Effects of Reef Proximity on the Structure of Fish Assemblages of Unconsolidated Substrata

Fish assemblages of unconsolidated sedimentary habitats on continental shelves are poorly described when compared to those of hard substrata. This lack of data restricts the objective management of these extensive benthic habitats. In the context of protecting representative areas of all community types, one important question is the nature of the transition from reefal to sedimentary fish assemblages. We addressed this question using Baited Remote Underwater Videos (BRUVs) to assess fish assemblages of sedimentary habitats at six distances from rocky reefs (0, 25, 50, 100, 200, and 400 m) at four sites in subtropical eastern Australia. Distance from reef was important in determining fish assemblage structure, and there was no overlap between reef sites and sedimentary sites 400 m from reef. While there was a gradient in assemblage structure at intermediate distances, this was not consistent across sites. All sites, however, supported a mixed ‘halo’ assemblage comprising both reef and sediment species at sampling stations close to reef. BRUVs used in conjunction with high-resolution bathymetric and backscatter spatial data can resolve differences in assemblage structure at small spatial scales (10s to 100s of metres), and has further application in unconsolidated habitats. Unless a ‘reef halo’ assemblage is being examined, a minimum of 200 m but preferably 400 m distance from any hard substrate is recommended when designing broader-scale assessments of fish assemblages of sedimentary habitats.     

Facies,paleoenvironment, carbonate platform and facies changes across Paleocene Eocene of the Taleh Zang Formation in the Zagros Basin,SW-Iran

The Paleocene–Eocene Taleh Zang Formation of the Zagros Basin is a sequence of shallow-water carbonates. We have studied carbonate platform, sedimentary environments and its changes based on the facies analysis with particular emphasis on the biogenic assemblages of the Late Paleocene Sarkan and Early Eocene Maleh kuh sections. In the Late Paleocene, nine microfacies types were distinguished, dominated by algal taxa and corals at the lower part and larger foraminifera at the upper part. The Lower Eocene section is characterised by 10 microfacies types, which are dominated by diverse larger foraminifera such as alveolinids, orbitolitids and nummulitids. The Taleh Zang Formation at the Sarkan and Maleh kuh sections represents sedimentation on a carbonate ramp.

The deepening trends show a gradual increase in perforate foraminifera, the deepest environment is marked by the maximum occurrence of perforate foraminifers (Nummulites), while the shallowing trends are composed mainly of imperforate foraminifera and also characterised by lack of fossils in tidal flat facies.

Based on the facies changes and platform evolution, three stages are assumed in platform development: I; algal and coralgal colonies (coralgal platform), II; coralgal reefs giving way to larger foraminifera, III; dominance of diverse and newly developing larger foraminifera lineages in oligotrophic conditions.     

Changes in Nematode Communities in Different Physiographic Sites of the Condor Seamount (North-East Atlantic Ocean) and Adjacent Sediments

Several seamounts are known as ‘oases’ of high abundances and biomass and hotspots of biodiversity in contrast to the surrounding deep-sea environments. Recent studies have indicated that each single seamount can exhibit a high intricate habitat turnover. Information on alpha and beta diversity of single seamount is needed in order to fully understand seamounts contribution to regional and global biodiversity. However, while most of the seamount research has been focused on summits, studies considering the whole seamount structure are still rather poor. In the present study we analysed abundance, biomass and diversity of nematodes collected in distinct physiographic sites and surrounding sediments of the Condor Seamount (Azores, North-East Atlantic Ocean). Our study revealed higher nematode biomass in the seamount bases and values 10 times higher in the Condor sediments than in the far-field site. Although biodiversity indices did not showed significant differences comparing seamount sites and far-field sites, significant differences were observed in term of nematode composition. The Condor summit harboured a completely different nematode community when compared to the other seamount sites, with a high number of exclusive species and important differences in term of nematode trophic diversity. The oceanographic conditions observed around the Condor Seamount and the associated sediment mixing, together with the high quality of food resources available in seamount base could explain the observed patterns. Our results support the hypothesis that seamounts maintain high biodiversity through heightened beta diversity and showed that not only summits but also seamount bases can support rich benthic community in terms of standing stocks and diversity. Furthermore functional diversity of nematodes strongly depends on environmental conditions link to the local setting and seamount structure. This finding should be considered in future studies on seamounts, especially in view of the potential impacts due to current and future anthropogenic threats.     

Quantifying production rates and size fractions of parrotfish‐derived sediment: A key functional role on Maldivian coral reefs

Coral reef fish perform numerous important functional roles on coral reefs. Of these, carbonate sediment production, as a by‐product of parrotfish feeding, is especially important for contributing to reef framework construction and reef‐associated landform development. However, only limited data exist on: (i) how production rates vary among reef habitats as a function of parrotfish assemblages, (ii) the relative importance of sediment produced from eroded, reworked, and endogenous sources, or (iii) the size fractions of sediment generated by different parrotfish species and size classes. These parameters influence not only overall reef‐derived sediment supply, but also influence the transport potential and depositional fate of this sedimentary material. Here, we show that parrotfish sediment production varies significantly between reef‐platform habitats on an atoll‐margin Maldivian reef. Highest rates of production (over 0.8 kg m⁻² year⁻¹) were calculated in three of the eight platform habitats; a rubble‐dominated zone, an Acropora spp. dominated zone, and a patch reef zone. Habitat spatial extent and differences in associated parrotfish assemblages strongly influenced the total quantities of sediment generated within each habitat. Nearly half of total parrotfish sediment production occurred in the rubble habitat, which comprised only 8% of the total platform area. Over 90% of this sedimentary material originated from eroded reef framework as opposed to being reworked existing or endogenously produced sediment, and comprised predominantly coral sands (predominantly 125–1000 µm in diameter). This is comparable to the dominant sand types and size fractions found on Maldivian reef islands. By contrast, nearly half of the sediment egested by parrotfish in the Acropora spp. dominated and patch reef habitats resulted from reworked existing sediments. These differences between habitats are a result of the different parrotfish assemblages supported. Endogenous carbonate production was found to be insignificant compared to the quantity of eroded and reworked material. Our findings have important implications for identifying key habitats and species which act as major sources of sediment for reef‐island systems.     

Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps,Guaymas Basin (Gulf of California)

Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the ‘BIG'' cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel ‘ANME-2c Sonora'' lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support alternative metabolic pathways than syntrophic anaerobic oxidation of methane.     

Diversity in obscurity: fossil flowers and the early history of angiosperms

In the second half of the nineteenth century, pioneering discoveries of rich assemblages of fossil plants from the Cretaceous resulted in considerable interest in the first appearance of angiosperms in the geological record. Darwin''s famous comment, which labelled the ‘rapid development’ of angiosperms an ‘abominable mystery’, dates from this time. Darwin and his contemporaries were puzzled by the relatively late, seemingly sudden and geographically widespread appearance of modern-looking angiosperms in Late Cretaceous floras. Today, the early diversification of angiosperms seems much less ‘rapid’. Angiosperms were clearly present in the Early Cretaceous, 20–30 Myr before they attained the level of ecological dominance reflected in some mid-Cretaceous floras, and angiosperm leaves and pollen show a distinct pattern of steadily increasing diversity and complexity through this interval. Early angiosperm fossil flowers show a similar orderly diversification and also provide detailed insights into the changing reproductive biology and phylogenetic diversity of angiosperms from the Early Cretaceous. In addition, newly discovered fossil flowers indicate considerable, previously unrecognized, cryptic diversity among the earliest angiosperms known from the fossil record. Lineages that today have an herbaceous or shrubby habit were well represented. Monocotyledons, which have previously been difficult to recognize among assemblages of early fossil angiosperms, were also diverse and prominent in many Early Cretaceous ecosystems.     

Giant Seismites and Megablock Uplift in the East African Rift: Evidence for Late Pleistocene Large Magnitude Earthquakes

In lieu of comprehensive instrumental seismic monitoring, short historical records, and limited fault trench investigations for many seismically active areas, the sedimentary record provides important archives of seismicity in the form of preserved horizons of soft-sediment deformation features, termed seismites. Here we report on extensive seismites in the Late Quaternary-Recent (≤ ~ 28,000 years BP) alluvial and lacustrine strata of the Rukwa Rift Basin, a segment of the Western Branch of the East African Rift System. We document examples of the most highly deformed sediments in shallow, subsurface strata close to the regional capital of Mbeya, Tanzania. This includes a remarkable, clastic ‘megablock complex’ that preserves remobilized sediment below vertically displaced blocks of intact strata (megablocks), some in excess of 20 m-wide. Documentation of these seismites expands the database of seismogenic sedimentary structures, and attests to large magnitude, Late Pleistocene-Recent earthquakes along the Western Branch of the East African Rift System. Understanding how seismicity deforms near-surface sediments is critical for predicting and preparing for modern seismic hazards, especially along the East African Rift and other tectonically active, developing regions.     

Sedimentation and overfishing drive changes in early succession and coral recruitment

Sedimentation and overfishing are important local stressors on coral reefs that can independently result in declines in coral recruitment and shifts to algal-dominated states. However, the role of herbivory in driving recovery across environmental gradients is often unclear. Here we investigate early successional benthic communities and coral recruitment across a sediment gradient in Palau, Micronesia over a 12-month period. Total sedimentation rates measured by ‘TurfPods’ varied from 0.03 ± 0.1 SE mg cm⁻² d⁻¹ at offshore sites to 1.32 ± 0.2 mg cm⁻² d⁻¹ at inshore sites. To assess benthic succession, three-dimensional settlement tiles were deployed at sites with experimental cages used to exclude tile access to larger herbivorous fish. Benthic assemblages exhibited rapid transitions across the sediment gradient within three months of deployment. At low levels of sedimentation (less than 0.6 mg cm⁻² d⁻¹), herbivory resulted in communities dominated by coral recruitment inducers (short turf algae and crustose coralline algae), whereas exclusion of herbivores resulted in the overgrowth of coral inhibitors (encrusting and upright foliose macroalgae). An ‘inducer threshold’ was found under increasing levels of sedimentation (greater than 0.6 mg cm⁻² d⁻¹), with coral inducers having limited to no presence in communities, and herbivore access to tiles resulted in sediment-laden turf algal assemblages, while exclusion of herbivores resulted in invertebrates (sponges, ascidians) and terrestrial sediment accumulation. A ‘coral recruitment threshold’ was found at 0.8 mg cm⁻² d⁻¹, below which net coral recruitment was reduced by 50% in the absence of herbivores, while recruitment was minimal above the threshold. Our results highlight nonlinear trajectories of benthic succession across sediment gradients and identify strong interactions between sediment and herbivory that have cascading effects on coral recruitment. Local management strategies that aim to reduce sedimentation and turbidity and manage herbivore fisheries can have measurable effects on benthic community succession and coral recruitment, enhancing reef resilience and driving coral recovery.     

Multi-Environment Model Estimation for Motility Analysis of Caenorhabditis elegans

The nematode Caenorhabditis elegans is a well-known model organism used to investigate fundamental questions in biology. Motility assays of this small roundworm are designed to study the relationships between genes and behavior. Commonly, motility analysis is used to classify nematode movements and characterize them quantitatively. Over the past years, C. elegans'' motility has been studied across a wide range of environments, including crawling on substrates, swimming in fluids, and locomoting through microfluidic substrates. However, each environment often requires customized image processing tools relying on heuristic parameter tuning. In the present study, we propose a novel Multi-Environment Model Estimation (MEME) framework for automated image segmentation that is versatile across various environments. The MEME platform is constructed around the concept of Mixture of Gaussian (MOG) models, where statistical models for both the background environment and the nematode appearance are explicitly learned and used to accurately segment a target nematode. Our method is designed to simplify the burden often imposed on users; here, only a single image which includes a nematode in its environment must be provided for model learning. In addition, our platform enables the extraction of nematode ‘skeletons’ for straightforward motility quantification. We test our algorithm on various locomotive environments and compare performances with an intensity-based thresholding method. Overall, MEME outperforms the threshold-based approach for the overwhelming majority of cases examined. Ultimately, MEME provides researchers with an attractive platform for C. elegans'' segmentation and ‘skeletonizing’ across a wide range of motility assays.     

Feeding effects of the keystone deposit feeder Ilyanassa obsoleta (Neogastropoda,Gastropoda) on sedimentary diatoms

Microphytobenthos (MPB), typically comprised mainly of diatoms, is a key contributor to nearshore energy flow and nutrient cycles. Deposit-feeding invertebrates are known to alter the structure and activity of MPB. The eastern mud snail Ilyanassa obsoleta can reach extremely high densities in estuaries of the northwestern Atlantic, and their deposit-feeding and locomotion strongly influence other invertebrates and microbes. Our objective was to explore quantitative and qualitative effects of this keystone deposit-feeder on diatoms of intertidal sediments. We gathered snails from mudflat and sandflat habitats and collected their fresh fecal pellets in the laboratory. DNA metabarcoding allowed us to characterize diatom assemblages of ingested sediments and feces. We noted selective feeding such that reduction in MPB biomass with gut passage was difficult to quantify. Diatom α-diversity was reduced with gut passage in snails from both sedimentary regimes. Mudflat and sandflat diatom assemblages were distinct and differed markedly between feces and sediment in mud-feeding snails, whereas the difference in sand-feeding snails was minor. The sandy habitat was dominated by a mix of epipelic and epipsammic diatoms. In contrast, mudflat samples were dominated by epipelic and planktonic diatoms. Compositional differences between sediment and feces reflected preferential removal of planktonic taxa. Our results suggest the importance of phytodetritus to the mud snail diet, particularly in hydrodynamically quiescent environments. Due to the natural spatial patchiness of the snails and the capacity for rapid microbial recolonization, field experiments are recommended to determine whether MPB community changes attributed to gut passage are manifested at the landscape scale.     

Paleoenvironmental model and sequence stratigraphy of the Asmari Formation in southwest Iran

The Asmari Formation is a thick carbonate succession of the Oligo-Miocene in southwest Iran (Zagros Basin). The Zagros Basin was a continental margin attached to the eastern edge of Africa throughout the Phanerozoic. The foraminiferal limestone from the Asmari Formation has been studied to determine its microfacies, paleoenvironments and sedimentary sequences. Based on analysis of larger benthic foraminiferal assemblages and microfacies features three major depositional environments are identified. These include open marine, barrier and lagoon-lower intertidal. These three are represented by eleven microfacies. A carbonate ramp platform is suggested for the depositional environment of the Asmari Formation. The inner ramp facies are characterized by wackestone-packstone, dominated by various taxa of imperforate foraminifera. The middle ramp facies represented by packstone-grainstone to floatstone with a diverse assemblage of larger hyaline foraminifera. The outer ramp is dominated by argillaceous wackestone, characterized by planktonic foraminifera and larger hyaline foraminifera. Two third-order sequences are identified based on deepening and shallowing patterns in microfacies, staking patterns and the distribution of Oligocene-Miocene foraminifers.     

Seasonal and spatial diversity of microbial communities in marine sediments of the South China Sea

This study was conducted to characterize the diversity of microbial communities in marine sediments of the South China Sea by means of 16S rRNA gene clone libraries. The results revealed that the sediment samples collected in summer harboured a more diverse microbial community than that collected in winter, Deltaproteobacteria dominated 16S rRNA gene clone libraries from both seasons, followed by Gammaproteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Firmicutes. Archaea phylotypes were also found. The majority of clone sequences shared greatest similarity to uncultured organisms, mainly from hydrothermal sediments and cold seep sediments. In addition, the sedimentary microbial communities in the coastal sea appears to be much more diverse than that of the open sea. A spatial pattern in the sediment samples was observed that the sediment samples collected from the coastal sea and the open sea clustered separately, a novel microbial community dominated the open sea. The data indicate that changes in environmental conditions are accompanied by significant variations in diversity of microbial communities at the South China Sea.     

Convective gas flow development and the maximum depths achieved by helophyte vegetation in lakes

Background and Aims

Convective gas flow in helophytes (emergent aquatic plants) is thought to be an important adaptation for the ability to colonize deep water. In this study, the maximum depths achieved by seven helophytes were compared in 17 lakes differing in nutrient enrichment, light attenuation, shoreline exposure and sediment characteristics to establish the importance of convective flow for their ability to form the deepest helophyte vegetation in different environments.

Methods

Convective gas flow development was compared amongst the seven species, and species were allocated to ‘flow absent’, ‘low flow’ and ‘high flow’ categories. Regression tree analysis and quantile regression analysis were used to determine the roles of flow category, lake water quality, light attenuation and shoreline exposure on maximum helophyte depths.

Key Results

Two ‘flow absent’ species were restricted to very shallow water in all lakes and their depths were not affected by any environmental parameters. Three ‘low flow’ and two ‘high flow’ species had wide depth ranges, but ‘high flow’ species formed the deepest vegetation far more frequently than ‘low flow’ species. The ‘low flow’ species formed the deepest vegetation most commonly in oligotrophic lakes where oxygen demands in sediments were low, especially on exposed shorelines. The ‘high flow’ species were almost always those forming the deepest vegetation in eutrophic lakes, with Eleocharis sphacelata predominant when light attenuation was low, and Typha orientalis when light attenuation was high. Depths achieved by all five species with convective flow were limited by shoreline exposure, but T. orientalis was the least exposure-sensitive species.

Conclusions

Development of convective flow appears to be essential for dominance of helophyte species in >0·5 m depth, especially under eutrophic conditions. Exposure, sediment characteristics and light attenuation frequently constrain them to a shallower depth than their flow capacity permits.Key words: Aeration, convective flow, exposure, helophytes, lakes, lakeshore vegetation, light attenuation, redox, regression tree, sediment motion, trophic state, waves     

Hinged Plakin Domains Provide Specialized Degrees of Articulation in Envoplakin,Periplakin and Desmoplakin

Envoplakin, periplakin and desmoplakin are cytoskeletal proteins that provide structural integrity within the skin and heart by resisting shear forces. Here we reveal the nature of unique hinges within their plakin domains that provides divergent degrees of flexibility between rigid long and short arms composed of spectrin repeats. The range of mobility of the two arms about the hinge is revealed by applying the ensemble optimization method to small-angle X-ray scattering data. Envoplakin and periplakin adopt ‘L’ shaped conformations exhibiting a ‘helicopter propeller’-like mobility about the hinge. By contrast desmoplakin exhibits essentially unrestricted mobility by ‘jack-knifing’ about the hinge. Thus the diversity of molecular jointing that can occur about plakin hinges includes ‘L’ shaped bends, ‘U’ turns and fully extended ‘I’ orientations between rigid blocks of spectrin repeats. This establishes specialised hinges in plakin domains as a key source of flexibility that may allow sweeping of cellular spaces during assembly of cellular structures and could impart adaptability, so preventing irreversible damage to desmosomes and the cell cytoskeleton upon exposure to mechanical stress.     

The effect of tubificid oligochaetes on the uptake of zinc by Lake Erie sediments

A laboratory experiment was conducted to determine the effect of tubificid worms on the flux of zinc into lake sediments. Forty-six cores of Lake Erie sediment, with and without (control) tubificid worm populations, were exposed to aquarium water with a zinc concentration of about 5 mg 1^–1 for 139 days. Pore water and exchangeable particulate zinc concentrations in the top 12 cm of sediment were periodically determined in pairs of cores — one with worms and one without worms — at 1 cm depth increments. After 139 days, pore water zinc concentrations in sediments with and without worms were nearly identical in the 0–1 cm interval (4.1 and 4.3 mg 1^–1 respectively), but were significantly greater in the sediments with worms in the 1–2 cm (4.4 vs. 0.3 mg^1–1) and the 2–3 cm (1.3 vs. 0.3 mg 1^–1) intervals. Exchangeable particulate zinc concentrations in the 0–1, 1–2, and 2–3 cm intervals in sediments with worms were 612.3, 750.7, and 191.5 µg g^–1 dry sediment respectively, whereas in sediments without worms, concentrations were 375.4, 5.9, and 3.2 µg g^–1 dry sediment. The increased flux of zinc into tubificid-inhabited sediments was caused by the conveyor belt feeding activity of the worms, which continuously exposed sedimentary particles to the overlying water. Movement of zinc into sediments with worms was dominated by adsorption and by particle movement, whereas movement of zinc into control sediments was by adsorption at the sediment-water interface and diffusion. The increased concentration of zinc in tubificid-inhabited sediments has important implications with respect to the trophic transfer of zinc through the aquatic food chain.     

The Obesogenic Quality of the Home Environment: Associations with Diet,Physical Activity,TV Viewing,and BMI in Preschool Children

Objectives

The home environment is thought to play a key role in early weight trajectories, although direct evidence is limited. There is general agreement that multiple factors exert small individual effects on weight-related outcomes, so use of composite measures could demonstrate stronger effects. This study therefore examined whether composite measures reflecting the ‘obesogenic’ home environment are associated with diet, physical activity, TV viewing, and BMI in preschool children.

Methods

Families from the Gemini cohort (n = 1096) completed a telephone interview (Home Environment Interview; HEI) when their children were 4 years old. Diet, physical activity, and TV viewing were reported at interview. Child height and weight measurements were taken by the parents (using standard scales and height charts) and reported at interview. Responses to the HEI were standardized and summed to create four composite scores representing the food (sum of 21 variables), activity (sum of 6 variables), media (sum of 5 variables), and overall (food composite/21 + activity composite/6 + media composite/5) home environments. These were categorized into ‘obesogenic risk’ tertiles.

Results

Children in ‘higher-risk’ food environments consumed less fruit (OR; 95% CI = 0.39; 0.27–0.57) and vegetables (0.47; 0.34–0.64), and more energy-dense snacks (3.48; 2.16–5.62) and sweetened drinks (3.49; 2.10–5.81) than children in ‘lower-risk’ food environments. Children in ‘higher-risk’ activity environments were less physically active (0.43; 0.32–0.59) than children in ‘lower-risk’ activity environments. Children in ‘higher-risk’ media environments watched more TV (3.51; 2.48–4.96) than children in ‘lower-risk’ media environments. Neither the individual nor the overall composite measures were associated with BMI.

Conclusions

Composite measures of the obesogenic home environment were associated as expected with diet, physical activity, and TV viewing. Associations with BMI were not apparent at this age.     

Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein

XPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively ‘opening’ these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a ‘kinetic gating’ mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how ‘opening’ is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed ‘open’ undamaged DNA in solution and that such ‘opening’ can largely occur without one or the other of the β-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound ‘open’ DNA adopts multiple conformations in solution notwithstanding the DNA’s original structure or the β-hairpins. Molecular dynamics simulations reveal compensatory roles of the β-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA ‘opening’ of undamaged sites and the dynamic nature of ‘open’ DNA may shed light on how the protein functions within and beyond nucleotide excision repair in cells.     

Can Natural Proteins Designed with ‘Inverted’ Peptide Sequences Adopt Native-Like Protein Folds?

We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to ‘swap’ certain short peptide sequences in naturally occurring proteins with their corresponding ‘inverted’ peptides and generate ‘artificial’ proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5–12 and 18 amino acid residues. Our analysis illustrates with examples that such ‘artificial’ proteins may be generated by identifying peptides with ‘similar structural environment’ and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides.     

Host Status of Different Potato (Solanum tuberosum) Varieties and Hatching in Root Diffusates of Globodera ellingtonae

Globodera ellingtonae was detected in Oregon in 2008. In order to make decisions regarding the regulation of this nematode, knowledge of its biology is required. We determined the host status of a diversity of potato (Solanum tuberosum) varieties in soil-based experiments and identified hatching stimulants in in vitro hatching assays. ‘Russet Burbank,’ ‘Desiree,’ ‘Modac,’ ‘Norland,’ ‘Umatilla,’ and ‘Yukon Gold’ were good hosts (RF > 14) for G. ellingtonae. Potato varieties ‘Maris Piper,’ ‘Atlantic,’ and ‘Satina,’ all which contain the Ro1 gene that confers resistance to G. rostochiensis, were not hosts for G. ellingtonae. In in vitro hatching assays, G. ellingtonae hatched readily in the presence of diffusates from potato (PRD) and tomato (Solanum lycopersicum; TRD). Egg hatch occurred in an average of between 87% and 90% of exposed cysts, with an average of between 144 and 164 juveniles emerging per cyst, from PRD- and TRD-treated cysts, respectively. This nematode hatched rapidly in the presence of PRD and TRD, with at least 66% of total hatch occurring by day 3 of exposure. There was no dose-response of egg hatch to concentrations of PRD or TRD ranging from 1:5 to 1:100 diffusate to water. When G. ellingtonae was exposed to root diffusates from 21 different plants, hatch occurred in 0% to 70% of exposed cysts, with an average of between 0 to 27 juveniles emerging per cyst. When root diffusate-exposed cysts were subsequently transferred to PRD to test viability, root diffusates from arugula (Eruca sativa), sudangrass (Sorghum bicolor subsp. drummondii), and common vetch (Vicia sativa) continued to inhibit egg hatch compared with the other root diffusates or water in which hatch occurred readily (60 to 182 juveniles emerging per cyst). Previously known hatching stimulants of G. rostochiensis and G. pallida, sodium metavanadate, sodium orthovanadate, and sodium thiocyanate, stimulated some egg hatch. Although, Globodera ellingtonae hatched readily in PRD and TRD and reproduced on potato, the pathogenicity of this nematode on potato remains to be determined.