Directed enzyme evolution: climbing fitness peaks one amino acid at a time

Directed evolution can generate a remarkable range of new enzyme properties. Alternate substrate specificities and reaction selectivities are readily accessible in enzymes from families that are naturally functionally diverse. Activities on new substrates can be obtained by improving variants with broadened specificities or by step-wise evolution through a sequence of more and more challenging substrates. Evolution of highly specific enzymes has been demonstrated, even with positive selection alone. It is apparent that many solutions exist for any given problem, and there are often many paths that lead uphill, one step at a time

Performance of tuberculin skin test measured against interferon gamma release assay as reference standard in children

Objectives. International guidelines differ in the threshold of tuberculin skin test (TST) induration regarded as indicating Mycobacterium (M.) tuberculosis infection. Interferon gamma release assay (IGRA) results were used as reference to assess performance of TST induration thresholds for detection of M. tuberculosis infection in children. Design. Systematic review which included studies containing data on TST, IGRA, and Bacillus Calmette-Gu´erin (BCG) status in children. Data bases searched were PubMed, EMBASE, and the Cochrane library. Specificities and sensitivities were calculated for TST thresholds 5, 10, and 15mm and correlated with age and geographical latitude. Results. Eleven studies with 2796 children were included. For BCG immunised children diameters of 5, 10, and 15mmhad median sensitivities of 87, 70, and 75%and specificities of 67, 93, and 90%, respectively. In non-BCG immunised children median sensitivities were 94, 95, and 83% and specificities 91, 95, and 97%. At the 10mm threshold age correlated negatively with sensitivity of TST

Nucleotide specificity of the enzymatic and motile activities of dynein, kinesin, and heavy meromyosin.

The substrate specificities of dynein, kinesin, and myosin substrate turnover activity and cytoskeletal filament-driven translocation were examined using 15 ATP analogues. The dyneins were more selective in their substrate utilization than bovine brain kinesin or muscle heavy meromyosin, and even different types of dyneins, such as 14S and 22S dynein from Tetrahymena cilia and the beta-heavy chain-containing particle from the outer-arm dynein of sea urchin flagella, could be distinguished by their substrate specificities. Although bovine brain kinesin and muscle heavy meromyosin both exhibited broad substrate specificities, kinesin-induced microtubule translocation varied over a 50-fold range in speed among the various substrates, whereas heavy meromyosin-induced actin translocation varied only by fourfold. With both kinesin and heavy meromyosin, the relative velocities of filament translocation did not correlate well with the relative filament-activated substrate turnover rates. Furthermore, some ATP analogues that did not support the filament translocation exhibited filament-activated substrate turnover rates. Filament-activated substrate turnover and power production, therefore, appear to become uncoupled with certain substrates. In conclusion, the substrate specificities and coupling to motility are distinct for different types of molecular motor proteins. Such nucleotide "fingerprints" of enzymatic activities of motor proteins may prove useful as a tool for identifying what type of motor is involved in powering a motility-related event that can be reconstituted in vitro

Broad and potent cross clade neutralizing antibodies with multiple specificities in the plasma of HIV-1 subtype C infected individuals.

Broadly Cross clade Neutralizing (BCN) antibodies are recognized as potential therapeutic tools and leads for the design of a vaccine that can protect human beings against various clades of Human Immunodeficiency Virus (HIV). In the present study, we screened plasma of 88 HIV-1 infected ART naïve individuals for their neutralization potential using a standard panel of 18 pseudoviruses belonging to different subtypes and different levels of neutralization. We identified 12 samples with good breadth of neutralization (neutralized >90% of the viruses). Four of these samples neutralized even the difficult-to-neutralize tier-3 pseudoviruses with great potency (GMT > 600). Analysis of neutralization specificities indicated that four samples had antibodies with multiple epitope binding specificities, viz. CD4-binding site (CD4BS), glycans in the V1/V2 and V3 regions and membrane proximal external region (MPER). Our findings indicate the strong possibility of identifying highly potent bNAbs with known or novel specificities from HIV-1 subtype C infected individuals from India that can be exploited as therapeutic tools or lead molecules for the identification of potential epitopes for design of a protective HIV-1 vaccine

Sparse Coding Predicts Optic Flow Specificities of Zebrafish Pretectal Neurons

Zebrafish pretectal neurons exhibit specificities for large-field optic flow patterns associated with rotatory or translatory body motion. We investigate the hypothesis that these specificities reflect the input statistics of natural optic flow. Realistic motion sequences were generated using computer graphics simulating self-motion in an underwater scene. Local retinal motion was estimated with a motion detector and encoded in four populations of directionally tuned retinal ganglion cells, represented as two signed input variables. This activity was then used as input into one of two learning networks: a sparse coding network (competitive learning) and backpropagation network (supervised learning). Both simulations develop specificities for optic flow which are comparable to those found in a neurophysiological study (Kubo et al. 2014), and relative frequencies of the various neuronal responses are best modeled by the sparse coding approach. We conclude that the optic flow neurons in the zebrafish pretectum do reflect the optic flow statistics. The predicted vectorial receptive fields show typical optic flow fields but also "Gabor" and dipole-shaped patterns that likely reflect difference fields needed for reconstruction by linear superposition.Comment: Published Conference Paper from ICANN 2018, Rhode

Inter-organizational communities of practice: specificities and stakes

Inter-organizational communities of practice (IOCoPs) are today an emergent research topic and studies in this area are still in an exploratory phase. Theoretical mechanisms are vaguely specified and empirical studies are incipient. For this reason, this paper firstly aims at presenting the specificities and stakes of such organizational forms, establishing reference points for further research in this field. We will introduce the main features of IOCoPs and explain why they do not represent a mere subcategory of CoPs, but a unit of analysis per se. In this paper, we will follow a thematic approach to indicate IOCoPs’ specificities and stakes. We will thus look at the IOCoPs’ actors (in part I), IOCoPs as original organizational forms (part II), then IOCoPs’ life cycle (part III). Finally, we will synthesize IOCoPs’ distinctive features and conclude with a discussion on key interests of IOCoPs for both practitioners and academics.Community of practice; inter-organizational relationships; professional practice; expertise; knowledge management; learning; organizational boundaries; life-cycle

Municipal transitions: The social, energy, and spatial dynamics of sociotechnical change in South Tyrol, Italy

With the aim of proposing recommendations on how to use social and territorial specificities as levers for wider achievement of climate and energy targets at local level, this research analyses territories as sociotechnical systems. Defining the territory as a sociotechnical system allows us to underline the interrelations between space, energy and society. Groups of municipalities in a region can be identified with respect to their potential production of renewable energy by means of well-known data-mining approaches. Similar municipalities linking together can share ideas and promote collaborations, supporting clever social planning in the transition towards a new energy system. The methodology is applied to the South Tyrol case study (Italy). Results show eight different spatially-based sociotechnical systems within the coherent cultural and institutional context of South Tyrol. In particular, this paper observes eight different systems in terms of (1) different renewable energy source preferences in semi-urban and rural contexts; (2) different links with other local planning, management, and policy needs; (3) different socio-demographic specificities of individuals and families; (4) presence of different kinds of stakeholders or of (5) different socio-spatial organizations based on land cover. Each energy system has its own specificities and potentialities, including social and spatial dimensions, that can address a more balanced, inclusive, equal, and accelerated energy transition at the local and translocal scale

Multiscreen serum analysis of highly sensitized renal dialysis patients for antibodies toward public and private class I HLA determinants: Implications for computer-predicted acceptable and unacceptable donor mismatches in kidney transplantation

A multiscreen serum analysis program has been developed that permits a determination of antibody specificity for the vast majority of highly sensitized patients awaiting transplantation. This program is based on a 2 x 2 table analysis of correlations between serum reactivity with an HLA-typed cell panel and incorporates two modifications. One implements the concept of public HLA determinants based on the serologic crossreactivity among class I HLA antigens. The other modification derives from the premise that most highly sensitized patients maintain the same PRA and antibody profiles over many months and even years. Monthly screening results for patients with persistent PRA values can therefore be combined for analysis. For 132 of 150 highly sensitized patients with >50% PRA, this multiscreen serum analysis program yielded information about antibody specificity toward public and private class IHLA determinants. The vast majority of patients (108 of 112) with PRA values between 50 and 89% showed antibody specificity generally toward one, two, or three public markers and/or the more common private HLA-A, B antigens. For 24 of 38 patients with >90% PRA, it was possible to define one or few HLA-specific antibodies. The primary objective of the multiscreen program was to develop an algorithm about computer-predicted acceptable and unacceptable donor HLA-A, B antigens for patients with preformed antibodies. A retrospective analysis of kidney transplants into 89 highly sensitized patients has demonstrated that allografts with unacceptable HLA-A, B mismatches had significantly lower actuarial survival rates than those with acceptable mismatches (P = 0.01). This was shown for both groups of 32 primary transplants (44% vs. 67% after 1 year) and 60 retransplants (50% vs. 68%). Also, serum creatinine levels were significantly higher in patients with unacceptable class I mismatches (3.0 vs. 8.4 mg% [P = 0.007] after 2 weeks; 3.9 vs. 9.1 mg% [P = 0.014] after 4 weeks). Histopathologic analysis of allograft tissue specimens from 47 transplant recipients revealed a significantly higher incidence of humoral rejection (P = 0.02), but not cellular rejection, in the unacceptable mismatch group. These results suggest that the multiscreen program can establish which donor HLA-A, B mismatches must be avoided in kidney transplantation for most highly sensitized patients. For 18 of 150 high PRA renal dialysis patients, the multiscreen program could not define HLA-specific antibody. Most patients had >90% PRA, and many of their sera appeared to contain IgM type nonspecific lympho- cytotoxins that could be inactivated by dithioerythreitol (DTE). Preliminary studies have shown that this treatment enabled the detection of HLA-specific antibodies upon subsequent screening on many occasions. These data suggest that non-HLA specific reactivity revealed by multiscreen analysis can often be removed by DTE treatment. Multiscreen analysis offers an attractive approach to regional organ-sharing programs for highly sensitized renal transplant candidates. It enables the development of an efficient strategy for donor selection based on the computer assignment of acceptable HLA-A, B mismatches for each patient. © 1990 by Williams and Wilkins

Discovering cultural differences (and similarities) in facial expressions of emotion

Understanding the cultural commonalities and specificities of facial expressions of emotion remains a central goal of Psychology. However, recent progress has been stayed by dichotomous debates (e.g., nature versus nurture) that have created silos of empirical and theoretical knowledge. Now, an emerging interdisciplinary scientific culture is broadening the focus of research to provide a more unified and refined account of facial expressions within and across cultures. Specifically, data-driven approaches allow a wider, more objective exploration of face movement patterns that provide detailed information ontologies of their cultural commonalities and specificities. Similarly, a wider exploration of the social messages perceived from face movements diversifies knowledge of their functional roles (e.g., the ‘fear’ face used as a threat display). Together, these new approaches promise to diversify, deepen, and refine knowledge of facial expressions, and deliver the next major milestones for a functional theory of human social communication that is transferable to social robotics

"Our Own Gayful Rest": A Postcolonial Archive

My subject is an archive of gay and lesbian activism that helps us understand a postcolonial counterpublic. The project I undertake is of historical recovery and theoretical elaboration of the specificities of postcolonial sexuality-based movements as necessary and long overdue supplements to global sexual activism