The biology of the Atherinids caught in the Swan-Avon river system

The ecology and taxonomy of the atherinids caught in the Swan-Avon River system was studied using data collected from monthly samples at ten main and some subsidiary sites. The study demonstrated that five species of atherinids from the three genera Allanetta, Atherinosoma and Pranesus utilise the estuary in different ways. One of the Atherinosoma species folllld in the estuary is currently unrecognised although it may previously have been described as Atherinosoma_ rockinghamensis (Whitley). The other species found in the river system are Atherinosoma elongata (Klunzinger), Atherinosoma presbyteroides (Richardson), Allanetta mugiloides (McCulloch) and Pranesus ogilbyi (Whitley). All the atherinid species spawned during the summer and in three Atherinosoma species and in Allanetta mugiloides the spawning period was protracted. The life cycle of these four species occupied one year. By contrast, in Pranesus ogilbyi the life cycle was either two or three years, with spawning occurring in the final two years of life. Although all of the species were opportunistic carnivores which fed in general on small invertebrates this study indicated that interspecific competition was reduced by a certain degree of selective feeding and by a tendency for slightly different distribution patterns. Pranesus ogilbyi, Allanetta mugiloides and Atherinosoma presbyteroides were marine species, while Atherinosoma elongata was estuarine and Atherinosoma rockinghamensis was largely restricted to fresh water. The feeding and breeding habits and pelagicnature as well as their large numbers in every part of the river system, mean that atherinids must be a very important component of the fauna of the estuary

Regional differences in store-operated Ca2+ entry in the epithelium of the intact human lens

An elevated level of Ca2+ is an important factor in cataract, yet precisely how Ca2+ enters the lens is unknown. Lens epithelial cells contain a range of G-protein–coupled receptors and receptor tyrosine kinases that induce increases in intracellular Ca2+. Receptor-associated Ca2+ influx is, therefore, likely to be an important route for Ca2+ influx to the lens. The authors investigated stimulated and passive Ca2+ influx in in situ human lens epithelium. Ca2+ changes in equatorial (E) and central anterior (CA) epithelial cells were monitored with the use of a Ca2+ indicator (Fluo4) and confocal microscopy. Gene expression was monitored by RT-PCR and immunoblotting. Adenosine triphosphate (ATP) induced Ca2+ responses that were smaller in CA than E. Ca2+ store depletion, using ATP (100 µM) or thapsigargin (1 µM), revealed greater relative store capacity and Ca2+ influx in E. Ca2+ influx was blocked by La3+ (0.5 µM) in both regions. Unstimulated Ca2+ influx was greater in E than CA. Greater expression of Orai1 and STIM1 was detected in E than in CA. Greater Ca2+ store capacity and Ca2+ influx in E compared with CA reflects underlying differences in proliferation and differentiation between the regions. The relatively small resting Ca2+ influx in CA epithelium suggests that store-operated Ca2+ entry (SOCE) is the main route of Ca2+ influx in these cells. Greater resting influx and SOCE in E cells suggests that these are a major route for Ca2+ influx into the lens. Increased expression of Orai1 and STIM1 in E could account for the differences in Ca2+ entry. Receptor activation will modulate Ca2+ influx, and inappropriate activity may contribute to cortical cataract

CHERI Performance Enhancement for a Bytecode Interpreter

During our port of the MicroPython bytecode interpreter to the CHERI-based Arm Morello platform, we encountered a number of serious performance degradations. This paper explores several of these performance issues in detail, in each case we characterize the cause of the problem, the fix, and the corresponding interpreter performance improvement over a set of standard Python benchmarks. While we recognize that Morello is a prototypical physical instantiation of the CHERI concept, we show that it is possible to eliminate certain kinds of software-induced runtime overhead that occur due to the larger size of CHERI capabilities (128 bits) relative to native pointers (generally 64 bits). In our case, we reduce a geometric mean benchmark slowdown from 5x (before optimization) to 1.7x (after optimization) relative to AArch64, non-capability, execution. The worst-case slowdowns are greatly improved, from 100x (before optimization) to 2x (after optimization). The key insight is that implicit pointer size presuppositions pervade systems code; whereas previous CHERI porting projects highlighted compile-time and execution-time errors exposed by pointer size assumptions, we instead focus on the performance implications of such assumptions.Comment: 9 pages, 9 figure

Parameter inference for stochastic biological models

PhD ThesisParameter inference is the field concerned with estimating reliable model parameters from data. In recent years there has been a trend in the biology community toward single cell technologies such as fluorescent flow cytometry, transcriptomics and mass cytometry: providing a rich array of stochastic time series and temporal distribution data for analysis. Deterministically, there are a wide range of parameter inference and global optimisation techniques available. However, these do not always scale well to non-deterministic (i.e., stochastic) settings — whereby the temporal evolution of the system can be described by a chemical master equation for which the solution is nearly always intractable, and the dynamic behaviour of a system is hard to predict. For systems biology, the inference of stochastic parameters remains a bottleneck for accurate model simulation. This thesis is concerned with the parameter inference problem for stochastic chemical reaction networks. Stochastic chemical reaction networks are most frequently modelled as a continuous time discretestate Markov chain using Gillespie’s stochastic simulation algorithm. Firstly, I present a new parameter inference algorithm, SPICE, that combines Gillespie’s algorithm with the cross-entropy method. The cross-entropy method is a novel approach for global optimisation inspired from the field of rare-event probability estimation. I then present recent advances in utilising the generalised method of moments for inference, and seek to provide these approaches with a direct stochastic simulation based correction. Subsequently, I present a novel use of a recent multi-level tau-leaping approach for simulating population moments efficiently, and use this to provide a simulation based correction to the generalised method of moments. I also propose a new method for moment closures based on the use of Padé approximants. The presented algorithms are evaluated on a number of challenging case studies, including bistable systems — e.g., the Schlögl System and the Genetic Toggle Switch — and real experimental data. Experimental results are presented using each of the given algorithms. We also consider ‘realistic’ data — i.e., datasets missing model species, multiple datasets originating from experiment repetitions, and datasets containing arbitrary units (e.g., fluorescence values). The developed approaches are found to be viable alternatives to existing state-ofthe-art methods, and in certain cases are able to outperform other methods in terms of either speed, or accuracyNewcastle/Liverpool/Durham BBSRC Doctoral Training Partnership for financial suppor

Iron ooid beds of the Carolinefjellet Formation, Spitsbergen, Norway

Iron ooid beds are unusual deposits that have been linked to greenhouse conditions and the transgressive flooding of shallow shelves, and which were globally prevalent during certain periods. Within the marine, Aptian-Albian, Carolinefjellet Formation of Spitsbergen, chamosite ooids have been found within distinctive sandstone beds at six localities, and at a consistent stratigraphic position within the basal Dalkjegla Member. Distinctive characteristics include the iron ooids themselves, a coarser grain size, intercalation with silty siderites, grading, cross-beds indicating offshore or longshore transport, and a lack of burrowing. The enclosing sands display planar and hummocky crossstratification and abundant oscillation ripple marks, and are interpreted as lagoon-attached bar complexes. The stratigraphic position and traits of the iron ooid sands are consistent with seaward storm transport and preservation within interbar swales. Ooids vary in shape considerably, and display evidence for multiple growth events. Nuclei of quartz, opaques, carbonate clasts and laminated crusts are typically encircled by finer grained tangential chamosite and opaque laminae, sometimes with outer overgrowths of calcite and/or radial chamosite. The Dalkjegla Member is the marine portion of a large-scale transgressive tract, attached to underlying fluvio-estuarine Helvetiafjellet Formation strata. A lagoonal environment associated with the basal shales of the Dalkjegla Member represents a logical setting, where riverine iron concentration and iron silicate growth could occur. The Spitsbergen iron ooid beds extend the known occurrence of Cretaceous examples, representing a less common High-Latitude example, and one not directly associated with a transgressive flooding surface

Combining Lipophilic dye, in situ Hybridization, Immunohistochemistry, and Histology

Going beyond single gene function to cut deeper into gene regulatory networks requires multiple mutations combined in a single animal. Such analysis of two or more genes needs to be complemented with in situ hybridization of other genes, or immunohistochemistry of their proteins, both in whole mounted developing organs or sections for detailed resolution of the cellular and tissue expression alterations. Combining multiple gene alterations requires the use of cre or flipase to conditionally delete genes and avoid embryonic lethality. Required breeding schemes dramatically enhance effort and cost proportional to the number of genes mutated, with an outcome of very few animals with the full repertoire of genetic modifications desired. Amortizing the vast amount of effort and time to obtain these few precious specimens that are carrying multiple mutations necessitates tissue optimization. Moreover, investigating a single animal with multiple techniques makes it easier to correlate gene deletion defects with expression profiles. We have developed a technique to obtain a more thorough analysis of a given animal; with the ability to analyze several different histologically recognizable structures as well as gene and protein expression all from the same specimen in both whole mounted organs and sections. Although mice have been utilized to demonstrate the effectiveness of this technique it can be applied to a wide array of animals. To do this we combine lipophilic dye tracing, whole mount in situ hybridization, immunohistochemistry, and histology to extract the maximal possible amount of data