Patterns of gene conversion in duplicated yeast histones suggest strong selection on a coadapted macromolecular complex

We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies

A National Plan of Action for Reducing the Incidental Catch of Seabirds in Longline Fisheries

Concerns about the incidental catch of seabirds in the world’s longline fisheries led to the endorsement of the International Plan of Action for Reducing the Incidental Catch of Seabirds in Longline Fisheries (IPOA–Seabirds) by the Food and Agriculture Organization of the United Nations’ Committee on Fisheries in February 1999. The voluntary IPOA–Seabirds applies to States with longline fisheries and would be implemented through the development of National Plans of Action, no later than early 2001. The U.S. NPOA–Seabirds contains the following themes: 1) Regional assessments of seabird interactions with longline fisheries; 2) If a problem exists, then actions should be taken – data collection; prescription of mitigation measures; research and development; and outreach about seabird bycatch; 3) Annual regional reports on the status of NPOA-Seabirds implementation; 4) Cooperative efforts between NMFS and FWS on seabird bycatch issues and research; and 5) A national commitment to advocate the development of National Plans of Action within international fora. By working cooperatively, fishermen, managers, regional fishery management councils, scientists, and the public will use this national framework to achieve a balanced solution to the seabird bycatch problem, promoting continuing sustainability of our national marine resources

Letter to the editor: Don't sell social science short

The News of the Week article that reports on Senator Kay Bailey Hutchison (R-TX) questioning the need to fund social science research at the National Science Foundation is alarming and shortsighted ("Senate panel chair asks why NSF funds social sciences," 12 May, p. 829). Social science research is at the fundamental core of basic research and has much to contribute to the economic viability of the United States. Twenty years of direct and jointly funded social and ecosystem science research at Colorado State University's Natural Resource Ecology Laboratory has produced deep insights into environmental and societal impacts of political upheaval, land use, and climate change in parts of Africa, Asia, and the Americas. Beyond greatly advancing our understanding of the coupled human-environmental system, the partnership of social and ecosystem science has brought scientists and decision-makers together to begin to develop solutions to difficult problems

Attenuated Central Nervous System Infection in Advanced HIV/AIDS With Combination Antiretroviral Therapy

Background Before the introduction of combination antiretroviral therapy (CART), neurological disease correlated with cerebrospinal fluid (CSF) levels of human immunodeficiency virus (HIV) RNA. Objective: To investigate the relationships among HIV RNA levels, immune activation markers, and neurological status in patients receiving CART. Design: Multicenter cohort study. Setting: Academic neurology departments. Patients: A total of 371 patients unselected for neurological complaints and with CD4 cell counts less than 200/μL or with cognitive symptoms and CD4 cell counts less than 300/μL were enrolled into the Northeastern AIDS Dementia cohort in 1998-2002. Diagnoses of HIV-associated dementia (HIV-D) and minor cognitive-motor disorder (MCMD) were obtained with a computerized algorithm. Plasma and CSF levels of HIV RNA, monocyte chemotactic protein 1, macrophage colony-stimulating factor, and tumor necrosis factor α were quantified. Results: The mean ± SD age was 41.5 ± 7.2 years, and the mean ± SD educational level was 12.3 ± 2.2 years. Seventy percent of the cohort was black, and 30% were women. The mean ± SD CD4 cell count was 136.8 ± 87.9/μL, and CART was used in 71%. Twenty-nine percent of the patients were unimpaired (n = 106), 36% had MCMD (n = 133), and 35% had HIV-D (n = 128). Mean log10 CSF HIV RNA copies per milliliter was 2.6 ± 0.8, with no differences among the neurological groups, even after adjustments for baseline CD4 cell counts and antiretroviral therapy. Cerebrospinal fluid HIV RNA was undetectable in 47% of unimpaired, 46% of MCMD, and 43% of HIV-D patients (P = .91). Plasma levels of monocyte chemotactic protein type 1 and tumor necrosis factor α correlated weakly with HIV RNA levels but did not distinguish those with neurological deficits. Conclusions: In contrast to observations in individuals not treated with CART, we found no relationship between CSF markers and neurological status in this CART-using cohort with advanced HIV/AIDS. This was not explicable by demographic differences or plasma virological control. CART may substantially attenuate the degree of central nervous system HIV infection and immune activation, and in CART users, CSF HIV RNA and immune activation markers may fail to discriminate milder degrees of HIV-D and MCMD

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome

Abstract Background Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal’s diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data. Results Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host. When the host sheep were fed a grain-based diet, the induced microbial metabolic network showed several critical differences from those seen on the evolved forage-based diet. Grain-based (e.g., concentrate) diets tend to be dominated by a smaller set of reactions that employ metabolites that are nearer in network space to the host’s metabolism. In addition, these reactions are more central in the network and employ substrates with shorter carbon backbones. Despite this apparent lower complexity, the concentrate-associated metabolic networks are actually more dissimilar from each other than are those of forage-fed animals. Because both groups of animals were initially fed on a forage diet, we propose that the diet switch drove the appearance of a number of different microbial networks, including a degenerate network characterized by an inefficient use of dietary nutrients. We used network simulations to show that such disparate networks are not an unexpected result of a diet shift. Conclusion We argue that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective. In particular, different diets induce predictable and significant differences in the enzymes used by the microbiome. Nonetheless, there are clearly a number of microbiomes of differing structure that show similar functional properties. Changes such as a diet shift uncover more of this type of diversity

Additional file 1: of Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome

Supplemental Figures 1-3 with captions; Supplemental Tables 1-3. (PDF 6395 kb