High-resolution computed tomography reconstructions of invertebrate burrow systems

The architecture of biogenic structures can be highly influential in determining species contributions to major soil and sediment processes, but detailed 3-D characterisations are rare and descriptors of form and complexity are lacking. Here we provide replicate high-resolution micro-focus computed tomography (μ-CT) data for the complete burrow systems of three co-occurring, but functionally contrasting, sediment-dwelling inter-tidal invertebrates assembled alone, and in combination, in representative model aquaria. These data (≤2,000 raw image slices aquarium−1, isotropic voxel resolution, 81 μm) provide reference models that can be used for the development of novel structural analysis routines that will be of value within the fields of ecology, pedology, geomorphology, palaeobiology, ichnology and mechanical engineering. We also envisage opportunity for those investigating transport networks, vascular systems, plant rooting systems, neuron connectivity patterns, or those developing image analysis or statistics related to pattern or shape recognition. The dataset will allow investigators to develop or test novel methodology and ideas without the need to generate a complete three-dimensional computation of exemplar architecture

Quantifying bioirrigation using ecological parameters: a stochastic approach†

Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O(2 )derived from the stochastic model, with the diffusion length scales constrained by O(2 )microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O(2 )concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O(2 )in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles

Towards reconciling structure and function in the nuclear pore complex

The spatial separation between the cytoplasm and the cell nucleus necessitates the continuous exchange of macromolecular cargo across the double-membraned nuclear envelope. Being the only passageway in and out of the nucleus, the nuclear pore complex (NPC) has the principal function of regulating the high throughput of nucleocytoplasmic transport in a highly selective manner so as to maintain cellular order and function. Here, we present a retrospective review of the evidence that has led to the current understanding of both NPC structure and function. Looking towards the future, we contemplate on how various outstanding effects and nanoscopic characteristics ought to be addressed, with the goal of reconciling structure and function into a single unified picture of the NPC

A quantitative systems view of the spindle assembly checkpoint

The idle assembly checkpoint acts to delay chromosome segregation until all duplicated sister chromatids are captured by the mitotic spindle. This pathway ensures that each daughter cell receives a complete copy of the genome. The high fidelity and robustness of this process have made it a subject of intense study in both the experimental and computational realms. A significant number of checkpoint proteins have been identified but how they orchestrate the communication between local spindle attachment and global cytoplasmic signalling to delay segregation is not yet understood. Here, we propose a systems view of the spindle assembly checkpoint to focus attention on the key regulators of the dynamics of this pathway. These regulators in turn have been the subject of detailed cellular measurements and computational modelling to connect molecular function to the dynamics of spindle assembly checkpoint signalling. A review of these efforts reveals the insights provided by such approaches and underscores the need for further interdisciplinary studies to reveal in full the quantitative underpinnings of this cellular control pathway

Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology

The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted relations connecting known and putative spindle proteins. The subsequent experimental validation of a number of predicted novel proteins confirmed not only their association with the spindle apparatus but also their role in mitosis. We found that 75% of our tested proteins are localizing to the spindle apparatus compared to a success rate of 35% when expert knowledge alone was used. We compare our results to the previously published MitoCheck study and see that our approach does validate some findings by this consortium. Further, we predict so-called “hidden spindle hub”, proteins whose network of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network. Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system

Zoofolkloristika: Prvi uvidi na putu prema novoj disciplini

The author notes that new, more complex researches of connections between animals, nature and connections to humans are needed in Slovenian and European folklore, literature and cultural studies, due to new ecological and ethical findings in the wider social and cultural environment and a changing order of the world, which has moved the focus from anthropocentrism into ecocentrism. The discussion builds upon various theoretical discourses, new concepts and multidisciplinary knowledge, to create the foundations, guidelines and directions for a new academic discipline of zoofolkloristics. Furthermore, new theoretical and analytical discourses should enable zoofolkloristics to provide an insight into changes in human attitudes to animals, in both folklore and within traditional and contemporary ritual practices, or their redefinition, and at the same time exert influence upon legal safety of non-human subjectivities.Autorica polazi od tvrdnje da su potrebna nova, kompleksnija istraživanja veza između životinja, prirode i poveznica s ljudima u slovenskoj i europskoj folkloristici, znanosti o književnosti i kulturnim studijima, zbog novih ekoloških i etičkih uvida u širu društveno-kulturnu okolinu i promjene u svijetu, koje su dovele do promjene od antropocentrizma k ekocentrizmu. U radu se na temelju različitih teorijskih diskursa, novih pojmova i multidisciplinarnog znanja stvaraju temelji, smjernice i pravci istraživanja u novoj znanstvenoj disciplini zoofolkloristike. Autorica tvrdi da bi etnologija, folkloristika i znanost o književnosti mogle imati ključnu ulogu u razvoju ekološke svijesti, znanstvenih terenskih istraživanja i kulturne ekologije te tako omogućiti prelazak iz ekologije u eshatologiju. Rad započinje opisom percepcije životinja i odnosa ljudi i životinja, gdje autorica govori o temeljnim pojmovima koji utječu na uvođenje ove nove znanstvene discipline, kao što su: životinja kao ispitanik, individualni pristup životinji, sinantropski i antropofilni pogled na čovjeka i životinju te antropomorfizam. Zatim se govori o povijesnim i suvremenim filozofsko-antropološkim diskursima o ljudskom pogledu na životinju te o teoriji specizma. Autorica razmatra predmet nove discipline te kaže da je u centru istraživanja životinja u folkloru u najširem mogućem smislu, u svim sferama narodne kulture, što se proučava iz novih gledišta, nove percepcije i recepcije; u pjesmama, pričama, bajkama, basnama, predajama, poslovicama, izrekama, zagonetkama, šalama, narodnom jeziku, kulturnim praksama, narodnom teatru, mitologiji, narodnoj medicini pa čak i u narodnoj glazbi. Nadalje, autorica daje pregled kulturnih istraživanja životinja u Europi i Sloveniji, te pokazuje da su rasprave o životinjama uglavnom objavljivane u 21. stoljeću, što bi moglo označavati da je riječ o prelasku u novu paradigmu ili čak i novu ontologiju. Autorica se bavi metodološkim i teorijskim pitanjima i pravcima u zoofolklorističkim istraživanjima koje klasificira prema kritičkom diskursu. Rad završava pregledom ciljeva zoofolkloristike, za koju tvrdi da ne bi smjela postati znanstvena disciplina koja nema aktivan utjecaj na društvenopolitički prostor u kojem koegzistiraju ljudski i ne-ljudski subjektiviteti

Low-Canopy Seagrass Beds Still Provide Important Coastal Protection Services

Contains fulltext : 117084.pdf (publisher's version ) (Open Access