Water quality and herbivory interactively drive coral-reef recovery patterns in American Samoa

Background

Compared with a wealth of information regarding coral-reef recovery patterns following major disturbances, less insight exists to explain the cause(s) of spatial variation in the recovery process.

Methodology/Principal Findings

This study quantifies the influence of herbivory and water quality upon coral reef assemblages through space and time in Tutuila, American Samoa, a Pacific high island. Widespread declines in dominant corals (Acropora and Montipora) resulted from cyclone Heta at the end of 2003, shortly after the study began. Four sites that initially had similar coral reef assemblages but differential temporal dynamics four years following the disturbance event were classified by standardized measures of ‘recovery status’, defined by rates of change in ecological measures that are known to be sensitive to localized stressors. Status was best predicted, interactively, by water quality and herbivory. Expanding upon temporal trends, this study examined if similar dependencies existed through space; building multiple regression models to identify linkages between similar status measures and local stressors for 17 localities around Tutuila. The results highlighted consistent, interactive interdependencies for coral reef assemblages residing upon two unique geological reef types. Finally, the predictive regression models produced at the island scale were graphically interpreted with respect to hypothesized site-specific recovery thresholds.

Conclusions/Significance

Cumulatively, our study purports that moving away from describing relatively well-known patterns behind recovery, and focusing upon understanding causes, improves our foundation to predict future ecological dynamics, and thus improves coral reef management.     

Linking functional morphology and feeding performance in larvae of two coral-reef fishes

Despite the well acknowledged phenomenon that the biology of marine teleost fish larvae is much different from that of juvenile and adult conspecifics, very little is known about the changes in design of the feeding apparatus as larvae develop from hatching through metamorphosis. Furthermore, our understanding of the consequences of these developmental changes for feeding performance is very limited. In this study, we examined the relationship between the development of the feeding apparatus and feeding performance in larvae of Amphiprion ocellaris and Pseudochromis fridmani using cluster analysis, multi-dimensional scaling (nMDS), and canonical correspondence analysis (CCA). Several patterns emerge from our analyses. First, the state of development of the feeding apparatus increased in complexity through ontogeny, from a simple, hyoid-driven system at the onset of exogenous feeding to a more complex feeding system involving all adult functional elements of the cranium just prior to metamorphosis. Although the feeding apparatus converged to the hyoid-opercular-mandible linkage state around metamorphosis in both species, P. fridmani had a lesser developed hyoid-mandible linkage system relative to A. ocellaris at the onset of first-feeding. Second, first-feeding larvae fed on smaller, less elusive zooplankton. In contrast, larvae that survived beyond the first-feeding stage fed on more diverse prey types, including larger, more elusive zooplankton. Third, intra- and inter-specific variation in the development of the feeding apparatus is associated with variation in feeding performance. The post-hatch developmental trajectory in both species showed a pattern consistent with stage (i.e., ontogenetic state)-specific shifts in morphology and performance. Furthermore, the number of developmental transitions in both feeding functional morphology and feeding performance differ between species that exhibit contrasting incubation periods.     

Diatom immigration drives biofilm recovery after chronic copper exposure

1. The impact of immigration on the recovery of diatom assemblages after chronic exposure to copper was investigated in laboratory microcosms. 2. We examined the recovery trajectories of copper‐contaminated biofilms after reducing copper stress and with or without the possibility of immigration from unimpaired communities. 3. The biofilms mixed with unimpaired communities returned to a ‘control’ assemblage structure within 6 weeks, with recovery patterns depending on the endpoint considered (i.e. 2 weeks for relative abundances of diatom species but 6 weeks for total diatom biomass). In contrast, no recovery was observed in assemblages placed under control conditions without external immigrants. 4. Immigration has important effects on the recovery of quantitative and qualitative characteristics of biofilms.     

Sleeping behavior and associations in a group of captive chimpanzees.

The present study investigated the sleeping behavior and preferences of a group of six adolescent chimpanzees at the Delta Regional Primate Research Center in Louisiana, USA. The study sought to relate sleeping partner preferences to other aspects of social relationships. Comparative observations between those chimpanzee behaviors seen in the wild and in this group are noted.     

Functional group dominance and not productivity drives species richness

Background: There is a lack of consensus about the productivity–richness relationship, with several recent studies suggesting that it is not productivity but other factors that are the important drivers that determine species richness.

Aims: Here, we examine the relationship between productivity, functional group dominance and plant species richness at the plot scale in Tibetan Plateau meadows. These alpine meadows are ideal to examine the species productivity-richness relationship because they have a very high species richness, a large gradient in productivity, and can be dominated by either graminoids (grasses and sedges) or forbs.

Methods: We measured plant species richness and above-ground biomass along a natural gradient of functional group abundance in 44 plots distributed across five natural, winter-grazed but otherwise undisturbed sites in the eastern part of the Qing-Hai Tibetan Plateau, in Gansu province, China in 2008.

Results: Graminoid abundance (i.e. graminoid biomass as percent of the total above-ground biomass) explained 39% of plot differences in species richness while neither productivity nor the biomass of the three most abundant plant species, either individually or combined, were a significant predictor of species richness.

Conclusions: Our results show that within these alpine meadows, a shift from graminoid to forb dominance, rather than the individual dominant species or productivity itself, is strongly correlated with species richness. Thus, differences in functional group abundance can be a strong driver of observed plant species richness patterns.     

Isolation drives taxonomic and functional nestedness in tropical reef fish faunas

Taxonomic nestedness, the degree to which the taxonomic composition of species‐poor assemblages represents a subset of richer sites, commonly occurs in habitat fragments and islands differing in size and isolation from a source pool. However, species are not ecologically equivalent and the extent to which nestedness is observed in terms of functional trait composition of assemblages still remains poorly known. Here, using an extensive database on the functional traits and the distributions of 6316 tropical reef fish species across 169 sites, we assessed the levels of taxonomical vs functional nestedness of reef fish assemblages at the global scale. Functional nestedness was considerably more common than taxonomic nestedness, and generally associated with geographical isolation, where nested subsets are gradually more isolated from surrounding reef areas and from the center of biodiversity. Because a nested pattern in functional composition implies that certain combinations of traits may be represented by few species, we identified these groups of low redundancy that include large herbivore‐detritivores and omnivores, small piscivores, and macro‐algal herbivores. The identified patterns of nestedness may be an outcome of the interaction between species dispersal capabilities, resource requirements, and gradients of isolation among habitats. The importance of isolation in generating the observed pattern of functional nestedness within biogeographic regions may indicate that disturbance in depauperate and isolated sites can have disproportionate effects on the functional structure of their reef fish assemblages.     

Intercropping drives plant phenotypic plasticity and changes in functional trait space

The relevance of intercropping, where two or more crop species are simultaneously grown on the same land space, is growing due to its potential for improving resource use and maintaining stable yields under variable weather conditions. However, the actual growth of intercropped species may differ resulting from the idiosyncratic effect of crop diversity, and with this, the realized benefits from intercrops are found to depend critically on the cultivar, species, management and environmental conditions. This study aimed to apply a trait-based approach, in which ecological niche spaces are defined through n-dimensional hypervolumes, to identify the contribution of species/cultivar, cultivation design (sole crop or intercrop) and management (low or high fertilization) to the trait diversity of four crop species, pea-barley and faba bean-wheat, when grown as sole crops and intercrops. Four traits were used as trait axes for the trait space analysis: canopy height, shoot biomass, tiller/node number, and grain yield. We found that trait spaces differed with crop species and cultivars, and whether they were grown as intercrops or sole crops. Trait spaces differed between high and low fertilization only for the cereals grown in the more productive site (i.e. Denmark). Species grown as intercrops had larger volumes than when grown as sole crops, as a result of trait plasticity. This response to intercropping was apparent in almost all the species grown in Sweden and Denmark, except for wheat in Denmark. The study demonstrated that individual species responded to intercropping compared to sole cropping through the plasticity of traits, which influenced the shape of the hypervolumes to divide up the trait space between the species. The findings are important in illustrating the plastic responses of arable crops, which are relevant for understanding the productivity of species grown in intercrops as compared to sole crops.     

Seasonal variation in the functional response of a coral-reef piscivore alters the inverse density-dependent mortality of its prey

Density-dependent processes are critical for regulating species’ populations, and piscivory of coral-reef fishes is frequently density dependent. However, the mechanism driving this density-dependent mortality is poorly understood, but may be caused by changes in a predator’s feeding rate at different prey densities (its functional response). An aquarium experiment replicated in winter and summer examined the functional response after 22 and 47 h of Cephalopholis cruentata feeding on Halichoeres pictus. With the exception of summer data after 47 h (density-independent mortality), mortality was inversely density dependent across all prey densities and increased with higher summer temperatures. The absence of an asymptotic pattern of inverse density-dependent mortality was caused by type II (summer) or dome-shaped type IV (winter) functional responses, with the benefits of schooling likely to cause the low mortality rates at higher prey densities. Predators’ functional responses may underlie the inverse density-dependent mortality reported in field studies of aggregating fishes.     

Cortical propagation tracks functional recovery after stroke

Stroke is a debilitating condition affecting millions of people worldwide. The development of improved rehabilitation therapies rests on finding biomarkers suitable for tracking functional damage and recovery. To achieve this goal, we perform a spatiotemporal analysis of cortical activity obtained by wide-field calcium images in mice before and after stroke. We compare spontaneous recovery with three different post-stroke rehabilitation paradigms, motor training alone, pharmacological contralesional inactivation and both combined. We identify three novel indicators that are able to track how movement-evoked global activation patterns are impaired by stroke and evolve during rehabilitation: the duration, the smoothness, and the angle of individual propagation events. Results show that, compared to pre-stroke conditions, propagation of cortical activity in the subacute phase right after stroke is slowed down and more irregular. When comparing rehabilitation paradigms, we find that mice treated with both motor training and pharmacological intervention, the only group associated with generalized recovery, manifest new propagation patterns, that are even faster and smoother than before the stroke. In conclusion, our new spatiotemporal propagation indicators could represent promising biomarkers that are able to uncover neural correlates not only of motor deficits caused by stroke but also of functional recovery during rehabilitation. In turn, these insights could pave the way towards more targeted post-stroke therapies.     

Assessment of functional recovery in tennis elbow

Objectives: (a) To investigate changes in muscular strength, fatigue and activity in recovered tennis elbow (RTE); (b) to assess the appropriateness of EMG and strength measurements in monitoring functional recovery in tennis elbow (TE).Methods: Study included three age-matched female groups of Control (C) (n = 8, no history of musculoskeletal problems), TE (n = 7, local tenderness at the lateral epicondyle and pain with resisted wrist and middle finger extension) and RTE (n = 6, asymptomatic for at least 6 months, no lateral epicondyle tenderness). Measurements included metacarpophalangeal (MCP), wrist, shoulder and grip isometric strength and EMG measures of muscle fatigue and activity for five forearm muscles (wrist extensors and flexors).Results: Strength was greater (p < 0.05) for all measurements in C compared to RTE and TE except for MCP extension. Only MCP extension was stronger in RTE than TE. EMG revealed increased activity of extensor carpi radialis (ECR) in RTE, decreased in TE.Conclusions: Despite attenuation of pain, global upper limb weakness in RTE indicated incomplete functional recovery. Increased strength of MCP extension may protect weakened wrist extensors from further injury. Monitoring the ECR activity as well as strength measurements may provide a useful assessment of functional recovery in TE.     

OPA1 drives macrophage metabolism and functional commitment via p65 signaling

Macrophages are essential players for the host response against pathogens, regulation of inflammation and tissue regeneration. The wide range of macrophage functions rely on their heterogeneity and plasticity that enable a dynamic adaptation of their responses according to the surrounding environmental cues. Recent studies suggest that metabolism provides synergistic support for macrophage activation and elicitation of desirable immune responses; however, the metabolic pathways orchestrating macrophage activation are still under scrutiny. Optic atrophy 1 (OPA1) is a mitochondria-shaping protein controlling mitochondrial fusion, cristae biogenesis and respiration; clear evidence shows that the lack or dysfunctional activity of this protein triggers the accumulation of metabolic intermediates of the TCA cycle. In this study, we show that OPA1 has a crucial role in macrophage activation. Selective Opa1 deletion in myeloid cells impairs M1-macrophage commitment. Mechanistically, Opa1 deletion leads to TCA cycle metabolite accumulation and defective NF-κB signaling activation. In an in vivo model of muscle regeneration upon injury, Opa1 knockout macrophages persist within the damaged tissue, leading to excess collagen deposition and impairment in muscle regeneration. Collectively, our data indicate that OPA1 is a key metabolic driver of macrophage functions.Subject terms: Cell death and immune response, Inflammation     

A Sleeping Beauty DNA transposon-based genetic sensor for functional screening of vitamin D3 analogues

Background  

Analogues of vitamin D3 are extensively used in the treatment of various illnesses, such as osteoporosis, inflammatory skin diseases, and cancer. Functional testing of new vitamin D3 analogues and formulations for improved systemic and topical administration is supported by sensitive screening methods that allow a comparative evaluation of drug properties. As a new tool in functional screening of vitamin D3 analogues, we describe a genomically integratable sensor for sensitive drug detection. This system facilitates assessment of the pharmacokinetic and pharmadynamic properties of vitamin D3 analogues. The tri-cistronic genetic sensor encodes a drug-sensoring protein, a reporter protein expressed from an activated sensor-responsive promoter, and a resistance marker.     

停止人为去除植物功能群后的高寒草甸多样性恢复过程与群落构建

已有大量研究利用功能性状或系统发育来推断群落构建机制, 然而不同过程可能会导致相似的格局。本文基于对甘南高寒草甸植物功能群去除处理后群落恢复过程的跟踪调查, 对比了物种多样性、功能多样性和系统发育多样性的动态变化, 并分析了物种定殖与消失过程对功能多样性和系统发育多样性变化的影响。结果表明: 去除不同数量功能群的群落中: (1)包括物种丰富度(SR)、Shannon-Wiener指数(H°)和Simpson指数(D)在内的传统物种多样性均随时间快速上升并与自然群落趋同, 不同群落的均匀度指数(J)随时间呈增加趋势并趋于相似; 功能多样性(FD)与系统发育多样性(PD)呈现出与物种多样性相似的动态变化趋势, 而平均配对距离(MPD/MPD_a、MFD/MFD_a)则向中等程度聚集。(2)不同群落的功能群和物种组成在短期内均恢复到与自然群落非常相似的程度。(3)物种定殖与消失过程的功能格局是群落恢复过程中趋同效应的主要驱动力。本研究揭示了高寒草甸植物功能群去除停止后群落短期内快速恢复的过程, 说明在小尺度且周边具有大范围未退化草甸的情况下, 无论物种多样性、功能多样性还是系统发育多样性都具有较快的恢复能力, 同时说明了利用群落系统发育多样性格局来推断群落构建机制的局限性。     

Prediction of functional sites in proteins using conserved functional group analysis

A detailed knowledge of a protein's functional site is an absolute prerequisite for understanding its mode of action at the molecular level. However, the rapid pace at which sequence and structural information is being accumulated for proteins greatly exceeds our ability to determine their biochemical roles experimentally. As a result, computational methods are required which allow for the efficient processing of the evolutionary information contained in this wealth of data, in particular that related to the nature and location of functionally important sites and residues. The method presented here, referred to as conserved functional group (CFG) analysis, relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologues. We show that CFG analysis can fully or partially predict the location of functional sites in approximately 96% of the 470 cases tested and that, unlike other methods available, it is able to tolerate wide variations in sequence identity. In addition, we discuss its potential in a structural genomics context, where automation, scalability and efficiency are critical, and an increasing number of protein structures are determined with no prior knowledge of function. This is exemplified by our analysis of the hypothetical protein Ydde_Ecoli, whose structure was recently solved by members of the North East Structural Genomics consortium. Although the proposed active site for this protein needs to be validated experimentally, this example illustrates the scope of CFG analysis as a general tool for the identification of residues likely to play an important role in a protein's biochemical function. Thus, our method offers a convenient solution to rapidly and automatically process the vast amounts of data that are beginning to emerge from structural genomics projects.     

Improved functional recovery of human granulocytes after cryopreservation

Human peripheral blood phagocytes (90% neutrophils) were cryopreserved with either 5 or 10% dimethyl sulfoxide (DMSO) and stored in the liquid phase of liquid nitrogen. Modifications to the freezing method included the elimination of dextran from the freezing medium, addition of the bulk of the DMSO at −5 °C, elimination of heparin and centrifugation from all postreconstitution procedures, and the use of deoxyribonuclease to minimize post-thaw granulocyte agglutination.Substantial numbers of the cryopreserved phagocytes, as assayed by nitroblue tetrazolium and chemotactic activity, showed comparable functional activity to fresh cells. Post-thaw cell dialysis further improved functional capacity although probably not as a consequence of DMSO removal.     

Integrase-directed recovery of functional genes from genomic libraries

Large population sizes, rapid growth and 3.8 billion years of evolution firmly establish microorganisms as a major source of the planet''s biological and genetic diversity. However, up to 99% of the microorganisms in a given environment cannot be cultured. Culture-independent methods that directly access the genetic potential of an environmental sample can unveil new proteins with diverse functions, but the sequencing of random DNA can generate enormous amounts of extraneous data. Integrons are recombination systems that accumulate open reading frames (gene cassettes), many of which code for functional proteins with enormous adaptive potential. Some integrons harbor hundreds of gene cassettes and evidence suggests that the gene cassette pool may be limitless in size. Accessing this genetic pool has been hampered since sequence-based techniques, such as hybridization or PCR, often recover only partial genes or a small subset of those present in the sample. Here, a three-plasmid genetic strategy for the sequence-independent recovery of gene cassettes from genomic libraries is described and its use by retrieving functional gene cassettes from the chromosomal integron of Vibrio vulnificus ATCC 27562 is demonstrated. By manipulating the natural activity of integrons, we can gain access to the caches of functional genes amassed by these structures.