Compositional Analysis of Lignocellulosic Feedstocks. 2. Method Uncertainties

The most common procedures for characterizing the chemical components of lignocellulosic feedstocks use a two-stage sulfuric acid hydrolysis to fractionate biomass for gravimetric and instrumental analyses. The uncertainty (i.e., dispersion of values from repeated measurement) in the primary data is of general interest to those with technical or financial interests in biomass conversion technology. The composition of a homogenized corn stover feedstock (154 replicate samples in 13 batches, by 7 analysts in 2 laboratories) was measured along with a National Institute of Standards and Technology (NIST) reference sugar cane bagasse, as a control, using this laboratory's suite of laboratory analytical procedures (LAPs). The uncertainty was evaluated by the statistical analysis of these data and is reported as the standard deviation of each component measurement. Censored and uncensored versions of these data sets are reported, as evidence was found for intermittent instrumental and equipment problems. The censored data are believed to represent the “best case” results of these analyses, whereas the uncensored data show how small method changes can strongly affect the uncertainties of these empirical methods. Relative standard deviations (RSD) of 1−3% are reported for glucan, xylan, lignin, extractives, and total component closure with the other minor components showing 4−10% RSD. The standard deviations seen with the corn stover and NIST bagasse materials were similar, which suggests that the uncertainties reported here are due more to the analytical method used than to the specific feedstock type being analyzed

Diurnal Differences in Intracellular Replication Within Splenic Macrophages Correlates With the Outcome of Pneumococcal Infection

Circadian rhythms affect the progression and severity of bacterial infections including those caused by Streptococcus pneumoniae, but the mechanisms responsible for this phenomenon remain largely elusive. Following advances in our understanding of the role of replication of S. pneumoniae within splenic macrophages, we sought to investigate whether events within the spleen correlate with differential outcomes of invasive pneumococcal infection. Utilising murine invasive pneumococcal disease (IPD) models, here we report that infection during the murine active phase (zeitgeber time 15; 15h after start of light cycle, 3h after start of dark cycle) resulted in significantly faster onset of septicaemia compared to rest phase (zeitgeber time 3; 3h after start of light cycle) infection. This correlated with significantly higher pneumococcal burden within the spleen of active phase-infected mice at early time points compared to rest phase-infected mice. Whole-section confocal microscopy analysis of these spleens revealed that the number of pneumococci is significantly higher exclusively within marginal zone metallophilic macrophages (MMMs) known to allow intracellular pneumococcal replication as a prerequisite step to the onset of septicaemia. Pneumococcal clusters within MMMs were more abundant and increased in size over time in active phase-infected mice compared to those in rest phase-infected mice which decreased in size and were present in a lower percentage of MMMs. This phenomenon preceded significantly higher levels of bacteraemia alongside serum IL-6 and TNF-alpha concentrations in active phase-infected mice following re-seeding of pneumococci into the blood. These data greatly advance our fundamental knowledge of pneumococcal infection by linking susceptibility to invasive pneumococcal infection to variation in the propensity of MMMs to allow persistence and replication of phagocytosed bacteria. These findings also outline a somewhat rare scenario whereby the active phase of an organism's circadian cycle plays a seemingly counterproductive role in the control of invasive infection

Gene Expression Signature of Cigarette Smoking and Its Role in Lung Adenocarcinoma Development and Survival

Tobacco smoking is responsible for over 90% of lung cancer cases, and yet the precise molecular alterations induced by smoking in lung that develop into cancer and impact survival have remained obscure.We performed gene expression analysis using HG-U133A Affymetrix chips on 135 fresh frozen tissue samples of adenocarcinoma and paired noninvolved lung tissue from current, former and never smokers, with biochemically validated smoking information. ANOVA analysis adjusted for potential confounders, multiple testing procedure, Gene Set Enrichment Analysis, and GO-functional classification were conducted for gene selection. Results were confirmed in independent adenocarcinoma and non-tumor tissues from two studies. We identified a gene expression signature characteristic of smoking that includes cell cycle genes, particularly those involved in the mitotic spindle formation (e.g., NEK2, TTK, PRC1). Expression of these genes strongly differentiated both smokers from non-smokers in lung tumors and early stage tumor tissue from non-tumor tissue (p<0.001 and fold-change >1.5, for each comparison), consistent with an important role for this pathway in lung carcinogenesis induced by smoking. These changes persisted many years after smoking cessation. NEK2 (p<0.001) and TTK (p = 0.002) expression in the noninvolved lung tissue was also associated with a 3-fold increased risk of mortality from lung adenocarcinoma in smokers.Our work provides insight into the smoking-related mechanisms of lung neoplasia, and shows that the very mitotic genes known to be involved in cancer development are induced by smoking and affect survival. These genes are candidate targets for chemoprevention and treatment of lung cancer in smokers

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

Hsp72 is targeted to the mitotic spindle by Nek6 to promote K-fiber assembly and mitotic progression

Hsp70 proteins represent a family of chaperones that regulate cellular homeostasis and are required for cancer cell survival. However, their function and regulation in mitosis remain unknown. In this paper, we show that the major inducible cytoplasmic Hsp70 isoform, Hsp72, is required for assembly of a robust bipolar spindle capable of efficient chromosome congression. Mechanistically, Hsp72 associates with the K-fiber-stabilizing proteins, ch-TOG and TACC3, and promotes their interaction with each other and recruitment to spindle microtubules (MTs). Targeting of Hsp72 to the mitotic spindle is dependent on phosphorylation at Thr-66 within its nucleotide-binding domain by the Nek6 kinase. Phosphorylated Hsp72 concentrates on spindle poles and sites of MT-kinetochore attachment. A phosphomimetic Hsp72 mutant rescued defects in K-fiber assembly, ch-TOG/TACC3 recruitment and mitotic progression that also resulted from Nek6 depletion. We therefore propose that Nek6 facilitates association of Hsp72 with the mitotic spindle, where it promotes stable K-fiber assembly through recruitment of the ch-TOG-TACC3 complex

A Trigger Enzyme in Mycoplasma pneumoniae: Impact of the Glycerophosphodiesterase GlpQ on Virulence and Gene Expression

Mycoplasma pneumoniae is a causative agent of atypical pneumonia. The formation of hydrogen peroxide, a product of glycerol metabolism, is essential for host cell cytotoxicity. Phosphatidylcholine is the major carbon source available on lung epithelia, and its utilization requires the cleavage of deacylated phospholipids to glycerol-3-phosphate and choline. M. pneumoniae possesses two potential glycerophosphodiesterases, MPN420 (GlpQ) and MPN566. In this work, the function of these proteins was analyzed by biochemical, genetic, and physiological studies. The results indicate that only GlpQ is an active glycerophosphodiesterase. MPN566 has no enzymatic activity as glycerophosphodiesterase and the inactivation of the gene did not result in any detectable phenotype. Inactivation of the glpQ gene resulted in reduced growth in medium with glucose as the carbon source, in loss of hydrogen peroxide production when phosphatidylcholine was present, and in a complete loss of cytotoxicity towards HeLa cells. All these phenotypes were reverted upon complementation of the mutant. Moreover, the glpQ mutant strain exhibited a reduced gliding velocity. A comparison of the proteomes of the wild type strain and the glpQ mutant revealed that this enzyme is also implicated in the control of gene expression. Several proteins were present in higher or lower amounts in the mutant. This apparent regulation by GlpQ is exerted at the level of transcription as determined by mRNA slot blot analyses. All genes subject to GlpQ-dependent control have a conserved potential cis-acting element upstream of the coding region. This element overlaps the promoter in the case of the genes that are repressed in a GlpQ-dependent manner and it is located upstream of the promoter for GlpQ-activated genes. We may suggest that GlpQ acts as a trigger enzyme that measures the availability of its product glycerol-3-phosphate and uses this information to differentially control gene expression

Growth zoning of garnet porphyroblasts: grain boundary and microtopographic controls

Chemical zoning in the outer few 10s of microns of garnet porphyroblasts has been investigated to assess the scale of chemical equilibrium with matrix minerals in a pelitic schist. Garnet porphyroblasts from the Late Proterozoic amphibolite‐facies regional metamorphic mica schists from Glen Roy in the Scottish Highlands contain typical prograde growth zoning patterns. Edge compositions have been measured via a combination of analysis of traverses across the planar edges of porphyroblast surfaces coupled to X‐ray mapping of small areas within polished thin sections at the immediate edge of the porphyroblasts. These approaches reveal local variation in garnet composition, especially of grossular (Ca) and almandine (Fe) components, with a range at the edge from &lt;7 mol% grs to &gt;16 mol% grs, across distances of less then 50 mm. This small‐scale patchy compositional zoning is as much variation as the core‐rim compositional zoning across the whole of a 3 mm porphyroblast. Ca and Fe heterogeneity occurs on a scale suggesting a combination of inefficient diffusive exchange across grain boundaries during prograde growth and the evolving microtopography of the porphyroblast surface control garnet composition. The latter creates haloes of compositional zoning adjacent to some inclusions, which typically extend from the inclusion towards the porphyroblast edge during further growth. The lack of a consistent equilibrium composition at the garnet edge is also apparent in the internal zoning of the porphyroblast and so processes occurring during entrapment of some mineral inclusions have a profound influence on the overall chemical zoning. Garnet compositions and associated zoning patterns are widely used by petrologists to reconstruct P‐T‐t paths for crustal rocks. The evidence of extremely localized (10‐50 mm scale) equilibrium during growth further undermines these approaches

Plio‐Quaternary exhumation history of the central Nepalese Himalaya: 2. Thermokinematic and thermochronometer age prediction model

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95647/1/tect1875.pd