On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem

The cophylogeny reconstruction problem is that of finding minimal cost explanations of differences between evolutionary histories of ecologically linked groups of biological organisms. We present a proof that shows that the general problem of reconciling evolutionary histories is NP-complete and provide a sharp boundary where this intractability begins. We also show that a related problem, that of finding Pareto optimal solutions, is NP-hard. As a byproduct of our results, we give a framework by which meta-heuristics can be applied to find good solutions to this problem

Extracting the MESA SR4000 Calibrations

Time-of-flight range imaging cameras are capable of acquiring depth images of a scene. Some algorithms require these cameras to be run in `raw mode', where any calibrations from the off-the-shelf manufacturers are lost. The calibration of the MESA SR4000 is herein investigated, with an attempt to reconstruct the full calibration. Possession of the factory calibration enables calibrated data to be acquired and manipulated even in “raw mode.” This work is motivated by the problem of motion correction, in which the calibration must be separated into component parts to be applied at different stages in the algorithm. There are also other applications, in which multiple frequencies are required, such as multipath interference correction. The other frequencies can be calibrated in a similar way, using the factory calibration as a base. A novel technique for capturing the calibration data is described; a retro-reflector is used on a moving platform, which acts as a point source at a distance, resulting in planar waves on the sensor. A number of calibrations are retrieved from the camera, and are then modelled and compared to the factory calibration. When comparing the factory calibration to both the “raw mode” data, and the calibration described herein, a root mean squared error improvement of 51:3mm was seen, with a standard deviation improvement of 34:9mm. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

A model selection approach to discover age-dependent gene expression patterns using quantile regression models

<p>Abstract</p> <p>Background</p> <p>It has been a long-standing biological challenge to understand the molecular regulatory mechanisms behind mammalian ageing. Harnessing the availability of many ageing microarray datasets, a number of studies have shown that it is possible to identify genes that have age-dependent differential expression (DE) or differential variability (DV) patterns. The majority of the studies identify "interesting" genes using a linear regression approach, which is known to perform poorly in the presence of outliers or if the underlying age-dependent pattern is non-linear. Clearly a more robust and flexible approach is needed to identify genes with various age-dependent gene expression patterns.</p> <p>Results</p> <p>Here we present a novel model selection approach to discover genes with linear or non-linear age-dependent gene expression patterns from microarray data. To identify DE genes, our method fits three quantile regression models (constant, linear and piecewise linear models) to the expression profile of each gene, and selects the least complex model that best fits the available data. Similarly, DV genes are identified by fitting and comparing two quantile regression models (non-DV and the DV models) to the expression profile of each gene. We show that our approach is much more robust than the standard linear regression approach in discovering age-dependent patterns. We also applied our approach to analyze two human brain ageing datasets and found many biologically interesting gene expression patterns, including some very interesting DV patterns, that have been overlooked in the original studies. Furthermore, we propose that our model selection approach can be extended to discover DE and DV genes from microarray datasets with discrete class labels, by considering different quantile regression models.</p> <p>Conclusion</p> <p>In this paper, we present a novel application of quantile regression models to identify genes that have interesting linear or non-linear age-dependent expression patterns. One important contribution of this paper is to introduce a model selection approach to DE and DV gene identification, which is most commonly tackled by null hypothesis testing approaches. We show that our approach is robust in analyzing real and simulated datasets. We believe that our approach is applicable in many ageing or time-series data analysis tasks.</p

Perspective using cross-species vaccination approaches to counter emerging infectious diseases

Since the initial use of vaccination in the eighteenth century, our understanding of human and animal immunology has greatly advanced and a wide range of vaccine technologies and delivery systems have been developed. The COVID-19 pandemic response leveraged these innovations to enable rapid development of candidate vaccines within weeks of the viral genetic sequence being made available. The development of vaccines to tackle emerging infectious diseases is a priority for the World Health Organization and other global entities. More than 70% of emerging infectious diseases are acquired from animals, with some causing illness and death in both humans and the respective animal host. Yet the study of critical host–pathogen interactions and the underlying immune mechanisms to inform the development of vaccines for their control is traditionally done in medical and veterinary immunology ‘silos’. In this Perspective, we highlight a ‘One Health vaccinology’ approach and discuss some key areas of synergy in human and veterinary vaccinology that could be exploited to accelerate the development of effective vaccines against these shared health threats

Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?

Australian spiny mountain crayfish (Euastacus, Parastacidae) and their ecotosymbiotic temnocephalan flatworms (Temnocephalida, Platyhelminthes) may have co-occurred and interacted through deep time, during a period of major environmental change. Therefore, reconstructing the history of their association is of evolutionary, ecological, and conservation significance. Here, time-calibrated Bayesian phylogenies of Euastacus species and their temnocephalans (Temnohaswellia and Temnosewellia) indicate near-synchronous diversifications from the Cretaceous. Statistically significant cophylogeny correlations between associated clades suggest linked evolutionary histories. However, there is a stronger signal of codivergence and greater host specificity in Temnosewellia, which co-occurs with Euastacus across its range. Phylogeography and analyses of evolutionary distinctiveness (ED) suggest that regional differences in the impact of climate warming and drying had major effects both on crayfish and associated temnocephalans. In particular, Euastacus and Temnosewellia show strong latitudinal gradients in ED and, conversely, in geographical range size, with the most distinctive, northern lineages facing the greatest risk of extinction. Therefore, environmental change has, in some cases, strengthened ecological and evolutionary associations, leaving host-specific temnocephalans vulnerable to coextinction with endangered hosts. Consequently, the extinction of all Euastacus species currently endangered (75%) predicts coextinction of approximately 60% of the studied temnocephalans, with greatest loss of the most evolutionarily distinctive lineages

Diagnóstico general y servicio prestado en la Cooperativa Agrícola Integral Unión de 4 Pinos R.L. Santiago Sacatepéquez, Guatemala C.A. y evaluación de Boscalid + Pyraclostrobin en la producción y prolongación de vida en anaquel del zucchini (Cucúrbita pepo L. subsp. pepo.)

La presente investigación se realizó en a Cooperativa Agrícola Integral Unión de 4 Pinos, R.L., Finca La Suiza, San Lucas Sacatepéquez, mediante el diagnóstico realizado en Finca La Suiza, área productora de Cooperativa Agrícola Integral Unión de 4 Pinos, determinando que la importancia de investigar el uso de nuevas tecnologías que aumenten la vida de anaquel del zucchini. La investigación consistió en la evaluación del efecto de los ingredientes activos Boscalid+Pyraclostrobin en la producción y prolongación de vida en anaquel del zucchini, para lo cual el ensayo fue dividido en dos etapas, la primera la producción en campo y la segunda el manejo postcosecha en planta empacadora. La primera parte fue realizada en Finca La Suiza, para lo cual se elaboró un plan de manejo fitosanitario, tomando como base el plan de manejo fitosanitario para el cultivo de zucchini Departamento Agrícola 2009, a la cual se incluyeron las aplicaciones de la estrobilurina (Boscalid+Pyraclostrobin) se evaluaron cuatro tratamientos, de los cuales uno era el testigo absoluto, dos tratamientos con 2 y 3 aplicaciones de la estrobilurina (Boscalid+Pyraclostrobin) en diferentes etapas fenológicas del cultivo y un cuarto tratamiento el manejo tradicional del Departamento Agrícola, asi como manejo postcosecha del producto, el cual fue sometido a un procedimiento de clasificación, lavado, desinfección, empaque y colocación en cuarto frio (4ºC) para determinar los días de vida en anaquel del zucchini

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

Ancient hepadnavirus sequences found in bird genomes reveal that this family of viruses, which includes the human hepatitis B virus, is much older than previously thought