Utilisation of key descriptors from protein sequence data to aid bioprocess route selection

The large-scale manufacture of biological products results in the generation of significant quantities of process information that can be used to inform future design decisions. Currently this information is not exploited to its full potential. The challenge is thus to identify and/or develop tools that allow the utilisation of this valuable resource. The main objective of the research reported in this paper was to investigate whether it was possible to utilise information, in particular that extracted from protein sequence data, from previous processes, with the goal of informing process route selection early in development. The approach adopted draws on tools in the areas of data mining and pattern recognition including the techniques of Fisher correlation score and self-organising maps. The methodology developed was applied to two case studies utilising data from the amino acid sequences of 41 proteins previously developed at Avecia Biologics, along with associated information relating to the downstream processing steps used during their large scale manufacture. The results demonstrate that information from previous processes can be used to inform process route selection

THE RHYTHM OF FAIRALL 9. I. OBSERVING THE SPECTRAL VARIABILITY WITH XMM-NEWTON AND NuSTAR

© 2016. The American Astronomical Society. All rights reserved. We present a multi-epoch X-ray spectral analysis of the Seyfert 1 galaxy Fairall 9. Our analysis shows that Fairall 9 displays unique spectral variability in that its ratio residuals to a simple absorbed power law in the 0.5-10 keV band remain constant with time in spite of large variations in flux. This behavior implies an unchanging source geometry and the same emission processes continuously at work at the timescale probed. With the constraints from NuSTAR on the broad-band spectral shape, it is clear that the soft excess in this source is a superposition of two different processes, one being blurred ionized reflection in the innermost parts of the accretion disk, and the other a continuum component such as a spatially distinct Comptonizing region. Alternatively, a more complex primary Comptonization component together with blurred ionized reflection could be responsible

NuSTAR observations of Mrk 766: Distinguishing reflection from absorption

We present two new NuSTAR observations of the narrow line Seyfert 1 (NLS1) galaxy Mrk 766 and give constraints on the two scenarios previously proposed to explain its spectrum and that of other NLS1s: relativistic reflection and partial covering. The NuSTAR spectra show a strong hard (> 15 keV) X-ray excess, while simultaneous soft X-ray coverage of one of the observations provided by XMM-Newton constrains the ionised absorption in the source. The pure reflection model requires a black hole of high spin (a > 0.92) viewed at a moderate inclination (i = 46 +1 −4 ). The pure partial covering model requires extreme parameters: the cut-off of the primary continuum is very low (22 +7 −5 keV) in one observation and the intrinsic X-ray emission must provide a large fraction (75%) of the bolometric luminosity. Allowing a hybrid model with both partial covering and reflection provides more reasonable absorption parameters and relaxes the constraints on reflection parameters. The fractional variability reduces around the iron K band and at high energies including the Compton hump, suggesting that the reflected emission is less variable than the continuum

A genome-wide association study identifies protein quantitative trait loci (pQTLs)

There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts - cis effects, and elsewhere in the genome - trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8×10 -57), CCL4L1 (p = 3.9×10-21), IL18 (p = 6.8×10-13), LPA (p = 4.4×10-10), GGT1 (p = 1.5×10-7), SHBG (p = 3.1×10-7), CRP (p = 6.4×10-6) and IL1RN (p = 7.3×10-6) genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R), altered secretion rates of different sized proteins (LPA), variation in gene copy number (CCL4L1) and altered transcription (GGT1). We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha) levels (p = 6.8×10-40), but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis locations. The identification of protein quantitative trait loci (pQTLs) may be a powerful complementary method of improving our understanding of disease pathways. © 2008 Melzer et al

NuSTAR and XMM-Newton observations of NGC 1365: Extreme absorption variability and a constant inner accretion disk

We present a spectral analysis of four coordinated NuSTAR+XMM-Newton observations of the Seyfert galaxy NGC 1365. These exhibit an extreme level of spectral variability, which is primarily due to variable line-of-sight absorption, revealing relatively unobscured states in this source for the first time. Despite the diverse range of absorption states, each of the observations displays the same characteristic signatures of relativistic reflection from the inner accretion disk. Through time-resolved spectroscopy we find that the strength of the relativistic iron line and the Compton reflection hump relative to the intrinsic continuum are well correlated, as expected if they are two aspects of the same broadband reflection spectrum. We apply self-consistent disk reflection models to these time-resolved spectra in order to constrain the inner disk parameters, allowing for variable, partially covering absorption to account for the vastly different absorption states observed. Each of the four observations is treated independently to test the consistency of the results obtained for the black hole spin and the disk inclination, which should not vary on observable timescales. We find both the spin and the inclination determined from the reflection spectrum to be consistent, confirming NGC 1365 hosts a rapidly rotating black hole; in all cases the dimensionless spin parameter is constrained to be a* > 0.97 (at 90% statistical confidence or better)

Perceiving Nasal Patency through Mucosal Cooling Rather than Air Temperature or Nasal Resistance

Adequate perception of nasal airflow (i.e., nasal patency) is an important consideration for patients with nasal sinus diseases. The perception of a lack of nasal patency becomes the primary symptom that drives these patients to seek medical treatment. However, clinical assessment of nasal patency remains a challenge because we lack objective measurements that correlate well with what patients perceive.The current study examined factors that may influence perceived patency, including air temperature, humidity, mucosal cooling, nasal resistance, and trigeminal sensitivity. Forty-four healthy subjects rated nasal patency while sampling air from three facial exposure boxes that were ventilated with untreated room air, cold air, and dry air, respectively. In all conditions, air temperature and relative humidity inside each box were recorded with sensors connected to a computer. Nasal resistance and minimum airway cross-sectional area (MCA) were measured using rhinomanometry and acoustic rhinometry, respectively. General trigeminal sensitivity was assessed through lateralization thresholds to butanol. No significant correlation was found between perceived patency and nasal resistance or MCA. In contrast, air temperature, humidity, and butanol threshold combined significantly contributed to the ratings of patency, with mucosal cooling (heat loss) being the most heavily weighted predictor. Air humidity significantly influences perceived patency, suggesting that mucosal cooling rather than air temperature alone provides the trigeminal sensation that results in perception of patency. The dynamic cooling between the airstream and the mucosal wall may be quantified experimentally or computationally and could potentially lead to a new clinical evaluation tool

Individual, facility and policy level influences on national coverage estimates for intermittent preventive treatment of malaria in pregnancy in Tanzania

BACKGROUND: Delivery of two doses of intermittent preventive treatment of malaria during pregnancy (IPTp) is a key strategy to reduce the burden of malaria in pregnancy in sub-Saharan Africa. However, different settings have reported coverage levels well below the target 80%. Antenatal implementation guidelines in Tanzania recommend IPTp first dose to be given at the second antenatal visit, and second dose at the third visit. This investigation measured coverage of IPTp at national level in Tanzania and examined the role of individual, facility, and policy level influences on achieved coverage. METHODS: Three national household and linked reproductive and child health (RCH) facility surveys were conducted July-August 2005, 2006, and 2007 in 210 clusters sampled using two-stage cluster sampling from 21 randomly selected districts. Female residents who reported a livebirth in the previous year were asked questions about malaria prevention during that pregnancy and individual characteristics including education, pregnancy history, and marital status. The RCH facility serving each cluster was also surveyed, and information collected about drug stocks, health education delivery, and the timing of antenatal care delivery by clinic users. RESULTS: The national IPTp coverage had declined over the survey period being 71% for first dose in 2005 falling to 65% in 2007 (chi2 2.9, p = 0.05), and 38% for second dose in 2005 but 30% in 2007 (chi2 4.4, p = 0.01). There was no evidence of any individual factors being associated with second dose coverage beyond living in an urban area. Availability of sulphadoxine-pyrimethamine at RCH had decreased year on year from 85% of clinics in stock in 2005 to 60% in 2007 (chi2 20.6, p < 0.001). This reduction was evident in rural but not urban clinics. If safety recommendations and national antenatal care guidelines for IPTp delivery were followed, in 2007 only 76% of pregnant women could have received IPTp first dose and only 46% could have received second dose. CONCLUSION: There is scope to improve IPTp first and second dose coverage at national scale within existing systems by improving stock at RCH, and by revising the existing guidelines to recommend delivery of IPTp after quickening, rather than at a pre-defined antenatal visit

Metabolic acceleration and the evolution of human brain size and life history.

Humans are distinguished from the other living apes in having larger brains and an unusual life history that combines high reproductive output with slow childhood growth and exceptional longevity. This suite of derived traits suggests major changes in energy expenditure and allocation in the human lineage, but direct measures of human and ape metabolism are needed to compare evolved energy strategies among hominoids. Here we used doubly labelled water measurements of total energy expenditure (TEE; kcal day(-1)) in humans, chimpanzees, bonobos, gorillas and orangutans to test the hypothesis that the human lineage has experienced an acceleration in metabolic rate, providing energy for larger brains and faster reproduction without sacrificing maintenance and longevity. In multivariate regressions including body size and physical activity, human TEE exceeded that of chimpanzees and bonobos, gorillas and orangutans by approximately 400, 635 and 820 kcal day(-1), respectively, readily accommodating the cost of humans' greater brain size and reproductive output. Much of the increase in TEE is attributable to humans' greater basal metabolic rate (kcal day(-1)), indicating increased organ metabolic activity. Humans also had the greatest body fat percentage. An increased metabolic rate, along with changes in energy allocation, was crucial in the evolution of human brain size and life history

Control of Centrin Stability by Aurora A

Aurora A is an oncogenic serine/threonine kinase which can cause cell transformation and centrosome amplification when over-expressed. Human breast tumors show excess Aurora A and phospho-centrin in amplified centrosomes. Here, we show that Aurora A mediates the phosphorylation of and localizes with centrin at the centrosome, with both proteins reaching maximum abundance from prophase through metaphase, followed by their precipitous loss in late stages of mitosis. Over-expression of Aurora A results in excess phospho-centrin and centrosome amplification. In contrast, centrosome amplification is not seen in cells over-expressing Aurora A in the presence of a recombinant centrin mutant lacking the serine phosphorylation site at residue 170. Expression of a kinase dead Aurora A results in a decrease in mitotic index and abrogation of centrin phosphorylation. Finally, a recombinant centrin mutation that mimics centrin phosphorylation increases centrin's stability against APC/C-mediated proteasomal degradation. Taken together, these results suggest that the stability of centrin is regulated in part by Aurora A, and that excess phosphorylated centrin may promote centrosome amplification in cancer

Reduced Serotonin Reuptake Transporter (SERT) Function Causes Insulin Resistance and Hepatic Steatosis Independent of Food Intake

Serotonin reuptake transporter (SERT) is a key regulator of serotonin neurotransmission and a major target of antidepressants. Antidepressants, such as selectively serotonin reuptake inhibitors (SSRIs), that block SERT function are known to affect food intake and body weight. Here, we provide genetic evidence that food intake and metabolism are regulated by separable mechanisms of SERT function. SERT-deficient mice ate less during both normal diet and high fat diet feeding. The reduced food intake was accompanied with markedly elevated plasma leptin levels. Despite reduced food intake, SERT-deficient mice exhibited glucose intolerance and insulin resistance, and progressively developed obesity and hepatic steatosis. Several lines of evidence indicate that the metabolic deficits of SERT-deficient mice are attributable to reduced insulin-sensitivity in peripheral tissues. First, SERT-deficient mice exhibited beta-cell hyperplasia and islet-mass expansion. Second, biochemical analyses revealed constitutively elevated JNK activity and diminished insulin-induced AKT activation in the liver of SERT-deficient mice. SERT-deficient mice exhibited hyper-JNK activity and hyperinsulinemia prior to the development of obesity. Third, enhancing AKT signaling by PTEN deficiency corrected glucose tolerance in SERT-deficient mice. These findings have potential implications for designing selective SERT drugs for weight control and the treatment of metabolic syndromes