FigSearch: a figure legend indexing and classification system

FigSearch is a prototype text-mining and classification system for figures from any corpus of full-text biological papers. The system allows users to search for figures that contain genes of interest and illustrate protein interactions. The retrieved figures are ranked by a score representing the likelihood to be of a certain type, in this case, schematic illustrations of protein interactions and signaling events. The system contains a Web interface for search, a module for classification of figures based on vector representations of figure legends and a module for indexing gene names. In a preliminary validation, the FigSearch system showed satisfactory performance according to domain experts in providing the most relevant graphical representations. This strategy may be easily extended to other figure types. Moreover, as more full-text data become available, such a system will find increased usefulness in identifying and presenting compressed biological knowledge. AVAILABILITY: A searchable Web interface, FigSearch, is accessible via http://pubgeneserver.uio.no/figsearch/ for all figures from the available corpus.     

Metal accumulation and metallothionein in brown trout, Salmo trutta, from two Norwegian rivers differently contaminated with Cd, Cu and Zn

In this work we have studied the accumulation of heavy metals in two brown trout (Salmo trutta) populations in their natural environment and the participation of metal binding to metallothionein (MT) in this process. Cd, Cu and Zn concentrations, total MT (including Cu MT) and Cd/Zn MT were measured in the gills, liver and kidney of trout inhabiting two rivers, one Cu-contaminated and the other Cd/Zn-contaminated, located at Røros, Central Norway. In both populations, high levels of Cu were found in the liver, whereas Cd was accumulated in liver and particularly in the kidney. The proportions of Cd/Zn MT and Cu MT in liver and kidney, but not in gills, reflected the accumulated and the environmental concentrations of these metals. The total Cu MT concentrations in the investigated tissues, however, were highest in trout from the river with the lowest ambient Cu concentration. It is suggested that MTs are of less importance in Cu-acclimated trout. The data also suggest that acclimation to a Cu-rich environment involves reduced Cu accumulation or increased Cu elimination. In trout from the Cd-rich environment, this metal was mainly bound to MT, whereas in trout from the Cu-rich environment Cd was also associated with non-MT proteins. These findings emphasize the importance to determine both Cd/Zn MT and Cu MT levels, when the participation of this protein in metal handling in trout tissues is investigated.     

Lithium ions enhance cysteine string protein gene expression in vivo and in vitro

Lithium is a well established pharmacotherapy for the treatment of recurrent manic-depressive illness. However, the mechanism by which lithium exerts its therapeutic action remains elusive. Here we report that lithium at 1 mM significantly increased the expression of cysteine string proteins (CSPs) in a pheochromocytoma cell line (PC12 cells) differentiated by nerve growth factor. These cells concomitantly exhibited increased expression of CSPs in their cell bodies and boutons. Enhanced CSP expression was also observed in the brain of rats fed a lithium-containing diet, which elevated serum lithium to a therapeutically relevant concentration of approximately 1.0 mM. However, both in vitro and in vivo, the expression of another synaptic vesicle protein, synaptophysin, and the t-SNARE, synaptosomal-associated protein of 25 kDa (SNAP-25), was not significantly altered by lithium. These observations indicate that lithium-induced changes of CSP gene expression may contribute to the therapeutic efficacy of this monovalent cation.     

Chlorpromazine interaction with glycerophospholipid liposomes studied by magic angle spinning solid state (13)C-NMR and differential scanning calorimetry

Phosphatidylserine (PS) extracted from pig brain and synthetic dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylcholine (DMPC) were used to make DPPC/DMPC and DPPC/PS large unilamellar liposomes with a diameter of approximately 1 microm. Chlorpromazine-HCl (CPZ), an amphipathic cationic psychotropic drug of the phenothiazine group, is known to partition into lipid bilayer membranes of liposomes with partition coefficients depending on the acyl chain length and to alter the bilayer structure in a manner depending on the phospholipid headgroups. The effects of adding CPZ to these membranes were studied by differential scanning calorimetry and proton cross polarization solid state magic angle spinning (13)C-nuclear magnetic resonance spectroscopy (CP-MAS-(13)C-NMR). CP-MAS-(13)C-NMR spectra of the DPPC (60%)/DMPC (40%) and the DPPC (54%)/DMPC (36%)/CPZ (10%) liposomes, show that CPZ has low or no interaction with the phospholipids of this neutral and densely packed bilayer. Conversely, the DPPC (54%)/PS (36%)/CPZ (10%) bilayer at 25 degrees C demonstrates interaction of CPZ with the phospholipid headgroups (PS). This CPZ interaction causes about 30% of the acyl chains to enter the gauche conformation with low or no CPZ interdigitation among the acyl chains at this temperature (25 degrees C). The DPPC (54%)/PS (36%)/CPZ (10%) bilayer at a sample temperature of 37 degrees C (T(C)=31.2 degrees C), shows CPZ interdigitation among the phospholipids as deduced from the finding that approximately 30% of the phospholipid acyl chains carbon resonances shift low-field by 5-15 ppm.     

When Inhibitors Do Not Inhibit: Critical Evaluation of Rational Drug Design Targeting Chorismate Mutase from Mycobacterium tuberculosis

Tuberculosis (TB) is a devastating disease that claims millions of lives every year. Hindered access or non‐compliance to medication, especially in developing countries, led to drug resistance, further aggravating the situation. With current standard therapies in use for over 50 years and only few new candidates in clinical trials, there is an urgent call for new TB drugs. A powerful tool for the development of new medication is structure‐guided design, combined with virtual screening or docking studies. Here, we report the results of a drug‐design project, which we based on a publication that claimed the structure‐guided discovery of several promising and highly active inhibitors targeting the secreted chorismate mutase (*MtCM) from Mycobacterium tuberculosis. We set out to further improve on these compounds and synthesized a series of new derivatives. Thorough evaluation of these molecules in enzymatic assays revealed, to our dismay, that neither the claimed lead compounds, nor any of the synthesized derivatives, show any inhibitory effects against *MtCM.     

Moose (Alces alces) calf survival rates in the presence of wolves (Canis lupus) in southeast Norway

Wolves (Canis lupus) are recolonizing Scandinavia and becoming a new limiting factor that should be taken into account in the management of moose (Alces alces). However, there is a lack of empirical estimates of moose survival after wolf recolonization. We investigated the effects of wolf abundance, moose litter size (single/twin calves), and climatic factors on annual and seasonal calf survival rates in a moose population in southeast Norway. We used data that were obtained over 7?years by radio-tracking and regular visual observations of 68 moose cows to determine the presence or absence of calves at heel. Annual and winter calf survival rates were 20–40 percentage points lower in the wolf territory compared with previous estimates of moose calf survival in similar areas that lacked wolves. Cause-specific studies of mortality would further enhance our ability to determine the relative role of various limiting factors. Our study suggests that moose managers should regulate quotas to buffer the lower survival rates after wolf recolonization.     

Insulin sensitivity after maximal and endurance resistance training

The purpose of the study was to compare the effects of maximal resistance training (MRT) vs. endurance resistance training (ERT) on improvements in insulin levels and glucose tolerance in overweight individuals at risk of developing type 2 diabetes. Eighteen participants with baseline values suggesting impaired glucose tolerance were randomly assigned to 1 of 2 groups. Group 1 engaged in supervised MRT (Bernstein inverted pyramid system: 5 × 3-4, 60-85% 1 repetition maximum [1RM]), 3 d·wk(-1) over 4 months, whereas members of group 2 acted as controls. Later, group 2 engaged in supervised ERT (3 × 12-15, 45-65% 1RM), 3 d·wk(-1) over a 4 month period with the 2 prebaselines as controls. Both interventions consisted of 8 exercises that included the entire body. Glucose (fasting and 2-hour test), insulin and C-peptide measures were assessed from pre to post in both groups. The MRT led to reduced blood levels of 2-hour glucose (p = 0.044) and fasting C-peptide (p = 0.023) and decreased insulin resistance (p = 0.040). The ERT caused a significant reduction in the blood levels of insulin (p = 0.023) and concomitant positive effects on % insulin sensitivity (p = 0.054) and beta-cell function (p = 0.020). The findings indicate that both MRT and ERT lead to decreased insulin resistance in people with a risk of developing type 2 diabetes; MRT led to a greater increase in glucose uptake capacity (in muscles), whereas ERT led to greater insulin sensitivity, supporting the recommendation of both MRT and ERT as primary intervention approaches for individuals at a risk of developing type 2 diabetes.     

INF2 promotes the formation of detyrosinated microtubules necessary for centrosome reorientation in T cells

T cell antigen receptor–proximal signaling components, Rho-family GTPases, and formin proteins DIA1 and FMNL1 have been implicated in centrosome reorientation to the immunological synapse of T lymphocytes. However, the role of these molecules in the reorientation process is not yet defined. Here we find that a subset of microtubules became rapidly stabilized and that their α-tubulin subunit posttranslationally detyrosinated after engagement of the T cell receptor. Formation of stabilized, detyrosinated microtubules required the formin INF2, which was also found to be essential for centrosome reorientation, but it occurred independently of T cell receptor–induced massive tyrosine phosphorylation. The FH2 domain, which was mapped as the INF2 region involved in centrosome repositioning, was able to mediate the formation of stable, detyrosinated microtubules and to restore centrosome translocation in DIA1-, FMNL1-, Rac1-, and Cdc42-deficient cells. Further experiments indicated that microtubule stabilization was required for centrosome polarization. Our work identifies INF2 and stable, detyrosinated microtubules as central players in centrosome reorientation in T cells.     

Cardiac Myocyte Excitation by Ultrashort High-Field Pulses

In unexcitable, noncardiac cells, ultrashort (nanosecond) high-voltage (megavolt-per-meter) pulsed electrical fields (nsPEF) can mobilize intracellular Ca²⁺ and create transient nanopores in the plasmalemma. We studied Ca²⁺ responses to nsPEF in cardiac cells. Fluorescent Ca²⁺ or voltage signals were recorded from isolated adult rat ventricular myocytes deposited in an electrode microchamber and stimulated with conventional pulses (CPs; 0.5-2.4 kV/cm, 1 ms) or nsPEF (10-80 kV/cm, 4 ns). nsPEF induced Ca²⁺ transients in 68/104 cells. Repeating nsPEF increased the likelihood of Ca²⁺ transient induction (61.8% for <10 nsPEF vs. 80.6% for ≥10 nsPEF). Repetitive Ca²⁺ waves arising at the anodal side and Ca²⁺ destabilization occurred after repeated nsPEF (12/29) or during steady-state single nsPEF delivery at 2 Hz. Removing extracellular Ca²⁺ abolished responses to nsPEF. Verapamil did not affect nsPEF-induced Ca²⁺ transients, but decreased responses to CP. Tetrodotoxin and KB-R7943 increased the repetition threshold in response to nsPEF: 1-20 nsPEF caused local anodal Ca²⁺ waves without Ca²⁺ transients, and ≥20 nsPEF caused normal transients. Ryanodine-thapsigargin and caffeine protected against nsPEF-induced Ca²⁺ waves and showed less recovery of diastolic Ca²⁺ levels than CP. Voltage recordings demonstrated action potentials triggered by nsPEF, even in the presence of tetrodotoxin. nsPEF can mobilize intracellular Ca²⁺ in cardiac myocytes by inducing action potentials. Anodal Ca²⁺ waves and resistance to Na⁺ and Ca²⁺ channel blockade suggest nonselective ion channel transport via sarcolemmal nanopores as a triggering mechanism.     

Here come the SUNs: a nucleocytoskeletal missing link

The nuclear envelope has traditionally been thought of as a barrier that separates the nucleoplasm from the cytoplasm in eukaryotic cells. Increasing evidence shows that the nuclear envelope also links the inside of the nucleus to the cytoskeleton. Here we discuss recent papers showing that this link occurs through complexes of lamins on the inner aspect of the inner nuclear membrane, transmembrane proteins of the inner nuclear membrane called SUNs and large nesprin isoforms localized specifically to the outer nuclear membrane. These discoveries have implications for nuclear positioning, nuclear migration and pathogenesis of inherited diseases that are caused by mutations in nuclear envelope proteins.