Mapping Interdisciplinary Fields: Efficiencies,Gaps and Redundancies in HIV/AIDS Research

While interdisciplinarity continues to increase in popularity among funders and other scientific organizations, its potential to promote scientific advances remains under-examined. For HIV/AIDS research, we examine the dynamics of disciplinary integration (or lack thereof) providing insight into a field''s knowledge base and those questions that remain unresolved. Drawing on the complete histories of two interdisciplinary journals, we construct bibliographic coupling networks based on overlapping citations to identify segregation into research clusters and estimate topic models of research content. We then compare how readily those bibliographic coupling clusters account for the structuring of topics covered within the field as it evolves over two decades. These comparisons challenge one-dimensional and/or cross-sectional approaches to interdisciplinarity. Some topics are increasingly coordinated across disciplinary boundaries (e.g., vaccine development); others remain relatively segmented into disconnected disciplinary domains for the full period (e.g., drug resistance). This divergence indicates heterogeneity in interdisciplinarity and emphasizes the need for critical approaches to studying the organization of science.     

Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation

The signal produced by fluorescence in situ hybridization (FISH) often is inconsistent among cells and sensitivity is low. Small DNA targets on the chromatin are difficult to detect. We report here an improved nick translation procedure for Texas red and Alexa Fluor 488 direct labeling of FISH probes. Brighter probes can be obtained by adding excess DNA polymerase I. Using such probes, a 30?kb yeast transgene, and the rp1, rp3 and zein multigene clusters were clearly detected.     

Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum

Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. Here we identify a Bifidobacterium longum protein with high sequence homology to type II DHQDs but no detectable DHQD activity under standard assay conditions. A crystal structure reveals that the B. longum protein adopts a DHQD-like tertiary structure but a distinct quaternary state. Apparently forming a dimer, the B. longum protein lacks the active site aspartic acid contributed from a neighboring protomer in the type II DHQD dodecamer. Relating to the absence of protein–protein interactions established in the type II DHQD dodecameric assembly, substantial conformational changes distinguish the would-be active site of the B. longum protein. As B. longum possess no other genes with homology to known DHQDs, these findings imply a unique DHQD activity within B. longum.     

Distinct signaling pathways regulate TLR2 co-stimulatory function in human T cells

Toll-like receptor 2 (TLR2) serves as a co-stimulatory receptor for human T cells by enhancing T cell receptor (TCR)-induced cytokine production and proliferation. However, it is unknown where signals from the TCR and TLR2 converge to enhance T cell activation. To address this gap, we examined changes in TCR-induced signaling following concurrent TLR2 activation in human T cells. Both proximal TCR-mediated signaling and early NFκB activation were not enhanced by TCR andTLR2 co-activation, potentially due to the association of TLR2 with TLR10. Instead, TLR2 co-induction did augment Akt and Erk1/Erk2 activation in human T cells. These findings demonstrate that TLR2 activates distinct signaling pathways in human T cells and suggest that alterations in expression of TLR2 co-receptors may contribute to aberrant T cell responses.     

Internal ethnicity in the ethnic economy

Internal ethnicity refers to ethnic subgroups within an immigrant group. An ‘ethnic economy’ includes the self‐employed and their co‐ethnic workers. Although most research treats the boundaries of ‘ethnic economy’ and its variant, the ‘ethnic enclave economy’, as though they were coterminous with those of national‐origin immigrant groups, this assumption is unreliable. Ethnic boundaries need not coincide with those of nationality origin when internal ethnicity exists. To test this hypothesis, we utilize survey data collected from a sample of Iranians in Los Angeles. Because this national‐origin immigrant group contains four ethno‐religious subgroups (Armenians, Bahais, Jews and Muslims), the Iranians in Los Angeles operated four distinctive ethnic economies, not one. Each ethno‐religious subgroup had its own ethnic economy, and these separate economies were only weakly tied to an encompassing Iranian ethnic economy.     

Neuroactive diol and acyloin metabolites from cone snail-associated bacteria

The bacterium Gordonia sp. 647 W.R.1a.05 was cultivated from the venom duct of the cone snail, Conus circumcisus. The Gordonia sp. organic extract modulated the action potential of mouse dorsal root ganglion neurons. Assay-guided fractionation led to the identification of the new compound circumcin A (1) and 11 known analogs (2–12). Two of these compounds, kurasoin B (7) and soraphinol A (8), were active in a human norepinephrine transporter assay with K_i values of 2575 and 867 nM, respectively. No neuroactivity had previously been reported for compounds in this structural class. Gordonia species have been reproducibly isolated from four different cone snail species, indicating a consistent association between these organisms.     

A snow microflora in the Cairngorm Mountains,Scotland

An association of snow algae and fungi from a corrie in the Cairngorms is described and illustrated. This is the first detailed account of a snow microflora from Britain, though Chlamydomonas nivalis was collected twice last century.     

Atomistic details of effect of disulfide bond reduction on active site of Phytase B from Aspergillus niger: A MD Study

The molecular integrity of the active site of phytases from fungi is critical for maintaining phytase function as efficient catalytic machines. In this study, the molecular dynamics (MD) of two monomers of phytase B from Aspergillus niger, the disulfide intact monomer (NAP) and a monomer with broken disulfide bonds (RAP), were simulated to explore the conformational basis of the loss of catalytic activity when disulfide bonds are broken. The simulations indicated that the overall secondary and tertiary structures of the two monomers were nearly identical but differed in some crucial secondary–structural elements in the vicinity of the disulfide bonds and catalytic site. Disulfide bonds stabilize the β-sheet that contains residue Arg66 of the active site and destabilize the α-helix that contains the catalytic residue Asp319. This stabilization and destabilization lead to changes in the shape of the active–site pocket. Functionally important hydrogen bonds and atomic fluctuations in the catalytic pocket change during the RAP simulation. None of the disulfide bonds are in or near the catalytic pocket but are most likely essential for maintaining the native conformation of the catalytic site.

Abbreviations

PhyB - 2.5 pH acid phophatese from Aspergillus niger, NAP - disulphide intact monomer of Phytase B, RAP - disulphide reduced monomer of Phytase B, Rg - radius of gyration, RMSD - root mean square deviation, MD - molecular dynamics.