The lysophospholipid acyltransferase antagonist CI-976 inhibits a late step in COPII vesicle budding

The mechanism of coat protein (COP)II vesicle fission from the endoplasmic reticulum (ER) remains unclear. Lysophospholipid acyltransferases (LPATs) catalyze the conversion of various lysophospholipids to phospholipids, a process that can promote spontaneous changes in membrane curvature. Here, we show that 2,2-methyl- N -(2,4,6,-trimethoxyphenyl)dodecanamide (CI-976), a potent LPAT inhibitor, reversibly inhibited export from the ER in vivo and the formation of COPII vesicles in vitro . Moreover, CI-976 caused the rapid and reversible accumulation of cargo at ER exit sites (ERESs) containing the COPII coat components Sec23/24 and Sec13/31 and a marked enhancement of Sar1p-mediated tubule formation from ERESs, suggesting that CI-976 inhibits the fission of assembled COPII budding elements. These results identify a small molecule inhibitor of a very late step in COPII vesicle formation, consistent with fission inhibition, and demonstrate that this step is likely facilitated by an ER-associated LPAT.     

Multi-scale measurements and modeling of denitrification in streams with varying flow and nitrate concentration in the upper Mississippi River basin, USA

Denitrification is an important net sink for NO₃ ^? in streams, but direct measurements are limited and in situ controlling factors are not well known. We measured denitrification at multiple scales over a range of flow conditions and NO₃ ^? concentrations in streams draining agricultural land in the upper Mississippi River basin. Comparisons of reach-scale measurements (in-stream mass transport and tracer tests) with local-scale in situ measurements (pore-water profiles, benthic chambers) and laboratory data (sediment core microcosms) gave evidence for heterogeneity in factors affecting benthic denitrification both temporally (e.g., seasonal variation in NO₃ ^? concentrations and loads, flood-related disruption and re-growth of benthic communities and organic deposits) and spatially (e.g., local stream morphology and sediment characteristics). When expressed as vertical denitrification flux per unit area of streambed (U _denit, in μmol N m^?2 h^?1), results of different methods for a given set of conditions commonly were in agreement within a factor of 2–3. At approximately constant temperature (~20 ± 4°C) and with minimal benthic disturbance, our aggregated data indicated an overall positive relation between U _denit (~0–4,000 μmol N m^?2 h^?1) and stream NO₃ ^? concentration (~20–1,100 μmol L^?1) representing seasonal variation from spring high flow (high NO₃ ^?) to late summer low flow (low NO₃ ^?). The temporal dependence of U _denit on NO₃ ^? was less than first-order and could be described about equally well with power-law or saturation equations (e.g., for the unweighted dataset, U _denit ≈26 * [NO₃ ^?]^0.44 or U _denit ≈640 * [NO₃ ^?]/[180 + NO₃ ^?]; for a partially weighted dataset, U _denit ≈14 * [NO₃ ^?]^0.54 or U _denit ≈700 * [NO₃ ^?]/[320 + NO₃ ^?]). Similar parameters were derived from a recent spatial comparison of stream denitrification extending to lower NO₃ ^? concentrations (LINX2), and from the combined dataset from both studies over 3 orders of magnitude in NO₃ ^? concentration. Hypothetical models based on our results illustrate: (1) U _denit was inversely related to denitrification rate constant (k1_denit, in day^?1) and vertical transfer velocity (v _f,denit, in m day^?1) at seasonal and possibly event time scales; (2) although k1_denit was relatively large at low flow (low NO₃ ^?), its impact on annual loads was relatively small because higher concentrations and loads at high flow were not fully compensated by increases in U _denit; and (3) although NO₃ ^? assimilation and denitrification were linked through production of organic reactants, rates of NO₃ ^? loss by these processes may have been partially decoupled by changes in flow and sediment transport. Whereas k1_denit and v _f,denit are linked implicitly with stream depth, NO₃ ^? concentration, and(or) NO₃ ^? load, estimates of U _denit may be related more directly to field factors (including NO₃ ^? concentration) affecting denitrification rates in benthic sediments. Regional regressions and simulations of benthic denitrification in stream networks might be improved by including a non-linear relation between U _denit and stream NO₃ ^? concentration and accounting for temporal variation.     

Mechanics of the right whale mandible: Full scale testing and finite element analysis

In an effort to better understand the mechanics of ship-whale collision and to reduce the associated mortality of the critically endangered North Atlantic right whale, a comprehensive biomechanical study has been conducted by the Woods Hole Oceanographic Institution and the University of New Hampshire. The goal of the study is to develop a numerical modeling tool to predict the forces and stresses during impact and thereby the resulting mortality risk to whales from ship strikes.Based on post-mortem examinations, jaw fracture was chosen as a fatal endpoint for the whales hit by a vessel. In this paper we investigate the overall mechanical behavior of a right whale mandible under transverse loading and develop a finite element analysis model of the bone. The equivalent elastic modulus of the cortical component of right whale mandible is found by comparing full-scale bending tests with the results of numerical modeling. The finite element model of the mandible can be used in conjunction with a vessel-whale collision event model to predict bone fracture for various ship strike scenarios.     

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

Metagenomic and metaproteomic analyses were utilized to determine the composition and function of complex air–water interface biofilms sampled from the hulls of two US Navy destroyers. Prokaryotic community analyses using PhyloChip-based 16S rDNA profiling revealed two significantly different and taxonomically rich biofilm communities (6,942 taxa) in which the majority of unique taxa were ascribed to members of the Gammaproteobacteria, Alphaproteobacteria and Clostridia. Although metagenomic sequencing indicated that both biofilms were dominated by prokaryotic sequence reads (> 91%) with the majority of the bacterial reads belonging to the Alphaproteobacteria, the Ship-1 metagenome harbored greater organismal and functional diversity and was comparatively enriched for sequences from Cyanobacteria, Bacteroidetes and macroscopic eukaryotes, whereas the Ship-2 metagenome was enriched for sequences from Proteobacteria and microscopic photosynthetic eukaryotes. Qualitative liquid chromatography-tandem mass spectrometry metaproteome analyses identified 678 unique proteins, revealed little overlap in species and protein composition between the ships and contrasted with the metagenomic data in that ~80% of classified and annotated proteins were of eukaryotic origin and dominated by members of the Bacillariophyta, Cnidaria, Chordata and Arthropoda (data deposited to the ProteomeXchange, identifier PXD000961). Within the shared metaproteome, quantitative ¹⁸O and iTRAQ analyses demonstrated a significantly greater abundance of structural proteins from macroscopic eukaryotes on Ship-1 and diatom photosynthesis proteins on Ship-2. Photosynthetic pigment composition and elemental analyses confirmed that both biofilms were dominated by phototrophic processes. These data begin to provide a better understanding of the complex organismal and biomolecular composition of marine biofilms while highlighting caveats in the interpretation of stand-alone environmental ‘-omics’ datasets.     

Integrating biology and economics in seagrass restoration: How much is enough and why?

Although success criteria for seagrass restoration have been in place for some time, there has been little consistency regarding how much habitat should be restored for every unit area lost (the replacement ratio). Extant success criteria focus on persistence, area, and habitat quality (shoot density). These metrics, while conservative, remain largely accepted for the seagrass ecosystem. Computation of the replacement ratio using economic tools has recently been integrated with seagrass restoration and is based on the intrinsic recovery rate of the injured seagrass beds themselves as compared with the efficacy of the restoration itself. In this application, field surveys of injured seagrass beds in the Florida Keys National Marine Sanctuary (FKNMS) were conducted over several years and provide the basis for computing the intrinsic recovery rate and thus, the replacement ratio. This computation is performed using the Habitat Equivalency Analysis (HEA) and determines the lost on-site services pertaining to the ecological function of an area as the result of an injury and sets this against the difference between intrinsic recovery and recovery afforded by restoration. Joining empirical field data with economic theory has produced a reasonable and typically conservative means of determining the level of restoration and this has been fully supported in Federal Court rulings. Having clearly defined project goals allows application of the success criteria in a predictable, consistent, reasonable, and fair manner.     

Capturing arthropod diversity in complex cave systems

Aim

Identify the optimal combination of sampling techniques to maximize the detection of diversity of cave‐dwelling arthropods.

Location

Central‐western New Mexico; north‐western Arizona; Rapa Nui, Chile.

Methods

From 26 caves across three geographically distinct areas in the Western Hemisphere, arthropods were sampled using opportunistic collecting, timed searches, and baited pitfall trapping in all caves, and direct intuitive searches and bait sampling at select caves. To elucidate the techniques or combination of techniques for maximizing sampling completeness and efficiency, we examined our sampling results using nonmetric multidimensional scaling (NMDS), analysis of similarity (ANOSIM), Wilcoxon signed‐rank tests, species richness estimators and species accumulation curves.

Results

To maximize the detection of cave‐dwelling arthropod species, one must apply multiple sampling techniques and specifically sample unique microhabitats. For example, by sampling cave deep zones and nutrient resource sites, we identified several undescribed cave‐adapted and/or cave‐restricted taxa in the south‐western United States and eight new species of presumed cave‐restricted arthropods on Rapa Nui that would otherwise have been missed. Sampling techniques differed in their detection of both management concern species (e.g., newly discovered cave‐adapted/restricted species, range expansions of cave‐restricted species and newly confirmed alien species) and specific taxonomic groups. Spiders were detected primarily with visual search techniques (direct intuitive searches, opportunistic collecting and timed searches), while most beetles were detected using pitfall traps. Each sampling technique uniquely identified species of management concern further strengthening the importance of a multi‐technique sampling approach.

Main conclusions

Multiple sampling techniques were required to best characterize cave arthropod diversity. For techniques applied uniformly across all caves, each technique uniquely detected between ~40% and 67% of the total species observed. Also, sampling cave deep zones and nutrient resource sites was critical for both increasing the number of species detected and maximizing the likelihood of detecting management concern species.

     

Expressed Sequences from Conidial, Mycelial, and Sexual Stages ofNeurospora crassa

In theNeurosporaGenome Project at the University of New Mexico, expressed sequence tags (ESTs) corresponding to three stages of the life cycle of the filamentous fungusNeurospora crassaare being analyzed. The results of a pilot project to identify expressed genes and determine their patterns of expression are presented. 1,865 partial complementary DNA (cDNA) sequences for 1,409 clones were determined using single-pass sequencing. Contig analysis allowed the identification of 838 unique ESTs and 156 ESTs present in multiple cDNA clones. For about 34% of the sequences, highly or moderately significant matches to sequences (of known and unknown function) in the NCBI database were detected. Approximately 56% of the ESTs showed no similarity to previously identified genes. Among genes with assigned function, about 43.3% were involved in metabolism, 32.9% in protein synthesis and 8.4% in RNA synthesis. Fewer were involved in defense (6%), cell signalling (3.4%), cell structure (3.4%) and cell division (2.6%).     

LOW-RESISTANCE JUNCTIONS BETWEEN CANCER CELLS IN VARIOUS SOLID TUMORS

Electrical coupling, which reveals the presence of specialized low-resistance intercellular junctions, has now been found in four types of tumors, Sarcoma 180, Novikoff hepatoma, and Morris hepatomas 3924-A and 7777. Coupled cancer cells were distinguished from coupled normal cells by intracellular marking techniques. Although the evidence suggests that coupling may be extensive in some cases, it is not possible to say that the coupling was normal. In particular, the results do not exclude less obvious defects in the specialized junctions, such as abnormal distribution or decreased permeability to molecules other than small inorganic ions. The results are discussed in relation to previous studies of coupling in Novikoff hepatomas and in cultures of S1801 and II cell lines.