Iterative approach to computational enzyme design

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes

Rapid diagnostic susceptibility testing of bacteria and fungi from clinical samples using silicon gratings

Bacterial and fungal infections persistently plague society and have amounted to one of the most prevalent issues in healthcare today. Thus, significant research effort is directed towards developing rapid diagnostic techniques for determination of the correct antibiotic (or antifungal) for a patient-tailored therapy. We have developed a rapid phenotypic antimicrobial susceptibility testing (AST) in which photonic 2D silicon microarrays are employed as both the optical transducer element and as a preferable solid-liquid interface for bacterial/fungal colonization. We harness the intrinsic ability of the micro-architectures to relay optical phase-shift reflectometric interference spectroscopic measurements (termed PRISM) and incorporate it into a platform for culture-free, label-free tracking of bacterial/fungal colonization, proliferation, and death. For example, bacteria proliferation within the microtopologies results in an increase in refractive index of the medium, yielding an increase in optical path difference, while cell death or bacteriostatic activity results in decreasing or unchanged values. The optical responses of bacteria, including clinical isolates and samples derived from patients at neighboring hospitals, to various concentrations of relevant antibiotics are tracked in real time, allowing for accurate determination of the minimum inhibitory concentration (MIC) values within 2-3 hours in comparison to assay times of <8 hours (using standard broth microdilution techniques or state-of-the-art clinical automated systems. This has opened the door to the observation of unique bacterial behaviors, as we can evaluate bacterial adhesion, growth, and antibiotic resistance on different micro-architectures, different surface chemistries, and even different strains. Motility, charge, and biofilm abilities have been explored for their effect of bacterial adhesion to the microstructures as we further develop our method of rapid, label-free AST for full clinical application. © 2019 SPIE

Characterization of different crystal forms of the α-glucosidase MalA from \u3ci\u3eSulfolobus solfataricus\u3c/i\u3e

MalA is an _-glucosidase from the hyperthermophilic archaeon Sulfolobus solfataricus. It belongs to glycoside hydrolase family 31, which includes several medically interesting α-glucosidases. MalA and its selenomethionine derivative have been overproduced in Escherichia coli and crystallized in four different crystal forms. Microseeding was essential for the formation of good-quality crystals of forms 2 and 4. For three of the crystal forms (2, 3 and 4) full data sets could be collected. The most suitable crystals for structure determination are the monoclinic form 4 crystals, belonging to space group P21, from which data sets extending to 2.5 Å resolution have been collected. Self-rotation functions calculated for this form and for the orthorhombic (P212121) form 2 indicate the presence of six molecules in the asymmetric unit related by 32 symmetry

Flow and Transport in Regions with Aquatic Vegetation

This review describes mean and turbulent flow and mass transport in the presence of aquatic vegetation. Within emergent canopies, the turbulent length scales are set by the stem diameter and spacing, and the mean flow is determined by the distribution of the canopy frontal area. Near sparse submerged canopies, the bed roughness and near-bed turbulence are enhanced, but the velocity profile remains logarithmic. For dense submerged canopies, the drag discontinuity at the top of the canopy generates a shear layer, which contains canopy-scale vortices that control the exchange of mass and momentum between the canopy and the overflow. The canopy-scale vortices penetrate a finite distance into the canopy, δe, set by the canopy drag. This length scale segregates the canopy into two regions: The upper canopy experiences energetic turbulent transport, controlled by canopy-scale vortices, whereas the lower canopy experiences diminished transport, associated with the smaller stem-scale turbulence. The canopy-scale vortices induce a waving motion in flexible blades, called a monami.National Science Foundation (U.S.) (EAR 0309188)National Science Foundation (U.S.) (EAR 0125056)National Science Foundation (U.S.) (EAR0738352)National Science Foundation (U.S.) (OCE0751358

Effectiveness of an Inpatient Movement Disorders Program for Patients with Atypical Parkinsonism

This paper investigated the effectiveness of an inpatient movement disorders program for patients with atypical parkinsonism, who typically respond poorly to pharmacologic intervention and are challenging to rehabilitate as outpatients. Ninety-one patients with atypical parkinsonism participated in an inpatient movement disorders program. Patients received physical, occupational, and speech therapy for 3 hours/day, 5 to 7 days/week, and pharmacologic adjustments based on daily observation and data. Differences between admission and discharge scores were analyzed for the functional independence measure (FIM), timed up and go test (TUG), two-minute walk test (TMW), Berg balance scale (BBS) and finger tapping test (FT), and all showed significant improvement on discharge (P > .001). Clinically significant improvements in total FIM score were evident in 74% of the patients. Results were similar for ten patients whose medications were not adjusted. Patients with atypical parkinsonism benefit from an inpatient interdisciplinary movement disorders program to improve functional status

Gender and class in Britain and France

This article examines the treatment of women's oppression in feminist theory, focusing on the engagement of second wave feminists with the concept of class and its relation to gender. This examination is carried out with reference to British and French feminisms, identifying the main trends and shifts that have developed over the last 35 years and noting that while these are undoubtedly influenced by a particular national context they are also shaped by increasing European integration and social, political and cultural exchanges at a global level. The authors find evidence of a number of similarities in the questions that feminist theorists have asked in Britain and France but also demonstrate that there are significant differences. They conclude that areas of convergent theoretical interests will extend along with cross-border flows of peoples and information

Revised Pediatric Reference Data for the Lateral Distal Femur Measured by Hologic Discovery/Delphi Dual-Energy X-Ray Absorptiometry

BackgroundLateral distal femur (LDF) scans by dual energy x-ray absorptiometry (DXA) are often feasible in children for whom other sites are not measurable. Pediatric reference data for LDF are not available for more recent DXA technology.AimsTo assess older pediatric LDF reference data, construct new reference curves for LDF bone mineral density (BMD), and demonstrate the comparability of LDF BMD to other measures of BMD and strength assessed by DXA and by peripheral quantitative computed tomography (pQCT).MethodsLDF, spine and whole body scans of 821 healthy children, 5 to 18 years of age, recruited at a single center were obtained using a Hologic Delphi/Discovery system. Tibia trabecular and total BMD (3% site), cortical geometry (38% site) (cortical thickness, section modulus, strain strength index) were assessed by pQCT. Sex and race-specific reference curves were generated using LMS-ChartMaker and Z-scores calculated and compared by correlation analysis.ResultsZ-scores for LDF BMD based on published findings demonstrated overestimation or underestimation of the prevalence of low BMD-for-age depending on the region of interest considered. Revised LDF reference curves were generated. The new LDF Z-scores were strongly and significantly associated with weight, BMI, spine and whole body BMD Z-scores, and all pQCT Z-scores.ConclusionThese findings demonstrate the comparability of LDF measurements to other clinical and research bone density assessment modes, and enable assessment of BMD in children with disabilities, who are particularly prone to low trauma fractures of long bones, and for whom traditional DXA measurement sites are not feasible

Teleost Growth Factor Independence (Gfi) Genes Differentially Regulate Successive Waves of Hematopoiesis

Growth Factor Independence (Gfi) transcription factors play essential roles in hematopoiesis, differentially activating and repressing transcriptional programs required for hematopoietic stem/progenitor cell (HSPC) development and lineage specification. In mammals, Gfi1a regulates hematopoietic stem cells (HSC), myeloid and lymphoid populations, while its paralog, Gfi1b, regulates HSC, megakaryocyte and erythroid development. In zebrafish, gfi1aa is essential for primitive hematopoiesis; however, little is known about the role of gfi1aa in definitive hematopoiesis or about additional gfi factors in zebrafish. Here, we report the isolation and characterization of an additional hematopoietic gfi factor, gfi1b. We show that gfi1aa and gfi1b are expressed in the primitive and definitive sites of hematopoiesis in zebrafish. Our functional analyses demonstrate that gfi1aa and gfi1b have distinct roles in regulating primitive and definitive hematopoietic progenitors, respectively. Loss of gfi1aa silences markers of early primitive progenitors, scl and gata1. Conversely, loss of gfi1b silences runx-1, c-myb, ikaros and cd41, indicating that gfi1b is required for definitive hematopoiesis. We determine the epistatic relationships between the gfi factors and key hematopoietic transcription factors, demonstrating that gfi1aa and gfi1b join lmo2, scl, runx-1 and c-myb as critical regulators of teleost HSPC. Our studies establish a comparative paradigm for the regulation of hematopoietic lineages by gfi transcription factors.Stem Cell and Regenerative Biolog