Analysis of early intermediate states of the nitrogenase reaction by regularization of EPR spectra.

Due to the complexity of the catalytic FeMo cofactor site in nitrogenases that mediates the reduction of molecular nitrogen to ammonium, mechanistic details of this reaction remain under debate. In this study, selenium- and sulfur-incorporated FeMo cofactors of the catalytic MoFe protein component from Azotobacter vinelandii are prepared under turnover conditions and investigated by using different EPR methods. Complex signal patterns are observed in the continuous wave EPR spectra of selenium-incorporated samples, which are analyzed by Tikhonov regularization, a method that has not yet been applied to high spin systems of transition metal cofactors, and by an already established grid-of-error approach.

New species of Pyrgulopsis Call & Pilsbry, 1886 (Mollusca: Caenogastropoda: Hydrobiidae) from two Chihuahuan Desert springs.

Two new populations of Pyrgulopsis were found in springs in the Chihuahuan desert region of Texas. Pyrgulopsis Call & Pilsbry, 1886 are a diverse group of snails occupying freshwater springs, usually narrow-range endemics limited to a single spring. Their small ranges confer substantial conservation concern as the drying or disturbance of a single spring can lead to their extinction.

Immunodominant surface epitopes power immune evasion in the African trypanosome.

The African trypanosome survives the immune response of its mammalian host by antigenic variation of its major surface antigen (the variant surface glycoprotein or VSG). Here we describe the antibody repertoires elicited by different VSGs. We show that the repertoires are highly restricted and are directed predominantly to distinct epitopes on the surface of the VSGs.

Two new species of Pyrgulopsis Call amp; Pilsbry, 1886 (Mollusca: Caenogastropoda: Hydrobiidae) from springs in the Rio Grande watershed in Texas.

Pyrgulopsis Call Pilsbry, 1886 is a genus of small (<5 mm) spring snails, usually endemic to single freshwater springs. Two new populations of Pyrgulopsis found in very small, isolated springs and spring runs in the mainstem Rio Grande watershed of western Texas are distinguished from congeners. Mitochondrial and nuclear sequences, morphometrics, and morphological characteristics support Pyrgulopsis rubra sp.

Structure and dynamics of the quaternary hunchback mRNA translation repression complex.

A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development.

Molecular basis of mRNA transport by a kinesin-1-atypical tropomyosin complex.

Kinesin-1 carries cargos including proteins, RNAs, vesicles, and pathogens over long distances within cells. The mechanochemical cycle of kinesins is well described, but how they establish cargo specificity is not fully understood. Transport of mRNA to the posterior pole of the oocyte is mediated by kinesin-1, also called kinesin heavy chain (Khc), and a putative cargo adaptor, the atypical tropomyosin, Tm1.

Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study.

Microscale thermophoresis (MST), and the closely related Temperature Related Intensity Change (TRIC), are synonyms for a recently developed measurement technique in the field of biophysics to quantify biomolecular interactions, using the (capillary-based) NanoTemper Monolith and (multiwell plate-based) Dianthus instruments. Although this technique has been extensively used within the scientific community due to its low sample consumption, ease of use, and ubiquitous applicability, MST/TRIC has not enjoyed the unambiguous acceptance from biophysicists afforded to other biophysical techniques like isothermal titration calorimetry (ITC) or surface plasmon resonance (SPR). This might be attributed to several facts, e.

Community-Wide Experimental Evaluation of the PROSS Stability-Design Method.

Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins.

Structure of trypanosome coat protein VSGsur and function in suramin resistance.

Suramin has been a primary early-stage treatment for African trypanosomiasis for nearly 100 yr. Recent studies revealed that trypanosome strains that express the variant surface glycoprotein (VSG) VSGsur possess heightened resistance to suramin. Here, we show that VSGsur binds tightly to suramin but other VSGs do not.

Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site.

As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the active-site FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer-Tropsch-type chemistry). The C-C bond forming capabilities of nitrogenase suggest that multiple CO or CO-derived ligands bind to the active site.

An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ADP-Ribosylation.

Strategies for installing authentic ADP-ribosylation (ADPr) at desired positions are fundamental for creating the tools needed to explore this elusive post-translational modification (PTM) in essential cellular processes. Here, we describe a phospho-guided chemoenzymatic approach based on the Ser-ADPr writer complex for rapid, scalable preparation of a panel of pure, precisely modified peptides. Integrating this methodology with phage display technology, we have developed site-specific as well as broad-specificity antibodies to mono-ADPr.

An unusually sculptured new species of Phreatodrobia Hershler amp; Longley (Mollusca: Caenogastropoda: Cochliopidae) from central Texas.

There are eight described species in Phreatodrobia, minute, phreatic (subterranean aquatic) snails, all stygobitic and endemic to the Edwards-Trinity Aquifer System of Texas. Two species were described from river drift (Pilsbry Ferriss 1906) and the others more recently by sampling the water flowing from wells or springs (Hershler Longley 1986b; Hershler Longley 1987). Recent sampling from spring orifices and the hyporheic zone of streams have extended the known ranges of the phreatic snails of the region and encountered unknown snails (Alvear et al.

Structure-based screening of binding affinities via small-angle X-ray scattering.

Protein-protein and protein-ligand interactions often involve conformational changes or structural rearrangements that can be quantified by solution small-angle X-ray scattering (SAXS). These scattering intensity measurements reveal structural details of the bound complex, the number of species involved and, additionally, the strength of interactions if carried out as a titration. Although a core part of structural biology workflows, SAXS-based titrations are not commonly used in drug discovery contexts.

A new species of stygobitic snail in the genus Hershler & Thompson, 1990 (Gastropoda, Cochliopidae) from the Appalachian Valley and Ridge of eastern Tennessee, USA.

A new species of cave snail (Littorinimorpha: Cochliopidae) in the genus is described from the dark zone of two caves in the Appalachian Valley and Ridge province in eastern Tennessee, United States. The Tennessee Cavesnail, Perez, Shoobs, Gladstone, & Niemiller, is distinguished from its only known congener, , by the absence of raised tubercles on its finely spirally striate protoconch, and its unique radular formula. Moreover, is genetically distinct from based on substantial divergence at the mitochondrial CO1 locus.

Embryonic exposure to environmentally relevant concentrations of triclosan impairs foraging efficiency in zebrafish larvae.

The ubiquitous and persistent contaminant triclosan is known to cause developmental and behavioral toxicity in fish, but few studies have evaluated the long-term effects of these responses. We used a phenotypically anchored approach to evaluate the behavioral responses caused by early exposure to environmentally relevant concentrations of triclosan to better understand the risk triclosan poses to fish. Zebrafish were exposed to 0, 0.

Geometric Morphometrics as a Tool to Evaluate Teratogenic Effects in Zebrafish (Danio rerio).

Geometric morphometrics allows for the characterization of shape using Cartesian geometric coordinates rather than linear or volumetric measurements, which are dependent upon size and are insufficient to capture geometric shape. By using landmarks on specimens, variations in position, orientation and scale between specimens can be removed to better compare variations in shape. This method has primarily been used in the fields of evolutionary biology and taxonomy.

Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor.

Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor.

The Dominance Concept Inventory: A Tool for Assessing Undergraduate Student Alternative Conceptions about Dominance in Mendelian and Population Genetics.

Despite the impact of genetics on daily life, biology undergraduates understand some key genetics concepts poorly. One concept requiring attention is dominance, which many students understand as a fixed property of an allele or trait and regularly conflate with frequency in a population or selective advantage. We present the Dominance Concept Inventory (DCI), an instrument to gather data on selected alternative conceptions about dominance.

Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase.

The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor.

Embryonic exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin impairs prey capture by zebrafish larvae.

As a ubiquitous, persistent environmental contaminant, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has the potential to cause lethal deformities in larval fishes. Few studies have examined its impacts on larval growth and craniofacial development in conjunction with feeding capability. The authors used morphological and behavioral assessments to demonstrate that feeding capability of larvae is impaired even when craniofacial structures are not grossly malformed.

The genetic drift inventory: a tool for measuring what advanced undergraduates have mastered about genetic drift.

Understanding genetic drift is crucial for a comprehensive understanding of biology, yet it is difficult to learn because it combines the conceptual challenges of both evolution and randomness. To help assess strategies for teaching genetic drift, we have developed and evaluated the Genetic Drift Inventory (GeDI), a concept inventory that measures upper-division students' understanding of this concept. We used an iterative approach that included extensive interviews and field tests involving 1723 students across five different undergraduate campuses.

The EvoDevoCI: a concept inventory for gauging students' understanding of evolutionary developmental biology.

The American Association for the Advancement of Science 2011 report Vision and Change in Undergraduate Biology Education encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary developmental biology, or "evo-devo." To assist in efforts to improve evo-devo instruction among undergraduate biology majors, we designed a concept inventory (CI) for evolutionary developmental biology, the EvoDevoCI.

Getting to evo-devo: concepts and challenges for students learning evolutionary developmental biology.

To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we find that instruction often addresses development cursorily, with most of the treatment embedded within instruction on evolution.