Moving targets: collective decisions and flexible choices in house-hunting ants

Many decisions involve a trade-off between commitment and flexibility. We show here that the collective decisions ants make over new nest sites are sometimes sufficiently flexible that the ants can change targets even after an emigration has begun. Our findings suggest that, in this context, the ants’ procedures are such that they can sometimes avoid ‘negative information cascades’ which might lock them into a poor choice. The ants are more responsive to belated good news of a higher quality nest than they are when the nest they had initially chosen degraded to become worse than an alternative. Our study confirms, in a new way, that ant colonies can be very powerful “search engines”.     

Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening

Systematic identification of direct protein-protein interactions is often hampered by difficulties in expressing and purifying the corresponding full-length proteins. By taking advantage of the modular nature of many regulatory proteins, we attempted to simplify protein-protein interactions to the corresponding domain-ligand recognition and employed peptide arrays to identify such binding events. A group of 12 Src homology (SH) 3 domains from eight human proteins (Swiss-Prot ID: SRC, PLCG1, P85A, NCK1, GRB2, FYN, CRK) were used to screen a peptide target array composed of 1536 potential ligands, which led to the identification of 921 binary interactions between these proteins and 284 targets. To assess the efficiency of the peptide array target screening (PATS) method in identifying authentic protein-protein interactions, we examined a set of interactions mediated by the PLCgamma1 SH3 domain by coimmunoprecipitation and/or affinity pull-downs using full-length proteins and achieved a 75% success rate. Furthermore, we characterized a novel interaction between PLCgamma1 and hematopoietic progenitor kinase 1 (HPK1) identified by PATS and demonstrated that the PLCgamma1 SH3 domain negatively regulated HPK1 kinase activity. Compared to protein interactions listed in the online predicted human interaction protein database (OPHID), the majority of interactions identified by PATS are novel, suggesting that, when extended to the large number of peptide interaction domains encoded by the human genome, PATS should aid in the mapping of the human interactome.     

Structure-templated predictions of novel protein interactions from sequence information

The multitude of functions performed in the cell are largely controlled by a set of carefully orchestrated protein interactions often facilitated by specific binding of conserved domains in the interacting proteins. Interacting domains commonly exhibit distinct binding specificity to short and conserved recognition peptides called binding profiles. Although many conserved domains are known in nature, only a few have well-characterized binding profiles. Here, we describe a novel predictive method known as domain–motif interactions from structural topology (D-MIST) for elucidating the binding profiles of interacting domains. A set of domains and their corresponding binding profiles were derived from extant protein structures and protein interaction data and then used to predict novel protein interactions in yeast. A number of the predicted interactions were verified experimentally, including new interactions of the mitotic exit network, RNA polymerases, nucleotide metabolism enzymes, and the chaperone complex. These results demonstrate that new protein interactions can be predicted exclusively from sequence information.     

Alveolar macrophage depletion is associated with increased surfactant pool sizes in adult rats.

Pulmonary surfactant is a lipid-protein material that is essential for normal lung function. Maintaining normal and consistent alveolar amounts of surfactant is in part dependent on clearance of surfactant by alveolar macrophages (AM). The present study utilized a rat model of AM depletion to determine the impact on surfactant pool sizes and function over time. Male Sprague-Dawley rats were anesthetized and intratracheally instilled with PBS-liposomes (PBS-L) or dichloromethylene diphosphonic acid (DMDP) containing liposomes (DMDP-L) and were killed at various time points up to 21 days for compliance measurements, AM cell counts, and surfactant analysis. AM numbers were significantly decreased 1, 2, and 3 days after instillation in DMDP-L vs. PBS-L, with 72% depletion at 3 days. AM numbers returned to normal levels by 5 days. In DMDP-L rats, there was a rapid increase in surfactant-phospholipid pools, showing a ninefold increase in the amount of surfactant in the lavage 3 days after liposome instillation. Surfactant accumulation progressed up to 7 days, with pools normalizing by 21 days. The increase in surfactant was due to increases in both subfractions of surfactant, the large aggregates (LA) and small aggregates. Surfactant protein A levels, relative to LA phospholipids, were not increased. There was a decreased extent of surfactant conversion in vitro for LA from DMDP-L rats compared with controls. It is concluded that the procedure of AM depletion significantly affects surfactant metabolism. The increased endogenous surfactant must be considered when utilizing the AM depletion model to study the role of these cells during lung insults.     

Cardiorespiratory and cerebrovascular responses to acute poikilocapnic hypoxia following intermittent and continuous exposure to hypoxia in humans.

We tested the hypothesis that intermittent hypoxia (IH) and/or continuous hypoxia (CH) would enhance the ventilatory response to acute hypoxia (HVR), thereby altering blood pressure (BP) and cerebral perfusion. Seven healthy volunteers were randomly selected to complete 10-12 days of IH (5-min hypoxia to 5-min normoxia repeated for 90 min) before ascending to mild CH (1,560 m) for 12 days. Seven other volunteers did not receive any IH before ascending to CH for the same 12 days. Before the IH and CH, following 12 days of CH and 12-13 days post-CH exposure, all subjects underwent a 20-min acute exposure to poikilocapnic hypoxia (inspired fraction of O(2), 0.12) in which ventilation, end-tidal gases, arterial O(2) saturation, BP, and middle cerebral artery blood flow velocity (MCAV) were measured continuously. Following the IH and CH exposures, the peak HVR was elevated and was related to the increase in BP (r = 0.66 to r = 0.88, respectively; P < 0.05) and to a reciprocal decrease in MCAV (r = 0.73 to r = 0.80 vs. preexposures; P < 0.05) during the hypoxic test. Following both IH and CH exposures, HVR, BP, and MCAV sensitivity to hypoxia were elevated compared with preexposure, with no between-group differences following the IH and/or CH conditions, or persistent effects following 12 days of sea level exposure. Our findings indicate that IH and/or mild CH can equally enhance the HVR, which, by either direct or indirect mechanisms, facilitates alterations in BP and MCAV.     

Amsterdam urban canals contain novel niches for methane-cycling microorganisms

Urbanised environments have been identified as hotspots of anthropogenic methane emissions. Especially urban aquatic ecosystems are increasingly recognised as important sources of methane. However, the microbiology behind these emissions remains unexplored. Here, we applied microcosm incubations and molecular analyses to investigate the methane-cycling community of the Amsterdam canal system in the Netherlands. The sediment methanogenic communities were dominated by Methanoregulaceae and Methanosaetaceae, with co-occurring methanotrophic Methanoperedenaceae and Methylomirabilaceae indicating the potential for anaerobic methane oxidation. Methane was readily produced after substrate amendment, suggesting an active but substrate-limited methanogenic community. Bacterial 16S rRNA gene amplicon sequencing of the sediment revealed a high relative abundance of Thermodesulfovibrionia. Canal wall biofilms showed the highest initial methanotrophic potential under oxic conditions compared to the sediment. During prolonged incubations the maximum methanotrophic rate increased to 8.08 mmol g_DW⁻¹ d⁻¹ that was concomitant with an enrichment of Methylomonadaceae bacteria. Metagenomic analysis of the canal wall biofilm lead to the recovery of a single methanotroph metagenome-assembled genome. Taxonomic analysis showed that this methanotroph belongs to the genus Methyloglobulus. Our results underline the importance of previously unidentified and specialised environmental niches at the nexus of the natural and human-impacted carbon cycle.     

Apex predator suppression is linked to restructuring of ecosystems via multiple ecological pathways

Removal of apex predators can drive ecological regime shifts owing to compensatory positive and negative population level responses by organisms at lower trophic levels. Despite evidence that apex predators can influence ecosystems though multiple ecological pathways, most studies investigating apex predators’ effects on ecosystems have considered just one pathway in isolation. Here, we provide evidence that lethal control of an apex predator, the dingo Canis dingo, drives shifts in the structure of Australia's tropical‐savannah ecosystems. We compared mammal assemblages and understorey structure at seven paired‐sites. Each site comprised an area where people poisoned dingoes and an area without dingo control. The effects of dingo control on mammals scaled with body size. Where dingoes were poisoned, we found greater activity of herbivorous macropods and feral cats, a mesopredator, but sparser understorey vegetation and lower abundances of native rodents. Our study suggests that ecological cascades arising from apex predators’ suppressive effects on herbivores and mesopredators occur simultaneously. Concordant effects of dingo removal across tropical‐savannah, forest and desert biomes suggest that dingoes once exerted ubiquitous top–down effects across Australia and provides support for calls that top–down forcing should be considered a fundamental process governing ecosystem structure.     

Interaction of sauger Sander canadensis and walleye Sander vitreus in a large,shallow northern river

The objectives of this study were to: (1) determine the relative abundance of sauger Sander canadensis and walleye S. vitreus within the Rainy River using a standardized index netting technique; (2) assess the life-history characteristics of the two species in a northern river; (3) examine the spatial distribution of the two species; (4) assess year-class synchrony. At a larger scale, relative abundance of S. canadensis and S. vitreus were similar among sections of the river. However, at a finer scale, S. canadensis were the dominant species over more area (24%) of the river than S. vitreus (12%). Life-history traits for both species were within the range reported for North American. Mortality rates were similar, suggesting that anglers were not affecting one species more than the other. Year-class strengths were not synchronous between S. canadensis and S. vitreus (r = 0.07). There was evidence of S. canadensis potentially outcompeting S. vitreus with a strong year class of S. canadensis followed by a very weak class of S. vitreus. Additionally, S. canadensis were larger than S. vitreus in most sections of the river when adjusted for mean size. However, the potential interspecific competition was not to the exclusion of S. vitreus. Turbidity was probably the factor that enable S. canadensis to survive sympatrically with S. vitreus given their inability to segregate by depth within the river.