Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines

To understand the structure and function of large molecular machines, accurate knowledge of their stoichiometry is essential. In this study, we developed an integrated targeted proteomics and super‐resolution microscopy approach to determine the absolute stoichiometry of the human nuclear pore complex (NPC), possibly the largest eukaryotic protein complex. We show that the human NPC has a previously unanticipated stoichiometry that varies across cancer cell types, tissues and in disease. Using large‐scale proteomics, we provide evidence that more than one third of the known, well‐defined nuclear protein complexes display a similar cell type‐specific variation of their subunit stoichiometry. Our data point to compositional rearrangement as a widespread mechanism for adapting the functions of molecular machines toward cell type‐specific constraints and context‐dependent needs, and highlight the need of deeper investigation of such structural variants.     

Association of Thymidylate Synthase Polymorphisms with Acute Pancreatitis and/or Peripheral Neuropathy in HIV-Infected Patients on Stavudine-Based Therapy

Background

Low expression thymidylate synthase (TS) polymorphism has been associated with increased stavudine triphosphate intracellular (d4T-TP) levels and the lipodystrophy syndrome. The use of d4T has been associated with acute pancreatitis and peripheral neuropathy. However, no relationship has ever been proved between TS polymorphisms and pancreatitis and/or peripheral neuropathy.

Methods

We performed a case-control study to assess the relationship of TS and methylene-tetrahydrofolate reductase (MTHFR) gene polymorphisms with acute pancreatitis and/or peripheral neuropathy in patients exposed to d4T. Student’s t test, Pearson’s correlations, one-way ANOVA with Bonferroni correction and stepwise logistic regression analyses were done.

Results

Forty-three cases and 129 controls were studied. Eight patients (18.6%) had acute pancreatitis, and 35 (81.4%) had peripheral neuropathy. Prior AIDS was more frequent in cases than in controls (OR = 2.36; 95%CI 1.10–5.07, P = 0.0247). L7ow expression TS and MTHFR genotype associated with increased activity were more frequent in patients with acute pancreatitis and/or peripheral neuropathy than in controls (72.1% vs. 46.5%, OR = 2.97; 95%CI: 1.33–6.90, P = 0.0062, and 79.1% vs. 56.6%, OR = 2.90, 95%CI: 1.23–7.41, P = 0.0142, respectively). Independent positive or negative predictors for the development of d4T-associated pancreatitis and/or peripheral neuropathy were: combined TS and MTHFR genotypes (reference: A+A; P = 0.002; OR_A+B = 0.34 [95%CI: 0.08 to 1.44], OR_B+A = 3.38 [95%CI: 1.33 to 8.57], OR_B+B = 1.13 [95%CI: 0.34 to 3.71]), nadir CD4 cell count >200 cells/mm³ (OR = 0.38; 95%CI: 0.17–0.86, P = 0.021), and HALS (OR = 0.39 95%CI: 0.18–0.85, P = 0.018).

Conclusions

Low expression TS plus a MTHFR genotype associated with increased activity is associated with the development of peripheral neuropathy in d4T-exposed patients.     

Synergistic action of xylanase and mannanase improves the total hydrolysis of softwood

The impact of xylan and glucomannan hydrolysis on cellulose hydrolysis was studied on five pretreated softwood substrates with different xylan and glucomannan contents, both varying from 0.2% to 6.9%, using mixtures of purified enzymes.The supplementation of pure cellulase mixture with non-specific endoglucanase TrCel7B and xylanase TrXyn11 enhanced the hydrolysis of all substrates, except the steam pretreated spruce, by more than 50%. The addition of endo-β-mannanase increased the overall hydrolysis yield by 20-25%, liberating significantly more glucose than theoretically present in glucomannan.When supplemented together, xylanolytic and mannanolytic enzymes acted synergistically with cellulases. Moreover, a linear correlation was observed between the hydrolysis of polysaccharides, irrespective of the composition, indicating that glucomannan and xylan form a complex network of polysaccharides around the cellulosic fibres extending throughout the lignocellulosic matrix. Both hemicellulolytic enzymes are crucial as accessory enzymes when designing efficient mixtures for the total hydrolysis of lignocellulosic substrates containing both hemicelluloses.     

Filamin depletion blocks endoplasmic spreading and destabilizes force-bearing adhesions

Cell motility is an essential process that depends on a coherent, cross-linked actin cytoskeleton that physically coordinates the actions of numerous structural and signaling molecules. The actin cross-linking protein, filamin (Fln), has been implicated in the support of three-dimensional cortical actin networks capable of both maintaining cellular integrity and withstanding large forces. Although numerous studies have examined cells lacking one of the multiple Fln isoforms, compensatory mechanisms can mask novel phenotypes only observable by further Fln depletion. Indeed, shRNA-mediated knockdown of FlnA in FlnB(-/-) mouse embryonic fibroblasts (MEFs) causes a novel endoplasmic spreading deficiency as detected by endoplasmic reticulum markers. Microtubule (MT) extension rates are also decreased but not by peripheral actin flow, because this is also decreased in the Fln-depleted system. Additionally, Fln-depleted MEFs exhibit decreased adhesion stability that appears in increased ruffling of the cell edge, reduced adhesion size, transient traction forces, and decreased stress fibers. FlnA(-/-) MEFs, but not FlnB(-/-) MEFs, also show a moderate defect in endoplasm spreading, characterized by initial extension followed by abrupt retractions and stress fiber fracture. FlnA localizes to actin linkages surrounding the endoplasm, adhesions, and stress fibers. Thus we suggest that Flns have a major role in the maintenance of actin-based mechanical linkages that enable endoplasmic spreading and MT extension as well as sustained traction forces and mature focal adhesions.     

Two heteropteran predators in relation to weed management in herbicide-tolerant corn

Deployment of genetically modified (GM), herbicide-tolerant corn may alter weed flora abundance and composition and may affect pests and their natural enemies. Among on-plant predators, Orius spp. are the prevalent group in Spain and were selected to study the impact of glyphosate use on predators. We also studied Nabis sp. which is commonly recorded on corn in the study area. For this, a 4-year study was conducted in NE Spain. Three different herbicide regimes were compared: two glyphosate (a broad-spectrum herbicide) treatments per season, no herbicide treatment, and one pre-emergence conventional treatment with selective herbicides against broadleaf and grassy weeds. Density of main arthropod herbivores and the above two predatory groups was recorded on plants. Differences between herbicide regimes were observed in the two functional groups studied, herbivores and heteropteran predators. The comparison of glyphosate-treated and untreated plots showed significant differences for both functional groups, but the differences between glyphosate-treated and conventionally treated plots for the two functional groups were lower. For Orius spp., annual density per plot was significantly correlated with annual density of leafhoppers and to a lesser extent, with aphids. Nabis sp. densities were never different between glyphosate-treated and conventionally treated plots, and Nabis sp. density showed no relation to any of the herbivores tested. We concluded that no significant changes in heteropteran predator densities may be expected from moderate alterations in weeds arising from the deployment of herbicide-tolerant corn varieties and that leafhoppers are probably the herbivore prey that most influences Orius spp. densities in corn in our study area.     

The cAMP/PKA pathway rapidly activates SIRT1 to promote fatty acid oxidation independently of changes in NAD(+)

The NAD(+)-dependent deacetylase SIRT1 is an evolutionarily conserved metabolic sensor of the Sirtuin family that mediates homeostatic responses to certain physiological stresses such as nutrient restriction. Previous reports have implicated fluctuations in intracellular NAD(+) concentrations as the principal regulator of SIRT1 activity. However, here we have identified a cAMP-induced phosphorylation of a highly conserved serine (S434) located in the SIRT1 catalytic domain that rapidly enhanced intrinsic deacetylase activity independently of changes in NAD(+) levels. Attenuation of SIRT1 expression or the use of a nonphosphorylatable SIRT1 mutant prevented cAMP-mediated stimulation of fatty acid oxidation and gene expression linked to this pathway. Overexpression of SIRT1 in mice significantly potentiated the increases in fatty acid oxidation and energy expenditure caused by either pharmacological β-adrenergic agonism or cold exposure. These studies support a mechanism of Sirtuin enzymatic control through the cAMP/PKA pathway with important implications for stress responses and maintenance of energy homeostasis.     

A reappraisal of the systematic affinities of Socotran,Arabian and East African scops owls (Otus,Strigidae) using a combination of molecular,biometric and acoustic data

We investigated phylogenetic relationships among Otus scops owls from Socotra Island, the Arabian Peninsula and East Africa using molecular, vocalization and biometric data. The Socotra Scops Owl Otus senegalensis socotranus, currently treated as a subspecies of the African Scops Owl Otus senegalensis, is more closely related to the Oriental Scops Owl Otus sunia and to the endemic Seychelles Scops Owl Otus insularis. Considerable mitochondrial genetic distance and significant morphological differentiation from its two closest relatives, as well as its distinctive vocalizations compared with O. insularis, strongly support recognition of Socotra Scops Owl as a full species. Unexpectedly, two taxa from the Arabian Peninsula, Pallid Scops Owl Otus brucei and African Scops Owl Otus senegalensis pamelae, represent very distinct lineages; O. brucei is basal to a clade that includes taxa found in the Indo‐Malayan region and on Indian Ocean islands. In contrast, O. s. pamelae occupies a well‐supported basal position within a clade of continental Afro‐Palaearctic taxa. The uncorrected‐p genetic distance between O. s. pamelae and its closest relatives (other populations of senegalensis from mainland Africa) is c. 4%. As O. s. pamelae is also well differentiated phylogenetically, morphologically and vocally from O. s. senegalensis, we recommend its elevation to species status, as Otus pamelae. Among mainland African O. senegalensis subspecies, Ethiopian populations appear to represent the most divergent lineage, whereas other lineages from Somalia, Kenya and South Africa are poorly differentiated. The large genetic distance between the Ethiopian haplotype and other African haplotypes (3.2%) suggests that the Ethiopian Otus may represent a cryptic taxon, and we recommend that more individuals be sampled to assess the taxonomic status of this population.     

Home range and territory of the Sardinian Warbler Sylvia melanocephala in Mediterranean shrubland

Capsule Singing territories were well separated.

Aims To examine the spatial distribution of Sardinian Warbler males during the breeding period in Mediterranean shrubland and, specifically, their territories, home ranges and spatial overlaps.

Methods We studied a 12-ha plot of Mediterranean shrubland in the 1997 to 1999 breeding seasons. Sardinian Warblers were captured using mist-nets, colour-ringed and their territories mapped. In 1999, seven breeding males were radiotracked in order to map home ranges.

Results The Sardinian Warbler had an average of 7.3 breeding pairs/10 ha in the study plot. The mean territory size was 8779 m² and the mean home range was 22 321 m². A positive relationship was found between the area of the home range and singing territory. Home ranges of males born in 1998 were about half the size of those of the oldest males. Paired males who moved with a female had smaller home ranges than those that were either unpaired or whose mate was incubating. The degree of home range overlap was high with some overlap between neighbouring territories. The estimate of home range area increased by 10% when the information generated by a mapping method was added and the estimated territory area increased by 31% when data generated by radiotracking were added. Transmitters remained attached to birds for an average of 9.63 ± 3.46 days (mean ± se).

Conclusions Singing territories were segregated to a considerable degree. In contrast, the wide overlaps among home ranges was best explained by the presence of food resources that the males exploit at the same time and also by the search for extra-pair copulation in nearby territories. We consider radiotracking in this species to be feasible and valid, with no evidence of negative effects on activity levels, weight or mortality.     

Inclusion of soil erosion impacts in life cycle assessment on a global scale: application to energy crops in Spain

Purpose

Despite the fundamental role of ecosystem goods and services in sustaining human activities, there is no harmonized and internationally agreed method for including them in life cycle assessment (LCA). The main goal of this study was to develop a globally applicable and spatially resolved method for assessing land use impacts on the erosion regulation ecosystem service.

Methods

Soil erosion depends much on location. Thus, unlike conventional LCA, the endpoint method was regionalized at the grid cell level (5 arcmin, approximately 10?×?10 km²) to reflect the spatial conditions of the site. Spatially explicit characterization factors were not further aggregated at broader spatial scales.

Results and discussion

Life cycle inventory data of topsoil and topsoil organic carbon (SOC) losses were interpreted at the endpoint level in terms of the ultimate damage to soil resources and ecosystem quality. Human health damages were excluded from the assessment. The method was tested on a case study of five 3-year agricultural rotations, two of them with energy crops, grown in several locations in Spain. A large variation in soil and SOC losses was recorded in the inventory step, depending on climatic and edaphic conditions. The importance of using a spatially explicit model and characterization factors is shown in the case study.

Conclusions

The regionalized assessment takes into account the differences in soil erosion-related environmental impacts caused by the great variability of soils. Taking this regionalized framework as the starting point, further research should focus on testing the applicability of the method through the complete life cycle of a product and on determining an appropriate spatial scale at which to aggregate characterization factors in order to deal with data gaps on the location of processes, especially in the background system. Additional research should also focus on improving the reliability of the method by quantifying and, insofar as it is possible, reducing uncertainty.     

Potent BRAF kinase inhibitors based on 2,4,5-trisubstituted imidazole with naphthyl and benzothiophene 4-substituents

The RAS–RAF–MEK–ERK pathway is hyperactivated in 30% of human cancers. BRAF is a serine–threonine kinase, belonging to this pathway that is mutated with high frequency in human melanoma and other cancers thus BRAF is an important therapeutic target in melanoma. We have designed inhibitors of BRAF based on 2,4,5-trisubstituted imidazoles with naphthyl and benzothiophene-4-substituents. Two compounds were discovered to be potent BRAF inhibitors: 1-(6-{2-[4-(2-dimethylamino-ethoxy)phenyl]-5-(pyridin-4-yl)-1H-imidazol-4-yl} benzo[b]thiophen-3-yl)-2,2,2-trifluoroethanol (1i) with BRAF IC₅₀ = 190 nM and with cellular GI₅₀ = 2100 nM, and 6-{2-[4-(2-dimethylamino-ethoxy)-phenyl]-5-pyridin-4-yl-3H-imidazol-4-yl}-naphthalen-1-ol (1q) with IC₅₀ = 9 nM and GI₅₀ = 220 nM.