Next-generation sequencing technologies and applications for human genetic history and forensics

Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics

What constitutes feeling safe at home? A qualitative interview study with frail older people receiving home care

Aim: To highlight experiences of what constitutes feeling safe at home among frail older people receiving home care. Design: Qualitative descriptive study. Methods: The sample consists of 12 individual recorded interviews with frail older people in their homes. Interviews were transcribed verbatim and analysed using qualitative content analysis. The data collection was performed in spring 2018. Results: The analysis resulted in three categories: "Having a feeling of\u27at-homeness\u27" describes the older people\u27s surrounding environment and their efforts to maintain independence; "being able to influence" describes the importance for older people to shape their care by being in control and having an opportunity for self-determination in the context of home care; and "being able to trust staff" relates to expecting staff\u27s knowledge and skills and to appreciating the staff\u27s ability to create positive relations

Surface Topography of Nitrided Steel Surfaces

\ua9 Published under licence by IOP Publishing Ltd. The effect of nitrocarburizing were investigated for two different steels, 42CrMo4 and 25CrMo4, with objective to evaluate the influence of initial surface topography on the resulting nitrocarburized surface with regard to surface topography and thickness of the compound layer. It was found that the nitrocarburizing process has an impact on the surface topography. The process creates a short-wave isotropic structure on the original surface and this is particularly evident for the smoother original surfaces. No significant effect on the compound layer thickness depending on the surface topography before heat treatment could be observed

Primary school teachers’ patterns in using communication-supporting strategies following a professional development program: lessons learned from an exploratory study with three teachers

Oral language skills underpin later literacy achievement and life prospects, and many children struggle with oral language for various reasons. Hence, it is crucial for teachers to provide a learning environment with rich opportunities for all children to practice their oral language. The aim of this exploratory study was to explore a professional development (PD) program designed to coach teachers in using communication-supporting strategies during verbal teacher-child interactions in regular classrooms. In focus were five strategies from the Communication Supporting Classroom Observation Tool. The study used a mixed-method case design with multiple observations across four time points over 10 weeks and a follow-up observation after two months. Outcome measures were collected at pre-and, post-intervention and at follow-up. The cases were two intervention teachers and one comparison teacher in second grade in Swedish primary schools. The teachers were directly observed and video-recorded during teacher-child structured small group conversations while discussing different texts with two groups of children each. The groups were mixed and comprised both children struggling with oral language as well as more typically developing children. To further understand the verbal interactions, the teachers’ amount of talk in relation to the children was analyzed in terms of the percentage distribution of the total number of words per minute. The overall patterns of strategy use showed that the two intervention teachers applied more varied strategies from the PD program during the intervention period, but this was not maintained at the follow-up. The amount of teacher talk appeared stable over time, with individual differences in the three teachers. We also discuss the teachers’ own insights and our experience in the design of the PD program, which may guide future research and applications of the PD program

Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents

<p>Abstract</p> <p>Background</p> <p>Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of <it>Bartonella grahamii</it>, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global <it>B. grahamii </it>population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.</p> <p>Results</p> <p>To study the population dynamics of <it>B. grahamii</it>, we analyzed the genomic diversity on a whole-genome scale of 27 <it>B. grahamii </it>strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the <it>fha </it>gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the <it>fha </it>gene or the plasmid.</p> <p>Conclusion</p> <p>Our study has revealed a geographic microstructure of <it>B. grahamii </it>in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.</p

Sex hormones and sperm parameters after adjuvant oxaliplatin-based treatment for colorectal cancer

Publisher Copyright: © 2022 The Author(s)Background: The incidence of colorectal cancer (CRC) in individuals of fertile age is increasing. Oxaliplatin is a cornerstone treatment in the adjuvant setting for stage III and high-risk stage II CRC. Limited data exist on possible side effects of oxaliplatin on fertility and gonadal function. More data is needed to guide possible fertility preservation procedures and aid evidence-based fertility counselling. Patients and methods: The aim of this study (EudraCT2006-002832-10) was to prospectively investigate sex hormones and sperm parameters after oxaliplatin-based adjuvant chemotherapy to clarify the risk of infertility and hypogonadism. Twenty males aged ≤55 years and 16 females aged ≤40 years were recruited from five hospitals in the Nordic countries. All had undergone radical surgery due to CRC and were given adjuvant oxaliplatin in combination with 5-fluorouracil. Measurement of luteinizing hormone (LH), follicle-stimulating hormone (FSH), testosterone, sex hormone binding globulin (SHBG) and semen analysis were done in males, while LH, FSH and oestradiol were measured in females. Measurements were done prior to chemotherapy, after completion of adjuvant treatment and at follow-up 1 and up to 5 years after end of treatment. Results: FSH and testosterone levels increased in males after chemotherapy treatment but were restored at follow-up. No patients developed hypogonadism. There was a trend towards a decrease in sperm concentration during treatment (p = 0.063). When comparing sperm concentration and rapid progressive motility of sperms prior to chemotherapy and at follow-up, there were no differences, and no patients became permanently azoospermic by treatment. No distinct altering of gonadal function could be observed in females. Conclusions: Oxaliplatin in combination with 5-fluorouracil seems to induce transient decrease in sperm concentration with recovery and a minor transient increase in FSH in males. No distinct altering of gonadal function was observed in females. The risk of infertility and hypogonadism in males and females after adjuvant oxaliplatin-based chemotherapy seems low.Peer reviewe

A carbon mass-balance budget for a periglacial catchment in West Greenland - Linking the terrestrial and aquatic systems

Climate change is predicted to have far reaching consequences for the mobility of carbon in arctic landscapes. On a regional scale, carbon cycling is highly dependent on interactions between terrestrial and aquatic parts of a catchment. Despite this, studies that integrate the terrestrial and aquatic systems and study entire catchments using site-specific data are rare. In this work, we use data partly published by Lindborg et al. (2016a) to calculate a whole-catchment carbon mass-balance budget for a periglacial catchment in West Greenland. Our budget shows that terrestrial net primary production is the main input of carbon (99% of input), and that most carbon leaves the system through soil respiration (90% of total export/storage). The largest carbon pools are active layer soils (53% of total carbon stock or 13 kg C m (2)), permafrost soils (30% of total carbon stock or 7.6 kg C m (2)) and lake sediments (13% of total carbon stock or 10 kg C m (2)). Hydrological transport of carbon from the terrestrial to aquatic system is lower than in wetter climates, but the annual input of 4100 kg C yr (1) (or 3.5 g C m (2) yr (1)) that enters the lake via runoff is still three times larger than the eolian input of terrestrial carbon. Due to the dry conditions, the hydrological export of carbon from the catchment is limited (5% of aquatic export/storage or 0.1% of total export/storage). Instead, CO2 evasion from the lake surface and sediment burial accounts for 57% and 38% of aquatic export/storage, respectively (or 0.8% and 0.5% of total export/storage), and Two-Boat Lake acts as a net source of carbon to the atmosphere. The limited export of carbon to downstream water bodies make our study system different from wetter arctic environments, where hydrological transport is an important export pathway for carbon. (C) 2019 The Author(s). Published by Elsevier B.V

Hard and transparent films formed by nanocellulose-TiO2 nanoparticle hybrids

T he formation of hybrids of nanofibrillated cellulose and titania nanoparticles in aqueous media has been studied. Their transparency and mechanical behavior have been assessed by spectrophotometry and nanoindentation. The results show that limiting the titania nanoparticle concentration below 16 vol% yields homogeneous hybrids with a very high Young's modulus and hardness, of up to 44 GPa and 3.4 GPa, respectively, and an optical transmittance above 80%. Electron microscopy shows that higher nanoparticle contents result in agglomeration and an inhomogeneous hybrid nanostructure with a concomitant reduction of hardness and optical transmittance. Infrared spectroscopy suggests that the nanostructure of the hybrids is controlled by electrostatic adsorption of the titania nanoparticles on the negatively charged nanocellulose surfaces