Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination.

The use of genetic markers, specifically Short Tandem Repeats (STRs), has been a valuable tool for identifying persons of interest. However, the ability to analyze additional markers including Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (INDELs) polymorphisms allows laboratories to explore other investigative leads. INDELs were chosen in this study because large panels can be differentiated by size, allowing them to be genotyped by capillary electrophoresis. Moreover, these markers do not produce stutter and are smaller in size than STRs, facilitating the recovery of genetic information from degraded samples. The INDEL Ancestry Informative Markers (AIMs) in this study were selected from the 1000 Genomes Project based on a fixation index (FST) greater than 0.50, high allele frequency divergence, and genetic distance. A total of 25 INDEL-AIMs were optimized and validated according to SWGDAM guidelines in a five-dye multiplex. To validate the panel, genotyping was performed on 155 unrelated individuals from four ancestral groups (Caucasian, African, Hispanic, and East Asian). Bayesian clustering and principal component analysis (PCA) were performed revealing clear separation among three groups, with some observed overlap within the Hispanic group. Additionally, the PCA results were compared against a training set of 793 samples from the 1000 Genomes Project, demonstrating consistent results. Validation studies showed the assay to be reproducible, tolerant to common inhibitors, robust with challenging casework type samples, and sensitive down to 125 pg. In conclusion, our results demonstrated the robustness and effectiveness of a 25 loci INDEL system for ancestry inference of four ancestries commonly found in the United States.

The right not to know: Non-disclosure of primary genetic test results and genetic counselors' response.

As part of clinical genetic counseling practice, patients may request that their primary genetic test results be disclosed to someone else, such as a relative or referring provider, or request that results be disclosed to no one (non-disclosure). In making these requests, patients employ the ethical principle of the "right not to know," which argues that autonomous individuals can choose not to know relevant health information. Although the right not to know has been well-studied in medicine in general, and in the return of genomic secondary findings, we are not aware of other studies that have explored the return of primary genetic test results when patients request non-disclosure or disclosure to another individual. This study aimed to describe common clinical scenarios in which these requests occur, how genetic counselors respond, and what ethical considerations they employ in their decision-making process. We recruited participants from the National Society of Genetic Counselors' (NSGC) "Student Research Surveys and Reminders" listserv and conducted semi-structured interviews with 11 genetic counselors in the United States who described genetic counseling cases where this occurred. Interviews were transcribed and coded inductively, and themes were identified. Case details varied, but in our study data the requests for non-disclosure were most commonly made by patients with poor, often oncologic, prognoses who requested their test results be disclosed to a family member instead of themselves. Genetic counselors considered similar factors in deciding how to respond to these requests: patient autonomy, medical actionability of results for the patient and family, the relationship between the patient and the person to whom results might be disclosed, and legal or practical concerns. Genetic counselors often made decisions on a case-by-case basis, depending on how relevant each of these factors were. This study adds to the growing body of literature regarding patients' "right not to know" and will hopefully provide guidance for genetic counselors who experience this situation in clinical practice.

Effect of plant chemical variation and mutualistic ants on the local population genetic structure of an aphid herbivore.

Plants exhibit impressive genetic and chemical diversity, not just between species but also within species, and the importance of plant intraspecific variation for structuring ecological communities is well known. When there is variation at the local population level, this can create a spatially heterogeneous habitat for specialised herbivores potentially leading to non-random distribution of individuals across host plants. Plant variation can affect herbivores directly and indirectly via a third species, resulting in variable herbivore growth rates across different host plants. Herbivores also exhibit within-species variation, with some genotypes better adapted to some plant variants than others. We genotyped aphids collected across 2 years from a field site containing ~200 patchily distributed host plants that exhibit high chemical diversity. The distribution of aphid genotypes, their ant mutualists, and other predators was assessed across the plants. We present evidence that the local distribution of aphid (Metopeurum fuscoviride) genotypes across host-plant individuals is associated with variation in the plant volatiles (chemotypes) and non-volatile metabolites (metabotypes) of their host plant tansy (Tanacetum vulgare). Furthermore, these interactions in the field were influenced by plant-host preferences of aphid-mutualist ants. Our results emphasise that plant intraspecific variation can structure ecological communities not only at the species level but also at the genetic level within species and that this effect can be enhanced through indirect interactions with a third species.

Secondary bacterial symbiont community in aphids responds to plant diversity.

Biodiversity is important for ecosystem functioning and biotic interactions. In experimental grasslands, increasing plant species richness is known to increase the diversity of associated herbivores and their predators. If these interactions can also involve endosymbionts that reside within a plant or animal host is currently unknown. In plant-feeding aphids, secondary bacterial symbionts can have strong fitness effects on the host, e.g. resistance to natural enemies or fungal pathogens. We examined the secondary symbiont community in three species of aphid, each feeding on a unique host plant across experimental plots that varied in plant species richness. Aphids were collected in May and June, and the symbiont community identified using species-specific PCR assays. Aphis fabae aphids were found to host six different symbiont species with individual aphids co-hosting up to four symbionts. Uroleucon jaceae and Macrosiphum rosae hosted two and three symbiont species, respectively. We found that, at the aphid population level, increasing plant species richness increased the diversity of the aphid symbiont community, whereas at the individual aphid level, the opposite was found. These effects are potentially driven by varying selective pressures across different plant communities of varying diversities, mediated by defensive protection responses and a changing cost-benefit trade-off to the aphid for hosting multiple secondary symbionts. Our work extends documented effects of plant diversity beyond visible biotic interactions to changes in endosymbiont communities, with potentially far-reaching consequences to related ecosystem processes.

Rehabilitation of a patient following hand replantation after near-complete distal forearm amputation.

STUDY DESIGN: Case report. INTRODUCTION: Reports of comprehensive rehabilitation following hand replantation are limited. PURPOSE OF THE STUDY: To describe hand therapy of a patient following hand replantation. METHODS: Right hand dominant 55 year-old male assessed 9 days following left hand replantation to treat distal forearm amputation. Patient presented with dorsal blocking orthotic. Initial status: AROM digits and thumb 0-20° extension, 0-40° flexion; absent light touch sensation; 0-1/5 hand strength. Patient underwent 70 hand therapy sessions over 13 months focusing on A/PROM, therapeutic exercise, neuromuscular re-education, and modalities to address functional limitations. RESULTS: Hand therapy discharge status: AROM digits and thumb form composite fist, thumb opposition to digit 3, light touch sensation (monofilament) 4.03 (digits 2, 4) and 4.17 (digits 1, 3, 5); 3- to 4-/5 hand strength. DISCUSSION: Hand therapy allowed for near complete functional return of the hand following replantation. CONCLUSION: Comprehensive Hand therapy aided restoration of adequate sensation and strength for functional use of the replanted hand. LEVEL OF EVIDENCE: 4.

Development of a novel five-dye panel for human identification insertion/deletion (INDEL) polymorphisms.

DNA analysis of forensic case samples relies on short tandem repeats (STRs), a key component of the combined DNA index system (CODIS) used to identify individuals. However, limitations arise when dealing with challenging samples, prompting the exploration of alternative markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) polymorphisms. Unlike SNPs, INDELs can be differentiated easily by size, making them compatible with electrophoresis methods. It is possible to design small INDEL amplicons (<200 bp) to enhance recovery from degraded samples. To this end, a set of INDEL Human Identification Markers (HID) was curated from the 1000 Genomes Project, employing criteria including a fixation index (FST) ≤ 0.06, minor allele frequency (MAF) >0.2, and high allele frequency divergence. A panel of 33 INDEL-HIDs was optimized and validated following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, utilizing a five-dye multiplex electrophoresis system. A small sample set (n = 79 unrelated individuals) was genotyped to assess the assay's performance. The validation studies exhibited reproducibility, inhibition tolerance, ability to detect a two-person mixture from a 4:1 to 1:6 ratio, robustness with challenging samples, and sensitivity down to 125 pg of DNA. In summary, the 33-loci INDEL-HID panel exhibited robust recovery with low-template and degraded samples and proved effective for individualization within a small sample set.

Floral presence and flower identity alter cereal aphid endosymbiont communities on adjacent crops.

Floral plantings adjacent to crops fields can recruit populations of natural enemies by providing flower nectar and non-crop prey to increase natural pest regulation. Observed variation in success rates might be due to changes in the unseen community of endosymbionts hosted by many herbivorous insects, of which some can confer resistance to natural enemies, for example, parasitoid wasps. Reduced insect control may occur if highly protective symbiont combinations increase in frequency via selection effects, and this is expected to be stronger in lower diversity systems.We used a large-scale field trial to analyse the bacterial endosymbiont communities hosted by cereal aphids Sitobion avenae collected along transects into strip plots of barley plants managed by either conventional or integrated (including floral field margins and reduced inputs) methods. In addition, we conducted an outdoor pot experiment to analyse endosymbionts in S. avenae aphids collected on barley plants that were either grown alone or alongside one of three flowering plants, across three time points.In the field, aphids hosted up to four symbionts. The abundance of aphids and parasitoid wasps was reduced towards the middle of all fields while aphid symbiont species richness and diversity decreased into the field in conventional, but not integrated, field-strips. The proportion of aphids hosting different symbiont combinations varied across cropping systems, with distances into the fields, and were correlated with parasitoid wasp abundances.In the pot experiment, aphids hosted up to six symbionts. Flower presence increased natural enemy abundance and diversity, and decreased aphid abundance. The proportion of aphids hosting different symbiont combinations varied across the flower treatment and time, and were correlated with varying abundances of the different specialist parasitoid wasp species recruited by different flowers. Synthesis and applications. Floral plantings and flower identity had community-wide impacts on the combinations of bacterial endosymbionts hosted by herbivorous insects, which correlated with natural enemy diversity and abundance. We recommend that integrated management practices incorporate floral resources within field areas to support a more functionally diverse and resilient natural enemy community to mitigate selection for symbiont-mediated pest resistance throughout the cropping area.

Part-night exposure to artificial light at night has more detrimental effects on aphid colonies than fully lit nights.

Artificial light at night (ALAN) threatens natural ecosystems globally. While ALAN research is increasing, little is known about how ALAN affects plants and interactions with other organisms. We explored the effects of ALAN on plant defence and plant-insect interactions using barley (Hordeum vulgare) and the English grain aphid (Sitobion avenae). Plants were exposed to 'full' or 'part' nights of 15-20 lux ALAN, or no ALAN 'control' nights, to test the effects of ALAN on plant growth and defence. Although plant growth was only minimally affected by ALAN, aphid colony growth and aphid maturation were reduced significantly by ALAN treatments. Importantly, we found strong differences between full-night and part-night ALAN treatments. Contrary to our expectations, part ALAN had stronger negative effects on aphid colony growth than full ALAN. Defence-associated gene expression was affected in some cases by ALAN, but also positively correlated with aphid colony size, suggesting that the effects of ALAN on plant defences are indirect, and regulated via direct disruption of aphid colonies rather than via ALAN-induced upregulation of defences. Mitigating ecological side effects of ALAN is a complex problem, as reducing exposure to ALAN increased its negative impact on insect herbivores. This article is part of the theme issue 'Light pollution in complex ecological systems'.

Four new mitochondrial genomes of the genus zosterops (aves: passeriformes: zosteropidae) from East Africa with a phylogenetic evaluation of the group.

The white-eye birds of the genus Zosterops have been recognized for their high speciation rates in the past, but the relationships of the East African populations are not yet fully resolved. We sequenced and annotated mitogenomes of four populations currently assigned to three East African white-eye species, Zosterops senegalensis, Z. abyssinicus and Z. poliogaster. For Z. senegalensis specimens from two distant populations were sequenced; for the other taxa we used samples collected at one site. The mitogenomes ranged between 17,827 and 17,974 bp, in size similar to previously published mitogenomes analyzed for this genus from other geographic regions. The mitogenomes contain the classical set of 13 coding genes, two structural rRNA genes and 22 tRNA genes. We constructed a phylogeny using all complete mitogenomes currently available for the genus. The phylogeny supports an Asian or Oceanic origin of the genus Zosterops. The East African species represent a monophyletic clade, but the two specimens of Zosterops senegalensis from different regions do not group together, supporting previous hypotheses of cryptic species within the genus. The new genetic resources provided here may help to further explore the relationships and evolution of the genus.

Surgical complications following ESIN for clavicular mid-shaft fractures do not limit functional or patient-perceived outcome.

Elastic intramedullary nailing (ESIN) has been proposed as an alternative minimal-invasive method for the operative management of mid-shaft fractures of the clavicle. However, a relevant complication rate has been reported in previous cohorts. The present retrospective single-centre study aimed to analyse the complications following ESIN in adult patients with clavicular mid-shaft fractures (Allman type I) and their impact on functional and patient-perceived outcome measures. Results were compared to a control group receiving locking plate osteosynthesis. The clinical course and outcome of operatively managed patients with clavicular mid-shaft fractures were retrospectively analysed. Patients were assigned to group A (ESIN) and group B (plate fixation). Radiological, functional (Constant Murley Shoulder Outcome Score (CS), the Disabilities of the Arm, Shoulder and Hand (DASH) Score, the Oxford Shoulder Score (OSS)), and patient perceived aesthetic and clinical outcome were measured. A total of 47 (33 male, 14 female) operatively managed patients with a mean age of 26.7 ± 14.9 years and a follow up time of 38.1 ± 19.4 months were analysed. 36 patients were treated by ESIN (Group A), whereas 11 patients received open reduction and internal plate fixation (Group B). Patients were operatively treated with a mean delay of 7.4 ± 9.3 days (group A: 6.6 ± 8.7 days, group B: 10.2 ± 11.1 days, p=0.326) between trauma and the surgical index procedure. There were no significant differences in the functional (CS: p=0.338, DASH: p=0.247, OSS: p=0.434) and patient-perceived (p=0.346) outcome measures between both groups. Surgical complications were noted in 14 patients (group A: 12, group B: 2) and non-union in 4 patients (group A: 3, group B: 1). There was no correlation between the recorded complications as assessed by the Clavien and Dindo classification and the functional as well as the patient-perceived outcome measures. Despite a relevant incidence rate of surgical complications, ESIN provides good to excellent functional and patient-perceived results in the treatment of clavicular mid-shaft fractures.

Searching for the Optimal Sampling Solution: Variation in Invertebrate Communities, Sample Condition and DNA Quality.

There is a great demand for standardising biodiversity assessments in order to allow optimal comparison across research groups. For invertebrates, pitfall or flight-interception traps are commonly used, but sampling solution differs widely between studies, which could influence the communities collected and affect sample processing (morphological or genetic). We assessed arthropod communities with flight-interception traps using three commonly used sampling solutions across two forest types and two vertical strata. We first considered the effect of sampling solution and its interaction with forest type, vertical stratum, and position of sampling jar at the trap on sample condition and community composition. We found that samples collected in copper sulphate were more mouldy and fragmented relative to other solutions which might impair morphological identification, but condition depended on forest type, trap type and the position of the jar. Community composition, based on order-level identification, did not differ across sampling solutions and only varied with forest type and vertical stratum. Species richness and species-level community composition, however, differed greatly among sampling solutions. Renner solution was highly attractant for beetles and repellent for true bugs. Secondly, we tested whether sampling solution affects subsequent molecular analyses and found that DNA barcoding success was species-specific. Samples from copper sulphate produced the fewest successful DNA sequences for genetic identification, and since DNA yield or quality was not particularly reduced in these samples additional interactions between the solution and DNA must also be occurring. Our results show that the choice of sampling solution should be an important consideration in biodiversity studies. Due to the potential bias towards or against certain species by Ethanol-containing sampling solution we suggest ethylene glycol as a suitable sampling solution when genetic analysis tools are to be used and copper sulphate when focusing on morphological species identification and facing financial restrictions in biodiversity studies.