) symbol manipulation. Turing-equivalent computation did not play the role in McCulloch and Pitts’s early cybernetic work that is sometimes attributed to it. Finally, various segments of the neuroscientific community invoke a notion of computation that differs from the Turing-equivalent notion.     

Chitotriosidase: the yin and yang

The enzyme chitotriosidase (ChT), the human analogue of chitinases from non-vertebrate species, is one of the most abundant and indicative proteins secreted by activated macrophages. Its enzymatic activity is elevated in serum of patients suffering from Gaucher’s disease type 1 and in some other inherited lysosomal storage disorders, as well as in diseases in which macrophages are activated. The last decade has witnessed the appearance of a substantial number of studies attempting to unravel its cellular functions, which have yet not been fully defined. A great deal of progress has been made in the study of the physiological roles of ChT. This review is looks at the key areas of investigations addressed to further illuminate whether ChT activation might have different functional meanings in various diseases. Received 7 June 2006; received after revision 24 July 2006; accepted 21 September 2006     

Identification and biological significance of 4-methyl-3Z,5-hexadienoic acid produced by males of the gall-forming tephritidsUrophora cardui (L.) andUrophora stylata (Fab.) (Diptera: Tephritidae)

Summary A new natural substance has been identified in the rectal ampullae of gall-forming fruit flies. The substance was found to be the only volatile compound in the rectal ampulla of maleUrophora cardui andUrophora stylata. GC-MS methods were used to characterize its structure as 4-methyl-3Z,5-hexadienoic acid. Physiological parameters such as the amount of the acid at different ages and under different conditions were investigated. The biological significance of the new volatile as an arresting pheromone was tested in several bioassays. The arrestant function could not be established, but the results gave hints of a territorial function between conspecific males. The results are discussed with respect to gland morphology and predictions of communication models among fruit flies.     

Looking forward,not back: Supporting structuralism in the present

The view that the fundamental kind properties are intrinsic properties enjoys reflexive endorsement by most metaphysicians of science. But ontic structural realists deny that there are any fundamental intrinsic properties at all. Given that structuralists distrust intuition as a guide to truth, and given that we currently lack a fundamental physical theory that we could consult instead to order settle the issue, it might seem as if there is simply nowhere for this debate to go at present. However, I will argue that there exists an as-yet untapped resource for arguing for ontic structuralism – namely, the way that fundamentality is conceptualized in our most fundamental physical frameworks. By arguing that physical objects must be subject to the ‘Goldilock's principle’ if they are to count as fundamental at all, I argue that we can no longer view the majority of properties defining them as intrinsic. As such, ontic structural realism can be regarded as the most promising metaphysics for fundamental physics, and that this is so even though we do not yet claim to know precisely what that fundamental physics is.     

AMP-activated protein kinase in skeletal muscle: From structure and localization to its role as a master regulator of cellular metabolism

The AMP-activated protein kinase (AMPK) is a metabolite sensing serine/threonine kinase that has been termed the master regulator of cellular energy metabolism due to its numerous roles in the regulation of glucose, lipid, and protein metabolism. In this review, we first summarize the current literature on a number of important aspects of AMPK in skeletal muscle. These include the following: (1) the structural components of the three AMPK subunits (i.e. AMPKα, β, and γ), and their differential localization in response to stimulation in muscle; (2) the biochemical regulation of AMPK by AMP, protein phosphatases, and its three known upstream kinases, LKB1, Ca²⁺/calmodulin-dependent protein kinase kinase (CaMKK), and transforming growth factor-β-activated kinase 1 (TAK1); (3) the pharmacological agents that are currently available for the activation and inhibition of AMPK; (4) the physiological stimuli that activate AMPK in muscle; and (5) the metabolic processes that AMPK regulates in skeletal muscle. Received 04 May 2008; received after revision 14 June 2008; accepted 14 July 2008     

Self and non-self discrimination is needed for the existence rather than deletion of autoimmunity: the role of regulatory T cells in protective autoimmunity

Autoimmune T cells have been viewed for decades as an outcome of immune system malfunction, and specifically as a failure to distinguish between components of self and non-self. The need for discrimination between self and non-self as a way to avoid autoimmunity has been repeatedly debated over the years. Recent studies suggest that autoimmunity, at least in the nervous system, is the bodys defense mechanism against deviations from the normal. The ability to harness neuroprotective autoimmunity upon need is evidently allowed by naturally occurring CD4+CD25+ regulatory T cells, which are themselves controlled by brain-derived compounds. These findings challenge widely accepted concepts of the need for discrimination between self and non-self, as they suggest that while such discrimination is indeed required, it is needed not as a way to avoid an anti-self response but to ensure its proper regulation. Whereas a response to non-self can be self-limited by a decreased presence of the relevant antigen, the response to self needs a mechanism for strict control, such as that provided by the naturally occurring regulatory T cells.Received 8 June 2004; accepted 6 July 2004