Measuring the Change in Soft Palate Length and Shape Following Maxillary Advancement: A Cohort Study in Patients with Orofacial Clefts.

OBJECTIVE: To evaluate a method of measuring the change in palatal length and shape following maxillary advancement using synchronous lateral videofluoroscopy and voice recording in order to understand how movement of the maxilla may affect VPI risk in patients with cleft lip and/or palate (CL/P). DESIGN: Retrospective cohort study of children with cleft lip and/or palate. SETTING: Single center, tertiary children's hospital. PARTICIPANTS: Patients with cleft lip and/or palate who underwent maxillary advancement between 2016-21 inclusive. INTERVENTIONS: Maxillary advancement surgery, including those who underwent concurrent mandibular procedures. MAIN OUTCOME MEASURES: The length of the soft palate and the genu angle were measured throughout palatal dynamic range. Pre- and post-operative measurements were compared using a one sided T-test, with subgroup analysis for patients with clinical VPI. RESULTS: Ten patients were examined. The mean distance of maxillary advancement was 10.5 mm. The average increase in pre-genu soft palate length was 2.8 mm in the resting position and 2.9 mm in the closed position. The genu angle decreased in the closed position by 16.3 degrees. CONCLUSIONS: The soft palate showed limited ability to lengthen following maxillary advancement and this may explain the risk of VPI. There was partial compensation by the muscle sling of the palate as demonstrated by a more acute post-operative genu angle and this suggests one reason for the variability of VPI reported. Future research is required to investigate how length and shape changes measured using this method can predict VPI risk.

Restoration of native saltmarshes can reverse arthropod assemblages and trophic interactions changed by a plant invasion.

Plant invasions profoundly impact both natural and managed ecosystems, and removal of the invasive plants addresses only part of the problem of restoring impacted areas. The rehabilitation of diverse communities and their ecosystem functions following removal of invasive plants is an important goal of ecological restoration. Arthropod assemblages and trophic interactions are important indicators of the success of restoration, but they have largely been overlooked in saltmarshes. We determined how arthropod assemblages and trophic interactions changed with the invasion of the exotic plant Spartina alterniflora and with the restoration of the native plant Phragmites australis following Spartina removal in a Chinese saltmarsh. We investigated multiple biotic and abiotic variables to gain insight into the factors underlying the changes in arthropod assemblages and trophic structure. We found that although Spartina invasion had changed arthropod diversity, community structure, feeding-guild composition, and the diets of arthropod natural enemies in the saltmarsh, these changes could be reversed by the restoration of native Phragmites vegetation following removal of the invader. The variation in arthropod assemblages and trophic structure were critically associated with four biotic and abiotic variables (aboveground biomass, plant density, leaf N, and soil salinity). Our findings demonstrate the positive effects of controlling invasive plants on biodiversity and nutrient cycling and provide a foundation for assessing the efficacy of ecological restoration projects in saltmarshes.

Inheritance of DNA methylation differences in the mangrove Rhizophora mangle.

The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

Artificial selection for host resistance to tumour growth and subsequent cancer cell adaptations: an evolutionary arms race.

BACKGROUND: Cancer progression is governed by evolutionary dynamics in both the tumour population and its host. Since cancers die with the host, each new population of cancer cells must reinvent strategies to overcome the host's heritable defences. In contrast, host species evolve defence strategies over generations if tumour development limits procreation. METHODS: We investigate this "evolutionary arms race" through intentional breeding of immunodeficient SCID and immunocompetent Black/6 mice to evolve increased tumour suppression. Over 10 generations, we injected Lewis lung mouse carcinoma cells [LL/2-Luc-M38] and selectively bred the two individuals with the slowest tumour growth at day 11. Their male progeny were hosts in the subsequent round. RESULTS: The evolved SCID mice suppressed tumour growth through biomechanical restriction from increased mesenchymal proliferation, and the evolved Black/6 mice suppressed tumour growth by increasing immune-mediated killing of cancer cells. However, transcriptomic changes of multicellular tissue organisation and function genes allowed LL/2-Luc-M38 cells to adapt through increased matrix remodelling in SCID mice, and reduced angiogenesis, increased energy utilisation and accelerated proliferation in Black/6 mice. CONCLUSION: Host species can rapidly evolve both immunologic and non-immunologic tumour defences. However, cancer cell plasticity allows effective phenotypic and population-based counter strategies.

Repeated Genetic and Adaptive Phenotypic Divergence across Tidal Elevation in a Foundation Plant Species.

AbstractMicrogeographic genetic divergence can create fine-scale trait variation. When such divergence occurs within foundation species, then it might impact community structure and ecosystem function and cause other cascading ecological effects. We tested for parallel microgeographic trait and genetic divergence in Spartina alterniflora, a foundation species that dominates salt marshes of the US Atlantic and Gulf coasts. Spartina is characterized by tall-form (1-2 m) plants at lower tidal elevations and short-form (<0.5 m) plants at higher tidal elevations, yet whether this trait variation reflects plastic and/or genetically differentiated responses to these environmental conditions remains unclear. In the greenhouse, seedlings raised from tall-form plants grew taller than those from short-form plants, indicating a heritable difference in height. When we reciprocally transplanted seedlings back into the field for a growing season, composite fitness (survivorship and seed production) and key plant traits (plant height and biomass allocation) differed interactively across origin and transplant zones in a manner indicative of local adaptation. Further, a survey of single nucleotide polymorphisms revealed repeated, independent genetic differentiation between tall- and short-form Spartina at five of six tested marshes across the native range. The observed parallel, microgeographic genetic differentiation in Spartina likely underpins marsh health and functioning and provides an underappreciated mechanism that might increase capacity of marshes to adapt to rising sea levels.

Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity.

PREMISE: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species because they create and define ecological communities, contributing disproportionately to ecosystem function. METHODS: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages. We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass Leymus chinensis. We examined the relationship between genetic and clonal diversities, their variation with patch size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species. RESULTS: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single multilocus lineages. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three. CONCLUSIONS: We found strong genetic structure among patches of L. chinensis. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.

Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics.

Contents Summary 738 I. Introduction 738 II. RRBS loci as genome-wide epigenetic markers 739 III. Exploiting functional annotation of RRBS loci 739 IV. Limitations of RRBS methods for nonmodel species 740 V. Maximising the impact of RRBS in plants 741 VI. Conclusions 741 Acknowledgements 741 SUMMARY: Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.

Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill.

Despite the severe impacts of the Deepwater Horizon oil spill, the foundation plant species Spartina alterniflora proved resilient to heavy oiling, providing an opportunity to identify mechanisms of response to the anthropogenic stress of crude oil exposure. We assessed plants from oil-affected and unaffected populations using a custom DNA microarray to identify genomewide transcription patterns and gene expression networks that respond to crude oil exposure. In addition, we used T-DNA insertion lines of the model grass Brachypodium distachyon to assess the contribution of four novel candidate genes to crude oil response. Responses in S. alterniflora to hydrocarbon exposure across the transcriptome as well as xenobiotic specific response pathways had little overlap with those previously identified in the model plant Arabidopsis thaliana. Among T-DNA insertion lines of B. distachyon, we found additional support for two candidate genes, one (ATTPS21) involved in volatile production, and the other (SUVH5) involved in epigenetic regulation of gene expression, that may be important in the response to crude oil. The architecture of crude oil response in S. alterniflora is unique from that of the model species A. thaliana, suggesting that xenobiotic response may be highly variable across plant species. In addition, further investigations of regulatory networks may benefit from more information about epigenetic response pathways.

Quantitative epigenetics and evolution.

Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited. To explicate these points, we show that epigenetics can influence all aspects of the phenotypic variance formula: VP (total phenotypic variance) = VG (genetic variance) + VE (environmental variance) + VGxE (genotype-by-environment interaction) + 2COVGE (the genotype-environment covariance) + Vɛ (residual variance), requiring new strategies to account for different potential sources of epigenetic effects on phenotypic variance. We also demonstrate how each of the components of phenotypic variance not only can be influenced by epigenetics, but can also have evolutionary consequences. We argue that no sources of epigenetic effects on phenotypic variance can be easily cast aside in a quantitative genetic research program that seeks to understand evolutionary processes.

Is pneumatic balloon dilation safe and effective primary modality of treatment for post-sleeve gastrectomy strictures? A retrospective study.

BACKGROUND: The optimal treatment of sleeve strictures has not been agreed upon at the current time. At our institution, we began using pneumatic balloon dilation to help resolve these obstructions in 2010. Herein we report our experience with pneumatic balloon dilation for the treatment of sleeve strictures. METHODS: From Jan 2010 to Dec 2016 we retrospectively reviewed our prospectively kept database for patients who developed a Laparoscopic Sleeve Gastrectomy (LSG) stricture within 90 days of surgery. If the stricture was found, then we dilated all our patients initially at 30 mm at 10 PSI for 10-20 min (14.5 min average) and increased the balloon size (30-40 mm) and duration (10-30 min) in subsequent sessions if the first session was unsuccessful. RESULTS: The review found that 1756 patients underwent either LSG or the first step of a Laparoscopic Duodenal Switch (LDS) (1409 LSG & 356 LDS). Of the 1756 patient 33 patients (24 underwent LSG, and 9 underwent LDS) developed a stricture as a complication of LSG. The average age of the patients was 46.4 (±9.6) years, and the average BMI was 43.7 (±6.4). The most common location for stricture was mid-body of the sleeve (54.5%). The average time from the primary surgery to diagnosis and first pneumatic dilation was 5.6 months (± 6.8) and 5.9 months (± 6.6) respectively. We successfully used pneumatic dilation in 31 (93.9%) of these patients to relieve the stricture. CONCLUSION: We conclude that pneumatic dilation is an effective procedure in patients with post sleeve gastrectomy stricture.

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

A matched cohort analysis of single anastomosis loop duodenal switch versus Roux-en-Y gastric bypass with 18-month follow-up.

BACKGROUND: The Roux-en-Y gastric bypass (GBP) has been considered the gold standard for many years. The loop duodenal switch (LDS) is a relatively new procedure that simplifies the complexity of the duodenal switch (BPDDS) by making it a single anastomosis procedure while at the same time giving it more intestinal absorption to reduce the rates of malnutrition associated with traditional BPDDS. This paper seeks to compare the 18-month weight loss outcomes and complications of the more standard GBP with the newer LDS in a single US center. METHODS: A retrospective matched cohort was analyzed on 108 patients who had either GBP (54 patients) or LDS (54 patients). Regression analysis was used to compare weight loss outcomes as measured by BMI and weight loss percentages. Complications gathered included bleeds, reoperations, diagnostic or therapeutic endoscopy (EGD), ulcers and chronic nausea. RESULTS: GBP and LDS have statistically similar weight loss at 18 months (39.6 vs 41 % weight loss, respectively). However, there were significantly more nausea complaints (26 vs 5), diagnostic endoscopies (EGD) (21 vs 3) and ulcers (6 vs 0) with the GBP than the LDS. CONCLUSION: LDS has comparable weight loss results to GBP. However, LDS has fewer 30-day and 18-month complications and patients suffer from less nausea postoperatively.

Sexual orientation of trans adults is not linked to outcome of transition-related health care, but worth asking.

Since the beginning of contemporary transition-related care at the outset of the 20th century, sexual orientation has ben considered to be closely connected with gender identity and the developmental trajectories of trans people. Specifically, health professionals have regarded the anticipated post-transitional heterosexual behaviour of trans adults as predictive of a good outcome of cross-sex hormones and gender-confirming surgeries. This article reviews the current literature according to the question of whether the sexual orientation of trans people is linked to outcome measures following transition-related interventions. A comprehensive review was undertaken using the Medline database, searching for empirical studies published between 2010 and 2015. Out of a total of 474 studies, only 10 studies reported a follow-up of trans adults and assessed sexual orientation in the study protocol at all. Sexual orientation was predominantly assessed as homosexual versus non-homosexual related to sex assigned at birth. Only one 1 of 10 follow-up studies found a significant association according to the outcome between groups differentiated by sexual orientation. Empirically there is no link between sexual orientation and outcome of transition-related health care for trans adults. In order to provide comprehensive health care, we recommend asking for sexual behaviours, attractions and identities, as well as for gender experiences and expressions; however, this knowledge should not drive, but simply inform, such comprehensive care.

Non-binary or genderqueer genders.

Some people have a gender which is neither male nor female and may identify as both male and female at one time, as different genders at different times, as no gender at all, or dispute the very idea of only two genders. The umbrella terms for such genders are 'genderqueer' or 'non-binary' genders. Such gender identities outside of the binary of female and male are increasingly being recognized in legal, medical and psychological systems and diagnostic classifications in line with the emerging presence and advocacy of these groups of people. Population-based studies show a small percentage--but a sizable proportion in terms of raw numbers--of people who identify as non-binary. While such genders have been extant historically and globally, they remain marginalized, and as such--while not being disorders or pathological in themselves--people with such genders remain at risk of victimization and of minority or marginalization stress as a result of discrimination. This paper therefore reviews the limited literature on this field and considers ways in which (mental) health professionals may assist the people with genderqueer and non-binary gender identities and/or expressions they may see in their practice. Treatment options and associated risks are discussed.

Opportunities and challenges of next-generation sequencing applications in ecological epigenetics.

Evolutionary theory posits that adaptation can result when populations harbour heritable phenotypic variation for traits that increase tolerance to local conditions. However, the actual mechanisms that underlie heritable phenotypic variation are not completely understood (Keller ). Recently, the potential role of epigenetic mechanisms in the process of adaptive evolution has been the subject of much debate (Pigliucci & Finkelman ). Studies of variation in DNA methylation in particular have shown that natural populations harbour high amounts of epigenetic variation, which can be inherited across generations and can cause heritable trait variation independently of genetic variation (Kilvitis et al. ). While we have made some progress addressing the importance of epigenetics in ecology and evolution using methylation-sensitive AFLP (MS-AFLP), this approach provides relatively few anonymous and dominant markers per individual. MS-AFLP are difficult to link to functional genomic elements or phenotype and are difficult to compare directly to genetic variation, which has limited the insights drawn from studies of epigenetic variation in natural nonmodel populations (Schrey et al. ). In this issue, Platt et al. provide an example of a promising approach to address this problem by applying a reduced representation bisulphite sequencing (RRBS) approach based on next-generation sequencing methods in an ecological context.

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.

Retention of Homeless Smokers in the Power to Quit Study.

INTRODUCTION: Concerns about retention are a major barrier to conducting studies enrolling homeless individuals. Since smoking is a major problem in homeless communities and research on effective methods of promoting smoking cessation is needed, we describe strategies used to increase retention and participant characteristics associated with retention in smoking cessation study enrolling homeless adults. METHODS: The parent study was a 2-group randomized controlled trial with 26-week follow-up enrolling 430 homeless smokers from emergency shelters and transitional housing units in Minneapolis/Saint Paul, MN, USA. Multiple strategies were used to increase retention, including conducting visits at convenient locations for participants, collecting several forms of contact information from participants, using a schedule that was flexible and included frequent low-intensity visits, and providing incentives. Participant demographics as well as characteristics related to tobacco and drug use and health status were analyzed for associations with retention using univariate and multivariate analysis. RESULTS: Overall retention was 75% at 26 weeks. Factors associated with increased retention included greater age; having healthcare coverage; history of multiple homeless episodes, lower stress level; and higher PHQ-9 (Patient Health Questionnaire-9) score. A history of excessive drinking and drug use were associated with decreased retention. CONCLUSIONS: It is possible to successfully retain homeless individuals in a smoking cessation study if the study is designed with participants' needs in mind.

Genome-wide patterns of Arabidopsis gene expression in nature.

Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PC(veg)) correlate to temperature and precipitation occurrence in the field. The largest PC(veg) axes included thermoregulatory genes while the second major PC(veg) was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.

Body image dissatisfaction and eating-related psychopathology in trans individuals: a matched control study.

High levels of body dissatisfaction have already been reported in the trans population; however, the root of this dissatisfaction, and its association with eating disordered behaviours, has not been studied in-depth. This study aims to assess eating disorder risk by comparing 200 trans people, 200 people with eating disorders and 200 control participants' scores on three subscales of the Eating Disorders Inventory-2 (EDI-2) and to further explore dissatisfaction in the trans participants using the Hamburg Body Drawing Scale (HBDS). The results showed that overall participants with eating disorders scored higher than trans or control groups on all EDI-2 measures, but that trans individuals had greater body dissatisfaction than control participants and, importantly, trans males had comparable body dissatisfaction scores to eating disordered males. Drive for thinness was greater in females (cis and trans) compared with males. In relation to HBDS body dissatisfaction, both trans males and trans females reported greatest dissatisfaction not only for gender-identifying body parts but also for body shape and weight. Overall, trans males may be at particular risk for eating disordered psychopathology and other body image-related behaviours.