Measuring the functional sequence complexity of proteins

<p>Abstract</p> <p>Background</p> <p>Abel and Trevors have delineated three aspects of sequence complexity, Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC) observed in biosequences such as proteins. In this paper, we provide a method to measure functional sequence complexity.</p> <p>Methods and Results</p> <p>We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.</p> <p>Conclusion</p> <p>For future extensions, measures of functional bioinformatics may provide a means to evaluate potential evolving pathways from effects such as mutations, as well as analyzing the internal structural and functional relationships within the 3-D structure of proteins.</p

Transport of larvae and detritus across the surf zone of a steep reflective pocket beach

The article of record as published may be found at http://dx.doi.org/10.3354/meps11223Larvae of many intertidal species develop offshore and must cross the surf zone to complete their onshore migration to adult habitats. Depending on hydrodynamics, the surf zone may limit this migration, especially on reflective rocky shores. As a logistically tractable analog of a rocky shore environment, we carried out a comprehensive biological and physical study of the hydrodynamics of a steep reflective sandy beach. Holoplankton and precompetent larval invertebrates were much less abundant within the surf zone than offshore, and their concentrations inside and outside the surf zone were not significantly correlated, suggesting that they were not entering the surf zone. Persistent offshore flow throughout the water column at the outer edge of the surf zone may prevent these organisms from entering the surf zone. In contrast, the concentrations of detritus and a competent larval invertebrate (i.e. cyprids), while also not significantly correlated with concentrations offshore, were frequently more concentrated in the surf zone than offshore. Within the surf zone, the concentration of detritus was significantly correlated with concentrations of competent larval invertebrates (barnacles, gastropods, polychaetes, and bopyrid amphipod) and organisms that may be associated with detritus (amphipods and harpacticoid copepods). These concentrations were significantly negatively correlated with average daily wave height. We hypothesize that detritus and larvae enter the surf zone near the bottom during calm wave conditions by a process of near-bottom streaming. Near-bottom streaming is associated with all surf zones and may be a general mechanism for onshore transport of larvae close to the coast.National Science FoundationGrant NSD-OCE#09273

Surf zones regulate larval supply and zooplankton subsidies to nearshore communities

The article of record as published may be located at http://doi.org/10.1002/lno.10609Surf zone hydrodynamics vary along shorelines potentially affecting the delivery of larvae and zooplankton subsidies to intertidal communities, and, hence, the intensity of postsettlement interactions, growth and reproduction of filter-feeding foundation species and planktivorous fishes. We investigated the ability of zooplankton assemblages to enter the wide surf zone of the rip-channeled, more dissipative beach at Sand City, California, and the narrow surf zone of the steep reflective beach at nearby Carmel River State Beach. Every day for a month, we surveyed zooplankton inside and outside the surf zone and concomitant larval settlement of the dominant invertebrate onshore at each site in this upwelling regime. At the more dissipative surf zone, all zooplankters were far more concentrated inside than outside the surf zone. Many taxa increased in the surf zone and the predominant invertebrate on beaches, Emerita analoga, settled abundantly when prevailing northwesterly winds relaxed and waves were small. At the reflective surf zone, concentrations of zooplankters of most taxa were far greater outside than inside the surf zone, and many taxa increased in the surf zone when waves were small. Twice as many taxa were positively correlated inside and outside the surf zone at the dissipative than the reflective surf zone, indicating that zooplankters were more freely exchanged although behavior also played a role. Thus, spatial and temporal variation in surf zone hydrodynamics may regulate subsidies of zooplankton food and larval recruits to nearshore communities with potential cascading effects on community dynamics and structure.Bodega Marine Laboratory and the Oregon Institute of Marine BiologyNSF-OCE-092719

Surfzone hydrodynamics as a key determinant of spatial variation in rocky intertidal communities.

Larvae of intertidal species develop at sea and must return to adult habitats to replenish populations. Similarly, nutrients, detritus and plankton provide important subsidies spurring growth and reproduction of macroalgae and filter-feeding invertebrates that form the foundation of intertidal communities. Together, these factors determine the density and intensity of interactions among community members. We hypothesized that spatial variation in surfzone hydrodynamics affects the delivery of plankton subsidies. We compared entire zooplankton communities inside and outside the surf zone daily while monitoring physical conditions for one month each at two shores with different surfzone characteristics. Opposite cross-shore distributions of larvae and other zooplankters occurred at the two sites: zooplankton was much more abundant inside the mildly sloping dissipative surf zone (DSZ) with rip currents and was more abundant outside the steep reflective surf zone (RSZ). Biophysical numerical simulations demonstrated that zooplankters were concentrated in rip channels of the DSZ and were mostly unable to enter the RSZ, indicating the hydrodynamic processes behind the observed spatial variation of zooplankters in the surf zone. Differences in the concentration of larvae and other zooplankters between the inner shelf and surf zone may be an underappreciated, key determinant of spatial variation in inshore communities

Persistent Differences in Horizontal Gradients in Phytoplankton Concentration Maintained by Surf Zone Hydrodynamics

The article of record as published may be located at http://link.springer.com/article/10.1007/s12237-017-0278-2Surf zones, regions of breaking waves, are at the interface between the shore and coastal ocean. Surf zone hydrodynamics may affect delivery of phytoplankton subsidies to the intertidal zone. Over a month of daily sampling at an intermediate surf zone with bathymetric rip currents and a reflective surf zone, we measured surf zone hydrodynamics and compared concentrations of coastal phytoplankton taxa in the surf zones to concentrations offshore. At the intermediate surf zone, ~80% of the variability in the concentration of coastal phytoplankton taxa within the surf zone was explained by their variation offshore; however, concentrations were much higher and lower than those offshore in samples from a bathymetric rip current and over the adjacent shoal, respectively. Hydrodynamics at this intermediate surf zone did not hinder the delivery of coastal phytoplankton to the surf zone, but the bathymetric rip current system appeared to redistribute phytoplankton concentrating them within eddies. At the reflective shore, we sampled surf zones at a beach and two adjacent rocky intertidal sites. Concentrations of typical coastal phytoplankton taxa were usually an order of magnitude or more lower than those offshore, even when offshore samples were collected just 20 m beyond the breakers. The phytoplankton assemblages inside and outside the surf zone often appeared to be disconnected. Surf zone hydrodynamics at the steep, reflective shore coupled with low phytoplankton concentrations in near-surface water appeared to limit delivery of phytoplankton subsidies to the surf zone. Surf zone hydrodynamics may be a key factor in the alongshore variation in phytoplankton subsidies to coastal communities.NSF-OCE no. 09273

Surfzone hydrodynamics as a key determinant of spatial variation in rocky intertidal communities.

Larvae of intertidal species develop at sea and must return to adult habitats to replenish populations. Similarly, nutrients, detritus and plankton provide important subsidies spurring growth and reproduction of macroalgae and filter-feeding invertebrates that form the foundation of intertidal communities. Together, these factors determine the density and intensity of interactions among community members. We hypothesized that spatial variation in surfzone hydrodynamics affects the delivery of plankton subsidies. We compared entire zooplankton communities inside and outside the surf zone daily while monitoring physical conditions for one month each at two shores with different surfzone characteristics. Opposite cross-shore distributions of larvae and other zooplankters occurred at the two sites: zooplankton was much more abundant inside the mildly sloping dissipative surf zone (DSZ) with rip currents and was more abundant outside the steep reflective surf zone (RSZ). Biophysical numerical simulations demonstrated that zooplankters were concentrated in rip channels of the DSZ and were mostly unable to enter the RSZ, indicating the hydrodynamic processes behind the observed spatial variation of zooplankters in the surf zone. Differences in the concentration of larvae and other zooplankters between the inner shelf and surf zone may be an underappreciated, key determinant of spatial variation in inshore communities

Variation in the abundance of Pseudo-nitzschia and domoic acid with surf zone type.

Most harmful algal blooms (HAB) originate away from the shore and, for them to endanger human health, they must be first transported to shore after which they must enter the surf zone where they can be feed upon by filter feeders. The last step in this sequence, entrance into the surf zone, depends on surf zone hydrodynamics. During two 30-day periods, we sampled Pseudo-nitzschia and particulate domoic acid (pDA) in and offshore of a more dissipative surf zone at Sand City, California (2010) and sampled Pseudo-nitzschia in and out of reflective surf zones at a beach and rocky shores at Carmel River State Beach, California (2011). At Sand City, we measured domoic acid in sand crabs, Emerita analoga. In the more dissipative surf zone, concentrations of Pseudo-nitzschia and pDA were an order of magnitude higher in samples from a rip current than in samples collected just seaward of the surf zone and were 1000 times more abundant than in samples from the shoals separating rip currents. Domoic acid was present in all the Emerita samples and varied directly with the concentration of pDA and Pseudo-nitzschia in the rip current. In the more reflective surf zones, Pseudo-nitzschia concentrations were 1-2 orders of magnitude lower than in samples from 125 and 20m from shore. Surf zone hydrodynamics affects the ingress of Pseudo-nitzschia into surf zones and the exposure of intertidal organisms to HABs on the inner shelf