Bioinformatics tools in predictive ecology: Applications to fisheries

This article is made available throught the Brunel Open Access Publishing Fund - Copygith @ 2012 Tucker et al.There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse

Positive-Buoyancy Rover for Under Ice Mobility

A buoyant rover has been developed to traverse the underside of ice-covered lakes and seas. The rover operates at the ice/water interface and permits direct observation and measurement of processes affecting freeze- over and thaw events in lake and marine environments. Operating along the 2- D ice-water interface simplifies many aspects of underwater exploration, especially when compared to submersibles, which have difficulty in station-keeping and precision mobility. The buoyant rover consists of an all aluminum body with two aluminum sawtooth wheels. The two independent body segments are sandwiched between four actuators that permit isolation of wheel movement from movement of the central tether spool. For normal operations, the wheels move while the tether spool feeds out line and the cameras on each segment maintain a user-controlled fixed position. Typically one camera targets the ice/water interface and one camera looks down to the lake floor to identify seep sources. Each wheel can be operated independently for precision turning and adjustments. The rover is controlled by a touch- tablet interface and wireless goggles enable real-time viewing of video streamed from the rover cameras. The buoyant rover was successfully deployed and tested during an October 2012 field campaign to investigate methane trapped in ice in lakes along the North Slope of Alaska

A Bayesian approach to star-galaxy classification

Star-galaxy classification is one of the most fundamental data-processing tasks in survey astronomy, and a critical starting point for the scientific exploitation of survey data. For bright sources this classification can be done with almost complete reliability, but for the numerous sources close to a survey's detection limit each image encodes only limited morphological information. In this regime, from which many of the new scientific discoveries are likely to come, it is vital to utilise all the available information about a source, both from multiple measurements and also prior knowledge about the star and galaxy populations. It is also more useful and realistic to provide classification probabilities than decisive classifications. All these desiderata can be met by adopting a Bayesian approach to star-galaxy classification, and we develop a very general formalism for doing so. An immediate implication of applying Bayes's theorem to this problem is that it is formally impossible to combine morphological measurements in different bands without using colour information as well; however we develop several approximations that disregard colour information as much as possible. The resultant scheme is applied to data from the UKIRT Infrared Deep Sky Survey (UKIDSS), and tested by comparing the results to deep Sloan Digital Sky Survey (SDSS) Stripe 82 measurements of the same sources. The Bayesian classification probabilities obtained from the UKIDSS data agree well with the deep SDSS classifications both overall (a mismatch rate of 0.022, compared to 0.044 for the UKIDSS pipeline classifier) and close to the UKIDSS detection limit (a mismatch rate of 0.068 compared to 0.075 for the UKIDSS pipeline classifier). The Bayesian formalism developed here can be applied to improve the reliability of any star-galaxy classification schemes based on the measured values of morphology statistics alone.Comment: Accepted 22 November 2010, 19 pages, 17 figure

A new, large-bodied omnivorous bat (Noctilionoidea: Mystacinidae) reveals lost morphological and ecological diversity since the Miocene in New Zealand

A new genus and species of fossil bat is described from New Zealand's only pre-Pleistocene Cenozoic terrestrial fauna, the early Miocene St Bathans Fauna of Central Otago, South Island. Bayesian total evidence phylogenetic analysis places this new Southern Hemisphere taxon among the burrowing bats (mystacinids) of New Zealand and Australia, although its lower dentition also resembles Africa's endemic sucker-footed bats (myzopodids). As the first new bat genus to be added to New Zealand's fauna in more than 150 years, it provides new insight into the original diversity of chiropterans in Australasia. It also underscores the significant decline in morphological diversity that has taken place in the highly distinctive, semi-terrestrial bat family Mystacinidae since the Miocene. This bat was relatively large, with an estimated body mass of ~40 g, and its dentition suggests it had an omnivorous diet. Its striking dental autapomorphies, including development of a large hypocone, signal a shift of diet compared with other mystacinids, and may provide evidence of an adaptive radiation in feeding strategy in this group of noctilionoid bats

Cryopreservation of lipid bilayers by LEA proteins from Artemia franciscana and trehalose

© 2016 Elsevier Inc. The capacity of Late Embryogenesis Abundant (LEA) proteins and trehalose to protect liposomes against freezing-induced damage was examined by measuring the leakage of 5(6)-carboxyfluorescein (CF). Liposomes were prepared to simulate the lipid compositions of the inner leaflet of the plasma membrane, outer mitochondrial membrane (OMM), and inner mitochondrial membrane (IMM). Two recombinant LEA proteins belonging to Group 3 (AfrLEA2 and AfrLEA3m) were expressed and purified from embryos of Artemia franciscana. Only OMM-like liposomes were significantly protected by AfrLEA2 and AfrLEA3m against freeze-thaw damage; at the highest protein:lipid mass ratio tested, leakage of CF was 56.3% of control with AfrLEA3m and 29.3% with AfrLEA2. By comparison, trehalose provided protection to all compositional types. The greatest stabilization during freezing occurred when trehalose was present on both sides of the bilayer. When mitochondria isolated from rat liver were freeze-thawed in trehalose solution, the OMM remained intact based on the absence of increased oxygen consumption when cytochrome c was added during oxidative phosphorylation (OXPHOS). Respiratory control ratios (OXPHOS/LEAK) were depressed by only 30% after freeze-thawing in trehalose compared to non-frozen controls, which indicated some retention of OXPHOS capacity by the IMM. Trehalose then was loaded into the matrix (0.24 μmol/mg mitochondrial protein) by transient opening of the permeability transition pore, a procedure optimized for retention of OMM integrity. Surprisingly, respiratory control ratios were not improved after freeze-thawing with external plus matrix trehalose, when compared to external trehalose alone. This result could perhaps be explained by insufficient accumulation of matrix trehalose

The Joint Effect of Task Similarity and Overparameterization on Catastrophic Forgetting -- An Analytical Model

In continual learning, catastrophic forgetting is affected by multiple aspects of the tasks. Previous works have analyzed separately how forgetting is affected by either task similarity or overparameterization. In contrast, our paper examines how task similarity and overparameterization jointly affect forgetting in an analyzable model. Specifically, we focus on two-task continual linear regression, where the second task is a random orthogonal transformation of an arbitrary first task (an abstraction of random permutation tasks). We derive an exact analytical expression for the expected forgetting - and uncover a nuanced pattern. In highly overparameterized models, intermediate task similarity causes the most forgetting. However, near the interpolation threshold, forgetting decreases monotonically with the expected task similarity. We validate our findings with linear regression on synthetic data, and with neural networks on established permutation task benchmarks.Comment: Accepted to the Twelfth International Conference on Learning Representations (ICLR 2024

Investigation of the role of Mg and Ca in the structure and durability of aluminoborosilicate glass

The structure and dissolution behaviour of Na 2 O·CaO·(15–x)Al 2 O 3 ·xB 2 O 3 ·SiO 2 and Na 2 O·MgO·(15–x)Al 2 O 3 ·xB 2 O 3 ·SiO 2 glasses, relevant to compositions of UK nuclear waste glass, have been investigated using nuclear magnetic resonance (NMR) spectroscopy and static dissolution experiments using the PCT protocol. Structural data from 11 B, 27 Al and 29 Si NMR analyses show that increasing the [B 2 O 3 ]/([Al 2 O 3 ] + [B 2 O 3 ]) ratio of the alkali-alkaline-earth aluminoborosilicate glasses led to an overall decrease in the proportion of non-silicate tetrahedral species ( IV Al + IV B) and a decrease in Si–O–X bonds (X[dbnd]B, Al). The Mg-containing glasses exhibited lower IV B fractions than their Ca-containing counterparts, which is thought to be due to the presence of IV Mg tetrahedra in the network. The measured corrosion rates were similar for both Ca and Mg-containing glasses although unexpectedly some Ca-containing glasses exhibited higher corrosion losses than the Mg-containing ones for time periods up to 112 d. However, there was evidence of a greater tendency to rate resumption in the Mg containing than the Ca containing ones. Alteration products were found to contain Ca, Si and Al with the Ca containing glasses and Ca, Mg, Si and Al with the Mg containing glasses; Na was not detected in the alteration products although its presence cannot be ruled out based on the data obtained

Challenges during diapause and anhydrobiosis: Mitochondrial bioenergetics and desiccation tolerance

© 2018 International Union of Biochemistry and Molecular Biology In preparation for the onset of environmental challenges like overwintering, food limitation, anoxia, or water stress, many invertebrates and certain killifish enter diapause. Diapause is a developmentally-programed dormancy characterized by suppression of development and metabolism. For embryos of Artemia franciscana (brine shrimp), the metabolic arrest is profound. These gastrula-stage embryos depress oxidative metabolism by ~99% during diapause and survive years of severe desiccation in a state termed anhydrobiosis. Trehalose is the sole fuel source for this developmental stage. Mitochondrial function during diapause is downregulated primarily by restricting substrate supply, as a result of inhibiting key enzymes of carbohydrate metabolism. Because proton conductance across the inner membrane is not decreased during diapause, the inference is that membrane potential must be compromised. In the absence of any intervention, the possibility exists that the F1Fo ATP synthase and the adenine nucleotide translocator may reverse, leading to wholesale hydrolysis of cellular ATP. Studies with anhydrobiotes like A. franciscana are revealing multiple traits useful for improving desiccation tolerance that include the expression and accumulation late embryogenesis abundant (LEA) proteins and trehalose. LEA proteins are intrinsically disordered in aqueous solution but gain secondary structure (predominantly α-helix) as water is removed. These protective agents stabilize biological structures including lipid bilayers and mitochondria during severe water stress. © 2018 IUBMB Life, 70(12):1251–1259, 2018

Quantification of cellular protein expression and molecular features of group 3 LEA proteins from embryos of Artemia franciscana

Late embryogenesis abundant (LEA) proteins are highly hydrophilic, low complexity proteins whose expression has been correlated with desiccation tolerance in anhydrobiotic organisms. Here, we report the identification of three new mitochondrial LEA proteins in anhydrobiotic embryos of Artemia franciscana, AfrLEA3m-47, AfrLEA3m-43, and AfrLEA3m-29. These new isoforms are recognized by antibody raised against recombinant AfrLEA3m, the original mitochondrial-targeted LEA protein previously reported from these embryos; mass spectrometry confirms all four proteins share sequence similarity. The corresponding messenger RNA (mRNA) species for the four proteins are readily amplified from total complementary DNA (cDNA) prepared from embryos. cDNA sequences of the four mRNAs are quite similar, but each has a stretch of sequence that is absent in at least one of the others, plus multiple single base pair differences. We conclude that all four mitochondrial LEA proteins are products of independent genes. Each possesses a mitochondrial targeting sequence, and indeed Western blots performed on extracts of isolated mitochondria clearly detect all four isoforms. Based on mass spectrometry and sodium dodecyl sulfate polyacrylamide gel electrophoresis migration, the cytoplasmic-localized AfrLEA2 exists primarily as a homodimer in A. franciscana. Quantification of protein expression for AfrLEA2, AfrLEA3m, AfrLEA3m-43, and AfrLEA3m-29 as a function of development shows that cellular concentrations are highest in diapause embryos and decrease during development to low levels in desiccation-intolerant nauplius larvae. When adjustment is made for mitochondria matrix volume, the effective concentrations of cytoplasmic versus mitochondrial group 3 LEA proteins are similar in vivo, and the values provide guidance for the design of in vitro functional studies with these proteins. © 2013 Cell Stress Society International

Detection of Galaxy Cluster Motions with the Kinematic Sunyaev-Zel'dovich Effect

Using high-resolution microwave sky maps made by the Atacama Cosmology Telescope, we for the first time detect motions of galaxy clusters and groups via microwave background .temperature distortions due to the kinematic Sunyaev.Zel'dovich effect. Galaxy clusters are identified by their constituent luminous galaxies observed by the Baryon Oscillation Spectroscopic Survey, part of the Sloan Digital Sky Survey III. The mean pairwise momentum of clusters is measured. at a statistical. significance of 3.8 sigma, and the signal is consistent with the growth of cosmic structure in the standard model of cosmolog