Comparison of methods for detection of pinworms in mice and rats

Though pinworm infestation remains common in laboratory rodent colonies, there is little information regarding current practices for pinworm detection and their relative efficacy. The authors surveyed research institutions to find out the prevalence of pinworm infestations and the detection methods they used. They also tested mice and rats from colonies that were known to be infested with Syphacia sp. and compared the following detection methods: perianal tape test, fecal flotation, fecal concentration, cecal content examination, cecal flotation and histological examination. Though the different methods yielded comparable efficacy overall, the authors recommend using more than one type of test to increase detection potential.     

Body size and postcranial robusticity of European Upper Paleolithic hominins

The robust diaphyses of Pleistocene hominins are said to indicate higher activity levels in these prehistoric humans than among people today. Thus, it could be argued that the prediction of body mass from fossil lower limb diaphyseal cortical area (CA) using recent human regressions might lead to erroneously high body mass estimates. This study uses three body mass prediction formulae based on the following features: reconstructed femoral 80% (subtrochanteric) CA, femoral head diameter (FH), and bi-iliac breadth and stature (BIB-St) among European Early and Late Upper Paleolithic (EUP and LUP) and recent humans from Africa and Europe. All three methods produce similar body mass estimates for all groups studied, including recent humans.Gleaning behavioral differences from these data is more difficult, as no significant differences in CA were found among the fossil and recent Europeans. It has been suggested that the EUP had less robust diaphyses than their LUP counterparts. However, here this result is only obtained when CA is size-standardized to femoral length(3) (Ruff et al., 1993, Am. J. phys. Anthrop.91, 21-53 Trinkaus et al., 1998, in Neandertals and Modern Humans in Western Asia, pp.391-404, New York: Plenum). This should not be interpreted as evidence for lower activity levels in the EUP, but rather as an artefact of standardization, for as Wolpoff (1999), Am. J. phys. Anthrop.109, 416-423 points out, these standardized variables are extremely sensitive to limb length differences, and the EUP have longer limbs than their LUP counterparts. With this in mind, these data do not support a pattern of behavioral differences between EUP and LUP humans, and therefore more sensitive measures than CA may be required to detect such differences.     

Clinical and necropsy findings associated with increased mortality among American alligators of Lake Griffin,Florida

From December, 1997, through November, 2000, 306 deaths were documented among adult and subadult American alligators (Alligator mississippiensis) of Lake Griffin, Florida (USA). Some live alligators were lethargic and unresponsive to approach. To determine the cause, we examined ten alligators captured from Lake Griffin between December 1997 and June 1999. Initially, four alligators, three of which were clinically unresponsive, were sacrificed for routine diagnostic necropsy. The other six Lake Griffin alligators, and five control alligators captured from Lake Woodruff National Wildlife Refuge, Florida, where mortality was negligible, were studied extensively by clinical neurologic examination, electromyography, hematology, serum chemical analyses, and blood culture, then sacrificed and necropsied. Samples of brain, spinal cord, peripheral nerves, skeletal muscle, and major internal organs were examined by light microscopy for abnormalities. Samples of nervous tissue also were examined by electron microscopy, and samples of various tissues were collected for toxicologic analyses. Clinical signs included swimming in circles, inability to submerge, lethargy, weakness, unresponsiveness, slow reflexes, dragging the dorsal surfaces of the hind feet, head tilt, and anisocoria. Lake Griffin alligators had significantly lower distal sciatic nerve conduction velocities than Lake Woodruff alligators, and the most severely affected alligators had the lowest velocities; but morphologic abnormalities in peripheral nerves were not evident in most cases. Three severely affected alligators had acute focal necrosis of the torus semicircularis in the midbrain, two had skeletal myofiber atrophy, another had diffuse nonsuppurative encephalomyelitis, and one mildly affected alligator had skeletal myodegeneration. The cause or causes have not yet been identified.     

Ectopic DICER-LIKE1 expression in P1/HC-Pro Arabidopsis rescues phenotypic anomalies but not defects in microRNA and silencing pathways

Expression of the viral silencing suppressor P1/HC-Pro in plants causes severe developmental anomalies accompanied by defects in both short interfering RNA (siRNA) and microRNA (miRNA) pathways. P1/HC-Pro transgenic lines fail to accumulate the siRNAs that mediate RNA silencing and are impaired in both miRNA processing and function, accumulating abnormally high levels of miRNA/miRNA* processing intermediates as well as miRNA target messages. Both miRNA and RNA silencing pathways require participation of DICER-LIKE (DCL) ribonuclease III-like enzymes. Here, we investigate the effects of overexpressing DCL1, one of four Dicers in Arabidopsis thaliana, on P1/HC-Pro-induced defects in development and small RNA metabolism. Expression of a DCL1 cDNA transgene (35S:DCL1) produced a mild gain-of-function phenotype and largely rescued dcl1 mutant phenotypes. The 35S:DCL1 plants were competent for virus-induced RNA silencing but were impaired in transgene-induced RNA silencing and in the accumulation of some miRNAs. Ectopic DCL1 largely alleviated developmental anomalies in P1/HC-Pro plants but did not correct the P1/HC-Pro-associated defects in small RNA pathways. The ability of P1/HC-Pro plants to suppress RNA silencing and the levels of miRNAs, miRNA*s, and miRNA target messages in these plants were essentially unaffected by ectopic DCL1. These data suggest that P1/HC-Pro defects in development do not result from general impairments in small RNA pathways and raise the possibility that DCL1 participates in processes in addition to miRNA biogenesis.     

Violation of an Evolutionarily Conserved Immunoglobulin Diversity Gene Sequence Preference Promotes Production of dsDNA-Specific IgG Antibodies

Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3), which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (D_H) gene segment sequence content by reading frame (RF) is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used D_H RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1), which is rearranged by inversion. To determine the effect of altering this germline bias in D_H gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type D_H sequence did not. Thus, germline bias against the use of arginine enriched D_H sequence helps to reduce the likelihood of producing self-reactive antibodies.     

Cardiomyopathy and response to enzyme replacement therapy in a male mouse model for Fabry disease

Fabry disease is an X-linked disorder of glycosphingolipid metabolism that results in progressive accumulation of neutral glycosphingolipids, (predominately globotriaosylceramide; GL-3) in lysosomes, as well as other cellular compartments and the extracellular space. Our aim was to characterize the cardiac phenotype of male knock-out mice that are deficient in alpha-galactosidase A activity, as a model for Fabry disease and test the efficacy of Enzyme Replacement Therapy with agalsidase-beta. Male mice (3-4 months of age) were characterized with awake blood pressure and heart rate measurements, cardiac echocardiography and electrocardiography measurements under light anesthesia, histological studies and molecular studies with real-time polymerase chain reaction. The Fabry knock-out mouse has bradycardia and lower blood pressure than control wild type (CB7BL/6J) mice. In Fabry knock-out mice, the cardiomyopathy associated mild hypertrophy at echography with normal systolic LV function and mild diastolic dysfunction. Premature atrial contractions were more frequent in without conduction defect. Heart weight normalized to tibial length was increased in Fabry knock-out mice. Ascending aorta dilatation was observed. Molecular studies were consistent with early stages of cardiac remodeling. A single dose of agalsidase-beta (3 mg/kg) did not affect the LV hypertrophy, function or heart rate, but did improve the mRNA signals of early cardiac remodeling. In conclusion, the alpha-galactosidase A deficient mice at 3 to 4 months of age have cardiac and vascular alterations similar to that described in early clinical stage of Fabry disease in children and adolescents. Enzyme replacement therapy affects cardiac molecular remodeling after a single dose.     

Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing

Little is known about the thermodynamic forces that drive the folding pathways of higher-order RNA structure. In this study, we employ calorimetric [isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC)] and spectroscopic (NMR and UV) methods to characterize the thermodynamics of the GAAA tetraloop-receptor interaction, utilizing a previously described bivalent construct. ITC studies indicate that the bivalent interaction is enthalpy driven and highly stable, with a binding constant (K(obs)) of 5.5x10(6) M(-1) and enthalpy (DeltaH(obs)(o)) of -33.8 kcal/mol at 45 degrees C in 20 mM KCl and 2 mM MgCl(2). Thus, we derive the DeltaH(obs)(o) for a single tetraloop-receptor interaction to be -16.9 kcal/mol at these conditions. UV absorbance data indicate that an increase in base stacking quality contributes to the enthalpy of complex formation. These highly favorable thermodynamics are consistent with the known critical role for the tetraloop-receptor motif in the folding of large RNAs. Additionally, a significant heat capacity change (DeltaC(p,obs)(o)) of -0.24 kcal mol(-1) K(-1) was determined by ITC. DSC and UV-monitored thermal denaturation experiments indicate that the bivalent tetraloop-receptor construct follows a minimally five-state unfolding pathway and suggest the observed DeltaC(p,obs)(o) for the interaction results from a temperature-dependent unbound receptor RNA structure.     

Quantifying irrigation cooling benefits to maize yield in the US Midwest

Irrigation is an important adaptation strategy to improve crop resilience to global climate change. Irrigation plays an essential role in sustaining crop production in water‐limited regions, as irrigation water not only benefits crops through fulfilling crops' water demand but also creates an evaporative cooling that mitigates crop heat stress. Here we use satellite remote sensing and maize yield data in the state of Nebraska, USA, combined with statistical models, to quantify the contribution of cooling and water supply to the yield benefits due to irrigation. Results show that irrigation leads to a considerable cooling on daytime land surface temperature (?1.63°C in July), an increase in enhanced vegetation index (+0.10 in July), and 81% higher maize yields compared to rainfed maize. These irrigation effects vary along the spatial and temporal gradients of precipitation and temperature, with a greater effect in dry and hot conditions, and decline toward wet and cool conditions. We find that 16% of irrigation yield increase is due to irrigation cooling, while the rest (84%) is due to water supply and other factors. The irrigation cooling effect is also observed on air temperature (?0.38 to ?0.53°C) from paired flux sites in Nebraska. This study highlights the non‐negligible contribution of irrigation cooling to the yield benefits of irrigation, and such an effect may become more important in the future with continued warming and more frequent droughts.     

Identification of a Precursor Pool of Ribosome Protein in Escherichia coli

Antibodies prepared against proteins from 50S ribosomes of Escherichia coli also reacted with the supernatant proteins of a cell-free extract of E. coli which was ribosome-free. A reaction of immunological identity (Ouchterlony tests) was demonstrated for one of these supernatant proteins and one protein found in 50S ribosomes. Isotope experiments involving a shift from (14)C-leucine medium to (12)C-leucine medium showed that these proteins are not formed by breakdown of ribosomes during the preparation of cell-free extracts, but instead represent a pool of ribosome protein which is utilized during growth. In shift experiments from (14)C-leucine to (12)C-leucine medium, the kinetics of disappearance of labeled supernatant ribosome proteins (as measured by reaction with antibody) indicated that half the pool is depleted in 0.1 generation time at 37 C in glucose-salts medium. The pool was also depleted under conditions of amino acid starvation of a "relaxed" strain which accumulated "relaxed" particles. Most, if not all, of the protein present in "relaxed" particles was derived from the pool. The pool represented about 3 to 4% of the total soluble proteins in the ribosome-free supernatant fluid of an E. coli extract.     

Bayesian model aggregation for ensemble‐based estimates of protein pKa values

This article investigates an ensemble‐based technique called Bayesian Model Averaging (BMA) to improve the performance of protein amino acid pK_a predictions. Structure‐based pK_a calculations play an important role in the mechanistic interpretation of protein structure and are also used to determine a wide range of protein properties. A diverse set of methods currently exist for pK_a prediction, ranging from empirical statistical models to ab initio quantum mechanical approaches. However, each of these methods are based on a set of conceptual assumptions that can effect a model's accuracy and generalizability for pK_a prediction in complicated biomolecular systems. We use BMA to combine eleven diverse prediction methods that each estimate pK_a values of amino acids in staphylococcal nuclease. These methods are based on work conducted for the pK_a Cooperative and the pK_a measurements are based on experimental work conducted by the García‐Moreno lab. Our cross‐validation study demonstrates that the aggregated estimate obtained from BMA outperforms all individual prediction methods with improvements ranging from 45 to 73% over other method classes. This study also compares BMA's predictive performance to other ensemble‐based techniques and demonstrates that BMA can outperform these approaches with improvements ranging from 27 to 60%. This work illustrates a new possible mechanism for improving the accuracy of pK_a prediction and lays the foundation for future work on aggregate models that balance computational cost with prediction accuracy. Proteins 2014; 82:354–363. © 2013 Wiley Periodicals, Inc.