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Making sense of rapidly evolving evidence on genetic associations is crucial to making genuine advances in human genomics and the eventual integration of this information in the practice of medicine and public health. Assessment of the strengths and weaknesses of this evidence, and hence the ability to synthesize it, has been limited by inadequate reporting of results. The STrengthening the REporting of Genetic Association studies (STREGA) initiative builds on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement and provides additions to 12 of the 22 items on the STROBE checklist. The additions concern population stratification, genotyping errors, modelling haplotype variation, Hardy-Weinberg equilibrium, replication, selection of participants, rationale for choice of genes and variants, treatment effects in studying quantitative traits, statistical methods, relatedness, reporting of descriptive and outcome data, and the volume of data issues that are important to consider in genetic association studies. The STREGA recommendations do not prescribe or dictate how a genetic association study should be designed but seek to enhance the transparency of its reporting, regardless of choices made during design, conduct, or analysis. [ABSTRACT FROM AUTHOR]

Objective: The present study examines the network structure and, using Bayesian network analysis, estimates the directional pathways among symptoms of posttraumatic stress disorder (PTSD), major depressive disorder (MDD), and levels of alcohol and cannabis use. Method: A sample of 1471 adults in the United States, who reported at least one potentially traumatic event, completed the PTSD Checklist (PCL-5), Patient Health Questionnaire (PHQ-9), and the Alcohol/Cannabis Use Disorders Identification Test (AUDIT/CUDIT). A regularized partial correlation network provided estimates of symptoms clusters and connections. Directional pathways within the network were then estimated using a directed acyclic graph (DAG). Results: Symptoms clustered in theoretically consistent ways. Risky behavior demonstrated the highest strength centrality and bridge strength. Neither alcohol nor cannabis use appeared central in the network, and DAG results suggested that MDD and PTSD symptoms are more likely to lead to substance use than the other way around. Conclusions: Results suggest that cannabis use is largely connected to alcohol use. Consistent with prior research, risky behavior appeared to be the primary bridge between substance use and PTSD. The direction of associations between substance use and psychological symptoms requires further attention.

Background: Energy demands associated with pregnancy and lactation are significant forces in mammalian evolution. To mitigate increased energy costs associated with reproduction, female mammals have evolved behavioural and physiological responses. Some species alter activity to conserve energy during pregnancy and lactation, while others experience changes in metabolism and fat deposition. Restructuring of gut microbiota with shifting reproductive states may also help females increase the energy gained from foods, especially during pregnancy. The goal of this study was to examine the relationships among behaviour, gut microbiota composition, and reproductive state in a wild, non-human primate to better understand reproductive ecology. We combined life history data with > 13,000 behavioural scans and 298 fecal samples collected longitudinally across multiple years from 33 white-faced capuchin monkey (Cebus imitator) females. We sequenced the V4 region of the 16S rRNA gene and used the DADA2 pipeline to analyze microbial diversity. We used PICRUSt2 to assess putative functions., Results: Reproductive state explained some variation in activity, but overall resting behaviours were relatively stable across pregnancy and lactation. Foraging was less frequent among females in the early stage of nursing compared to the cycling stage, though otherwise remained at comparable levels. Maximum temperature was a strong, significantly positive predictor of resting, while social dominance had a small but significantly negative effect on resting. Ecological variables such as available fruit biomass and rainfall had a small but significantly positive effects on measures of foraging time. Gut microbial community structure, including richness, alpha diversity, and beta diversity remained stable across the reproductive cycle. In pairwise comparisons, pregnant females exhibited increased relative abundances of multiple microbial ASVs, suggesting small changes in relation to reproductive state. Reproductive state was not linked to differential abundance of putative metabolic pathways., Conclusions: Previous data suggest that activity budget and the gut microbiome shifts considerably during reproduction. The present study finds that both activity and gut microbial communities are less associated with reproduction compared to other predictors, including ecological contexts. This suggests that behavioural flexibility and gut microbial community plasticity is contrained by ecological factors in this population. These data contribute to a broader understanding of plasticity and stability in response to physiological shifts associated with mammalian reproduction., (© 2023. The Author(s).)

Neurons are the cells of the nervous system and are responsible for every thought, movement and perception. Immune cells are the cells of the immune system, constantly protecting from foreign pathogens. Understanding the interaction between the two systems is especially important in disease states such as autoimmune or neurodegenerative disease. Unfortunately, this interaction is typically detrimental to the host. However, recent efforts have focused on how neurons and immune cells interact, either directly or indirectly, following traumatic injury to the nervous system. The outcome of this interaction can be beneficial - leading to successful neural repair, or detrimental - leading to functional deficits, depending on where the injury occurs. This review will discuss our understanding of neuron-immune cell interactions after traumatic injury to both the peripheral and central nervous system., (Copyright © 2021 Elsevier B.V. and Japan Neuroscience Society. All rights reserved.)

Background: Tonic immobility (TI) is a reflexive, involuntary response that causes motor inhibition, vocal suppression, and analgesia. TI is elicited by extreme fear and perception of entrapment in a life-threatening situation. Research suggests that TI is a frequent peritraumatic response and may be related to subsequent posttraumatic stress disorder (PTSD). However, findings are mixed and, as of yet, no systematic or meta-analytic review examining associations between TI and PTSD has been published., Objective: We systematically and meta-analytically reviewed the literature and investigated whether TI is associated with the development, severity, and course of PTSD. Additionally, we evaluated whether different types of traumatic events are differentially associated with TI, and whether TI severity differs according to sex., Methods: A systematic literature search was conducted using Embase, PubMed, PsycINFO, and Scopus. Meta-analyses were performed on the included articles., Results: We identified 27 eligible articles. We found a significant association between TI and PTSD symptom severity (r = 0.39, 95% CI: 0.34-0.44; p < .0001). TI was more severe among females (Cohen's d=0.37, 95% CI: 0.25-0.48; p < .0001) and was more often elicited in situations involving interpersonal violence. We found limited longitudinal data to perform a meta-analysis of the association between TI and the development and/or course of PTSD. However, the literature available seems to support the role of TI in both the development and course of PTSD., Conclusions: Peritraumatic TI is associated with PTSD symptom severity, occurs more often during interpersonal violence, and is more severe among females. More longitudinal research is needed to investigate the role of TI in psychopathology development and course., Competing Interests: Declaration of Competing Interest None., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Potentially traumatic events may lead to the development of a wide range of adverse psychological responses, including symptoms of anxiety, depression, and (complex) posttraumatic stress disorder (PTSD). Despite the high prevalence of potentially traumatic events in Iran, there is no population data nor evidence-based instrument to screen for cross-diagnostic psychological responses to trauma. The Global Psychotrauma Screen (GPS) is a transdiagnostic self-report instrument for the detection of trauma-related symptoms, as well as risk and protective factors related to the impact of potentially traumatic events., Objective: The present study seeks to 1) translate and cross-culturally adapt the GPS in the Persian (Farsi) language and 2) examine the psychometric properties of the Persian GPS., Method: The translation and adaptation were performed using the Sousa and Rojjanasrirat (2011) method. A pilot study (n = 30) was carried out to test the content validity and test-retest reliability of the GPS. Next, in a representative sample (n = 800) of residents of Kermanshah City, the GPS, the General Health Questionnaire (GHQ) and the PTSD Checklist for DSM-5 (PCL-5) were administered. Construct validity of the Persian GPS was assessed using exploratory and confirmatory factor analysis. Additionally, we evaluated the convergent validity and internal consistency of the GPS., Results: Exploratory and confirmatory factor analyses indicated a three-factor model as the best solution with factors representing 1) Negative Affect, 2) Core PTSD symptoms and 3) Dissociative symptoms. The GPS total symptom score had high internal consistency and high convergent validity with related measures. A GPS total symptom cut-off score of nine was optimal for indicating a probable PTSD diagnosis based on the PCL-5. About half (52%) of the current sample met criteria for probable PTSD., Conclusions: The current findings suggest that the GPS can be effectively adapted for use in a non-Western society and, specifically, that the Persian GPS represents a useful, reliable and valid tool for screening of trauma-related symptoms in Iran., (© 2023. The Author(s).)

A growing body of research demonstrates the association between neighborhood context and health. The underlying biological mechanisms of this association are not fully understood. We conducted a systematic review of studies that investigated the association between neighborhood context and telomere length (TL), a DNA-protein complex that shortens after cell division. Short TL is linked to age-related diseases and may be impacted by chronic stress. Nineteen eligible articles identified through PubMed and Scopus met inclusion criteria. Results demonstrated inconsistent support for the relationship between neighborhood disadvantage and short TL. However, findings across several studies provide evidence for an inverse association between perceived neighborhood problems and TL, suggesting that TL may be an important factor in understanding health vulnerabilities associated specifically with negative perceptions of the neighborhood context., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

The potential mental health consequences of the coronavirus disease 2019 (COVID-19) pandemic are widely acknowledged; however, limited research exists regarding the nature and patterns of stress responses to COVID-19-related potentially traumatic events (PTEs) and the convergence/divergence with responses to other (non-COVID-19-related) PTEs. Network analysis can provide a useful method for evaluating and comparing these symptom structures. The present study includes 7034 participants from 86 countries who reported on mental health symptoms associated with either a COVID-19-related PTE (n = 1838) or other PTE (n = 5196). Using network analysis, we compared the centrality and connections of symptoms within and between each group. Overall, results show that the COVID-19-related network includes transdiagnostic symptom associations similar to networks tied to PTEs unrelated to the pandemic. Findings provide evidence for a shared centrality of depression across networks and theoretically consistent connections between symptoms. Network differences included stronger connections between avoidance-derealization and hypervigilance-depression in the COVID-19 network. Present findings support the conceptualization of psychological responses to pandemic-related PTEs as a network of highly interconnected symptoms and support the use of a transdiagnostic approach to the assessment and treatment of mental health challenges related to the COVID-19 pandemic., (Copyright © 2021. Published by Elsevier Ltd.)

Background : The mental health impact of the COVID-19 crisis may differ from previously studied stressful events in terms of psychological reactions, specific risk factors, and symptom severity across geographic regions worldwide. Objective : To assess the impact of COVID-19 on a wide range of mental health symptoms, to identify relevant risk factors, to identify the effect of COVID-19 country impact on mental health, and to evaluate regional differences in psychological responses to COVID-19 compared to other stressful events. Method : 7034 respondents (74% female) participated in the worldwide Global Psychotrauma Screen - Cross-Cultural responses to COVID-19 study (GPS-CCC ), reporting on mental health symptoms related to COVID-19 ( n = 1838) or other stressful events ( n = 5196) from April to November 2020. Results : Events related to COVID-19 were associated with more mental health symptoms compared to other stressful events, especially symptoms of PTSD, anxiety, depression, insomnia, and dissociation. Lack of social support, psychiatric history, childhood trauma, additional stressful events in the past month, and low resilience predicted more mental health problems for COVID-19 and other stressful events. Higher COVID-19 country impact was associated with increased mental health impact of both COVID-19 and other stressful events. Analysis of differences across geographic regions revealed that in Latin America more mental health symptoms were reported for COVID-19 related events versus other stressful events, while the opposite pattern was seen in North America. Conclusions : The mental health impact of COVID-19-related stressors covers a wide range of symptoms and is more severe than that of other stressful events. This difference was especially apparent in Latin America. The findings underscore the need for global screening for a wide range of mental health problems as part of a public health approach, allowing for targeted prevention and intervention programs., Competing Interests: Wissam El-Hage received personal fees from Air Liquide, EISAI, Janssen, Lundbeck, Nordic Pharma, Otsuka, UCB, Roche and Chugai. No potential competing interest was reported by the other authors., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Gay, bisexual, and queer (GBQ) men are at higher risk of negative body image. As having a negative body image is related to negative mood, sexual, and health outcomes, identifying and providing community-friendly tools for GBQ men is important. This paper describes the creation and evaluation of Rainbow Reflections, a comic anthology developed to promote awareness of and communication about body image. Rainbow Reflections includes comics from 38 trans- and cis-GBQ artists who drew inspiration from personal narratives based on pre-determined themes in the empirical literature and interactive inserts based on evidence-based practice. To evaluate Rainbow Reflections, 167 trans- and cis-GBQ men completed pre-post measures before/after viewing a selection of comics and responded to an open-ended question about their experience. Overall, participants rated the comic book positively, with a majority (61.1%) indicating that they would recommend the book to a friend. After viewing the comics, participants reported greater comfort with initiating conversations about body image, greater satisfaction with their bodies, and reported higher estimates of how common body image concerns are for queer men. Themes that emerged from open-ended responses included participants reflecting on personal struggles (~ 30%), relating with the stories of others (~ 22%), reflecting on the standards of queer men (~ 18%), recognizing cis-privilege (~ 11%), reflecting on others' struggles (~ 9%), negative feedback about the comics (~ 7%), and balancing masculine and feminine (~ 3%). Results of the study provide preliminary evidence for Rainbow Reflections as an effective community-friendly tool to promote awareness of and communication about body image for GBQ men.

The senses play critical roles in helping animals evaluate foods, including fruits that can change both in colour and scent during ripening to attract frugivores. Although numerous studies have assessed the impact of colour on fruit selection, comparatively little is known about fruit scent and how olfactory and visual data are integrated during foraging. We combine 25 months of behavioural data on 75 wild, white-faced capuchins (Cebus imitator) with measurements of fruit colours and scents from 18 dietary plant species. We show that frequency of fruit-directed olfactory behaviour is positively correlated with increases in the volume of fruit odours produced during ripening. Monkeys with red-green colour blindness sniffed fruits more often, indicating that increased reliance on olfaction is a behavioural strategy that mitigates decreased capacity to detect red-green colour contrast. These results demonstrate a complex interaction among fruit traits, sensory capacities and foraging strategies, which help explain variation in primate behaviour.

Great strides in gene discovery have been made using a multitude of methods to associate phenotypes with genetic variants, but there still remains a substantial gap between observed symptoms and identified genetic defects. Herein, we use the convergence of various genetic and genomic techniques to investigate the underpinnings of a constellation of phenotypes that include prostate cancer (PCa) and sensorineural hearing loss (SNHL) in a human subject. Through interrogation of the subject's de novo, germline, balanced chromosomal translocation, we first identify a correlation between his disorders and a poorly annotated gene known as lipid droplet associated hydrolase (LDAH). Using data repositories of both germline and somatic variants, we identify convergent genomic evidence that substantiates a correlation between loss of LDAH and PCa. This correlation is validated through both in vitro and in vivo models that show loss of LDAH results in increased risk of PCa and, to a lesser extent, SNHL. By leveraging convergent evidence in emerging genomic data, we hypothesize that loss of LDAH is involved in PCa and other phenotypes observed in support of a genotype-phenotype association in an n-of-one human subject.

Internet interventions face significant challenges in recruitment and attrition rates are typically high and problematic. Finding innovative yet scientifically valid avenues for attaining and retaining participants is therefore of considerable importance. The main goal of this study was to compare recruitment process and participants characteristics between two similar randomized control trials of mood management interventions. One of the trials (Bunge et al., 2016) was conducted with participants recruited from Amazon's Mechanical Turk (AMT), and the other trial recruited via Unpaid Internet Resources (UIR)., Methods: The AMT sample (Bunge et al., 2016) consisted of 765 adults, and the UIR sample (recruited specifically for this study) consisted of 329 adult US residents. Participants' levels of depression, anxiety, confidence, motivation, and perceived usefulness of the intervention were assessed. The AMT sample was financially compensated whereas the UIR was not., Results: AMT yielded higher recruitment rates per month ( p <  . 05 ). At baseline, the AMT sample reported significantly lower depression and anxiety scores ( p  < .001 and p  < .005, respectively) and significantly higher mood, motivation, and confidence (all p  < .001) compared to the UIR sample. AMT participants spent significantly less time on the site ( p <  . 05 ) and were more likely to complete follow-ups than the UIR sample ( p <  . 05 ). Both samples reported a significant increase in their level of confidence and motivation from pre- to post-intervention. AMT participants showed a significant increase in perceived usefulness of the intervention ( p  < .0001), whereas the UIR sample did not ( p  = .1642)., Conclusions: By using AMT, researchers can recruit very rapidly and obtain higher retention rates; however, these participants may not be representative of the general online population interested in clinical interventions. Considering that AMT and UIR participants differed in most baseline variables, data from clinical studies resulting from AMT samples should be interpreted with caution.

Background: Most users of unsupported Internet interventions visit that site only once, therefore there is a need to create interventions that can be offered as a single brief interaction with the user., Objective: The main goal of this study was to compare the effect of a one-session unsupported Internet intervention on participants' clinical symptoms (depressive and anxiety symptoms) and related variables (mood, confidence and motivation)., Method: A total of 765 adults residing in the United States took part in a randomized controlled trial. Participants were randomly assigned to one of five brief plain text interventions lasting 5-10 min. The interventions designed to address depressive symptoms were: thoughts (increasing helpful thoughts), activities (increasing activity level), sleep hygiene, assertiveness (increasing assertiveness awareness), Own Methods (utilizing methods that were previously successful). They were followed-up one week after consenting., Results: A main effect of time was observed for both depression (F(1, 563) = 234.70, p  < 0.001) and anxiety (F(1, 551) = 170.27, p  < 0.001). In all cases, regardless of assigned condition and Major Depressive Episode status, mean scores on both positive outcomes (mood, confidence and motivation) and negative outcome scores (depression and anxiety) improved over time., Conclusions: Brief unsupported Internet interventions can improve depressive symptoms at one-week follow-up. Further outcome data and research implications will be discussed.

The putative RNA helicase encoded by the Arabidopsis gene At1g32490 is a homolog of the yeast splicing RNA helicases Prp2 and Prp22. We isolated a temperature-sensitive allele (rsw12) of the gene in a screen for root radial swelling mutants. Plants containing this allele grown at the restrictive temperature showed weak radial swelling, were stunted with reduced root elongation, and contained reduced levels of cellulose. The role of the protein was further explored by microarray analysis. By using both fold change cutoffs and a weighted gene coexpression network analysis (WGCNA) to investigate coexpression of genes, we found that the radial swelling phenotype was not linked to genes usually associated with primary cell wall biosynthesis. Instead, the mutation has strong effects on expression of secondary cell wall related genes. Many genes potentially associated with secondary walls were present in the most significant WGCNA module, as were genes coding for arabinogalactans and proteins with GPI anchors. The proportion of up-regulated genes that possess introns in rsw12 was above that expected if splicing was unrelated to the activity of the RNA helicase, suggesting that the helicase does indeed play a role in splicing in Arabidopsis. The phenotype may be due to a change in the expression of one or more genes coding for cell wall proteins.

Activation of the Kelch-like ECH-associated protein 1/nuclear factor (erythroid-derived 2)-like 2 and heat-shock protein 90/heat-shock factor-1 signal-transduction pathways plays a central role in combatting cellular oxidative damage and related endoplasmic reticulum stress. Electrophilic compounds have been shown to be activators of these transcription-mediated responses through S-alkylation of specific regulatory proteins. Previously, we reported that a prototype compound (D1, a small molecule representing a proelectrophilic, para-hydroquinone species) exhibited neuroprotective action by activating both of these pathways. We hypothesized that the para-hydroquinone moiety was critical for this activation because it enhanced transcription of these neuroprotective pathways to a greater degree than that of the corresponding ortho-hydroquinone isomer. This notion was based on the differential oxidation potentials of the isomers for the transformation of the hydroquinone to the active, electrophilic quinone species. Here, to further test this hypothesis, we synthesized a pair of para- and ortho-hydroquinone-based proelectrophilic compounds and measured their redox potentials using analytical cyclic voltammetry. The redox potential was then compared with functional biological activity, and the para-hydroquinones demonstrated a superior neuroprotective profile., (© The Author(s) 2015.)

This study evaluates the capability, efficacy and practicality of a combined approach based on solvent extraction and chemical reduction to simultaneously degrade polycyclic aromatic hydrocarbons (PAHs) and their oxygenated derivatives (OPAHs) in spiked soil. The spiked soil was washed using a composite organic solvent consisting of ethanol and ethyl lactate (1:1, v/v) and then degradation of the extracted contaminants using zero-valent magnesium. The extraction conditions were optimized at 25 °C with solvent-soil ratio of 2:1 (v/w) and the ensuing degradation efficiency ranged from 79% to 88% for the OPAHs, and 66% to 87% for the PAHs after 24 h of reaction at pH of 6.1. The reductive degradation of the spiked contaminants followed pseudo-first-order kinetics; however, comparing the kinetic results of this study to soil-free studies, the degradation rates are significantly reduced. It can be inferred that extracted organic or inorganic components from the soil medium hinder the degradation process, possibly by reducing the reactivity of the activated metal. Furthermore, to our understanding, this study is the first report on the simultaneous degradation of these priority pollutants and their oxygenated derivatives. The experimental results encourage the application of this magnesium/co-solvent system for future pilot-scale remediation studies.

Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases.

The shape of plants depends on cellulose, a biopolymer that self-assembles into crystalline, inextensible microfibrils (CMFs) upon synthesis at the plasma membrane by multi-enzyme cellulose synthase complexes (CSCs). CSCs are displaced in directions predicted by underlying parallel arrays of cortical microtubules, but CMFs remain transverse in cells that have lost the ability to expand unidirectionally as a result of disrupted microtubules. These conflicting findings suggest that microtubules are important for some physico-chemical property of cellulose that maintains wall integrity. Using X-ray diffraction, we demonstrate that abundant microtubules enable a decrease in the degree of wall crystallinity during rapid growth at high temperatures. Reduced microtubule polymer mass in the mor1-1 mutant at high temperatures is associated with failure of crystallinity to decrease and a loss of unidirectional expansion. Promotion of microtubule bundling by over-expressing the RIC1 microtubule-associated protein reduced the degree of crystallinity. Using live-cell imaging, we detected an increase in the proportion of CSCs that track in microtubule-free domains in mor1-1, and an increase in the CSC velocity. These results suggest that microtubule domains affect glucan chain crystallization during unidirectional cell expansion. Microtubule disruption had no obvious effect on the orientation of CMFs in dark-grown hypocotyl cells. CMFs at the outer face of the hypocotyl epidermal cells had highly variable orientation, in contrast to the transverse CMFs on the radial and inner periclinal walls. This suggests that the outer epidermal mechanical properties are relatively isotropic, and that axial expansion is largely dependent on the inner tissue layers., (© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.)

Cellulose synthases form rosette terminal complexes in the plasma membranes of Streptophyta and various linear terminal complexes in other taxa. The sequence of a putative CESA from Griffithsia monilis (Rhodophyta, Floridiophyceae) was deduced using a cloning strategy involving degenerate primers, a cDNA library screen, and 5' and 3' rapid amplification of cDNA ends (RACE). RACE identified two alternative transcriptional starts and four alternative polyadenylation sites. The first translation start codon provided an open reading frame of 2610 bp encoding 870 amino acids and was PCR amplified without introns from genomic DNA. Southern hybridization indicated one strongly hybridizing gene with possible weakly related genes or pseudogenes. Amino acid sequence analysis identified a family 48 carbohydrate-binding module (CBM) upstream of the protein's first predicted transmembrane domain. There are broad similarities in predicted 3D structures of the family 48 modules from CESA, from several glycogen- and starch-binding enzymes, and from protein kinases, but there are substitutions at some residues thought to be involved in ligand binding. The module in G. monilis CESA will be on the cytoplasmic face of the plasma membrane so that it could potentially bind either low molecular weight ligands or starch which is cytosolic rather than inside membrane-bound plastids in red algae. Possible reasons why red algal CESAs have evolved family 48 modules perhaps as part of a system to regulate cellulose synthase activity in relation to cellular carbohydrate status are briefly discussed.

We understand few details about how the arrangement and interactions of cell wall polymers produce the mechanical properties of primary cell walls. Consequently, we cannot quantitatively assess if proposed wall structures are mechanically reasonable or assess the effectiveness of proposed mechanisms to change mechanical properties. As a step to remedying this, we developed WallGen, a Fortran program (available on request) building virtual cellulose-hemicellulose networks by stochastic self-assembly whose mechanical properties can be predicted by finite element analysis. The thousands of mechanical elements in the virtual wall are intended to have one-to-one spatial and mechanical correspondence with their real wall counterparts of cellulose microfibrils and hemicellulose chains. User-defined inputs set the properties of the two polymer types (elastic moduli, dimensions of microfibrils and hemicellulose chains, hemicellulose molecular weight) and their population properties (microfibril alignment and volume fraction, polymer weight percentages in the network). This allows exploration of the mechanical consequences of variations in nanostructure that might occur in vivo and provides estimates of how uncertainties regarding certain inputs will affect WallGen's mechanical predictions. We summarize WallGen's operation and the choice of values for user-defined inputs and show that predicted values for the elastic moduli of multinet walls subject to small displacements overlap measured values. "Design of experiment" methods provide systematic exploration of how changed input values affect mechanical properties and suggest that changing microfibril orientation and/or the number of hemicellulose cross-bridges could change wall mechanical anisotropy.

Making sense of rapidly evolving evidence on genetic associations is crucial to making genuine advances in human genomics and the eventual integration of this information in the practice of medicine and public health. Assessment of the strengths and weaknesses of this evidence, and hence, the ability to synthesize it, has been limited by inadequate reporting of results. The STrengthening the REporting of Genetic Association (STREGA) studies initiative builds on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement and provides additions to 12 of the 22 items on the STROBE checklist. The additions concern population stratification, genotyping errors, modeling haplotype variation, Hardy-Weinberg equilibrium, replication, selection of participants, rationale for choice of genes and variants, treatment effects in studying quantitative traits, statistical methods, relatedness, reporting of descriptive and outcome data, and the volume of data issues that are important to consider in genetic association studies. The STREGA recommendations do not prescribe or dictate how a genetic association study should be designed, but seek to enhance the transparency of its reporting, regardless of choices made during design, conduct, or analysis.

Genes involved in the hearing process have been identified through both positional cloning efforts following genetic linkage studies of families with heritable deafness and by candidate gene approaches based on known functional properties or inner ear expression. The latter method of gene discovery may employ a tissue- or organ-specific approach. Through characterization of a human fetal cochlear cDNA library, we have identified transcripts that are preferentially and/or highly expressed in the cochlea. High expression in the cochlea may be suggestive of a fundamental role for a transcript in the auditory system. Herein we report the identification and characterization of a transcript from the cochlear cDNA library with abundant cochlear expression and unknown function that was subsequently determined to represent osteoglycin (OGN). Ogn-deficient mice, when analyzed by auditory brainstem response and distortion product otoacoustic emissions, have normal hearing thresholds.

Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.

Evidence from genetics, co-precipitation and bimolecular fluorescence complementation suggest that three CESAs implicated in making primary wall cellulose in Arabidopsis thaliana form a complex. This study shows the complex has a M(r) of approximately 840 kDa in detergent extracts and that it has undergone distinctive changes when extracts are prepared from some cellulose-deficient mutants. The mobility of CESAs 1, 3, and 6 in a Triton-soluble microsomal fraction subject to blue native polyacrylamide gel electrophoresis was consistent with a M(r) of about 840 kDa. An antibody specific to any one CESA pulled down all three CESAs consistent with their occupying the same 840 kDa complex. In rsw1, a CESA1 missense mutant, extracts of seedlings grown at the permissive temperature have an apparently normal CESA complex that was missing from extracts of seedlings grown at the restrictive temperature where CESAs precipitated independently. In prc1-19, with no CESA6, CESAs 1 and 3 were part of a 420 kDa complex in extracts of light-grown seedlings that was absent from extracts of dark-grown seedlings where the CESAs precipitated independently. Two CESA3 missense mutants retained apparently normal CESA complexes as did four cellulose-deficient mutants defective in proteins other than CESAs. The 840 kDa complex could contain six CESA subunits and, since loss of plasma membrane rosettes accompanies its loss in rsw1, the complex could form one of the six particles which electron microscopy reveals in rosettes.

Dynamin-related proteins are large GTPases that deform and cause fission of membranes. The DRP1 family of Arabidopsis thaliana has five members of which DRP1A, DRP1C, and DRP1E are widely expressed. Likely functions of DRP1A were identified by studying rsw9, a null mutant of the Columbia ecotype that grows continuously but with altered morphology. Mutant roots and hypocotyls are short and swollen, features plausibly originating in their cellulose-deficient walls. The reduction in cellulose is specific since non-cellulosic polysaccharides in rsw9 have more arabinose, xylose, and galactose than those in wild type. Cell plates in rsw9 roots lack DRP1A but still retain DRP1E. Abnormally placed and often incomplete cell walls are preceded by abnormally curved cell plates. Notwithstanding these division abnormalities, roots and stems add new cells at wild-type rates and organ elongation slows because rsw9 cells do not grow as long as wild-type cells. Absence of DRP1A reduces endocytotic uptake of FM4-64 into the cytoplasm of root cells and the hypersensitivity of elongation and radial swelling in rsw9 to the trafficking inhibitor monensin suggests that impaired endocytosis may contribute to the development of shorter fatter roots, probably by reducing cellulose synthesis.

Genes with a role in the auditory system have been mapped by genetic linkage analysis of families with heritable deafness and then cloned through positional candidate gene approaches. Another positional method for gene discovery is to ascertain deaf individuals with balanced chromosomal translocations and identify disrupted or disregulated genes at the site(s) of rearrangement. We report herein the use of fluorescence in situ hybridization (FISH) to map the breakpoint regions on each derivative chromosome of a de novo apparently balanced translocation, t(8;9)(q12.1;p21.3)dn, in a deaf individual. Chromosomal breakpoints were assigned initially by GTG-banding of metaphase chromosomes and then BAC probes chosen to map precisely the breakpoints by FISH experiments. To facilitate cloning of the breakpoint sequences, further refinement of the breakpoints was performed by FISH experiments using PCR products and by Southern blot analysis. The chromosome 9 breakpoint disrupts methylthioadenosine phosphorylase (MTAP); no known or predicted genes are present at the chromosome 8 breakpoint. Disruption of MTAP is hypothesized to lead to deafness due to the role of MTAP in metabolizing an inhibitor of polyamine synthesis. Drosophila deficient for the MTAP ortholog, CG4,802, were created and their hearing assessed; no hearing loss phenotype was observed. A knockout mouse model for MTAP deficiency was also created and no significant hearing loss was detected in heterozygotes for Mtap. Homozygous Mtap-deficient mice were embryonic lethal., ((c) 2007 Wiley-Liss, Inc)

The Arabidopsis radial swelling mutant rsw10 showed ballooning of root trichoblasts, a lower than wild-type level of cellulose and altered levels of some monosaccharides in non-cellulosic polysaccharides. Map-based cloning showed that the mutated gene (At1g71100) encodes a ribose 5-phosphate isomerase (RPI) and that the rsw10 mutation replaces a conserved glutamic acid residue with lysine. Although RPI is intimately involved with many biochemical pathways, media supplementation experiments suggest that the visible phenotype results from a defect in the production of pyrimidine-based sugar-nucleotide compounds, most likely uridine 5'-diphosphate-glucose, the presumed substrate of cellulose synthase. Two of three RPI sequences in the nuclear genome are cytoplasmic, while the third has a putative chloroplast transit sequence. The sequence encoding both cytoplasmic enzymes could complement the mutation when expressed behind the CaMV 35S promoter, while fusion of the RSW10 promoter region to the GUS reporter gene established that the gene is expressed in many aerial tissues as well as the roots. The prominence of the rsw10 phenotype in roots probably reflects RSW10 being the only cytosolic RPI in this tissue and the gene encoding the plastid RPI being relatively weakly expressed. We could not, however, detect a decrease in total RPI activity in root extracts. The rsw10 phenotype is prominent near the root tip where cells undergo division, endoreduplication and cell expansion and so are susceptible to a restriction in de novo pyrimidine production. The two cytosolic RPIs probably arose in an ancient duplication event, their present expression patterns representing subfunctionalization of the expression of the original ancestral gene.

CesA1 and CesA3 are thought to occupy noninterchangeable sites in the cellulose synthase making primary wall cellulose in Arabidopsis (Arabidopsis thaliana L. Heynh). With domain swaps and deletions, we show that sites C terminal to transmembrane domain 2 give CesAs access to their individual sites and, from dominance and recessive behavior, deduce that certain CesA alleles exclude others from accessing each site. Constructs that swapped or deleted N-terminal domains were stably transformed into the wild type and into the temperature-sensitive mutants rsw1 (Ala-549Val in CesA1) and rsw5 (Pro-1056Ser in CesA3). Dominant-positive behavior was assayed as root elongation at the restrictive temperature and dominant-negative effects were observed at the permissive temperature. A protein with the catalytic and C-terminal domains of CesA1 and the N-terminal domain of CesA3 promoted growth only in rsw1 consistent with it accessing the CesA1 site even though it contained the CesA3 N-terminal domain. A protein having the CesA3 catalytic and C-terminal domains linked to the CesA1 N-terminal domain dramatically affected growth, but only in the CesA3 mutant. This is consistent with the operation of the same access rule taking this chimeric protein to the CesA3 site. In this case, however, the transgene behaved as a genotype-specific dominant negative, causing a 60% death rate in rsw5, but giving no visible phenotype in wild type or rsw1. We therefore hypothesize that possession of CesA3(WT) protects Columbia and rsw1 from the lethal effects of this chimeric protein, whereas the mutant protein (CesA3(rsw5)) does not.

The coordinated expansion of cells is essential to the formation of correctly shaped plant tissues and organs. Members of the radially swollen (rsw) class of temperature-sensitive arabidopsis mutants were isolated in a screen for reduced anisotropic expansion, by selecting plants with radially swollen root tips. Here we describe rsw6, in which cortical microtubules in the root epidermis are well organized in parallel arrays within cells, but neighboring cells frequently contain arrays differing in their mean orientation by up to 90 degrees. Microtubules in rsw6 are more resistant to oryzalin-induced depolymerization than wild-type microtubules, and their reorientation is accompanied by swelling of the epidermal cells. The reorientation phenotype is blocked by taxol and by the depolymerization of actin filaments. We propose that rsw6 microtubule organization is functional on a local level, but defective on a global scale. The rsw6 mutant provides a unique tool with which to study the coordination of microtubule organization at a multicellular level.

Vesicle trafficking delivers proteins to intracellular and extracellular compartments, cellulose synthase to the plasma membrane, and non-cellulosic polysaccharides to the cell wall. The Arabidopsis genome potentially encodes 19 proteins with sequence similarities to ARFs (ADP-ribosylation factors) and its relatives such as ARLs (ARF-like proteins). ARFs are essential for vesicle coating and uncoating in all eukaryotic cells, while ARLs play more diverse roles. Nine proteins, six of them highly similar, are possible ARFs, three are putative ARL orthologues and the remainder were designated ARF-related proteins. The functions of the six highly similar, putative ARFs in whole plant development were probed by suppressing their expression with antisense. Antisense plants were severely stunted because cell production rate and final cell size were both reduced. Changed time-to-flowering, apical dominance, and fertility may reflect alterations to hormonal and other signalling pathways with which ARFs may interact. No gross changes in targeting or compartmentalization were seen in antisense plants containing GFP targeted to the ER and Golgi and changes in cell wall composition were limited to increases in some non-cellulosic polysaccharides and a relatively small decrease in cellulose. The reasons why these effects are less drastic than the effects on endomembranes and wall composition that are seen in short-term experiments with brefeldin A and with dominant negative ARF mutants are discussed.

Cellulose microfibril deposition patterns define the direction of plant cell expansion. To better understand how microfibril alignment is controlled, we examined microfibril orientation during cortical microtubule disruption using the temperature-sensitive mutant of Arabidopsis thaliana, mor1-1. In a previous study, it was shown that at restrictive temperature for mor1-1, cortical microtubules lose transverse orientation and cells lose growth anisotropy without any change in the parallel arrangement of cellulose microfibrils. In this study, we investigated whether a pre-existing template of well-ordered microfibrils or the presence of well-organized cortical microtubules was essential for the cell to resume deposition of parallel microfibrils. We first transiently disrupted the parallel order of microfibrils in mor1-1 using a brief treatment with the cellulose synthesis inhibitor 2,6-dichlorobenzonitrile (DCB). We then analysed the alignment of recently deposited cellulose microfibrils (by field emission scanning electron microscopy) as cellulose synthesis recovered and microtubules remained disrupted at the mor1-1 mutant's non-permissive culture temperature. Despite the disordered cortical microtubules and an initially randomized wall texture, new cellulose microfibrils were deposited with parallel, transverse orientation. These results show that transverse cellulose microfibril deposition requires neither accurately transverse cortical microtubules nor a pre-existing template of well-ordered microfibrils. We also demonstrated that DCB treatments reduced the ability of cortical microtubules to form transverse arrays, supporting a role for cellulose microfibrils in influencing cortical microtubule organization.

As critical determinants of growth anisotropy in plants, cortical microtubules are thought to constrain the movement of cellulose synthase complexes and thus align newly deposited cellulose microfibrils. We tested this cellulose synthase constraint model using the temperature-sensitive mor1-1 mutant of Arabidopsis. Contrary to predictions, the disruption of cortical microtubules in mor1-1 root epidermal cells led to left-handed root twisting and radial swelling but did not alter the transverse orientation of cellulose microfibrils. We also found that drug-dependent disassembly or hyperstabilization of cortical microtubules did not alter the parallel order of cellulose microfibrils. By measuring cellulose content in mor1-1 seedlings, we verified that cellulose synthesis is not reduced at the restrictive temperature. The independence of cortical microtubule organization and cellulose microfibril alignment was supported by the observation that double mutants of mor1-1 and rsw1-1, the cellulose-deficient mutant with misaligned microfibrils, had additive phenotypes. Our results suggest that cortical microtubules regulate growth anisotropy by some mechanism other than cellulose microfibril alignment or synthesis.

Background: In some patients with vitamin B-12 deficiency mistakenly treated with folic acid, anemia resolved but neurologic complications became worse (masking). Fortification of enriched cereal grains with folic acid has raised concerns that people who consume large quantities of cereal grains, particularly the elderly, may be at increased risk of masking. It is unclear, however, what proportion of people with low vitamin B-12 concentrations do not have anemia and whether the proportion is increasing., Objective: We investigated whether fortification has increased the proportion of patients with low vitamin B-12 but without anemia., Design: We reviewed the laboratory results of every patient for whom a vitamin B-12 concentration was measured at the Veterans Affairs Medical Center in Washington, DC, between 1992 and 2000. Those with a low vitamin B-12 concentration (< 258 pmol/L) had their hematocrits and mean cell volumes checked. The proportion without anemia was examined by year before, during, and after folic acid fortification began., Results: There were 1573 subjects with a low vitamin B-12 concentration. The proportion without anemia did not increase significantly from the prefortification period (39.2%) to the period of optional fortification (45.5%) and the postfortification period (37.6%). These findings did not change when the analysis was limited to patients aged > 60 y or when a more conservative definition of low vitamin B-12 (< 150 pmol/L) was used., Conclusions: Despite evidence that folic acid exposure has increased dramatically since food fortification began, this population showed no evidence of an increase in low vitamin B-12 concentrations without anemia. If confirmed, these results would indicate that food fortification has not caused a major increase in masking of vitamin B-12 deficiency.

rsw3 is a temperature-sensitive mutant of Arabidopsis thaliana showing radially swollen roots and a deficiency in cellulose. The rsw3 gene was identified by a map-based strategy, and shows high similarity to the catalytic alpha-subunits of glucosidase II from mouse, yeast and potato. These enzymes process N-linked glycans in the ER, so that they bind and then release chaperones as part of the quality control pathway, ensuring correct protein folding. Putative beta-subunits for the glucosidase II holoenzyme identified in the Arabidopsis and rice genomes share characteristic motifs (including an HDEL ER-retention signal) with beta-subunits in mammals and yeast. The genes encoding the putative alpha- and beta-subunits are single copy and, like the rsw3 phenotype, widely expressed. rsw3 reduces cell number more strongly than cell size in stamen filaments and probably stems. Most features of the rsw3 phenotype are shared with other cellulose-deficient mutants, but some--notably, production of multiple rosettes and a lack of secreted seed mucilage--are not and may reflect glucosidase II affecting processes other than cellulose synthesis. The rsw3 root phenotype develops more slowly than the rsw1 and rsw2 phenotypes when seedlings are transferred to the restrictive temperature. This is consistent with rsw3 reducing glycoprotein delivery from the ER to the plasma membrane whereas rsw1 and rsw2 act more rapidly by affecting the properties of already delivered enzymes.

Recent research has provided insights into how plants make cellulose - the major structural material of their cell walls and the basis of the cotton and wood fibre industries. Arabidopsis thaliana mutants impaired in cellulose production are defective in genes encoding membrane-bound glycosyltransferases, an endo-1,4-beta-glucanase and several enzymes involved in the N-glycosylation and quality-control pathways of the endoplasmic reticulum. The glycosyltransferases form the rosette terminal complexes seen in plasma membranes making cellulose. Synthesis might start by making lipoglucans, which, in turn, might form the substrate for the endo-1,4-beta-glucanase, before being elongated to form the long, crystalline microfibrils that assemble in the cell wall.

The anisotropic growth of plant cells depends on cell walls having anisotropic mechanical properties, which are hypothesized to arise from aligned cellulose microfibrils. To test this hypothesis and to identify genes involved in controlling plant shape, we isolated mutants in Arabidopsis thaliana in which the degree of anisotropic expansion of the root is reduced. We report here the characterization of mutants at two new loci, RADIALLY SWOLLEN 4 (RSW4) and RSW7. The radial swelling phenotype is temperature sensitive, being moderate (rsw7) or negligible (rsw4) at the permissive temperature, 19 degrees C, and pronounced at the restrictive temperature, 30 degrees C. After transfer to 30 degrees C, the primary root's elongation rate decreases and diameter increases, with all tissues swelling radially. Swelling is accompanied by ectopic cell production but swelling is not reduced when the extra cell production is eliminated chemically. A double mutant was generated, whose roots swell constitutively and more than either parent. Based on analytical determination of acid-insoluble glucose, the amount of cellulose was normal in rsw4 and slightly elevated in rsw7. The orientation of cortical microtubules was examined with immunofluorescence in whole mounts and in semi-thin plastic sections, and the orientation of microfibrils was examined with field-emission scanning electron microscopy and quantitative polarized-light microscopy. In the swollen regions of both mutants, cortical microtubules and cellulose microfibrils are neither depleted nor disoriented. Thus, oriented microtubules and microfibrils themselves are insufficient to limit radial expansion; to build a wall with high mechanical anisotropy, additional factors are required, supplied in part by RSW4 and RSW7.

Polysaccharide analyses of mutants link several of the glycosyltransferases encoded by the 10 CesA genes of Arabidopsis to cellulose synthesis. Features of those mutant phenotypes point to particular genes depositing cellulose predominantly in either primary or secondary walls. We used transformation with antisense constructs to investigate the functions of CesA2 (AthA) and CesA3 (AthB), genes for which reduced synthesis mutants are not yet available. Plants expressing antisense CesA1 (RSW1) provided a comparison with a gene whose mutant phenotype (Rsw1(-)) points mainly to a primary wall role. The antisense phenotypes of CesA1 and CesA3 were closely similar and correlated with reduced expression of the target gene. Reductions in cell length rather than cell number underlay the shorter bolts and stamen filaments. Surprisingly, seedling roots were unaffected in both CesA1 and CesA3 antisense plants. In keeping with the mild phenotype compared with Rsw1(-), reductions in total cellulose levels in antisense CesA1 and CesA3 plants were at the borderline of significance. We conclude that CesA3, like CesA1, is required for deposition of primary wall cellulose. To test whether there were important functional differences between the two, we overexpressed CesA3 in rsw1 but were unable to complement that mutant's defect in CesA1. The function of CesA2 was less obvious, but, consistent with a role in primary wall deposition, the rate of stem elongation was reduced in antisense plants growing rapidly at 31 degrees C.

As auditory genes and deafness-associated mutations are discovered at a rapid rate, exciting opportunities have arisen to uncover the molecular mechanisms underlying hearing and hearing impairment. Single genes have been identified to be pathogenic for dominant or recessive forms of nonsyndromic hearing loss, syndromic hearing loss, and, in some cases, even multiple forms of hearing loss. Modifier loci and genes have been found, and investigations into their role in the hearing process will yield valuable insight into the fundamental processes of the auditory system.

Cellulose microfibrils containing crystalline beta-1,4-glucan provide the major structural framework in higher-plant cell walls. Genetic analyses of Arabidopsis thaliana now link specific genes to plant cellulose production just as was achieved some years earlier with bacteria. Cellulose-deficient mutants have defects in several members of one family within a complex glycosyltransferase superfamily and in one member of a small family of membrane-bound endo-1,4-beta-glucanases. The mutants also accumulate a readily extractable beta-1,4-glucan that has short chains which, in at least one case, are lipid linked. Cellulose could be made by direct extension of the glucan chain by the glycosyltransferase or, as the mutant suggests, by an indirect route which makes lipid-linked oligosaccharides. Models discussed incorporate the known enzymes and lipo-glucan and raise the possibility that different CesA glycosyltransferases may catalyse different steps.

An 8.5-kb cosmid containing the KORRIGAN gene complements the cellulose-deficient rsw2-1 mutant of Arabidopsis. Three temperature-sensitive alleles of rsw2 show single amino acid mutations in the putative endo-1,4-beta-glucanase encoded by KOR. The F1 from crosses between kor-1 and rsw2 alleles shows a weak, temperature-sensitive root phenotype. The shoots of rsw2-1 seedlings produce less cellulose and accumulate a short chain, readily extractable glucan resembling that reported for rsw1 (which is defective in a putative glycosyltransferase required for cellulose synthesis). The double mutant (rsw2-1 rsw1) shows further reductions in cellulose production relative to both single mutants, constitutively slow root growth, and enhanced temperature-sensitive responses that are typically more severe than in either single mutant. Abnormal cytokinesis and severely reduced birefringent retardation in elongating root cell walls of rsw2 link the enzyme to cellulose production for primary cell walls and probably cell plates. The Rsw2(-) phenotype generally resembles the Kor(-) and cellulose-deficient Rsw1(-) phenotypes, but anther dehiscence is impaired in Rsw2-1(-). The findings link a second putative enzyme activity to cellulose synthesis in primary cell walls of Arabidopsis and further increases the parallels to cellulose synthesis in Agrobacterium tumefaciens where the celA and celC genes are required and encode a putative glycosyltransferase and an endo-1,4-beta-glucanase related to RSW1 and KOR, respectively.