Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

Towards Establishment of a Rice Stress Response Interactome

Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein–protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance

Resident Research and Scholarly Activity in Internal Medicine Residency Training Programs

OBJECTIVES: 1) To describe how internal medicine residency programs fulfill the Accreditation Council for Graduate Medical Education (ACGME) scholarly activity training requirement including the current context of resident scholarly work, and 2) to compare findings between university and nonuniversity programs. DESIGN: Cross-sectional mailed survey. SETTING: ACGME-accredited internal medicine residency programs. PARTICIPANTS: Internal medicine residency program directors. MEASUREMENTS: Data were collected on 1) interpretation of the scholarly activity requirement, 2) support for resident scholarship, 3) scholarly activities of residents, 4) attitudes toward resident research, and 5) program characteristics. University and nonuniversity programs were compared. MAIN RESULTS: The response rate was 78%. Most residents completed a topic review with presentation (median, 100%) to fulfill the requirement. Residents at nonuniversity programs were more likely to complete case reports (median, 40% vs 25%; P =.04) and present at local or regional meetings (median, 25% vs 20%; P =.01), and were just as likely to conduct hypothesis-driven research (median, 20% vs 20%; P =.75) and present nationally (median, 10% vs 5%; P =.10) as residents at university programs. Nonuniversity programs were more likely to report lack of faculty mentors (61% vs 31%; P <.001) and resident interest (55% vs 40%; P =.01) as major barriers to resident scholarship. Programs support resident scholarship through research curricula (47%), funding (46%), and protected time (32%). CONCLUSIONS: Internal medicine residents complete a variety of projects to fulfill the scholarly activity requirement. Nonuniversity programs are doing as much as university programs in meeting the requirement and supporting resident scholarship despite reporting significant barriers

Therapy of recurrent high grade gliomas with surgery, and autologous mitogen activated IL-2 stimulated killer (MAK) Lymphocytes: I. Enhancement of MAK lytic activity and cytokine production by PHA and clinical use of PHA

Nineteen patients with recurrent high grade gliomas were treated in a phase I/II trial with aggressive debulking of the tumor, mitogen activated IL-2 stimulated peripheral blood lymphocytes (MAK cells), and rIL-2. Phytohemagglutin (PHA) was introduced into the tumor site in 16 patients prior to implanting MAK cells and IL-2 in an attempt to trigger more effective lysis of the tumor in vivo. In vitro both TNF bioactivity and cytolytic activity of long term cultured MAK (LMAK) cells were dramatically enhanced by adding PHA to the cultures of these activated PBL. Three of eleven patients (27%) had a decrease in size of the enhancing lesion on CT and/or MRI. Seven (37%) patients clinically improved. Median survival after therapy was 30 weeks. PHA was shown to be safe in vivo and more effective than IL-2 triggering enhanced effector function in vitro