Valuable Community Resource Research Articles

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

BackgroundThe ambient temperature of all habitats is a key physical property that shapes the biology of microbes inhabiting them. The optimal growth temperature (OGT) of a microbe, is therefore a key piece of data needed to understand evolutionary adaptations manifested in their genome sequence. Unfortunately there is no growth temperature database or easily downloadable dataset encompassing the majority of cultured microorganisms. We are thus limited in interpreting genomic data to identify temperature adaptations in microbes.ResultsIn this work I significantly contribute to closing this gap by mining data from major culture collection centres to obtain growth temperature data for a nonredundant set of 21,498 microbes. The dataset (https://doi.org/10.5281/zenodo.1175608) contains mainly bacteria and archaea and spans psychrophiles, mesophiles, thermophiles and hyperthermophiles. Using this data a full 43% of all protein entries in the UniProt database can be annotated with the growth temperature of the species from which they originate. I validate the dataset by showing a Pearson correlation of up to 0.89 between growth temperature and mean enzyme optima, a physiological property directly influenced by the growth temperature. Using the temperature dataset I correlate the genomic occurance of enzyme functional annotations with growth temperature. I identify 319 enzyme functions that either increase or decrease in occurrence with temperature. Eight metabolic pathways were statistically enriched for these enzyme functions. Furthermore, I establish a correlation between 33 domains of unknown function (DUFs) with growth temperature in microbes, four of which (DUF438, DUF1524, DUF1957 and DUF3458_C) were significant in both archaea and bacteria.ConclusionsThe growth temperature dataset enables large-scale correlation analysis with enzyme function- and domain-level annotations. Growth-temperature dependent changes in their occurrence highlight potential evolutionary adaptations. A few of the identified changes are previously known, such as the preference for menaquinone biosynthesis through the futalosine pathway in bacteria growing at high temperatures. Others represent important starting points for future studies, such as DUFs where their occurrence change with temperature. The growth temperature dataset should become a valuable community resource and will find additional, important, uses in correlating genomic, transcriptomic, proteomic, metabolomic, phenotypic or taxonomic properties with temperature in future studies.

P076A community resource using gene feature enumeration to generate accurate allele calls and sequence annotations for HLA and KIR

Aim A publicly available service for accurately annotating and assigning allele names to consensus sequences would be a valuable community resource. We have developed such a service for HLA and KIR consensus sequences. Methods Gene feature enumeration (GFE) notation was developed as a way to retain sequence variation outside of the current nomenclature. We generated GFE notation for every sequence in the IPD-IMGT/HLA and -KIR Databases, and loaded the results into a neo4j graph database (neo4j.b12x.org), which includes KIR, HLA, GFE and sequence feature nodes. Our allele-calling tool (ACT) annotates sequences and converts those annotations to GFE notation. The ACT uses these GFE notations and the graph database to make allele calls by finding alleles that share similar GFE notations. A RESTful service web-interface makes the ACT easy to use and allows for cross-platform compatibility (act.b12x.org). We used 118,585 Be the Match® donors typed at high resolution with consensus sequences available for HLA-A, B, C, DRB3/4/5, DRB1, DQB1 and DPB1 to test the ACT. We compared the allele calls generated by the ACT to the lab-reported allele calls using the same IPD-IMGT/HLA release as the labs and IPD-IMGT/HLA release 3.31.0. To test the ACT with KIR, we took all the KIR sequences that were characterized in IPD-KIR release 2.7.0 and made allele calls with the ACT using release 2.6.0. Results The allele calls made by the ACT matched the lab reported typing 100% of the time for class I and 99.5% of the time for class II when using the same IMGT release as the lab. When using the 3.31.0 IPD-IMGT/HLA release, the ACT extended third field assignments to the fourth field for 98% of donors for at least one locus. On average, the ACT took 3 s to annotate a sequence and make an allele call for class I and 9 s for class II sequences. The ACT made accurate allele calls for all KIR sequences that were characterized in 2.7.0. Conclusions Accurate allele calls and sequence annotations can be made when using our GFE-based ACT. The ACT can also be used to extend the nomenclature for allele assignments made with previous IPD-IMGT/HLA releases. This service will allow anyone to easily convert HLA and KIR consensus sequences into detailed sequence annotations and allele names.

An annotated CNS transcriptome of the medicinal leech, Hirudo verbana: De novo sequencing to characterize genes associated with nervous system activity.

The medicinal leech is one of the most venerated model systems for the study of fundamental nervous system principles, ranging from single-cell excitability to complex sensorimotor integration. Yet, molecular analyses have yet to be extensively applied to complement the rich history of electrophysiological study that this animal has received. Here, we generated the first de novo transcriptome assembly from the entire central nervous system of Hirudo verbana, with the goal of providing a molecular resource, as well as to lay the foundation for a comprehensive discovery of genes fundamentally important for neural function. Our assembly generated 107,704 contigs from over 900 million raw reads. Of these 107,704 contigs, 39,047 (36%) were annotated using NCBI’s validated RefSeq sequence database. From this annotated central nervous system transcriptome, we began the process of curating genes related to nervous system function by identifying and characterizing 126 unique ion channel, receptor, transporter, and enzyme contigs. Additionally, we generated sequence counts to estimate the relative abundance of each identified ion channel and receptor contig in the transcriptome through Kallisto mapping. This transcriptome will serve as a valuable community resource for studies investigating the molecular underpinnings of neural function in leech and provide a reference for comparative analyses.

Association between clinical observations and a mobile crisis team's level of care recommendations.

Mobile mental health crisis programs are a widely used and valuable community resource. Literature analyzing the service, however, is sparse and descriptive in nature. This study uses multinomial logistic regression to analyze clinical data from a mobile crisis program in Pennsylvania over 12 months. 793 individuals recommended to various levels of care were analyzed. Clinical and demographic presentations were used as predictor variables and level of care recommendation as outcome variable. Several clinical presentations were found to increase the likelihood of various levels of care recommendations. These findings are discussed in light of current suicide intervention and data-driven practice.

P055 GFE ACT: A community resource for calling HLA allele names from consensus sequences with gene feature enumeration notation

Aim A publicly available service for assigning HLA allele names to consensus sequences would be a valuable community resource. Our aim was to use existing technologies to develop a publicly available, graph-based HLA allele calling service. Methods Gene feature enumeration (GFE) notation has been developed as a way of describing sequence variation outside of current HLA nomenclature. We generated GFE notation for every sequence in the IPD-IMGT/HLA Database, and loaded the results into a neo4j graph database ( neo4j.b12x.org ), which includes HLA, GFE and sequence feature nodes. We developed an allele calling tool (ACT) that leverages this graph to return an HLA allele call and GFE notation from submitted consensus sequence. ACT uses the GFE service ( gfe.b12x.org ) to convert the consensus sequences to GFE notation, and then searches the graph database for HLA alleles that share the most features with the generated GFE. A RESTful service interface makes ACT easy to use and allows for cross-platform compatibility ( act.b12x.org ). We used 30,000 Be the Match® donors typed at high resolution and with consensus sequences available for HLA-A, B, and C to test ACT. We compared the HLA calls ACT produced to the allele names reported by the typing labs. Comparisons were made with and without mapping alleles to their G group equivalent. Results When mapping alleles to their respective G group equivalent, the reported HLA typing for all 30,000 donors matched the ACT typing to the 2nd field with no ambiguity. Without mapping alleles to their G groups, the number of exact matches to the 4th field at HLA-A, B and C was 17,142 (57%), 16,540 (55%) and 10,024 (33%), respectively. Using G groups, ambiguity at the 4th field was reduced substantially; the number of exact matches increased to 29,914 (99.7%), 29,733 (99.1%) and 29,985 (99.9%) for HLA-A, B, and C, respectively. In 75 instances, ACT called alleles at a higher resolution than reported by the typing lab. Conclusions HLA class I allele names can be accurately called from consensus sequences using our GFE-based ACT. This service will allow anyone to easily convert HLA class I consensus sequences into the corresponding GFE notation and HLA allele name. Class II HLA and KIR are already represented in the graph, and we plan to extend ACT functions to these loci.

Immigrants and Foreign Firm Performance

Studies have demonstrated that foreign firms locate where immigrants from their home countries reside and have suggested that doing so can improve performance. We argue that to properly assess how immigrants impact the performance of co-national firms, research must account for heterogeneity in how independent foreign firms (owned by individual foreigners) versus multinational corporation (MNC) subsidiaries (owned by a foreign corporate parent) benefit from immigrant communities. Independent firms have a greater need for resources from the immigrant community and depend more on their individual managers’ personal connections within the community to obtain such resources. Subsidiaries of MNCs can instead rely on the impersonal organizational resources of their parent firm (e.g., brand, reputation, channels) to access valuable immigrant community resources. Using data on foreign firms in Russia during 2006–2011, we find that immigrants improve the profitability of co-national independent firms only if they are managed by immigrant chief executive officers (CEOs), whereas co-national MNC subsidiaries profit from immigrants regardless of their CEOs’ nationality. Our study suggests that although organizations benefit from the resources of co-national immigrant communities in foreign markets, the means by which they activate them—personal or impersonal—systematically vary across different types of firms.

EQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato.

Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome and identified approximately 7,200 eQTL regulating the steady-state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hot spots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity as well as hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression, but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive eQTL analysis details the influence of these loci on plant phenotypes and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.

Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response

The utility of tumor-derived cell lines is dependent on their ability to recapitulate underlying genomic aberrations and primary tumor biology. Here, we sequenced the exomes of 25 bladder cancer (BCa) cell lines and compared mutations, copy number alterations (CNAs), gene expression and drug response to BCa patient profiles in The Cancer Genome Atlas (TCGA). We observed a mutation pattern associated with altered CpGs and APOBEC-family cytosine deaminases similar to mutation signatures derived from somatic alterations in muscle-invasive (MI) primary tumors, highlighting a major mechanism(s) contributing to cancer-associated alterations in the BCa cell line exomes. Non-silent sequence alterations were confirmed in 76 cancer-associated genes, including mutations that likely activate oncogenes TERT and PIK3CA, and alter chromatin-associated proteins (MLL3, ARID1A, CHD6 and KDM6A) and established BCa genes (TP53, RB1, CDKN2A and TSC1). We identified alterations in signaling pathways and proteins with related functions, including the PI3K/mTOR pathway, altered in 60% of lines; BRCA DNA repair, 44%; and SYNE1–SYNE2, 60%. Homozygous deletions of chromosome 9p21 are known to target the cell cycle regulators CDKN2A and CDKN2B. This loci was commonly lost in BCa cell lines and we show the deletions extended to the polyamine enzyme methylthioadenosine (MTA) phosphorylase (MTAP) in 36% of lines, transcription factor DMRTA1 (27%) and antiviral interferon epsilon (IFNE, 19%). Overall, the BCa cell line genomic aberrations were concordant with those found in BCa patient tumors. We used gene expression and copy number data to infer pathway activities for cell lines, then used the inferred pathway activities to build a predictive model of cisplatin response. When applied to platinum-treated patients gathered from TCGA, the model predicted treatment-specific response. Together, these data and analysis represent a valuable community resource to model basic tumor biology and to study the pharmacogenomics of BCa.

Sex Differences in the Relationship between Park Proximity and Features and Child and Youth Physical Activity

This study examined the association of park proximity and features with child and youth physical activity, including differences by sex, among 191 young people in Kansas City, Missouri. Logistic regression examined the relationship between each park variable and the likelihood of children and youth engaging in a greater amount of physical activity. All young people with a playground within a half-mile or a baseball field within one mile of home, females who had a park within a half-mile, and males with a park within one mile were more likely to achieve a greater amount of physical activity. The findings further previous research indicating that parks are valuable community resources that can play an important role in the battle against obesity and chronic disease in children and youth across the U.S.

High‐density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

AbstractMiscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker‐assisted selection. Thus, a high‐density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High‐density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site‐associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM, with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra‐striped trait, which was segregating in this population. Three QTL for zebra‐striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra‐striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.

New signaling pathways govern the host response to C. albicans infection in various niches.

Candida albicans, the major invasive fungal pathogen of humans, can cause both debilitating mucosal infections and fatal invasive infections. Understanding the complex nature of the host–pathogen interaction in each of these contexts is essential to developing desperately needed therapies to treat fungal infections. RNA-seq enables a systems-level understanding of infection by facilitating comprehensive analysis of transcriptomes from multiple species (e.g., host and pathogen) simultaneously. We used RNA-seq to characterize the transcriptomes of both C. albicans and human endothelial cells or oral epithelial cells during in vitro infection. Network analysis of the differentially expressed genes identified the activation of several signaling pathways that have not previously been associated with the host response to fungal pathogens. Using an siRNA knockdown approach, we demonstrate that two of these pathways—platelet-derived growth factor BB (PDGF BB) and neural precursor-cell-expressed developmentally down-regulated protein 9 (NEDD9)—govern the host–pathogen interaction by regulating the uptake of C. albicans by host cells. Using RNA-seq analysis of a mouse model of hematogenously disseminated candidiasis (HDC) and episodes of vulvovaginal candidiasis (VVC) in humans, we found evidence that many of the same signaling pathways are activated during mucosal (VVC) and/or disseminated (HDC) infections in vivo. Our analyses have uncovered several signaling pathways at the interface between C. albicans and host cells in various contexts of infection, and suggest that PDGF BB and NEDD9 play important roles in this interaction. In addition, these data provide a valuable community resource for better understanding host-fungal pathogen interactions.

A formative evaluation of social media campaign to reduce adolescent dating violence.

BackgroundThe Emory Jane Fonda Center implemented the Start Strong Atlanta social marketing campaign, “Keep It Strong ATL”, in 2007 to promote the development of healthy adolescent relationships and to foster the prevention of adolescent dating abuse among 11-14 year olds.ObjectiveA formative evaluation was conducted to understand whether messages directed at the target audience were relevant to the program’s relationship promotion and violence prevention goals, and whether the “Web 2.0” social media channels of communication (Facebook, Twitter, YouTube, Flickr, Tumblr, and Pinterest) were reaching the intended audience.MethodsMixed methodologies included qualitative interviews and a key informant focus group, a cross-sectional survey, and web analytics. Qualitative data were analyzed using constant comparative methodology informed by grounded theory. Descriptive statistics were generated from survey data, and web analytics provided user information and traffic patterns.ResultsResults indicated that the Keep It Strong ATL social marketing campaign was a valuable community resource that had potential for broader scope and greater reach. The evaluation team learned the importance of reaching adolescents through Web 2.0 platforms, and the need for message dissemination via peers. Survey results indicated that Facebook (ranked 6.5 out of 8) was the highest rated social media outlet overall, and exhibited greatest appeal and most frequent visits, yet analytics revealed that only 3.5% of “likes” were from the target audience. These results indicate that the social media campaign is reaching predominantly women (76.5% of viewership) who are outside of the target age range of 11-14 years.ConclusionsWhile the social media campaign was successfully launched, the findings indicate the need for a more focused selection of communication channels, timing of media updates to maximize visibility, balancing message tone and delivery, and incorporating differentiated messaging for the target audiences. Collaboration with parents and community partners is also emphasized in order to expand the campaign’s reach and create more channels to disseminate relationship promotion and dating violence prevention messaging to the intended audience.

Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).

The non-human primate reference transcriptome resource (NHPRTR, available online at http://nhprtr.org/) aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. In the 2012 Phase I of the NHPRTR project, 19 billion fragments or 3.8 terabases of transcriptome sequences were collected from pools of ∼20 tissues in 15 species and subspecies. Here we describe a major expansion of NHPRTR by adding 10.1 billion fragments of tissue-specific RNA-seq data. For this effort, we selected 11 of the original 15 NHP species and subspecies and constructed total RNA libraries for the same ∼15 tissues in each. The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes. This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects. Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.

Longitudinal Trends in Equity of Park Accessibility in Yokohama, Japan: An Investigation into the Role of Causal Mechanisms

Despite an increasing interest in issues surrounding environmental equity, much research evidence to date is based on studies adopting cross-sectional approaches which do not adequately capture the processes and mechanisms generating inequities. Longitudinal studies may better inform policy measures to remedy inequity between populations, but the few that have been undertaken have mostly been focused solely on environmental risks—ignoring access to amenities. As a case study, we adopt a longitudinal approach in this work to investigate the association between sociodemographic indicators and public park provision over an eighteen-year period in the city of Yokohama, Japan. We show that inequities in park provision are present over the whole time period. Hedonic modelling shows that park accessibility is positively associated with house and land prices in the city. Our results suggested some, relatively weak, evidence of two causal processes: New parks are located in more affluent communities; yet new parks also appear to encourage further move-in of affluent populations. We suggest that park provision by administrative authorities in less-affluent neighbourhoods may be required to maintain equity in access to these valuable community resources. Economic incentives, such as subsidy provision, may have a role to play to encourage park provision by developers.

Functional Genomic Analyses of Two Morphologically Distinct Classes of Drosophila Sensory Neurons: Post-Mitotic Roles of Transcription Factors in Dendritic Patterning

BackgroundNeurons are one of the most structurally and functionally diverse cell types found in nature, owing in large part to their unique class specific dendritic architectures. Dendrites, being highly specialized in receiving and processing neuronal signals, play a key role in the formation of functional neural circuits. Hence, in order to understand the emergence and assembly of a complex nervous system, it is critical to understand the molecular mechanisms that direct class specific dendritogenesis.Methodology/Principal FindingsWe have used the Drosophila dendritic arborization (da) neurons to gain systems-level insight into dendritogenesis by a comparative study of the morphologically distinct Class-I (C-I) and Class-IV (C-IV) da neurons. We have used a combination of cell-type specific transcriptional expression profiling coupled to a targeted and systematic in vivo RNAi functional validation screen. Our comparative transcriptomic analyses have revealed a large number of differentially enriched/depleted gene-sets between C-I and C-IV neurons, including a broad range of molecular factors and biological processes such as proteolytic and metabolic pathways. Further, using this data, we have identified and validated the role of 37 transcription factors in regulating class specific dendrite development using in vivo class-specific RNAi knockdowns followed by rigorous and quantitative neurometric analysis.Conclusions/SignificanceThis study reports the first global gene-expression profiles from purified Drosophila C-I and C-IV da neurons. We also report the first large-scale semi-automated reconstruction of over 4,900 da neurons, which were used to quantitatively validate the RNAi screen phenotypes. Overall, these analyses shed global and unbiased novel insights into the molecular differences that underlie the morphological diversity of distinct neuronal cell-types. Furthermore, our class-specific gene expression datasets should prove a valuable community resource in guiding further investigations designed to explore the molecular mechanisms underlying class specific neuronal patterning.

Microbiomes of built environments: 2011 symposium highlights and workgroup recommendations

The air we breathe inside buildings dominates overall inhalation exposure to most air pollutants, whether of indoor or outdoor origin. The same is true for our exposure to microorganisms. Over the past three decades much has been learned about chemicals (in gas and particle phases) in building air, including typical levels, sources, fate, and control. Far less has been learned about the types, sources, and fate of microorganisms in buildings, and about how building design, and operation and maintenance affect microorganisms in buildings. Knowledge creation has been constrained by historical reliance on culture-based methods that can yield only partial or biased assessments of microbial community structure, sometimes dramatically underestimating uncultivable organisms, and failing to detect fragments of organisms that may themselves influence human health. However, in the past several years, advances in culture-independent analytical methods have significantly increased knowledge related to microbial communities and diversity in buildings. We are positioned to make even stronger gains in the coming years.

Development and Testing of a Community Stakeholder Park Audit Tool

Parks are valuable community resources, and auditing park environments is important for understanding their influence on physical activity and health. However, few tools exist that engage citizens in this process. The purpose of this study was to develop a user-friendly tool that would enable diverse stakeholders to quickly and reliably audit community parks for their potential to promote physical activity. A secondary aim was to examine community stakeholders' reactions to the process of developing and using the new tool. The study employed a sequential, multiphase process including three workshops and field testing to ensure the new instrument was the product of input and feedback from a variety of potential stakeholders and was psychometrically sound. All study stages, including data collection and analysis, occurred in 2010. Stakeholder recommendations were combined with reviews of existing instruments to create the new Community Park Audit Tool (CPAT). The CPAT contains four sections titled Park Information, Access and Surrounding Neighborhood, Park Activity Areas, and Park Quality and Safety. Inter-rater analyses demonstrated strong reliability for the vast majority of the items in the tool. Further, stakeholders reported a range of positive reactions resulting from their engagement in the project. The CPAT provides a reliable and user-friendly means of auditing parks for their potential to promote physical activity. Future use of the CPAT can facilitate greater engagement of diverse groups in evaluating and advocating for improved parks and overall healthy community design.

Cord blood stem cell banking: a snapshot of the Italian situation

In Italy, the law does not permit the setting up of private banks to preserve cord blood (CB) stem cells for personal use. However, since 2007 the right to export and preserve them in private laboratories located outside Italy has existed, and an increasing number of women are requesting this collection of umbilical CB at delivery to enable storage of stem cells for autologous use. Since private banks recruit clients mainly via the Internet, we examined the content of 24 Italian-language websites that offer stem cells storage (from CB or amniotic fluid), to assess what information is available. We found that the majority of private banks give no clear information about the procedures of collection, processing, and banking of CB units and that the standards offered by private CB banks strongly differ in terms of exclusion or acceptance criteria from the public banks. These factors may well influence the overall quality of the CB units stored in private CB banks. Of note, during the period 2007 to 2009, the number collected for autologous use did not create a downward trend on the number of units stored in public CB banks for allogeneic use. CB is a valuable community resource but expectant parents should be better informed as to the quality variables necessary for its storage, both by institutions and by professionals. Currently, most of the advertising is insufficient to justify the expense and the hopes pinned on autologous use of CB stem cells.

Characterization of a 6K oligonucleotide turkey skeletal muscle microarray

Consumer demand for lean, inexpensive meat products has driven the domestic turkey (Meleagris gallopavo) industry to unprecedented production; however, this has coincided with an increase in growth-induced myopathies and meat quality defects. With the aim of developing a new tool for the study of turkey growth and development at the muscle transcriptome level, a 6K oligonucleotide microarray was constructed, the Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray. Skeletal muscle samples were collected at three critical stages in muscle development: 18-day embryo (hyperplasia), 1-day post-hatch (hypertrophy), and 16-week (market age) from two genetic lines of turkeys: RBC2, a line maintained without selection pressure, and F, a line selected from the RBC2 line for increased 16-week body weight. Oligonucleotides were designed from sequences obtained from skeletal muscle cDNA libraries from the three developmental stages. Several unique controls, including mismatch and distance controls and scrambled sequences, were designed for 30 genes. Quality control hybridizations were completed, confirming the validity and repeatability of the array. Control features were evaluated across two larger experiments comparing developmental stage within genetic line or genetic line within each developmental stage, totaling 70 arrays. Mismatch and scrambled sequences appeared to be useful controls of specific hybridization for most genes. In addition, quantitative real-time RT-PCR confirmed microarray results. This creation and assessment of the TSKMLO array provides a valuable community resource for the study of gene expression changes related to turkey muscle growth and development.

Taking stock:Indoor Airis an international, multidisciplinary, research journal

Taking stock:<i>Indoor Air</i>is an international, multidisciplinary, research journal