Measuring Diversity of the National Institutes of Health-Funded Workforce.

PURPOSE: To measure diversity within the National Institutes of Health (NIH)-funded workforce. The authors use a relevant labor market perspective to more directly understand what the NIH can influence in terms of enhancing diversity through NIH policies. METHOD: Using the relevant labor market (defined as persons with advanced degrees working as biomedical scientists in the United States) as the conceptual framework, and informed by accepted economic principles, the authors used the American Community Survey and NIH administrative data to calculate representation ratios of the NIH-funded biomedical workforce from 2008 to 2012 by race, ethnicity, sex, and citizenship status, and compared this against the pool of characteristic individuals in the potential labor market. RESULTS: In general, the U.S. population during this time period was an inaccurate comparison group for measuring diversity of the NIH-funded scientific workforce. Measuring accurately, we found the representation of women and traditionally underrepresented groups in NIH-supported postdoc fellowships and traineeships and mentored career development programs was greater than their representation in the relevant labor market. The same analysis found these demographic groups are less represented in the NIH-funded independent investigator pool. CONCLUSIONS: Although these findings provided a picture of the current NIH-funded workforce and a foundation for understanding the federal role in developing, maintaining, and renewing diverse scientific human resources, further study is needed to identify whether junior- and early-stage investigators who are part of more diverse cohorts will naturally transition into independent NIH-funded investigators, or whether they will leave the workforce before achieving independent researcher status.

Sex differences in application, success, and funding rates for NIH extramural programs.

PURPOSE: The authors provide an analysis of sex differences in National Institutes of Health (NIH) award programs to inform potential initiatives for promoting diversity in the research workforce. METHOD: In 2010, the authors retrieved data for NIH extramural grants in the electronic Research Administration Information for Management, Planning, and Coordination II database and used statistical analysis to determine any sex differences in securing NIH funding, as well as subsequent success of researchers who had already received independent NIH support. RESULTS: Success and funding rates for men and women were not significantly different in most award programs. Furthermore, in programs where participation was lower for women than men, the disparity was primarily related to a lower percentage of women applicants compared with men, rather than decreased success rates or funding rates. However, for subsequent grants, both application and funding rates were generally higher for men than for women. CONCLUSIONS: Cross-sectional analysis showed that women and men were generally equally successful at all career stages, but longitudinal analysis showed that men with previous experience as NIH grantees had higher application and funding rates than women at similar career points. On average, although women received larger R01 awards than men, men had more R01 awards than women at all points in their careers. Therefore, while greater participation of women in NIH programs is under way, further action will be required to eradicate remaining sex differences.

Moving toward paradigm-shifting research in health disparities through translational, transformational, and transdisciplinary approaches.

Translational, transdisciplinary, and transformational research stands to become a paradigm-shifting mantra for research in health disparities. A windfall of research discoveries using these 3 approaches has increased our understanding of the health disparities in racial, ethnic, and low socioeconomic status groups. These distinct but related research spheres possess unique environments, which, when integrated, can lead to innovation in health disparities science. In this article, we review these approaches and propose integrating them to advance health disparities research through a change in philosophical position and an increased emphasis on community engagement. We argue that a balanced combination of these research approaches is needed to inform evidence-based practice, social action, and effective policy change to improve health in disparity communities.

Genomics research: world survey of public funding.

BACKGROUND: Over the past two decades, genomics has evolved as a scientific research discipline. Genomics research was fueled initially by government and nonprofit funding sources, later augmented by private research and development (R&D) funding. Citizens and taxpayers of many countries have funded much of the research, and have expectations about access to the resulting information and knowledge. While access to knowledge gained from all publicly funded research is desired, access is especially important for fields that have broad social impact and stimulate public dialogue. Genomics is one such field, where public concerns are raised for reasons such as health care and insurance implications, as well as personal and ancestral identification. Thus, genomics has grown rapidly as a field, and attracts considerable interest. RESULTS: One way to study the growth of a field of research is to examine its funding. This study focuses on public funding of genomics research, identifying and collecting data from major government and nonprofit organizations around the world, and updating previous estimates of world genomics research funding, including information about geographical origins. We initially identified 89 publicly funded organizations; we requested information about each organization's funding of genomics research. Of these organizations, 48 responded and 34 reported genomics research expenditures (of those that responded but did not supply information, some did not fund such research, others could not quantify it). The figures reported here include all the largest funders and we estimate that we have accounted for most of the genomics research funding from government and nonprofit sources. CONCLUSION: Aggregate spending on genomics research from 34 funding sources averaged around $2.9 billion in 2003-2006. The United States spent more than any other country on genomics research, corresponding to 35% of the overall worldwide public funding (compared to 49% US share of public health research funding for all purposes). When adjusted to genomics funding intensity, however, the United States dropped below Ireland, the United Kingdom, and Canada, as measured both by genomics research expenditure per capita and per Gross Domestic Product.

The epsilon subunit of DNA polymerase III Is involved in the nalidixic acid-induced SOS response in Escherichia coli.

Quinolone antibacterial drugs such as nalidixic acid target DNA gyrase in Escherichia coli. These inhibitors bind to and stabilize a normally transient covalent protein-DNA intermediate in the gyrase reaction cycle, referred to as the cleavage complex. Stabilization of the cleavage complex is necessary but not sufficient for cell killing--cytotoxicity apparently results from the conversion of cleavage complexes into overt DNA breaks by an as-yet-unknown mechanism(s). Quinolone treatment induces the bacterial SOS response in a RecBC-dependent manner, arguing that cleavage complexes are somehow converted into double-stranded breaks. However, the only proteins known to be required for SOS induction by nalidixic acid are RecA and RecBC. In hopes of identifying additional proteins involved in the cytotoxic response to nalidixic acid, we screened for E. coli mutants specifically deficient in SOS induction upon nalidixic acid treatment by using a dinD::lacZ reporter construct. From a collection of SOS partially constitutive mutants with disruptions of 47 different genes, we found that dnaQ insertion mutants are specifically deficient in the SOS response to nalidixic acid. dnaQ encodes DNA polymerase III epsilon subunit, the proofreading subunit of the replicative polymerase. The deficient response to nalidixic acid was rescued by the presence of the wild-type dnaQ gene, confirming involvement of the epsilon subunit. To further characterize the SOS deficiency of dnaQ mutants, we analyzed the expression of several additional SOS genes in response to nalidixic acid using real-time PCR. A subset of SOS genes lost their response to nalidixic acid in the dnaQ mutant strain, while two tested SOS genes (recA and recN) continued to exhibit induction. These results argue that the replication complex plays a role in modulating the SOS response to nalidixic acid and that the response is more complex than a simple on/off switch.

Formation and processing of stalled replication forks--utility of two-dimensional agarose gels.

Replication forks can be stalled by tightly bound proteins, DNA damage, nucleotide deprivation, or defects in the replication machinery. It is now appreciated that processing of stalled replication forks is critical for completion of DNA replication and maintenance of genome stability. In this chapter, we detail the use of two-dimensional (2D) agarose gels with Southern hybridization for the detection and analysis of blocked replication forks in vivo. This kind of 2D gel electrophoresis has been used extensively for analysis of replication initiation mechanisms for many years, and more recently has become a valuable tool for analysis of fork stalling. Although the method can provide valuable information when forks are stalled in random locations (e.g., after UV damage or nucleotide deprivation), it is even more informative with site-specific fork blockage, for example, blocks caused by tightly bound replication terminator proteins or by drug-stabilized topoisomerase cleavage complexes.

Genetic analysis of the requirements for SOS induction by nalidixic acid in Escherichia coli.

Nalidixic acid, the prototype antibacterial quinolone, induces the SOS response by a mechanism that requires the RecBCD nuclease/helicase. A key step inferred for this induction pathway is the conversion of a drug-induced gyrase cleavage complex into a DNA break that can be processed by RecBC. We tried to clarify the nature of this step by searching for additional gene products that are specifically necessary for SOS induction following nalidixic acid treatment. A transposon library of approximately 19,000 insertion mutants yielded 18 mutants that were substantially reduced for SOS induction following nalidixic acid but not UV treatment, and which were also hypersensitive to nalidixic acid. All 18 mutants turned out to have insertions in recB or recC. As expected, recA insertion mutants were uncovered as being uninducible by either nalidixic acid or UV treatment. Insertions in 11 other genes were found to cause partial defects in SOS induction by one or both pathways, providing possible leads in understanding the detailed mechanisms of SOS induction. Overall, these results suggest that nalidixic acid-induced DNA breaks are generated either by RecBC itself, by redundant activities, and/or by an essential protein that could not be uncovered with transposon mutagenesis.

Norfloxacin-induced DNA gyrase cleavage complexes block Escherichia coli replication forks, causing double-stranded breaks in vivo.

Antibacterial quinolones inhibit type II DNA topoisomerases by stabilizing covalent topoisomerase-DNA cleavage complexes, which are apparently transformed into double-stranded breaks by cellular processes such as replication. We used plasmid pBR322 and two-dimensional agarose gel electrophoresis to examine the collision of replication forks with quinolone-induced gyrase-DNA cleavage complexes in Escherichia coli. Restriction endonuclease-digested DNA exhibited a bubble arc with discrete spots, indicating that replication forks had been stalled. The most prominent spot depended upon the strong gyrase binding site of pBR322, providing direct evidence that quinolone-induced cleavage complexes block bacterial replication forks in vivo. We differentiated between stalled forks that do or do not contain bound cleavage complex by extracting DNA under different conditions. Resealing conditions allow gyrase to efficiently reseal the transient breaks within cleavage complexes, while cleavage conditions cause the latent breaks to be revealed. These experiments showed that some stalled forks did not contain a cleavage complex, implying that gyrase had dissociated in vivo and yet the fork had not restarted at the time of DNA isolation. Additionally, some branched plasmid DNA isolated under resealing conditions nonetheless contained broken DNA ends. We discuss a model for the creation of double-stranded breaks by an indirect mechanism after quinolone treatment.

Drosophila melanogaster topoisomerase IIIalpha preferentially relaxes a positively or negatively supercoiled bubble substrate and is essential during development.

Eukaryotic type IA topoisomerases are important for the normal function of the cell, and in some cases essential for the organism, although their role in DNA metabolism remains to be elucidated. In this study, we cloned Drosophila melanogaster topoisomerase (topo) IIIalpha from an embryonic cDNA library and expressed and purified the protein to >95% homogeneity. This enzyme partially relaxes a hypernegatively supercoiled plasmid substrate consistent with other purified topo IIIs. A novel, covalently closed bubble substrate was prepared for this study, which topo IIIalpha fully relaxed, regardless of the handedness of the supercoils. Experiments with the bubble substrate demonstrate that topo IIIalpha has much different reaction preferences from those obtained by plasmid substrate-based assays. This is presumably due to the fact that solution conditions can affect the structure of plasmid based substrates and therefore their suitability as a substrate. A mutant allele of the Top3alpha gene, Top3alpha191, was isolated through imprecise excision mutagenesis of an existing P-element inserted in the first intron of the gene. Top3alpha191 is recessive lethal, with most of the homozygous individuals surviving to pupation but never emerging to adulthood. Whereas this mutation can be rescued by a Top3alpha transgene, ubiquitous overexpression of D. melanogaster topo IIIbeta cannot rescue this allele.