Perfect Hash Families: The Generalization to Higher Indices

Perfect hash families are often represented as combinatorial arrays encoding partitions of kitems into v classes, so that every t or fewer of the items are completely separated by at least a specified number of chosen partitions. This specified number is the index of the hash family. The case when each t-set must be separated at least once has been extensively researched; they arise in diverse applications, both directly and as fundamental ingredients in a column replacement strategy for a variety of combinatorial arrays. In this paper, construction techniques and algorithmic methods for constructing perfect hash families are surveyed, in order to explore extensions to the situation when each t-set must be separated by more than one partition.https://digitalcommons.usmalibrary.org/books/1029/thumbnail.jp

Subunit asymmetry and roles of conformational switching in the hexameric AAA+ ring of ClpX

The hexameric AAA+ ring of Escherichia coli ClpX, an ATP-dependent machine for protein unfolding and translocation, functions with the ClpP peptidase to degrade target substrates. For efficient function, ClpX subunits must switch between nucleotide-loadable (L) and nucleotide-unloadable (U) conformations, but the roles of switching are uncertain. Moreover, it is controversial whether working AAA+-ring enzymes assume symmetric or asymmetric conformations. Here, we show that a covalent ClpX ring with one subunit locked in the U conformation catalyzes robust ATP hydrolysis, with each unlocked subunit able to bind and hydrolyze ATP, albeit with highly asymmetric position-specific affinities. Preventing U↔L interconversion in one subunit alters the cooperativity of ATP hydrolysis and reduces the efficiency of substrate binding, unfolding and degradation, showing that conformational switching enhances multiple aspects of wild-type ClpX function. These results support an asymmetric and probabilistic model of AAA+-ring activity.National Institutes of Health (U.S.) (Grant GM-101988)Massachusetts Institute of Technology (Poitras Predoctoral Fellowship

Clara cell adhesion and migration to extracellular matrix

<p>Abstract</p> <p>Background</p> <p>Clara cells are the epithelial progenitor cell of the small airways, a location known to be important in many lung disorders. Although migration of alveolar type II and bronchiolar ciliated epithelial cells has been examined, the migratory response of Clara cells has received little attention.</p> <p>Methods</p> <p>Using a modification of existing procedures for Clara cell isolation, we examined mouse Clara cells and a mouse Clara-like cell line (C22) for adhesion to and migration toward matrix substrate gradients, to establish the nature and integrin dependence of migration in Clara cells.</p> <p>Results</p> <p>We observed that Clara cells adhere preferentially to fibronectin (Fn) and type I collagen (Col I) similar to previous reports. Migration of Clara cells can be directed by a fixed gradient of matrix substrates (haptotaxis). Migration of the C22 cell line was similar to the Clara cells so integrin dependence of migration was evaluated with this cell line. As determined by competition with an RGD containing-peptide, migration of C22 cells toward Fn and laminin (Lm) 511 (formerly laminin 10) was significantly RGD integrin dependent, but migration toward Col I was RGD integrin independent, suggesting that Clara cells utilize different receptors for these different matrices.</p> <p>Conclusion</p> <p>Thus, Clara cells resemble alveolar type II and bronchiolar ciliated epithelial cells by showing integrin mediated pro-migratory changes to extracellular matrix components that are present in tissues after injury.</p

Mechanochemical basis of protein degradation by a double-ring AAA+ machine

Molecular machines containing double or single AAA+ rings power energy-dependent protein degradation and other critical cellular processes, including disaggregation and remodeling of macromolecular complexes. How the mechanical activities of double-ring and single-ring AAA+ enzymes differ is unknown. Using single-molecule optical trapping, we determine how the double-ring ​ClpA enzyme from Escherichia coli, in complex with the ​ClpP peptidase, mechanically degrades proteins. We demonstrate that ​ClpA unfolds some protein substrates substantially faster than does the single-ring ​ClpX enzyme, which also degrades substrates in collaboration with ​ClpP. We find that ​ClpA is a slower polypeptide translocase and that it moves in physical steps that are smaller and more regular than steps taken by ​ClpX. These direct measurements of protein unfolding and translocation define the core mechanochemical behavior of a double-ring AAA+ machine and provide insight into the degradation of proteins that unfold via metastable intermediates.Howard Hughes Medical InstituteNational Institutes of Health (U.S.) (Grant AI-16892

Potent interaction of flavopiridol with MRP1

The multidrug resistance protein 1 (MRP1) is an ATP-dependent transport protein for organic anions, as well as neutral or positively charged anticancer agents. In this study we show that flavopiridol, a synthetic flavonoid currently studied in phase 1 trials for its anti-proliferative characteristics, interacts with MRP1 in a potent way. Flavopiridol, as well as other (iso)flavonoids stimulate the ATPase activity of MRP1 in a dose-dependent way at low micromolar concentrations. A new specific monoclonal antibody against MRP1 (MIB6) inhibits the (iso)flavonoid-induced ATPase activity of plasma membrane vesicles prepared from the MRP1 overexpressing cell line GLC4/ADR. The accumulation of daunorubicin in GLC4/ADR cells is increased by flavopiridol and by other non-glycosylated (iso)flavonoids that interact with MRP1 ATPase activity. However, flavopiridol is the only tested compound that affects the daunorubicin accumulation when present at concentrations below 1 μM. Glycosylated (iso)flavonoids do not affect MRP1-mediated transport or ATPase activity. Finally, MRP1 overexpressing and transfected cells are resistant to flavopiridol, but not to other (iso)flavonoids tested. These findings may be of relevance for the development of anticancer therapies with flavopiridol. © 1999 Cancer Research Campaig

Quantifying the effectiveness of climate change mitigation through forest plantations and carbon sequestration with an integrated land-use model

<p>Abstract</p> <p>Background</p> <p>Carbon plantations are introduced in climate change policy as an option to slow the build-up of atmospheric carbon dioxide (CO₂) concentrations. Here we present a methodology to evaluate the potential effectiveness of carbon plantations. The methodology explicitly considers future long-term land-use change around the world and all relevant carbon (C) fluxes, including all natural fluxes. Both issues have generally been ignored in earlier studies.</p> <p>Results</p> <p>Two different baseline scenarios up to 2100 indicate that uncertainties in future land-use change lead to a near 100% difference in estimates of carbon sequestration potentials. Moreover, social, economic and institutional barriers preventing carbon plantations in natural vegetation areas decrease the physical potential by 75–80% or more.</p> <p>Nevertheless, carbon plantations can still considerably contribute to slowing the increase in the atmospheric CO₂concentration but only in the long term. The most conservative set of assumptions lowers the increase of the atmospheric CO₂concentration in 2100 by a 27 ppm and compensates for 5–7% of the total energy-related CO₂emissions. The net sequestration up to 2020 is limited, given the short-term increased need for agricultural land in most regions and the long period needed to compensate for emissions through the establishment of the plantations. The potential is highest in the tropics, despite projections that most of the agricultural expansion will be in these regions. Plantations in high latitudes as Northern Europe and Northern Russia should only be established if the objective to sequester carbon is combined with other activities.</p> <p>Conclusion</p> <p>Carbon sequestration in plantations can play an important role in mitigating the build-up of atmospheric CO₂. The actual magnitude depends on natural and management factors, social barriers, and the time frame considered. In addition, there are a number of ancillary benefits for local communities and the environment. Carbon plantations are, however, particularly effective in the long term. Furthermore, plantations do not offer the ultimate solution towards stabilizing CO₂concentrations but should be part of a broader package of options with clear energy emission reduction measures.</p

Inhibition of the inositol kinase Itpkb augments calcium signaling in lymphocytes and reveals a novel strategy to treat autoimmune disease

Emerging approaches to treat immune disorders target positive regulatory kinases downstream of antigen receptors with small molecule inhibitors. Here we provide evidence for an alternative approach in which inhibition of the negative regulatory inositol kinase Itpkb in mature T lymphocytes results in enhanced intracellular calcium levels following antigen receptor activation leading to T cell death. Using Itpkb conditional knockout mice and LMW Itpkb inhibitors these studies reveal that Itpkb through its product IP4 inhibits the Orai1/Stim1 calcium channel on lymphocytes. Pharmacological inhibition or genetic deletion of Itpkb results in elevated intracellular Ca2+ and induction of FasL and Bim resulting in T cell apoptosis. Deletion of Itpkb or treatment with Itpkb inhibitors blocks T-cell dependent antibody responses in vivo and prevents T cell driven arthritis in rats. These data identify Itpkb as an essential mediator of T cell activation and suggest Itpkb inhibition as a novel approach to treat autoimmune disease

Alcohol use and misuse: What are the contributions of occupation and work organization conditions?

<p>Abstract</p> <p>Background</p> <p>This research examines the specific contribution of occupation and work organization conditions to alcohol use and misuse. It is based on a social-action model that takes into account agent personality, structures of daily life, and macro social structures.</p> <p>Methods</p> <p>Data come from a representative sample of 10,155 workers in Quebec, Canada. Multinomial regression models corrected for sample design effect have been used to predict low-risk and high-risk drinking compared to non-drinkers. The contribution of occupation and work organization conditions (skill used, decision authority, physical and psychological demands, hours worked, irregular work schedule, harassment, unionization, job insecurity, performance pay, prestige) have been adjusted for family situation, social network outside the workplace, and individual characteristics.</p> <p>Results</p> <p>Compared to non-qualified blue-collars, both low-risk and high-risk drinking are associated with qualified blue-collars, semi-qualified white-collars, and middle managers; high-risk drinking is associated with upper managers. For constraints-resources related to work organization conditions, only workplace harassment is an important determinant of both low-risk and high-risk drinking, but it is modestly moderated by occupation. Family situation, social support outside work, and personal characteristics of individuals are also associated with alcohol use and misuse. Non-work factors mediated/suppressed the role of occupation and work organization conditions.</p> <p>Conclusion</p> <p>Occupation and workplace harassment are important factors associated with alcohol use and misuse. The results support the theoretical model conceptualizing alcohol use and misuse as being the product of stress caused by constraints and resources brought to bear simultaneously by agent personality, structures of daily life, and macro social structures. Occupational alcohol researchers must expand their theoretical perspectives to avoid erroneous conclusions about the specific role of the workplace.</p

Nutritional status and growth of indigenous Xavante children, Central Brazil

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to characterize the nutritional status of Xavante Indian children less than 10 years of age in Central Brazil and to evaluate the hypothesis of an association between child nutrition and socioeconomic differentiation in this population.</p> <p>Methods</p> <p>A cross-sectional study was conducted in July 2006 that included all children under the age of 10 from the Xavante village Pimentel Barbosa in Mato Grosso, Brazil. The data collected included weight, height, and sociodemographic information. Sociodemographic data were used to generate two indices ("income" and "wealth") and to determine the proportion of adults in each household. Descriptive analyses were performed for weight-for-age (W/A), height-for-age (H/A), and weight-for-height (W/H) using the NCHS and the WHO growth references. Univariate and multivariate analyses were conducted using H/A and W/A as a response variables.</p> <p>Results</p> <p>Of a total of 246 children under the age of ten residing in the village, 232 (94.3%) were evaluated. Following the NCHS reference, 5.6% of children under the age of ten presented low W/A and 14.7% presented low H/A. Among children under the age of five, deficit percentages for weight and height were 4.5% and 29.9%, respectively, following the WHO curves. Among children < 2 years of age, H/A index variability was found to be directly related to child's age and inversely related to the proportion of adults in the household. Maternal BMI was positively associated with growth for children from 2 to 4 years of age, explaining 11.5% of the z-score variability for the H/A index. For children 5 years of age and older, the wealth index and maternal height were positively associated with H/A. No significant associations were found using W/A as the dependent variable.</p> <p>Conclusion</p> <p>This study demonstrated that undernutrition, in particular linear growth deficit, is a notable health issue for Xavante children. These findings contrast with the nutritional profile observed among Brazilian children nationally, which is characterized by a sharp decline in child undernutrition in recent decades, even in the poorest regions of the country. This discrepancy calls attention to the persistent health disparities that exist between indigenous and non-indigenous people in Brazil.</p

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

<p>Abstract</p> <p>Background</p> <p>Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome.</p> <p>Methods</p> <p>We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays.</p> <p>Results</p> <p>Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.</p> <p>We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the <it>SLC45A3-ELK4 </it>e4-e2 TIC to <it>ERG</it>-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines.</p> <p>Conclusions</p> <p>Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as <it>MSMB-NCOA4</it>, may play functional roles in cancer.</p