Dissociation of multiply charged negative ions for hirudin (54–65), fibrinopeptide B, and insulin A (oxidized)

AbstractCollision-induced dissociation (CID) was performed on multiply deprotonated ions from three commercial peptides: hirudin (54–65), fibrinopeptide B, and oxidized insulin chain A. Ions were produced by electrospray ionization in a Fourier transform ion cyclotron resonance mass spectrometer. Each of these peptides contains multiple acidic residues, which makes them very difficult to ionize in the positive mode. However, the peptides deprotonate readily making negative ion studies a viable alternative. The CID spectra indicated that the likely deprotonation sites are acidic residues (aspartic, glutamic, and cysteic acids) and the C-terminus. The spectra are rife with c, y, and internal ions, although some a, b, x, and z ions form. Many of the fragment ions were formed from cleavage adjacent to acidic residues, both N- and C-terminal to the acidic site. In addition, neutral loss (e.g., NH3, CH3, H2O, and CO2) was prevalent from both the parent ions and from fragment ions. These neutral eliminations were often indicative of specific amino acid residues. The fragmentation patterns from several charge states of the parent ions, when combined, provide significant primary sequence information. These results suggest that negative mode CID of multiply deprotonated ions provides useful structural information and can be worthwhile for highly acidic peptides that do not form positive ions in abundance

RANDOM MODELS WITH DIRECT AND COMPETITION GENETIC EFFECTS

Livestock producers often select for animals which are genetically superior for yield. Competition among animals in the same pen may affect yield of pen mates. If competitiveness has a genetic component, selection should be for direct genetic effects for yield and for genetic effects of competitiveness on yield of penmates (Muir and Schinkel, 2002). This simulation study examined estimates of variance components from models which ignored competition effects. A population structure of 642 related animals was created. Random effects were residual and pen effects and direct and competition genetic values with genetic correlation. Conclusions, based on 400 replications for 16 different sets of variance parameters, were that competition effects, if ignored, may inflate estimates of pen variance and of direct genetic variance and that ignoring pen effects may increase estimates of the genetic correlation and both genetic variances. Key words: Associative Effects, Genetic Correlation, REM

The Late Medieval Agrarian Crisis and Black Death plague epidemic in medieval Denmark: a paleopathological and paleodietary perspective

The medieval period of Denmark (11th-16th centuries) witnessed two of the worst demographic, health, and dietary catastrophes in history: the Late Medieval Agrarian Crisis (LMAC) and the Black Death plague epidemic. Historians have argued that these events resulted in a change in subsistence from a cereal grain to a more pastorallyfocused diet, and that the population decimation resulted in improved living conditions. This dissertation bioarchaeologically examines the impact of these historically described events on the diet and health of the population from Jutland, Denmark. I examine the stable isotopic ratios of carbon and nitrogen, dental caries, cribra orbitalia, porotic hyperostosis, periosteal reactions, and femur length to examine the samples for dietary and health differences due to sex, time period, site and social status. The results suggest that there are few chronological differences in diet or health in these samples. There are greater disparities among the sites, as peasants from the rural site had a more terrestrially-based diet and poorer health than the urban sites. While there is little difference in diet by sex, there is a disparity in health between the sexes. However, the direction of difference varies by site, suggesting that the relative treatment of the sexes was not universal in Denmark. While the results indicate there is little difference in health by status, there are dietary differences, as elites had a more marinebased diet than peasants. This research indicates the importance of bioarchaeological analysis in the interpretation of historical events. The recording of history is dependent on the viewpoint of the recorder and may not accurately reflect the importance of events on the the population itself. Bioarchaeological techniques examine skeletal material from the individuals in question and may provide a better understanding of the consequences of historic events on the population, such as the effects of the LMAC and Black Death on the population of Denmark. This research reveals that, contrary to historical expectation, these events did not have a measurable impact on Danish diet or health. Thus, the use of historical documentation and bioarchaeological analyses provides a richer understanding of these historical events

Evaluation of intake and feed efficiency measures in beef cattle

Four experiments were conducted to evaluate intake and measures of feed efficiency in beef cattle. In Exp. 1 and 2, measures of feed efficiency were calculated on Angus and SimAngus heifers (Exp.1; n = 623, and Exp. 2; 404); and heifers were classified as either high, medium, or low residual feed intake (RFI), residual BW gain (RG), residual intake and BW gain (RIG), and DMI. The objective of these experiments was to determine the relationship between post-weaning feed efficiency and intake in heifers, and subsequent cow performance, reproduction, and longevity as 2-and 5-yr-old cows. As heifer RFI improved, cow forage DMI was reduced in both 2-and 5-yr old cows (P < 0.01) and resulted in more desirable 2-yr old cow efficiency (P < 0.01). Heifer RFI classification did not affect (P ≥ 0.07) reproductive traits, cow production traits, or herd longevity up to 5 yr of age. Heifer RG classification did not affect (P ≥ 0.08) reproductive traits; cow production traits, cow efficiency, or DMI in 2-yr-old cows. As heifer RIG improved, 2-yr-old cow forage DMI was reduced (P < 0.01) during lactation, resulting in more desirable cow efficiency (P=0.02). Heifer RIG classification did not affect (P ≥ 0.12) reproductive traits; calf birth or weaning BW; cow BW, milk production, 12th rib fat thickness, or BCS in 2-yr old cows. Heifer DMI was highly correlated (P < 0.05) to cow forage intake as both 2- and 5-yr-old cows. Heifers classified as low DMI were least frequently (P < 0.01) kept as replacements and were youngest (P = 0.04) at first calving. Calves from 2-yr-old cows, classified as high DMI heifers, had the greatest (P < 0.01) birth BW; yet, there were no differences (P=0.60) in weaning BW. Intake classification had no effect (P ≥ 0.07) on cow BCS, 12th rib fat thickness, or milk production in either 2- or 5-yr-old cows. Cows, classified as low DMI heifers, weighed the least (P = 0.02) and had reduced (P < 0.01) hip heights as both 2- and 5-yr old cows. Cows, classified as low DMI heifers, had reduced (P ≤ 0.01) DMI, improved (P = 0.01) cow efficiency, and a greater percentage of females remaining in the herd at 5 yr of age. These data indicate that females classified as more efficient have reduced cow DMI without compromising production traits and longevity. Heifer DMI is an accurate predictor of cow forage intake at different biological time points in life. In Exp. 3, measures of feed efficiency were determined in Angus and Simmental X Angus heifers (n=263), and heifers were classified within feed intake and efficiency groups as described in Exp. 1 and 2. The objective of this experiment was to determine the relationship between measures of heifer feed efficiency and mature cow intake of forage of divergent quality. At 5 or 6-yr of age, cows were evaluated for voluntary forage intake of high-quality forage (HQDMI) and poor-quality forage (PQDMI). Heifer RFI classification had no effect on cow production traits; yet, cows classified with the least desirable heifer RFI had the greatest (P ≤ 0.05) HQDMI and PQDMI. Heifer RG classification had no effect on cow production traits or DMI. Heifer RIG classification had no effect on cow traits. Cows classified as low RIG heifers had the greatest (P = 0.02) HQDMI; yet, only tended to have the greatest PQDMI (P = 0.09). Cows classified as high DMI heifers were heavier (P = 0.05) and had greater (P < 0.01) DMI than cows classified as low or medium DMI heifers. This study suggests that feed costs can be reduced by selection for heifer RFI, RIG, and DMI. In Exp. 4, Charolais crossbred heifers and steers (n=628) endured two performance and intake tests during the growing and finishing phases of the feedlot phase. Objectives were to determine the effects of test period duration, timing, and diet type on measures of feed efficiency in feedlot calves. Dry matter intake and RFI were repeatable (r=0.56; P<0.01, and 0.63; P<0.01, respectively) for both periods of grain-fed steers. Average daily gain was not repeatable (r=0.11; P=0.06) across both test periods for steers. However, growing and finishing ADG were correlated (r=0.58; P<0.01, and r=0.69; P<0.01, respectively) to total feeding period ADG. Regardless of test length, from 7 to 70d, DMI was correlated (r≥0.87; P<0.01) to total DMI during the growing period. Heifer forage DMI was correlated (r=0.58; P<0.01) to grain DMI. Forage and grain RFI were moderately correlated (r=0.40; P<0.01) for heifers. These data indicate that DMI is repeatable across varying stages of maturity in cattle, and accurate feed efficiency measures can be obtained in either the growing or finishing period. The relationship of forage and grain DMI and efficiency in heifers suggests that measures of DMI and feed efficiency are relevant, regardless of diet fed. Intake evaluation periods can be shortened without losing accuracy in predicting individual animal DMI; and measures of feed efficiency can be calculated by decoupling performance and intake information. Collectively, these experiments provide insight into the effects of DMI and feed efficiency on many production traits; and the potential methods in which both feedlot and cow-calf producers can improve profitability within their operations

Environmental Policy Update 2012: Development Strategies and Environmental Policy in East Africa

The seven chapters that comprise this report explore ways to integrate sustainability goals and objectives into Ethiopia's current development strategies

The differential regulation of Lck kinase phosphorylation sites by CD45 is critical for T cell receptor signaling responses

SummaryThe molecular mechanisms whereby the CD45 tyrosine phosphatase (PTPase) regulates T cell receptor (TCR) signaling responses remain to be elucidated. To investigate this question, we have reconstituted CD45 (encoded by Ptprc)-deficient mice, which display severe defects in thymic development, with five different expression levels of transgenic CD45RO, or with mutant PTPase null or PTPase-low CD45R0. Whereas CD45 PTPase activity was absolutely required for the reconstitution of thymic development, only 3% of wild-type CD45 activity restored T cell numbers and normal cytotoxic T cell responses. Lowering the CD45 expression increased CD4 lineage commitment. Peripheral T cells with very low activity of CD45 phosphatase displayed reduced TCR signaling, whereas intermediate activity caused hyperactivation of CD4+ and CD8+ T cells. These results are explained by a rheostat mechanism whereby CD45 differentially regulates the negatively acting pTyr-505 and positively acting pTyr-394 p56lck tyrosine kinase phosphorylation sites. We propose that high wild-type CD45 expression is necessary to dephosphorylate p56lck pTyr-394, suppressing CD4 T+ cell lineage commitment and hyperactivity

Towards a state-space geometry of neural responses to natural scenes: A steady-state approach

Our understanding of information processing by the mammalian visual system has come through a variety of techniques ranging from psychophysics and fMRI to single unit recording and EEG. Each technique provides unique insights into the processing framework of the early visual system. Here, we focus on the nature of the information that is carried by steady state visual evoked potentials (SSVEPs). To study the information provided by SSVEPs, we presented human participants with a population of natural scenes and measured the relative SSVEP response. Rather than focus on particular features of this signal, we focused on the full state-space of possible responses and investigated how the evoked responses are mapped onto this space. Our results show that it is possible to map the relatively high-dimensional signal carried by SSVEPs onto a 2-dimensional space with little loss. We also show that a simple biologically plausible model can account for a high proportion of the explainable variance (~73%) in that space. Finally, we describe a technique for measuring the mutual information that is available about images from SSVEPs. The techniques introduced here represent a new approach to understanding the nature of the information carried by SSVEPs. Crucially, this approach is general and can provide a means of comparing results across different neural recording methods. Altogether, our study sheds light on the encoding principles of early vision and provides a much needed reference point for understanding subsequent transformations of the early visual response space to deeper knowledge structures that link different visual environments

Sites of Biosynthesis of Outer and Inner Membrane Proteins of Neurospora crassa Mitochondria

Outer and inner membranes of Neurospora crassa mitochondria were separated by the combined swelling, shrinking, sonication procedure. Membranes were characterized by electron microscopy and by marker enzyme activities. A red carotenoid pigment was found to be concentrated in the outer membrane. The inner mitochondrial membrane was resolved into about 20 protein bands on polyacrylamide gel electrophoresis, whereas the outer membrane shows essentially one single protein band. Only negligible incorporation of radioactive amino acids occurs into outer membrane when isolated mitochondria are synthesizing polypeptide chains. In agreement with this observation labeling of outer membrane protein is almost entirely blocked, when whole Neurospora cells are incubated with radioactive amino acids in the presence of cycloheximide, an inhibitor of cytoplasmic protein synthesis. Finally, the essential electrophoretic protein band from outer membrane does not become labeled when mitochondria are incubated with radioactive amino acids either in vitro or in vivo in the presence of cycloheximide. It is concluded that the vast majority, if not all, of the outer membrane protein is synthesized by the cytoplasmic system and that polypeptide chains formed by the mitochondrial ribosomes are integrated into the inner mitochondrial membrane