Diverse organic-mineral associations in Jezero crater, Mars.

The presence and distribution of preserved organic matter on the surface of Mars can provide key information about the Martian carbon cycle and the potential of the planet to host life throughout its history. Several types of organic molecules have been previously detected in Martian meteorites1 and at Gale crater, Mars2-4. Evaluating the diversity and detectability of organic matter elsewhere on Mars is important for understanding the extent and diversity of Martian surface processes and the potential availability of carbon sources1,5,6. Here we report the detection of Raman and fluorescence spectra consistent with several species of aromatic organic molecules in the Máaz and Séítah formations within the Crater Floor sequences of Jezero crater, Mars. We report specific fluorescence-mineral associations consistent with many classes of organic molecules occurring in different spatial patterns within these compositionally distinct formations, potentially indicating different fates of carbon across environments. Our findings suggest there may be a diversity of aromatic molecules prevalent on the Martian surface, and these materials persist despite exposure to surface conditions. These potential organic molecules are largely found within minerals linked to aqueous processes, indicating that these processes may have had a key role in organic synthesis, transport or preservation.

Challenges in ageing persons with haemophilia.

As treatments for individuals with inherited bleeding disorders improve, life expectancy increases and is approaching that of the normal population. Concomitant with this we are now seeing the problems of ageing in the bleeding disorder population. Although the clear-cut association between low clotting factor levels and risk of bleeding is well recognised, a relationship between high levels, some non-factor therapies and thrombotic risk also exists. The management of thrombosis in persons with inherited bleeding disorders is complex but manageable with modern treatments and collaboration in decision making between health care professionals and patients. Despite the improvements in treatment and reduction in bleeding, mostly musculoskeletal pain continues to be a major issue with advancing age. The management of pain amongst older people with haemophilia who may have multiple comorbidities should involve a person-centred, holistic, multi-disciplinary approach to support and optimise long-term physical functioning and overall quality of life.

Inequities in access to palliative and end-of-life care in the black population in Canada: a scoping review.

BACKGROUND: Improving equity and early access to palliative care for underserved populations in Canada is a priority. Little is known regarding access to palliative and end-of-life care in the Black population. METHODS: We undertook a scoping review using the framework by Arksey and O'Malley to identify knowledge, access gaps, and experiences of palliative and end-of-life care among Blacks living with life-limiting illnesses in Canada. Primary studies, discussion papers, books, and reports were considered eligible. We followed a comprehensive search strategy developed by an information scientist. Searches were performed in the following bibliographic databases: Medline, EMBASE, PsycINFO via OVID, CINAHL via EBSCOhost, Scopus and Cochrane Library via Wiley. The search strategy was derived from three main concepts: (1) Black people; (2) Canada and Canadian provinces; (3) Palliative, hospice, or end-of-life care. No publication date or language limits were applied. Titles and abstracts were screened for eligibility by one reviewer and full text by two independent reviewers. RESULTS: The search yielded 233 articles. Nineteen articles were selected for full-text review, and 7 articles met the inclusion criteria. These studies were published between 2010 and 2021, and conducted in the provinces of Ontario and Nova Scotia only. Studies used both quantitative and qualitative methods and included cancer decedents, next of kin, family caregivers and religious leaders. Sample sizes in various studies ranged from 6 - 2,606 participants. Included studies reported a general lack of understanding about palliative and end-of-life care, positive and negative experiences, and limited access to palliative and end-of-life care for Blacks, across all care settings. CONCLUSION: Findings suggest limited knowledge of palliative care and inequities in access to palliative and end-of-life care for Blacks living with life-limiting illnesses in 2 Canadian provinces. There is an urgent need for research to inform tailored and culturally acceptable strategies to improve understanding and access to palliative care and end-of-life care among Blacks in Canada.

Community Group-Based Physical Activity Programs for Immigrant Older Adults: A Systematic Realist Review.

Physical activity program interventions often lack sensitivity to the needs of older immigrant adults. The objective of this systematic realist review is to explain how, why, for whom, and under which circumstances community group-based physical activity programs work for immigrant older adults. The initial program theory was developed using prior research, team expertise, social cognitive theory, and knowledge user consultations. The program theory was tested and refined via a systematic review of the literature. Database searches were conducted in MEDLINE, EMBASE, CINAHL, Scopus, Cochrane Library, Sports Medicine and Education Index, and SPORTDiscus. A total of 22 sources of evidence met inclusion criteria and included intervention studies, systematic reviews, and a discussion paper. Intervention studies were appraised using the Mixed Methods Appraisal Tool. The final program theory constituted eight context-mechanism-outcome configurations that highlight the importance of facilitator characteristics, access to safe spaces, group dynamics, and social support. A limitation was the small number and variable quality of included evidence. Physical activity programs that target immigrant older adults must strengthen physical and psychological safety and maximize opportunities for role modeling and socialization. This research was supported by the Alberta Health Services Seniors Health Strategic Clinical Network and is registered in PROSPERO (ID#258179).

Physical activity, physical fitness and cardiometabolic risk amongst adults with moderate and severe haemophilia.

AIM: This study aimed to examine physical activity (PA), physical fitness and cardiometabolic risk amongst people with moderate and severe haemophilia (PwMSH). METHODS: The following domains were examined: PA (accelerometry); functional aerobic capacity (6-Minute Walk Test); grip strength (dynamometry); balance (One Leg Stand Test); body composition (anthropometry and bioimpedance analysis); blood pressure; arterial stiffness; and cardiometabolic disorders. RESULTS: A total of 53 PwMSH (44 years) and 33 controls (43 years; p = .679) were recruited. Compared to controls, PwMSH were significantly less active in moderate and vigorous PA parameters (all p < .05), and less physically fit indicated by 6-Minute Walk distance (p < .0005), grip strength (p = .040) and balance (p < .0005). PwMSH had higher rates of abdominal adiposity compared to controls measured by waist circumference indices (all p < .05). Resting blood pressure and arterial stiffness were not significantly different (p = .797 and .818, respectively). With respect to overall PA, World Health Organisation recommended targets for adults were achieved by the majority of both groups (haemophilia: 72.9% vs. controls: 90.0%; p = .069). Importantly, the number of PwMSH who achieved guideline recommended PA via longer, sustained bouts of moderate-vigorous PA was significantly lower compared to controls (18.8% vs. 56.7%; p = .001). Lastly, clinically diagnosed hypertension, insulin resistance and hyperlipidaemia were more prevalent amongst PwMSH compared to controls. CONCLUSION: Low levels of PA and physical fitness, and significant rates of abdominal adiposity and hypertension may collectively influence the risk and severity of various cardiometabolic and/or musculoskeletal health issues amongst ageing PwMSH. Personalised multi-disciplinary health interventions involving PA, dietary and health psychology input for PwMSH warrant future investigation.

A cross-sectional follow-up study of physical activity in adults with moderate and severe haemophilia.

AIM: To conduct a cross-sectional follow-up assessment of physical activity (PA) in people with moderate and severe haemophilia (PwMSH) from the Irish Personalised Approach to the Treatment of Haemophilia (iPATH) study. METHODS: Between June-December 2021, participants' PA was measured over one week using accelerometery, and was compared with their previously measured data from the original iPATH assessment. Self-awareness of PA and the impact of the Covid-19 pandemic on PA, pain, mobility and function were retrospectively examined using a survey. RESULTS: Of 30 participants who returned surveys [n = 19, severe (FVIII, <.01 IU/mL); n = 4, moderate (FVIII, .01-.05 IU/mL); n = 7, severe (FIX, <.01 IU/mL); age: 47 (36, 55) years], 28 completed accelerometery (follow-up time: 3 years). There were no significant differences in accelerometer PA (all p > .05), but achievement of World Health Organisation guidelines increased (67.9%-75.0%; p = .646). Increased self-awareness of PA was reported by 76.7%, and 66.7% reported desires to become more physically active. Compared to normal, most reported either no differences or lower levels of PA during lockdown restrictions. Self-reported PA increased for most when restrictions eased from April 2021 onwards. Beyond the pandemic, concerns included pain and access to exercise resources. CONCLUSION: Self-reported PA throughout the pandemic was variable, whilst there were no significant differences in objectively measured PA between assessment periods, despite reports of increased self-awareness and desires to be physically active at follow-up. Further qualitative research is needed to design personalised PA and health interventions, capturing perspectives of patients, their families, and multi-disciplinary haemophilia healthcare providers.

Synchronous Web-Based Psychotherapy for Mental Disorders From a Health Quality Perspective: Scoping Review.

BACKGROUND: The COVID-19 pandemic necessitated rapid changes to health care delivery, including a shift from in-person to digitally delivered psychotherapy. While these changes helped ensure timely psychotherapy provision, many concerns exist, including clinical, cultural, practical, privacy, and security issues. OBJECTIVE: This scoping review systematically mapped existing peer-reviewed research on synchronous, therapist-delivered web-based psychotherapy for individuals with a diagnosed mental illness. Data were analyzed through the lens of the Alberta Quality Matrix for Health (AQMH) to assess to what degree this literature addresses key indicators of health care quality. This analysis aided in the identification and organization of knowledge gaps with regard to web-based psychotherapies, highlighting potential disparities between previously prioritized dimensions of care and those requiring further attention. METHODS: This review adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines. We included peer-reviewed primary research studies in the English language investigating synchronous, therapist-delivered remote psychotherapy delivered to adults (aged 18 years and older) with a Diagnostic and Statistical Manual of Mental Disorders or International Statistical Classification of Diseases diagnosed mental illness. All other citations were excluded. Relevant studies were identified through MEDLINE, APA PsycINFO, Embase (OVID), Web of Science: Core Collection (Clarivate), Cochrane Library (Wiley), and Scopus (Elsevier) databases. Databases were searched on March 18, 2021. For every publication that was taken into consideration, the data were charted independently by 2 reviewers, and in the event of a discrepancy, the principal investigator validated the choice of either extractor. Results were thematically described according to the 6 AQMH dimensions: acceptability, accessibility, appropriateness, effectiveness, efficiency, and safety. RESULTS: From 13,209 publications, 48 articles were included, largely from North American studies. Most studies measured treatment effectiveness (n=48, 100%) and acceptability (n=29, 60%) health quality dimensions. Over 80% (40/48) of studies investigated either a cognitive or exposure intervention for either posttraumatic stress disorder or a mood or anxiety disorder, generally indicating comparable results to in-person therapy. Safety (n=5, 10%) was measured in fewer studies, while treatment accessibility, appropriateness, and efficiency were not explicitly measured in any study, although these dimensions were mentioned as a future direction, hypothesis, or potential outcome. CONCLUSIONS: In relation to web-based therapist-delivered psychotherapies for those with a diagnosed mental illness, important aspects of health care quality (accessibility, appropriateness, efficiency, and safety) have received little scientific examination, underscoring a need to address these gaps. There are also significant issues related to the generalizability of this literature, including the underrepresentation of many geographic regions, cultures, populations, clinical contexts, and psychotherapy modalities. Qualitative research in underrepresented populations and settings may uncover important patient and contextual factors important for the future implementation of quality web-based psychotherapy.

A Scoping Review on Community-Based Programs to Promote Physical Activity in Older Immigrants.

Older immigrants are at higher risks for inactivity due to cultural, environmental, and social barriers in the postmigration context. Community-based physical activity (PA) programs increase PA in older adults, yet little is known about approaches that specifically target older immigrants. This scoping review explores the literature on community-based programs that increase PA and physical fitness in immigrant older adults and identifies barriers and facilitators to PA program participation in this population. A systematic search of electronic databases and gray literature was conducted, and a total of 11 articles met the inclusion criteria after full-text screening. A range of populations and PA program characteristics are described, yet there is a lack of studies on older immigrant men, Black older immigrants, and immigrants from Arab and African countries. There is a need for further research to develop evidence-informed PA programs for this diverse population.

Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10-/- Mice.

BACKGROUND & AIMS: Perturbations in the early-life gut microbiome are associated with increased risk for complex immune disorders like inflammatory bowel diseases. We previously showed that maternal antibiotic-induced gut dysbiosis vertically transmitted to offspring increases experimental colitis risk in interleukin (IL) 10 gene deficient (IL10-/-) mice, a finding that may result from the loss/lack of essential microbes needed for appropriate immunologic education early in life. Here, we aimed to identify key microbes required for proper development of the early-life gut microbiome that decrease colitis risk in genetically susceptible animals. METHODS: Metagenomic sequencing followed by reconstruction of metagenome-assembled genomes was performed on fecal samples of IL10-/- mice with and without antibiotic-induced dysbiosis to identify potential missing microbial members needed for immunologic education. One high-value target strain was then engrafted early and/or late into the gut microbiomes of IL10-/- mice with antibiotic-induced dysbiosis. RESULTS: Early-, but not late-, life engraftment of a single dominant Bacteroides strain of non-antibiotic-treated IL10-/- mice was sufficient to restore the development of the gut microbiome, promote immune tolerance, and prevent colitis in IL10-/- mice that had antibiotic-induced dysbiosis. CONCLUSIONS: Restitution of a keystone microbial strain missing in the early-life antibiotic-induced gut dysbiosis results in recovery of the microbiome, proper development of immune tolerance, and reduced risk for colitis in genetically prone hosts.

Incentive-Based Sexually Transmitted and Blood-Borne Infections Screening in High-Income Countries: A Systematic Review.

BACKGROUND: Despite increasing access to treatment and screening, rates of sexually transmitted and blood-borne infections (STBBI) continue to rise in high-income countries. The high cost of undiagnosed and untreated STBBI negatively affects individuals, health care systems, and societies. The use of monetary and nonmonetary incentives may increase STBBI screening uptake in high-income countries. Incentivized screening programs are most effective when developed specific to context and target population. METHODS: Our review was performed according to the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement and the Cochrane Handbook for Systematic Reviews of Interventions. Inclusion criteria were as follows: English language, high-income countries, primary research studies, and older than 16 years. Study quality was assessed using Joanna Briggs Institute quality assessment tools. RESULTS: The search yielded 6219 abstracts. Thirteen articles met the inclusion criteria. Studies took place in the United States, the United Kingdom, and Australia. Populations screened included: postsecondary and tertiary students, parolees or probationers, youth, and inner-city emergency department patients. Incentivized STBBI screened were human immunodeficiency virus (n = 5), chlamydia (n = 7), and multiple infections (n = 1). Incentives offered were monetary (cash/gift cards/not specified) (n = 10), nonmonetary (n = 1), and mixed (n = 2). Both monetary and nonmonetary incentives enhance STBBI screening in high-income countries. CONCLUSION: Incentivized screening programs are most effective when developed specific to context and target population. Further research is needed to analyze incentivized screening across similar study designs and to evaluate long-term effectiveness.

Pain and functional disability amongst adults with moderate and severe haemophilia from the Irish personalised approach to the treatment of haemophilia (iPATH) study.

OBJECTIVES: To establish the prevalence of pain and functional disability in Irish adults with moderate and severe haemophilia, and to examine demographic and lifestyle influences. METHODS: Males ≥18 years with moderate or severe haemophilia participated. Pain and function were examined using the PROBE questionnaire. RESULTS: Of 49 participants [median age 44 (IQR 32, 52) years], most had severe haemophilia (Factor VIII = 30; Factor IX = 13) and were on regular prophylaxis (88%). Those with moderate haemophilia (Factor VIII = 5; Factor IX = 1) treated on demand (12%). Acute (72%) and chronic pain (71%), functional difficulties (58%), and analgesic requirements (92%) were prevalent. Age was significantly associated with more advanced haemophilic arthropathy (p = .002), chronic pain (p = .029) and functional difficulties (p = .036). Adults who reported chronic pain commenced prophylaxis significantly later in life [32 (20, 51) vs. 8 (1, 23) years; p = .004]. Physical activity was significantly lower in those with functional difficulties (p < .05). A disparity between self-perceived 'target joints' and clinically defined target joints was also identified (76% vs. 23%). CONCLUSION: Haemophilic arthropathy, pain and functional disability were prevalent amongst Irish adults with moderate and severe haemophilia. Age-dependent lifestyle, analgesic and treatment influences on pain and function warrant further investigation.

Improvement in cognitive impairment following a 12-week aerobic exercise intervention in individuals with non-cirrhotic chronic hepatitis C.

Cognitive impairment occurs in 30%-50% of patients with non-cirrhotic chronic hepatitis C virus (HCV) infection. Exercise is beneficial in preventing and treating cognitive impairment and cardiometabolic abnormalities in many chronic inflammatory diseases, but there are few studies investigating the impact of exercise in HCV infection. The study aimed to assess the effect of a 12-week aerobic exercise intervention on cognition and extrahepatic manifestations in individuals with HCV. In this nonrandomized controlled pilot study, individuals with HCV participated in a 12-week aerobic exercise intervention. Outcome measures included cognition (Montreal Cognitive Assessment [MOCA], Trail Making Test A & B [TMT-A; TMT-B], Digit Symbol Test [DST]), cardiorespiratory fitness (estimated V˙O2max ), physical activity (accelerometry), anthropometry, quality of life (depression; fatigue; sleep quality) and biochemical markers. Outcomes were assessed at baseline (T0), intervention completion (T1) and 12 weeks after intervention completion (T2). Thirty-one patients completed the study (exercise group n = 13, control group n = 18). In the exercise group, cognition improved at T1 in the TMT-A (31% mean improvement, p = 0.019), TMT-B (15% mean improvement, p = 0.012) time and MOCA (14% mean improvement, p ≤ 0.001). These improvements were not maintained at T2. Depression (p = 0.038), sleep quality (p = 0.002), fatigue (p = 0.037) and estimated V˙O2max (7.8 mL kg-1  min-1 [22%] mean increase, p = 0.004) also improved at T1. In conclusion, this study demonstrates the benefits of a 12-week aerobic exercise intervention in improving cognition, quality of life and cardiorespiratory fitness in individuals with HCV. Larger studies are needed to confirm these findings and strategies for continued exercise engagement in individuals with HCV are warranted for sustained benefits.

A systematic review of physical activity in people with haemophilia and its relationship with bleeding phenotype and treatment regimen.

INTRODUCTION: Although the measurement of physical activity (PA) amongst people with haemophilia (PWH) has become increasingly widespread in recent years, the relationship between PA and bleeding phenotype remains poorly understood. In addition, the influence of various treatment regimens on this relationship has not been defined. AIM: This review aimed to systematically assess the data that are available regarding PA levels amongst PWH, as well as the relationship between PA and bleeding. METHODS: A systematic search of the online databases EMBASE, Cochrane, MEDLINE Ovid, CINAHL and Web of Science was conducted by two independent reviewers. Quality assessment was undertaken using the AXIS Critical Appraisal Tool for Cross-sectional Studies and the STROBE checklist. RESULTS: Of 1902 sources identified overall, 36 articles were included. Low-to-moderate transparency of reporting and various sources of bias were identified. PA levels varied amongst heterogeneous samples of PWH. The relationship between PA and bleeds was inconclusive, although there was evidence that improvements in treatment over recent decades have appeared to enable PWH to become more physically active. CONCLUSION: Based upon the limited available evidence, the relationship between PA and bleeding phenotype in PWH remains unclear. However, with the development of improved prophylaxis treatment regimens in recent years, there is evidence that PA levels have increased, especially amongst people with severe haemophilia. The use of validated outcome measures of PA and more robust reporting of bleeds and treatment regimen are warranted in future research, especially in a rapidly evolving era of new treatments for PWH.

Tools for assessment of acute psychological distress in critical illness: A scoping review.

OBJECTIVES: Patients' experience of psychological distress in the intensive care unit (ICU) is associated with adverse effects, reduced satisfaction, and delayed physical and psychological recovery. There are no specific guidelines for the assessment and management of acute psychological distress during hospitalisation in the ICU. We reviewed existing tools for the assessment of acute psychological distress in ICU patients, examined evidence on their metric properties, and identified potential gaps and methodological considerations. METHOD: A scoping review based on literature searches (Cumulative Index to Nursing and Allied Health Literature, Medical Literature Analysis and Retrieval System Online, Excerpta Medica Database, PsycINFO, Scopus, Health and Psychosocial Instruments, Dissertations and Theses Global, and Google Scholar) and predefined eligibility criteria was conducted as per current scoping review guidelines. FINDINGS: Overall, 14 assessment tools were identified having been developed in diverse ICU settings. The identified tools assess mainly anxiety and depressive symptoms and ICU stressors, and investigators have reported various validity and reliability metrics. It was unclear whether available tools can be used in specific groups, such as noncommunicative patients and patients with delirium, brain trauma, stroke, sedation, and cognitive impairments. CONCLUSION: Available tools have methodological limitations worth considering in future investigations. Given the high prevalence of psychiatric morbidity in ICU survivors, rigorously exploring the metric integrity of available tools used for anxiety, depressive, and psychological distress symptom assessment in the vulnerable ICU population is a practice and research priority. RELEVANCE TO CLINICAL PRACTICE: These results have implications for the selection and implementation of psychological distress assessment methods as a means for promoting meaningful patient-centred clinical outcomes and humanising ICU care experiences.

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism.

In Neurospora crassa, the transcription factor COL-26 functions as a regulator of glucose signaling and metabolism. Its loss leads to resistance to carbon catabolite repression. Here, we report that COL-26 is necessary for the expression of amylolytic genes in N. crassa and is required for the utilization of maltose and starch. Additionally, the Δcol-26 mutant shows growth defects on preferred carbon sources, such as glucose, an effect that was alleviated if glutamine replaced ammonium as the primary nitrogen source. This rescue did not occur when maltose was used as a sole carbon source. Transcriptome and metabolic analyses of the Δcol-26 mutant relative to its wild type parental strain revealed that amino acid and nitrogen metabolism, the TCA cycle and GABA shunt were adversely affected. Phylogenetic analysis showed a single col-26 homolog in Sordariales, Ophilostomatales, and the Magnaporthales, but an expanded number of col-26 homologs in other filamentous fungal species. Deletion of the closest homolog of col-26 in Trichoderma reesei, bglR, resulted in a mutant with similar preferred carbon source growth deficiency, and which was alleviated if glutamine was the sole nitrogen source, suggesting conservation of COL-26 and BglR function. Our finding provides novel insight into the role of COL-26 for utilization of starch and in integrating carbon and nitrogen metabolism for balanced metabolic activities for optimal carbon and nitrogen distribution.

Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics.

Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a well-resolved phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but was unable to resolve higher-level organization of groups. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity, biology, and evolution.

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data.

Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.

Genome-wide analysis of lectin receptor-like kinases in Populus.

BACKGROUND: Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants. RESULTS: Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs. CONCLUSIONS: This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.

Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.

The genus Amanita encompasses both symbiotic, ectomycorrhizal fungi and asymbiotic litter decomposers; all species are derived from asymbiotic ancestors. Symbiotic species are no longer able to degrade plant cell walls. The carbohydrate esterases family 1 (CE1s) is a diverse group of enzymes involved in carbon metabolism, including decomposition and carbon storage. CE1 genes of the ectomycorrhizal A. muscaria appear diverged from all other fungal homologues, and more similar to CE1s of bacteria, suggesting a horizontal gene transfer (HGT) event. In order to test whether AmanitaCE1s were acquired horizontally, we built a phylogeny of CE1s collected from across the tree of life, and describe the evolution of CE1 genes among Amanita and relevant lineages of bacteria. CE1s of symbiotic Amanita were very different from CE1s of asymbiotic Amanita, and are more similar to bacterial CE1s. The protein structure of one CE1 gene of A. muscaria matched a depolymerase that degrades the carbon storage molecule poly((R)-3-hydroxybutyrate) (PHB). Asymbiotic Amanita do not carry sequence or structural homologues of these genes. The CE1s acquired through HGT may enable novel metabolisms, or play roles in signaling or defense. This is the first evidence for the horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal fungi.