Terrestrial vegetation and the seasonal cycleof dissolved silica in a southern New Englandcoastal river

The Pawcatuck river watershed (797 km²) is located in southern Rhode Island and northeastern Connecticut. The predominant lithology of the area is granite, and over 60% of the watershed remains forested with mixed hardwoods (primarily oak) and eastern white pine. As part of a larger study of nutrient and sediment exports from the watershed to Little Narragansett Bay, we measured dissolved silica (SiO₂) (DSi) concentrations at the river mouth over 70 times between January 14, 2002 and November 29, 2002. Annual export of DSi during our study was 40 × 10⁶ mol or 50 kmol km⁻². The United States Geological Survey (USGS) obtained DSi concentrations at this site, at varying frequencies, from 1978 to the present, which allowed for a historical comparison of this study with previous years. River DSi concentrations exhibited a strong seasonal signal that did not vary in a regular way with water discharge or water temperature. DSi and dissolved inorganic nitrogen (DIN) concentrations were significantly related over the annual cycle (p<0.0001) and both decreased substantially during the spring. Dissolved inorganic phosphorus (DIP) did not covary at any time with silica or nitrogen, suggesting that in-stream biological uptake was not responsible for the seasonal decline in silica. The spring decline in river silica concentrations may be due to silica uptake by terrestrial vegetation. We estimate a net forest silica accretion rate of 41 kmol km⁻² y⁻¹, a value that is stoichiometrically consistent with other measurements of net carbon accretion in nearby forests.     

Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production

The development and advent of mutagenesis tools for solventogenic clostridial species in recent years has allowed for the increased refinement of industrially relevant strains. In this study we have utilised CLEAVE™, a CRISPR/Cas genome editing system developed by Green Biologics Ltd., to engineer a strain of Clostridium saccharoperbutylacetonicum N1-4(HMT) with potentially useful solvents titres and energy metabolism. As one of two enzymes responsible for the conversion of glyceraldehyde-3-phosphate (GAP) to 3-phosphoglyceric acid in glycolysis, it was hypothesised that deletion of gapN would increase ATP and NADH production that could in turn improve solvent production. Herein, whole genome sequencing has been used to evaluate CLEAVE™ and the successful knockout of gapN, demonstrating a clean knockout with no other detectable variations from the wild type sequence. Elevated solvent levels were detected during the first 24 h of batch fermentation, indicating an earlier shift to solventogenesis. A 2.4-fold increase in ATP concentration was observed, and quantitation of NAD(P)H derivatives revealed a more reducing cytoplasm for the gapN strain. These findings expand our understanding of clostridium carbon metabolism and report a new approach to optimising biofuel production.     

Fine‐scale oceanographic drivers of reef manta ray (Mobula alfredi) visitation patterns at a feeding aggregation site

Globally, reef manta rays (Mobula alfredi) are in decline and are particularly vulnerable to exploitation and disturbance at aggregation sites. Here, passive acoustic telemetry and a suite of advanced oceanographic technologies were used for the first time to investigate the fine‐scale (5‐min) influence of oceanographic drivers on the visitation patterns of 19 tagged M. alfredi to a feeding aggregation site at Egmont Atoll in the Chagos Archipelago. Boosted regression trees indicate that tag detection probability increased with the intrusion of cold‐water bores propagating up the atoll slope through the narrow lagoon inlet during flood tide, potentially transporting zooplankton from the thermocline. Tag detection probability also increased with warmer near‐surface temperature close to low tide, with near‐surface currents flowing offshore, and with high levels of backscatter (a proxy of zooplankton biomass). These combinations of processes support the proposition that zooplankton carried from the thermocline into the lagoon during the flood may be pumped back out through the narrow inlet during an ebb tide. These conditions provide temporally limited feeding opportunities for M. alfredi, which are tied on the tides. Results also provide some evidence of the presence of Langmuir Circulation, which transports and concentrates zooplankton, and may partly explain why M. alfredi occasionally remained at the feeding location for longer than that two hours. Identification of these correlations provides unique insight into the dynamic synthesis of fine‐scale oceanographic processes which are likely to influence the foraging ecology of M. alfredi at Egmont Atoll, and elsewhere throughout their range.     

Trafficking of Vacuolar Sorting Receptors: New Data and New Problems

Vacuolar sorting receptors bind cargo ligands early in the secretory pathway and show that multivesicular body-vacuole fusion requires a Rab5/Rab7 GTPase conversion with consequences for retromer binding.To serve the purposes of controlled protein turnover, eukaryotic cells compartmentalize the required acid hydrolases in specialized digestive organelles: lysosomes in animals and vacuoles in yeasts and plants. Therefore, a reliable system must be in operation to prevent such proteolytic enzymes being released at the cell surface. Such a mechanism requires that acid hydrolases be identified and diverted away from the secretory flow to the plasma membrane (PM). This process is facilitated by receptors that recognize specific motifs in the hydrolases that are absent in secretory proteins. The most well-known example of this is the mannosyl 6-phosphate receptor (MPR), which is responsible for the sorting of lysosomal enzymes; indeed, it has become a paradigm for protein sorting in most cell biology textbooks. It entails the recognition of phosphomannan cargo ligands by MPRs in the trans-Golgi network (TGN) followed by the sequestration of the MPR-ligand complexes into specific transport vectors (clathrin-coated vesicles [CCVs]). These are then transported to an endosomal compartment (the early endosome [EE]) having a more acidic pH than the TGN, thereby causing the ligands to separate from the MPRs. The MPRs are subsequently recycled back to the TGN via retromer-coated carriers for another round of trafficking (for review, see Braulke and Bonifacino, 2009; Seaman, 2012).Many plant scientists support a scenario for the sorting of soluble vacuolar proteins and the trafficking of their receptors (vacuolar sorting receptors [VSRs]) that closely resembles that of the MPR system of mammalian cells (Hwang, 2008; De Marcos Lousa et al., 2012; Kang et al., 2012; Sauer et al., 2013; Xiang et al., 2013). This working model is based on three key observations: (1) VSRs were first identified in detergent-solubilized CCV fractions isolated from developing pea (Pisum sativum) cotyledons; (2) CCVs are regularly seen budding off the TGN in thin-sectioned plant cells; and (3) depending on the organism, VSRs and VSR-reporter constructs are found concentrated either in the TGN or in multivesicular prevacuolar compartments (PVCs) under steady-state conditions (Robinson and Pimpl, 2014a, 2014b, and refs. therein). Unfortunately, information on VSRs has not been obtained from a single experimental system. Although much work on Arabidopsis (Arabidopsis thaliana) VSR mutants has been published (for review, see De Marcos Lousa et al., 2012) and the majority of immunogold electron microscopic localization experiments have been performed in Arabidopsis, the majority of the fluorescence localizations, particularly with regard to VSR trafficking, have been carried out by transient expression in tobacco (Nicotiana tabacum; agroinfiltration for leaves and electroporation for protoplasts). Nevertheless, it should be stressed that sorting motifs for acid hydrolases and their corresponding receptors in the three major eukaryotic organismal groups differ considerably (Robinson et al., 2012). In addition, the secretory and endocytic pathways of plant cells contrast significantly with mammalian cells, the most important distinctions being (1) the lack of an intermediate compartment between the endoplasmic reticulum (ER) and the Golgi apparatus in plants, (2) that plants have motile Golgi stacks rather than a perinuclear Golgi complex, and (3) the absence of an independent EE in plants, the function of which is assumed by the TGN (Contento and Bassham, 2012). While these differences do not automatically negate the validity of the above working model for VSR trafficking, they at least legitimize a more thorough analysis of the supporting data than has previously been the case (Robinson and Pimpl, 2014a, 2014b).The principal issues at stake are as follows. Where do VSRs bind and release their cargo ligands? What is the actual mechanism resulting in the separation of secretory from vacuolar cargo molecules? What is/are the precise role(s) of TGN-derived CCVs? And where does retromer pick up VSRs and where are they delivered to? The impact of several new publications on these points of dispute is the subject of this article.     

Bmp signaling is required for development of primary lens fiber cells

We have investigated the role of Bmp signaling in development of the mouse lens using three experimental strategies. First, we have shown that the Bmp ligand inhibitor noggin can suppress the differentiation of primary lens fiber cells in explant culture. Second, we have expressed a dominant-negative form of the type 1 Bmp family receptor Alk6 (Bmpr1b -- Mouse Genome Informatics) in the lens in transgenic mice and shown that an inhibition of primary fiber cell differentiation can be detected at E13.5. Interestingly, the observed inhibition of primary fiber cell development was asymmetrical and appeared only on the nasal side of the lens in the ventral half. Expression of the inhibitory form of Alk6 was driven either by the alpha A-cystallin promoter or the ectoderm enhancer from the Pax6 gene in two different transgenes. These expression units drive transgene expression in distinct patterns that overlap in the equatorial cells of the lens vesicle at E12.5. Despite the distinctions between the transgenes, they caused primary fiber cell differentiation defects that were essentially identical, which implied that the equatorial lens vesicle cells were responding to Bmp signals in permitting primary fiber cells to develop. Importantly, E12.5 equatorial lens vesicle cells showed cell-surface immunoreactivity for bone-morphogenetic protein receptor type 2 and nuclear immunoreactivity for the active, phosphorylated form of the Bmp responsive Smads. This indicated that these cells had the machinery for Bmp signaling and were responding to Bmp signals. We conclude that Bmp signaling is required for primary lens fiber cell differentiation and, given the asymmetry of the differentiation inhibition, that distinct differentiation stimuli may be active in different quadrants of the eye.     

Experimental effects of elevated salinity on three benthic invertebrates in Pyramid Lake,Nevada

Salinity of Pyramid Lake increased from 3.7 to 5.5 between 1933 and 1980. Concern over future reductions in overall species richness prompted experiments to assess responses of dominant lake organisms to elevated salinity. Salinity tolerances of three important benthic invertebrates, Hyalella aztecta, Chironomus utahensis, and Heterocypris sp., were tested in controlled laboratory bioassays and also in a semi-natural environment consisting of large (47 m³) mesocosms.Densities of H. azteca in mesocosms were significantly lower at salinities of 8.0 and 11.0 compared with 5.6 controls in year one, but not in 8.5 salinity mesocosms in year two. The 96-h LC₅₀ for H. azteca was high at 19.5. Short-term mortalities of C. utahensis were 100% at salinities of 13.3 and greater. Fifty-seven percent fewer larvae matured from third to fourth instar at 8.9 than at 5.5 salinity in 17 day subacute bioassays. Furthermore, larval chironomid densities and emergence of adults from mesocosms were significantly reduced at salinities of 8.0 and higher compared with controls. Mortality of Heterocypris sp. was 50% at a salinity of 18.6 in laboratory bioassays and populations in mesocosms ranged between 40 and 100% lower at salinities of 8.0 and 11.0 than in controls.Multiple generation mesocosm experiments indicated all three invertebrates were more sensitive to elevated salinity than results of short-term bioassays. Our studies suggest populations of these invertebrates may be reduced from present levels if Pyramid Lake's salinity were to double, although none are expected to be extirpated. Food habit shifts and reduced production of lake fishes are likely consequences of salinity-induced disruption in the benthic invertebrate forage base.     

An Analysis of the Organization of Vocal Communication in the Titi Monkey Callicebus moloch

Vocalizations of titi monkeys were recorded from 6 groups at two sites in the llanos of Colombia during 8 months of study. Frequency and temporal measurements from spectrograms of recordings, and differences in their patterns of use, were used to characterize call types. Animals repeat calls to form phrases, and combine phrases to form sequences. The six sequence types, defined by different transition probabilities between phrases, varied in proportion in different contexts. To examine the effect of order of phrases on response, I played back artificially constructed sequences to subject groups. I discuss hierarchical and sequential mechanisms as generators' of vocal sequences, and draw comparisons with models of human language.