Promoting Healthy Families and Communities for Boys and Young Men of Color

This report talks about boys and young men of color who are at risk for poor health and developmental outcomes beginning at birth and persisting through childhood, adolescence, and young adulthood. As a result of household poverty and residence in segregated neighborhoods of concentrated disadvantage, they are disproportionately bombarded by environmental threats -- often without the benefits of supportive systems of prevention, protection, and care. This exposure to chronic stress undermines cognitive, social-emotional, and regulatory human development as well as the immune system. The parents of boys and young men of color are similarly affected, which affects boys directly in utero and interferes with their parents' abilities to promote their health and development and to protect them from harm as they mature

Site specific genetic incorporation of azidophenylalanine in Schizosaccharomyces pombe

The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNATyr and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins

Cervicitis as a Clinical Indicator of Gonococcal and Chlamydial Infections in Pregnancy

Objective: We undertook the present study to attempt to apply clinical indicators predictive of cervical infection in nongravid populations with either Neisseria gonorrhoeae or Chlamydia trachomatis to our pregnant population and to determine the significance of the clinical diagnosis of “cervicitis.

Rapid default transition of CD4 T cell effectors to functional memory cells

The majority of highly activated CD4 T cell effectors die after antigen clearance, but a small number revert to a resting state, becoming memory cells with unique functional attributes. It is currently unclear when after antigen clearance effectors return to rest and acquire important memory properties. We follow well-defined cohorts of CD4 T cells through the effector-to-memory transition by analyzing phenotype, important functional properties, and gene expression profiles. We find that the transition from effector to memory is rapid in that effectors rested for only 3 d closely resemble canonical memory cells rested for 60 d or longer in the absence of antigen. This is true for both Th1 and Th2 lineages, and occurs whether CD4 T cell effectors rest in vivo or in vitro, suggesting a default pathway. We find that the effector–memory transition at the level of gene expression occurs in two stages: a rapid loss of expression of a myriad of effector-associated genes, and a more gradual gain of expression of a cohort of genes uniquely associated with memory cells rested for extended periods

AgBase: a unified resource for functional analysis in agriculture

Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource ‘AgBase’ (). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data are available from the AgBase proteogenomics link. We contribute Gene Ontology (GO) annotations and we provide a two tier system of GO annotations for users. The ‘GO Consortium’ gene association file contains the most rigorous GO annotations based solely on experimental data. The ‘Community’ gene association file contains GO annotations based on expert community knowledge (annotations based directly from author statements and submitted annotations from the community) and annotations for predicted proteins. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the GO is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an online mechanism for agricultural researchers to submit requests for GO annotations

Innovation in Teacher Preparation: - Using Performance Expectations and Annotated Video to Facilitate Reflection.

CalStateTEACH (CST) is a California State University statewide, online, site-supported teacher preparation program that prepares candidates primarily for teaching in elementary school. Teacher candidates engage in academic work online and participate in field experiences at a local school each term. The program promotes innovation, technology integration, and reflection (Mishra, Koehler, & Henrikson, 2011) via the Observation Event (OE) in the clinical practice component of the program. Data collected over three terms in the program is used to monitor candidate progress. The OE is a lesson planning interface that was developed to give teacher candidates greater control over the classroom observation process by determining the lesson focus and pedagogical proficiency levels based on California Teaching Performance Expectations (TPE) (California Commission for Teacher Credentialing [CCTC], 2013). The 13 TPEs are skills a teacher candidate needs to develop by the end of a teachertraining program. These are grouped within the broad range of categories in the Standards for the Teaching Profession: Making Subject Matter Comprehensible to Learners, Assessing Student Learning, Engaging and Supporting Students in Learning, Planning Instruction and Designing Learning Experiences for Students, and Creating and Maintaining Effective Environments forStudent Learning (CCTC, 2009). See Figure 1. Candidates begin preparing for the OE by completing a lesson plan and choosing two or three TPEs indicating which aspects of teaching they intend to demonstrate, providing a rationale for that expectation. The elements of the electronic lesson plan include a preconference self-evaluation rationale for proficiency level performance and a reflective video feedback loop for teacher candidates. In the preconference self-evaluation, candidates rank their pedagogical proficiency levels for the TPEs by selecting exploring, applying, proficient, or exemplary, and providing a rationale for the ranking. Faculty mentors provide feedback to the candidate on the lesson plan prior to observing the lesson. &nbsp

Evaluation of Item Candidates: The PROMIS Qualitative Item Review

One of the PROMIS (Patient-Reported Outcome Measurement Information System) network's primary goals is the development of a comprehensive item bank for patient-reported outcomes of chronic diseases. For its first set of item banks, PROMIS chose to focus on pain, fatigue, emotional distress, physical function, and social function. An essential step for the development of an item pool is the identification, evaluation, and revision of extant questionnaire items for the core item pool. In this work, we also describe the systematic process wherein items are classified for subsequent statistical processing by the PROMIS investigators. Six phases of item development are documented: identification of extant items, item classification and selection, item review and revision, focus group input on domain coverage, cognitive interviews with individual items, and final revision before field testing. Identification of items refers to the systematic search for existing items in currently available scales. Expert item review and revision was conducted by trained professionals who reviewed the wording of each item and revised as appropriate for conventions adopted by the PROMIS network. Focus groups were used to confirm domain definitions and to identify new areas of item development for future PROMIS item banks. Cognitive interviews were used to examine individual items. Items successfully screened through this process were sent to field testing and will be subjected to innovative scale construction procedures

Further evidence of the limited role of candidate genes in relation to infant–mother attachment outcomes

In this paper, we examine the associations between specific candidate genes (DRD2, DRD4, COMT, biallelic and tri-allelic 5HTTLPR, and OXTR) and infant attachment outcomes as main effects and in conjunction with maternal sensitivity. The sample included 200 infants (97 European American, 94 African-American, and 9 biracial) and their mothers. Maternal sensitivity and overtly negative maternal behavior were observed when infants were 6 months and 1 year old in distress-eliciting contexts, attachment was assessed via the Strange Situation at age 1, and DNA samples were collected when children were 2 years old. Consistent with recent research in large samples, there was little evidence that these genes are associated with attachment security, disorganization, or distress as main effects (in additive, dominant, and homozygous models) or in conjunction with maternal sensitivity or overtly negative behavior (primarily dominance models). Furthermore, there was little evidence that associations vary as a function of race

The Proteogenomic Mapping Tool

<p>Abstract</p> <p>Background</p> <p>High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be mapped back to their source genome location quickly and exactly. Previously, the tools to do this have been limited to custom scripts designed by individual research groups to analyze their own data, are generally not widely available, and do not scale well with large eukaryotic genomes.</p> <p>Results</p> <p>The Proteogenomic Mapping Tool includes a Java implementation of the Aho-Corasick string searching algorithm which takes as input standardized file types and rapidly searches experimentally observed peptides against a given genome translated in all 6 reading frames for exact matches. The Java implementation allows the application to scale well with larger eukaryotic genomes while providing cross-platform functionality.</p> <p>Conclusions</p> <p>The Proteogenomic Mapping Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data.</p

Socioeconomic impacts of innovative dairy supply chain practices. The case of the Laiterie du Berger in the Senegalese Sahel

This study analyzes the Laiterie Du Berger (LDB)'s milk supply chain and its contribution to strengthening the food security and socioeconomic resources of Senegalese Sahelian pastoral households. Porter's value chain model is used to characterize the innovations introduced by the LDB dairy in its milk inbound logistics and supplier relationships. A socioeconomic food security index and qualitative data are used to assess the dairy's supply chain's contribution to strengthen smallholder households' livelihoods. Data for this research were obtained through individual surveys, focus groups and in-depth interviews of LDB managers and milk suppliers. Results show that milk income contributes significantly to household food security. Suppliers who stabilize their dairy income between rainy and dry seasons, diversify income sources and have larger herds are more likely to remain food secure. The LDB innovations contribute by helping herders access biophysical and economic resources, leading to better livestock feed and household food security. (Résumé d'auteur