Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination

Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome

Catchment survey in the Karonga District: a landscape-scale analysis of provisioning and core reduction strategies during the Middle Stone Age of northern Malawi

The landscape of northern Malawi is defined by several river catchments that drain from the highlands in the west into Lake Malawi in the east. Many thousands of Middle Stone Age (MSA) artefacts are present on the surface, in particular, in areas where sedimentary units assigned to the Chitimwe Beds are exposed. The unique configuration of the region and its exposures makes it possible to address landscape-scale questions about MSA behaviour that augment information derived from excavated assemblages. In this study, data are derived from initial results of surveys conducted in 2012 which focussed on how lithic raw materials (in the form of cobbles) and core technology (in the form of mapped and analysed cores) are distributed across the landscape relative to different landforms, geologies and one another. These data are used to examine if differences in core reduction technology occur in different catchment areas with different raw material quantities and qualities, and to test hypotheses about lithic provisioning scenarios. This allows for examination of core reduction technologies in relation to raw material sources via surface finds, on a larger regional scale than is usually possible from excavations. Different catchments show differences in the type and quality of the raw material, with higher-quality quartzites occurring in the North Rukuru catchment and declining to the south. This is reflected in the types of materials that MSA people chose to use for the production of stone tools. However, differences in raw material selection and distance from cobbles did not influence preferred core reduction strategies, and most cores cluster together near cobble sources. This suggests that throughout the MSA in the study area, core reduction strategies were highly conserved even while raw material use remained flexible, and cores were not regularly transported as part of a provisioning strategy

Tortoise taphonomy and tortoise butchery patterns at Blombos Cave, South Africa

Tortoises are one of the most common faunal components at many Palaeolithic archaeological sites across the Old World. They provide protein, fat, and other 'animal' resources in a 'collectable' package. However, for most sites their interpretation as human food debris is based only on association, rather than demonstrated through taphonomic analysis. Because of their very different anatomical configuration compared to mammals, it is difficult to conduct such analyses by directly applying the taphonomic methods used to interpret large mammal assemblages. Tortoise-specific taphonomic analysis is presented here for the Still Bay layers at the important Middle Stone Age (MSA) site of Blombos Cave (BBC), Western Cape, South Africa. Research on MSA subsistence systems at sites such as BBC has almost exclusively relied on analysis of large ungulate remains, in spite of the fact that many of these key sites contain equal or greater numbers of tortoise fragments. In this analysis we show that human modification is common on the BBC tortoises, and that there are consistent patterns of fragmentation and burning that indicate set processing sequences including cooking while in the shell, hammerstone percussion, and human chewing of limbs. The almost exclusive dominance of the angulate tortoise, Chersina angulata, is confirmed by full skeletal element analyses rather than only counts of single elements such as humeri. The sex distribution can be reconstructed for this species, and is female-biased. For all tortoise assemblages, taxonomic and skeletal element abundance data should be calculated from a sample of complete elements, or at minimum the entoplastron and humerus. A sample of shell and limb/girdle elements should also be subjected to microscopic bone surface modification analysis, as modifications are often rare or subtle but highly informative. Using this approach, analysis of breakage patterns, bone surface modification, and burning patterns can be understood together to specifically reconstruct tortoise collection, processing, and human dietary significance across a range of archaeological sites

Motor unit discharge variability is increased in mild-to-moderate Parkinson\u27s disease

Individuals with Parkinson\u27s disease (PD) demonstrate deficits in muscle activation such as decreased amplitude and inappropriate bursting. There is evidence that some of these disturbances are more pronounced in extensor vs. flexor muscles. Surface EMG has been used widely to quantify muscle activation deficits in PD, but analysis of discharge of the underlying motor units may provide greater insight and be more sensitive to changes early in the disease. Of the few studies that have examined motor unit discharge in PD, the majority were conducted in the first dorsal interosseous, and no studies have measured motor units from extensor and flexor muscles within the same cohort. The objective of this study was to characterize the firing behavior of single motor units in the elbow flexor and extensor muscles during isometric contractions in people with mild-to-moderate PD. Ten individuals with PD (off-medication) and nine healthy controls were tested. Motor unit spike times were recorded via intramuscular EMG from the biceps and triceps brachii muscles during 30-s isometric contractions at 10% maximum voluntary elbow flexion and elbow extension torque, respectively. We selected variables of mean motor unit discharge rate, discharge variability, and torque variability to evaluate motor abnormalities in the PD group. The effects of group, muscle, and group-by-muscle on each variable were determined using separate linear mixed models. Discharge rate and torque variability were not different between groups, but discharge variability was significantly higher in the PD group for both muscles combined

An experimental investigation of cut mark production and stone tool attrition

Abstract In discussions of Paleolithic hominin behavior it is often assumed that cut marks are an unwanted byproduct of butchery activities, and that their production causes the dulling of stone tool edges. It is also presumed that Paleolithic butchers would have refrained from making cut marks to extend the use life of their tools. We conducted a series of butchery experiments designed to test the hypothesis that cut marks affect the use life of tools. Results suggest cut marks are not associated with edge attrition of simple flake tools, and therefore it is unlikely that Paleolithic butchers would have avoided contact between bone surfaces and tool edges. Edge attrition is, however, significantly greater during skinning and disarticulation than during defleshing. This suggests that skinning and disarticulation activities would require more tool edges relative to butchery events focused purely on defleshing. Differences between the number of cut-marked bones relative to the number of stone artifacts deposited at taphonomically comparable archaeological localities may be explicable in terms of different types of butchery activities conducted there, rather than strictly the timing of carcass access by hominins. Archaeological localities with higher artifact discard rates relative to raw material availability may represent an emphasis on activities associated with higher edge attrition (e.g. skinning or disarticulation)

Prioritization of Features for Mobile Apps for Families in a Federal Nutrition Program for Low-Income Women, Infants, and Children: User-Centered Design Approach

Background: The Special Supplemental Nutrition Assistance Program for Women, Infants, and Children (WIC) is a federal nutrition program that provides nutritious food, education, and health care referrals to low-income women, infants, and children up to the age of 5 years. Although WIC is associated with positive health outcomes for each participant category, modernization and efficiency are needed at the clinic and shopping levels to increase program satisfaction and participation rates. New technologies, such as electronic benefits transfer (EBT), online nutrition education, and mobile apps, can provide opportunities to improve the WIC experience for participants. Objective: This formative study applies user-centered design principles to inform the layout and prioritization of features in mobile apps for low-income families participating in the WIC program. Methods: To identify and prioritize desirable app features, caregivers (N=22) of the children enrolled in WIC participated in individual semistructured interviews with a card sorting activity. Interviews were transcribed verbatim and analyzed using constant comparative analysis for themes. App features were ranked and placed into natural groupings by each participant. The sum and average of the rankings were calculated to understand which features were prioritized by the users. Natural groupings of features were labeled according to participant descriptions. Results: Natural groupings focused on the following categories: clinics/appointments, shopping/stores, education/assessments, location, and recipes/food. Themes from the interviews triangulated the results from the ranking activity. The priority app features were balance checking, an item scanner, and appointment scheduling. Other app features discussed and ranked included appointment reminders, nutrition training and quizzes, shopping lists, clinic and store locators, recipe gallery, produce calculator, and dietary preferences/allergies. Conclusions: This study demonstrates how a user-centered design process can aid the development of an app for low-income families participating in WIC to inform the effective design of the app features and user interface

Weak Coupling Among Barrier Loci and Waves of Neutral and Adaptive Introgression Across an Expanding Hybrid Zone

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species’ ranges, whereas putative cases of adaptive introgression had exceptionally wide clines with centers shifted toward one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per-generation dispersal between 200 and 400 m, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range-limited species

Reimagining Restitution: New Approaches to Support Youth and Communities

Courts began ordering youth restitution in the 1960s as a less restrictive sanction than probation or incarceration for mostly white youth. Since then, restitution has been linked to higher recidivism rates and heightened racial and economic disparities in the juvenile justice system. This report provides an overview of the historical and current landscape of restitution imposed on youth, the impact of restitution on youth, victims and communities, and provides recommendations for how jurisdictions can reimagine restitution

Peptide-Based Scaffolds Support Human Cortical Progenitor Graft Integration to Reduce Atrophy and Promote Functional Repair in a Model of Stroke

Stem cell transplants offer significant hope for brain repair following ischemic damage. Pre-clinical work suggests that therapeutic mechanisms may be multi-faceted, incorporating bone-fide circuit reconstruction by transplanted neurons, but also protection/regeneration of host circuitry. Here, we engineered hydrogel scaffolds to form "bio-bridges" within the necrotic lesion cavity, providing physical and trophic support to transplanted human embryonic stem cell-derived cortical progenitors, as well as residual host neurons. Scaffolds were fabricated by the self-assembly of peptides for a laminin-derived epitope (IKVAV), thereby mimicking the brain's major extracellular protein. Following focal ischemia in rats, scaffold-supported cell transplants induced progressive motor improvements over 9 months, compared to cell- or scaffold-only implants. These grafts were larger, exhibited greater neuronal differentiation, and showed enhanced electrophysiological properties reflective of mature, integrated neurons. Varying graft timing post-injury enabled us to attribute repair to both neuroprotection and circuit replacement. These findings highlight strategies to improve the efficiency of stem cell grafts for brain repair