Coming out: the experience of LGBT+ people in STEM

Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three openly LGBT+ researchers on their experiences in biology.

Polarization enhancement technique for nuclear quadrupole resonance detection

We demonstrate a dramatic increase in the signal-to-noise ratio (SNR) of a nuclear quadrupole resonance (NQR) signal by using a polarization enhancement technique. By first applying a static magnetic field to pre-polarize one spin subsystem of a material, and then allowing that net polarization to be transferred to the quadrupole subsystem, we increased the SNR of a sample of ammonium nitrate by one-order of magnitude.

Case definitions, diagnostic algorithms, and priorities in encephalitis: consensus statement of the international encephalitis consortium

BACKGROUND

Encephalitis continues to result in substantial morbidity and mortality worldwide. Advances in diagnosis and management have been limited, in part, by a lack of consensus on case definitions, standardized diagnostic approaches, and priorities for research.

METHODS

In March 2012, the International Encephalitis Consortium, a committee begun in 2010 with members worldwide, held a meeting in Atlanta to discuss recent advances in encephalitis and to set priorities for future study.

RESULTS

We present a consensus document that proposes a standardized case definition and diagnostic guidelines for evaluation of adults and children with suspected encephalitis. In addition, areas of research priority, including host genetics and selected emerging infections, are discussed.

CONCLUSIONS

We anticipate that this document, representing a synthesis of our discussions and supported by literature, will serve as a practical aid to clinicians evaluating patients with suspected encephalitis and will identify key areas and approaches to advance our knowledge of encephalitis.

Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula

Genome-wide association study (GWAS) has revolutionized the search for the genetic basis of complex traits. To date, GWAS have generally relied on relatively sparse sampling of nucleotide diversity, which is likely to bias results by preferentially sampling high-frequency SNPs not in complete linkage disequilibrium (LD) with causative SNPs. To avoid these limitations we conducted GWAS with >6 million SNPs identified by sequencing the genomes of 226 accessions of the model legume Medicago truncatula. We used these data to identify candidate genes and the genetic architecture underlying phenotypic variation in plant height, trichome density, flowering time, and nodulation. The characteristics of candidate SNPs differed among traits, with candidates for flowering time and trichome density in distinct clusters of high linkage disequilibrium (LD) and the minor allele frequencies (MAF) of candidates underlying variation in flowering time and height significantly greater than MAF of candidates underlying variation in other traits. Candidate SNPs tagged several characterized genes including nodulation related genes SERK2, MtnodGRP3, MtMMPL1, NFP, CaML3, MtnodGRP3A and flowering time gene MtFD as well as uncharacterized genes that become candidates for further molecular characterization. By comparing sequence-based candidates to candidates identified by in silico 250K SNP arrays, we provide an empirical example of how reliance on even high-density reduced representation genomic makers can bias GWAS results. Depending on the trait, only 30–70% of the top 20 in silico array candidates were within 1 kb of sequence-based candidates. Moreover, the sequence-based candidates tagged by array candidates were heavily biased towards common variants; these comparisons underscore the need for caution when interpreting results from GWAS conducted with sparsely covered genomes.

Requirement for the SLP-76 adaptor GADS in T cell development

GADS is an adaptor protein implicated in CD3 signaling because of its ability to link SLP-76 to LAT. A GADS-deficient mouse was generated by gene targeting, and the function of GADS in T cell development and activation was examined. GADS- CD4-CD8- thymocytes exhibited a severe block in proliferation but still differentiated into mature T cells. GADS- thymocytes failed to respond to CD3 cross-linking in vivo and were impaired in positive and negative selection. Immunoprecipitation experiments revealed that the association between SLP-76 and LAT was uncoupled in GADS- thymocytes. These observations indicate that GADS is a critical adaptor for CD3 signaling.

Autoreactive B cells escape clonal deletion by expressing multiple antigen receptors

IgH and L chain transgenes encoding a phosphocholine (PC)-specific Ig receptor were introduced into recombinase-activating gene (Rag-2-/-) knockout mice. The PC-specific B cells that developed behaved like known autoreactive lymphocytes. They were 1) developmentally arrested in the bone marrow, 2) unable to secrete Ab, 3) able to escape clonal deletion and develop into B1 B cells in the peritoneal cavity, and 4) rescued by overexpression of bcl-2. A second IgL chain was genetically introduced into Rag-2-/- knockout mice expressing the autoreactive PC-specific Ig receptor. These dual L chain-expressing mice had B cells in peripheral lymphoid organs that coexpressed both anti-PC Ab as well as Ab employing the second available L chain that does not generate an autoreactive PC-specific receptor. Coexpression of the additional Ig molecules rescued the autoreactive anti-PC B cells and relieved the functional anergy of the anti-PC-specific B cells, as demonstrated by detection of circulating autoreactive anti-PC-Abs. We call this novel mechanism by which autoreactive B cells can persist by compromising allelic exclusion receptor dilution. Rescue of autoreactive PC-specific B cells would be beneficial to the host because these Abs are vital for protection against pathogens such as Streptococcus pneumoniae.

Early detection of Rasmussen's syndrome by brain SPECT imaging

The authors describe a patient with Rasmussen's syndrome detected by grossly abnormal results of Tc-99m HMPAO SPECT brain imaging obtained with a single-headed camera. Results of magnetic resonance imaging and cerebrospinal fluid examinations were normal.

Determination of cefsulodin, cefmenoxime, and cefadroxil as residues on surfaces

Cefsulodin, cefmenoxime, and cefadroxil are degraded instantaneously in aqueous sodium hypochlorite, sodium hypochlorite-detergent, or alkaline detergent solutions. These alkaline solutions are used to clean surfaces that have been exposed to the cephalosporins. The cleaned surfaces are monitored for residual drug levels (microgram) using a wet swab-dry swab technique. After extraction from the swabs, the content of the respective cephalosporin is determined in the solution by high-performance liquid chromatography. The limit of detection for each of the compounds is 0.1 microgram/ml. Recoveries from nonporous surfaces ranged from 56 to 102%.

Psychological test and demographic variables associated with retention of narcotic addicts in treatment

The relationships of psychological and demographic variables to retention in treatment of narcotic addicts were examined. Age and race were not related to retention. The IQ's of subjects retained longer seemed to be higher but the relationship did not reach statistical significance with this sample size. Legal pressure was clearly associated with longer retention as were higher scores on the Suitable for Treatment Scale. Legal pressure seemed to exert its major influence early in treatment. Treatment center variables and patient variables probably interact to determine retention.

Exposure and contamination of the air and employees of a pentachlorophenol plant, Idaho--1972

A pentachlorophenol (PCP) wood treatment plant was studied to determine PCP exposure to people by occupation and to the plant by work area. This plant operates on a year-round basis with a 25 percent increase in production from May through October. Approximately 2.5 million board feet of timber are processed annually. Samples were taken in the morning of the second work week of each month for 5 consecutive months. Samples consisted of serum and urine from the employees and air from locations throughout the plant work area. All samples were analyzed for PCP residue. Peripheral blood was used to culture cells to investigate possible chromosomal aberrations.