Using BLAT to find sequence similarity in closely related genomes.

The BLAST-Like Alignment Tool (BLAT) is used to find genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole-genome random reads to the human genome at a higher speed. It is freely available either on the Web or as a downloadable stand-alone program. BLAT search results provide a link for visualization in the University of California, Santa Cruz (UCSC) Genome Browser, where associated biological information may be obtained. Three example protocols are given: using an mRNA sequence to identify the exon-intron locations and associated gene in the genomic sequence of the same species, using a protein sequence to identify the coding regions in a genomic sequence and to search for gene family members in the same species, and using a protein sequence to find homologs in another species.

The informationist: building evidence for an emerging health profession.

BACKGROUND: To encourage evidence-based practice, an Annals of Internal Medicine editorial called for a new professional on clinical teams: an informationist trained in science or medicine as well as information science. OBJECTIVES: The study explored the effects of informationists on information behaviors of clinical research teams, specifically, frequency of seeking information for clinical or research decisions, range of resources consulted, perceptions about access to information, confidence in adequacy of literature searches, and effects on decision making and practice. It also explored perceptions about training and experience needed for successful informationists. METHODS: Exploratory focus groups and key interviews were followed by baseline and follow-up surveys conducted with researchers and clinicians receiving the service. Survey data were analyzed with Pearson's chi-square or Fisher's exact test. RESULTS: Comparing 2006 to 2004 survey responses, the researchers found that study participants reported: seeking answers to questions more frequently, spending more time seeking or using information, believing time was less of an obstacle to finding or using information, using more information resources, and feeling greater satisfaction with their ability to find answers. Participants' opinions on informationists' qualifications evolved to include both subject knowledge and information searching expertise. CONCLUSION: Over time, clinical research teams with informationists demonstrated changes in their information behaviors, and they valued an informationist's subject matter expertise more.

Inquiring Informationists: A Qualitative Exploration of Our Role.

OBJECTIVE: The goal of this study is to explore the impact of an informationist program at the National Institutes of Health (NIH) Library and to provide a basis for further program assessment. In 2001 the NIH Library began its informationist program, where librarians with training in both biomedicine and information science work alongside researchers. The goal of the program is to facilitate researchers' access to and usage of information resources. METHODS: The researchers used qualitative interviews with key informants to characterize the current informationist services of user groups. Subjects were selected to capture a variety of activities that would show patterns of how the program assists the researchers of various NIH groups. Following the interviews, the authors extracted recurring and significant themes from the subjects' comments. RESULTS: Interview subjects provided their views on the informationists' skills, impact, and team participation. Research results documented that informationists helped find resources, provided instruction, and worked as part of the research team. The NIH groups currently using this service value their informationists' knowledge of library resources and their ability to access information needs quickly. The informationists' skills in finding information save the researchers time, increase the efficiency of the research team, and complement the contributions of other team members. Training by informationists was found useful. Informationist services led to increased self-reported library use, albeit in some cases this use was entirely via the informationist. CONCLUSIONS: Informationists saved researchers time by obtaining requested information, finding esoteric or unfamiliar resources, and providing related training. These activities appeared to be facilitated by the acceptance of the informationist as part of the research team. This exploratory study provides background that should be useful in future, more extensive evaluations.

Informationist education.

The National Institutes of Health (NIH) funds biomedical research and conducts its own research. One way the NIH Library supports this work is by providing librarians with biomedical training and encouraging them to become embedded with researchers and administrators. Some of these "informationists" have degrees in scientific or health fields, and all engage in ongoing training, mostly through coursework at local institutions and at NIH itself. This article elaborates on the training of NIH informationists. Past research has indicated that patrons welcome librarians with biomedical training, which may in turn lead to greater communication between librarians and researchers.

Color change as a potential behavioral strategy.

Within species, color morphs may enhance camouflage, improve communication and/or confer reproductive advantage. However, in the male cichlid Astatotilapia burtoni, body color may also signal a behavioral strategy. A. burtoni live in a lek-like social system in Lake Tanganyika, Africa where bright blue or yellow territorial (T) males (together ~10-30% of the population) are reproductively capable and defend territories containing food with a spawning site. In contrast, non-territorial (NT) males are smaller, cryptically colored, shoal with females and have regressed gonads. Importantly, males switch between these social states depending on their success in aggressive encounters. Yellow and blue morphs were thought to be adaptations to particular habitats, but they co-exist both in nature and in the laboratory. Importantly, individual males can switch colors so we asked whether color influences behavioral and hormonal profiles. When pairing territorial males with opposite colored fish, yellow males became dominant over blue males significantly more frequently. Moreover, yellow T males had significantly higher levels of 11-ketotosterone than blue T males while only blue NT males had higher levels of the stress hormone cortisol compared to the other groups. Thus color differences alone predict dominance status and hormone profiles in T males. Since T males can and do change color, this suggests that A. burtoni may use color as a flexible behavioral strategy.