Interim progress report on a study of the utility of data obtainable from otoliths to management of Humpback Chub (Gila cypha) in the Grand Canyon

Daily growth increments of otoliths of fishes have been useful in many fishery applications since they have been demonstrated to provide a precise method of ageing individuals and reconstructing individual growth and, possibly, movement or habitat histories. These techniques have not been previously applied to humpback chub, but are believed to have considerable potential for providing knowledge of this difficult to sample and little-understood species. Large temperature and water quality gradients apparently traversed by individuals of this species in the Grand Canyon are of a magnitude likely to produce structural and/or chemical signals in the crystalline calcareous otoliths. If so, since otoliths grow by accretion of daily increments (much like trees develop yearly growth rings), and are stable structures, which unlike scales, are not susceptible to reabsorption except in the most extreme conditions, they retain a structural and chemical chronology of habitats occupied. If the relationships of ambient physical and chemical conditions to otolith structure and composition can be described, a chronology of habitat occupancy and growth for individuals could theoretically be reconstructed with daily precision. Such reconstructions of growth rates, birth dates, movement histories, and possibly, birth place (based on chemistry at otolith formation or during early life), could provide extremely valuable life-history information regarding timing of spawning, cohort recruitment, mortality rates, and data on other population parameters critical for management of this endangered species. The feasibility of using otoliths and opercles of humpback chub for age estimation of individuals has been preliminarily investigated by examining otoliths and opercles from a total of 47 juvenile (ages 0 through 1 +)and 43 adult (estimated ages 2- 23) specimens collected in the Little Colorado River (71 specimens) and mainstream Colorado River (19 specimens) at various places in the Grand Canyon between 1988 and 1992. Studies are continuing, and at this point, due to both sample size and numerous other limitations, and ongoing refinements of techniques, conclusions made here are highly preliminary. Structures prepared and examined included opercles of 35 specimens, one asteriscus from each of 47 specimens and a lapillus from each of 56 specimens. Seventeen specimens were evaluated using all three calcareous structures (lapillus, asteriscus and opercle). The sagitta was also examined, but found to be unsuitable for ageing purposes due to its long, delicate form and irregular increments after the larval/juvenile stage. Additional lapilli have been removed from other available specimens, and a complete inventory of specimens available for further study of calcified structures is provided. Studies of micro-spatial variation in chemical composition of selected lapilli is in progress, using the highly accurate proton probe at the Institute of Geological and Nuclear Sciences in Lower Hutt, New Zealand. This method of analysis shows great promise of overcoming what has been indicated in recent literature to be significant inaccuracies of other techniques (Energy Dispersive X-ray diffraction and Wave Length dispersive X-ray diffraction) used in many of the published studies of microspatial elemental analysis of otoliths.Arizona Game and Fish DepartmentIntegrative Biolog

Stereochemistry of Polypeptide Conformation in Coarse Grained Analysis

The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed predominantly from {\alpha}-helices and {\beta}-sheets, they nevertheless adopt diverse tertiary structure, each folded as dictated by its unique amino-acid sequence. Despite such uniqueness, however, the functioning of many proteins involves changes between quite different conformations. The study of large-scale conformational changes, particularly in large systems, is facilitated by a coarse-grained representation such as provided by virtually bonded C{\alpha} atoms. We have developed a virtual atom molecular mechanics (VAMM) force field to describe conformational dynamics in proteins and a VAMM-based algorithm for computing conformational transition pathways. Here we describe the stereochemical analysis of proteins in this coarse-grained representation, comparing the relevant plots in coarse-grained conformational space to the corresponding Ramachandran plots, having contoured each at levels determined statistically from residues in a large database. The distributions shown for an all-{\alpha} protein, two all-{\beta} proteins and one {\alpha}+{\beta} protein serve to relate the coarse-grained distributions to the familiar Ramachandran plot.Comment: 12 pages, 3 figures, Postprint of book chapter submitted to the Biomolecular Forms and Functions, M. Bansal and N. Srinivasan, Eds. copyright (2013) [copyright World Scientific Publishing Company

Viral pathogens and acute lung injury: investigations inspired by the SARS epidemic and the 2009 H1N1 influenza pandemic.

Acute viral pneumonia is an important cause of acute lung injury (ALI), although not enough is known about the exact incidence of viral infection in ALI. Polymerase chain reaction-based assays, direct fluorescent antigen (DFA) assays, and viral cultures can detect viruses in samples from the human respiratory tract, but the presence of the virus does not prove it to be a pathogen, nor does it give information regarding the interaction of viruses with the host immune response and bacterial flora of the respiratory tract. The severe acute respiratory syndrome (SARS) epidemic and the 2009 H1N1 influenza pandemic provided a better understanding of how viral pathogens mediate lung injury. Although the viruses initially infect the respiratory epithelium, the relative role of epithelial damage and endothelial dysfunction has not been well defined. The inflammatory host immune response to H1N1 infection is a major contributor to lung injury. The SARS coronavirus causes lung injury and inflammation in part through actions on the nonclassical renin angiotensin pathway. The lessons learned from the pandemic outbreaks of SARS coronavirus and H1N1 capture key principles of virally mediated ALI. There are pathogen-specific pathways underlying virally mediated ALI that converge onto a common end pathway resulting in diffuse alveolar damage. In terms of therapy, lung protective ventilation is the cornerstone of supportive care. There is little evidence that corticosteroids are beneficial, and they might be harmful. Future therapeutic strategies may be targeted to specific pathogens, the pathogenetic pathways in the host immune response, or enhancing repair and regeneration of tissue damage

Fishes of Texas Project: Data Visualization and Analysis Tools

Poster presentation presented at the 2020 Texas Chapter of the American Fisheries Society annual meeting in Waco, Texas on January 24, 2020.The Fishes of Texas Project (FoTX) (http://fishesoftexas.org) database currently has 124,452 specimen-vouchered occurrence records spanning > 150 years with over 400,000 new records (including non-vouchered sources such as literature, anecdotal, and photo-based) in the process of being imported. Continual data growth prompted creation of new tools to dynamically assess (as the data evolve) the state of data coverage across various dimensions to increase user understanding and accessibility to the data and improve overall utility of the project. We produced species sampling curves, temporal species accumulation graphs, and heat maps of collecting event density over time and space for each river sub-basin within Texas. A QGIS plugin was also created to better assess the suspect status of incoming records. Each type of visualization has basic documentation, easily accessible statistical summaries, flexible queries, and exploration tools to help reveal variations in sampling density over both temporal and spatial dimensions. We highlight here the San Bernard River as an example of a notably under-sampled sub-basin (as indicated by diverse forms of evidence). With addition of future records, these dynamic tools will continue to illustrate taxonomic and spatial sampling deficiencies that in turn will help guide conservation planning.Texas Parks and Wildlife Department, under the U.S. Fish and Wildlife Service State Wildlife Grant Program, grant TX T-180-R-1, F17AF01129 (CFDA# 15.634)Integrative Biolog

Documentation Related to a 1991 Observation of Sturgeon in the Rio Grande – Río Bravo, USA (Texas) and Mexico (Coahuila)

This digital archive provides a compilation of previously unpublished information regarding a 1991 observation of a live sturgeon (Family Acipenseridae) in the Rio Grande-Río Bravo of the USA and Mexico. Though a few specimens collected in the 19th century support occurrence of sturgeon in this river basin, lack of credible, recent records has often led to this species not being recognized as part of the basin’s native fish fauna, and certainly not part of its modern fish community. The second and third authors of this document manage the Fishes of Texas Project (Hendrickson, Dean A., & Cohen, Adam E. (2015). Fishes of Texas Project Database (version 2.0). Texas Advanced Computing Center, University of Texas at Austin. http://doi.org/10.17603/C3WC70) and knew of the unpublished 1991 observation of sturgeon reported here. They requested the content provided here from first author (Platania) who provided what follows below (verbatim as received in April 2018) and permission to archive it for public access.Integrative Biolog

Electronic and Optical Properties of Vacancy Defects in Transition Metal Dichalcogenides

A detailed first-principle study has been performed to evaluate the electronic and optical properties of single-layer (SL) transition metal dichalcogenides (TMDCs) (MX${}_2$; M= transition metal such as Mo, W and X= S, Se, Te), in the presence of vacancy defects (VDs). Defects usually play an important role in tailoring electronic, optical, and magnetic properties of semiconductors. We consider three types of VDs in SL TMDCs i) $X$-vacancy, $X_{2}$-vacancy, and iii) $M$-vacancy. We show that VDs lead to localized defect states (LDS) in the band structure, which in turn give rise to sharp transitions in in-plane and out-of-plane optical susceptibilities, $\chi_{\parallel}$ and $\chi_{\perp}$. The effects of spin orbit coupling (SOC) are also considered. We find that SOC splitting in LDS is directly related to the atomic number of the transition metal atoms. Apart from electronic and optical properties we also find magnetic signatures (local magnetic moment of $\sim\mu_{B}$) in MoSe$_{2}$ in the presence of Mo vacancy, which breaks the time reversal symmetry and therefore lifts the Kramers degeneracy. We show that a simple qualitative tight binding model (TBM), involving only the hopping between atoms surrounding the vacancy with an on-site SOC term, is sufficient to capture the essential features of LDS. In addition, the existence of the LDS can be understood from the solution of the 2D Dirac Hamiltonian by employing infinite mass boundary conditions. In order to provide a clear description of the optical absorption spectra, we use group theory to derive the optical selection rules between LDS for both $\chi_{\parallel}$ and $\chi_{\perp}$.Comment: 14 pages, 11 figure

Simulation Studies of the NLC with Improved Ground Motion Models

The performance of various systems of the Next Linear Collider (NLC) have been studied in terms of ground motion using recently developed models. In particular, the performance of the beam delivery system is discussed. Plans to evaluate the operation of the main linac beam-based alignment and feedback systems are also outlined.Comment: Submitted to XX International Linac Conferenc

Assessment in Finland: A Scholarly Reflection on One Country’s Use of Formative, Summative, and Evaluative Practices

Finland’s high test scores have prompted international comparisons of educational policy. This article explores the use of assessment in Finland, particularly the intended use of student assessment and evaluation of schools as described in the National Curriculum. This article explores Finnish educational policy through the lens of formative and summative assessment in attempt to gain further understanding of the differences between Finland and the United States