Molecular Exploration of the First-Century Tomb of the Shroud in Akeldama, Jerusalem

The Tomb of the Shroud is a first-century C. E. tomb discovered in Akeldama, Jerusalem, Israel that had been illegally entered and looted. The investigation of this tomb by an interdisciplinary team of researchers began in 2000. More than twenty stone ossuaries for collecting human bones were found, along with textiles from a burial shroud, hair and skeletal remains. The research presented here focuses on genetic analysis of the bioarchaeological remains from the tomb using mitochondrial DNA to examine familial relationships of the individuals within the tomb and molecular screening for the presence of disease. There are three mitochondrial haplotypes shared between a number of the remains analyzed suggesting a possible family tomb. There were two pathogens genetically detected within the collection of osteological samples, these were Mycobacterium tuberculosis and Mycobacterium leprae. The Tomb of the Shroud is one of very few examples of a preserved shrouded human burial and the only example of a plaster sealed loculus with remains genetically confirmed to have belonged to a shrouded male individual that suffered from tuberculosis and leprosy dating to the first-century C.E. This is the earliest case of leprosy with a confirmed date in which M. leprae DNA was detected

In Vitro Assembly of Multiple DNA Fragments Using Successive Hybridization

Construction of recombinant DNA from multiple fragments is widely required in molecular biology, especially for synthetic biology purposes. Here we describe a new method, successive hybridization assembling (SHA) which can rapidly do this in a single reaction in vitro. In SHA, DNA fragments are prepared to overlap one after another, so after simple denaturation-renaturation treatment they hybridize in a successive manner and thereby assemble into a recombinant molecule. In contrast to traditional methods, SHA eliminates the need for restriction enzymes, DNA ligases and recombinases, and is sequence-independent. We first demonstrated its feasibility by constructing plasmids from 4, 6 and 8 fragments with high efficiencies, and then applied it to constructing a customized vector and two artificial pathways. As SHA is robust, easy to use and can tolerate repeat sequences, we expect it to be a powerful tool in synthetic biology

Ethical Surveillance: Applying Deep Learning and Contextual Awareness for the Benefit of Persons Living with Dementia

A significant proportion of the population has become used to sharing private information on the internet with their friends. This information can leak throughout their social network and the extent that personal information propagates can depend on the privacy policy of large corporations. In an era of artificial intelligence, data mining, and cloud computing, is it necessary to share personal information with unidentified people? Our research shows that deep learning is possible using relatively low capacity computing. When applied, this demonstrates promising results in spatio-temporal positioning of subjects, in prediction of movement, and assessment of contextual risk. A private surveillance system is particularly suitable in the care of those who may be considered vulnerable

Canalization and developmental stability in the Brachyrrhine mouse

The semi-dominant Br mutation affects presphenoid growth, producing the facial retrognathism and globular neurocranial vault that characterize heterozygotes. We analysed the impact of this mutation on skull shape, comparing heterozygotes to wildtype mice, to determine if the effects are skull-wide or confined to the sphenoid region targeted by the mutation. In addition, we examined patterns of variability of shape for the skull as a whole and for three regions (basicranium, face and neurocranium). We found that the Br mice differed significantly from wildtype mice in skull shape in all three regions as well as in the shape of the skull as a whole. However, the significant increases in variance and fluctuating asymmetry were found only in the basicranium of mutant mice. These results suggest that the mutation has a significant effect on the underlying developmental architecture of the skull, which produces an increase in phenotypic variability that is localized to the anatomical region in which the mean phenotype is most dramatically affected. These results suggest that the same developmental mechanisms that produce the change in phenotypic mean also produce the change in variance.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75710/1/j.1469-7580.2006.00527.x.pd

Strategies for implementing genomic selection in family-based aquaculture breeding schemes: double haploid sib test populations

<p>Abstract</p> <p>Background</p> <p>Simulation studies have shown that accuracy and genetic gain are increased in genomic selection schemes compared to traditional aquaculture sib-based schemes. In genomic selection, accuracy of selection can be maximized by increasing the precision of the estimation of SNP effects and by maximizing the relationships between test sibs and candidate sibs. Another means of increasing the accuracy of the estimation of SNP effects is to create individuals in the test population with extreme genotypes. The latter approach was studied here with creation of double haploids and use of non-random mating designs.</p> <p>Methods</p> <p>Six alternative breeding schemes were simulated in which the design of the test population was varied: test sibs inherited maternal (<it>Mat</it>), paternal (<it>Pat</it>) or a mixture of maternal and paternal (<it>MatPat</it>) double haploid genomes or test sibs were obtained by maximum coancestry mating (<it>MaxC</it>), minimum coancestry mating (<it>MinC</it>), or random (<it>RAND</it>) mating. Three thousand test sibs and 3000 candidate sibs were genotyped. The test sibs were recorded for a trait that could not be measured on the candidates and were used to estimate SNP effects. Selection was done by truncation on genome-wide estimated breeding values and 100 individuals were selected as parents each generation, equally divided between both sexes.</p> <p>Results</p> <p>Results showed a 7 to 19% increase in selection accuracy and a 6 to 22% increase in genetic gain in the <it>MatPat</it> scheme compared to the <it>RAND</it> scheme. These increases were greater with lower heritabilities. Among all other scenarios, i.e. <it>Mat, Pat, MaxC</it>, and <it>MinC</it>, no substantial differences in selection accuracy and genetic gain were observed.</p> <p>Conclusions</p> <p>In conclusion, a test population designed with a mixture of paternal and maternal double haploids, i.e. the <it>MatPat</it> scheme, increases substantially the accuracy of selection and genetic gain. This will be particularly interesting for traits that cannot be recorded on the selection candidates and require the use of sib tests, such as disease resistance and meat quality.</p

Applied screening tests for the detection of superior face recognition.

In recent years there has been growing interest in the identification of people with superior face recognition skills, for both theoretical and applied investigations. These individuals have mostly been identified via their performance on a single attempt at a tightly controlled test of face memory-the long form of the Cambridge Face Memory Test (CFMT+). The consistency of their skills over a range of tests, particularly those replicating more applied policing scenarios, has yet to be examined systematically. The current investigation screened 200 people who believed they have superior face recognition skills, using the CFMT+ and three new, more applied tests (measuring face memory, face matching and composite-face identification in a crowd). Of the sample, 59.5% showed at least some consistency in superior face recognition performance, although only five individuals outperformed controls on overall indices of target-present and target-absent trials. Only one participant outperformed controls on the Crowds test, suggesting that some applied face recognition tasks require very specific skills. In conclusion, future screening protocols need to be suitably thorough to test for consistency in performance, and to allow different types of superior performer to be detected from the outset. Screening for optimal performers may sometimes need to directly replicate the task in question, taking into account target-present and target-absent performance. Self-selection alone is not a reliable means of identifying those at the top end of the face recognition spectrum

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page