The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae.

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.

The human fungal pathogen Aspergillus fumigatus can produce the highest known number of meiotic crossovers.

Sexual reproduction involving meiosis is essential in most eukaryotes. This produces offspring with novel genotypes, both by segregation of parental chromosomes as well as crossovers between homologous chromosomes. A sexual cycle for the opportunistic human pathogenic fungus Aspergillus fumigatus is known, but the genetic consequences of meiosis have remained unknown. Among other Aspergilli, it is known that A. flavus has a moderately high recombination rate with an average of 4.2 crossovers per chromosome pair, whereas A. nidulans has in contrast a higher rate with 9.3 crossovers per chromosome pair. Here, we show in a cross between A. fumigatus strains that they produce an average of 29.9 crossovers per chromosome pair and large variation in total map length across additional strain crosses. This rate of crossovers per chromosome is more than twice that seen for any known organism, which we discuss in relation to other genetic model systems. We validate this high rate of crossovers through mapping of resistance to the laboratory antifungal acriflavine by using standing variation in an undescribed ABC efflux transporter. We then demonstrate that this rate of crossovers is sufficient to produce one of the common multidrug resistant haplotypes found in the cyp51A gene (TR34/L98H) in crosses among parents harboring either of 2 nearby genetic variants, possibly explaining the early spread of such haplotypes. Our results suggest that genomic studies in this species should reassess common assumptions about linkage between genetic regions. The finding of an unparalleled crossover rate in A. fumigatus provides opportunities to understand why these rates are not generally higher in other eukaryotes.

Honey bees infer source location from the dances of returning foragers.

Honeybees (Apis mellifera carnica) communicate the direction and distance to a food source by means of a waggle dance. We ask whether bees recruited by the dance use it only as a flying instruction, with the technical form of a polar vector, or also translate it into a location vector that enables them to set courses directed toward the food source from arbitrary locations within their familiar territory. The flights of recruits captured on exiting the hive and released at distant sites were tracked by radar. The recruits performed first a straight flight in approximately the compass direction indicated by the dance. However, this "vector" portion of their flights and the ensuing tortuous "search" portion were strongly and differentially affected by the release site. Searches were biased toward the true location of the food and away from the location specified by translating the origin for the danced polar vector to the release site. We conclude that by following the dance recruits get two messages, a polar flying instruction (bearing and range from the hive) and a location vector that enables them to approach the source from anywhere in their familiar territory. The dance communication is much richer than thought so far.

Biophysical and structural characterization of the impacts of MET phosphorylation on tepotinib binding.

The receptor tyrosine kinase MET is activated by hepatocyte growth factor binding, followed by phosphorylation of the intracellular kinase domain (KD) mainly within the activation loop (A-loop) on Y1234 and Y1235. Dysregulation of MET can lead to both tumor growth and metastatic progression of cancer cells. Tepotinib is a highly selective, potent type Ib MET inhibitor and approved for treatment of non-small cell lung cancer harboring METex14 skipping alterations. Tepotinib binds to the ATP site of unphosphorylated MET with critical π-stacking contacts to Y1230 of the A-loop, resulting in a high residence time. In our study, we combined protein crystallography, biophysical methods (surface plasmon resonance, differential scanning fluorimetry), and mass spectrometry to clarify the impacts of A-loop conformation on tepotinib binding using different recombinant MET KD protein variants. We solved the first crystal structures of MET mutants Y1235D, Y1234E/1235E, and F1200I in complex with tepotinib. Our biophysical and structural data indicated a linkage between reduced residence times for tepotinib and modulation of A-loop conformation either by mutation (Y1235D), by affecting the overall Y1234/Y1235 phosphorylation status (L1195V and F1200I) or by disturbing critical π-stacking interactions with tepotinib (Y1230C). We corroborated these data with target engagement studies by fluorescence cross-correlation spectroscopy using KD constructs in cell lysates or full-length receptors from solubilized cellular membranes as WT or activated mutants (Y1235D and Y1234E/1235E). Collectively, our results provide further insight into the MET A-loop structural determinants that affect the binding of the selective inhibitor tepotinib.

The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae.

Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibility (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad-spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non-host species. This phenomenon of resistance in L. saligna is called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant-pathogen interaction triggered by pathogen recognition receptors, including nucleotide-binding leucine-rich repeat (NLR) proteins and receptor-like kinases (RLKs). We report a chromosome-level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis of Bremia-infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidates for determinants of the NHR phenotype of L. saligna.

Use of EQ-5D-5L for Assessing Patient-Reported Outcomes in a National Register for Specialized Rehabilitation.

OBJECTIVE: To compare problems reported on EQ-5D-5L dimensions, index, and EQ visual analog scale (VAS) scores in patients receiving specialized rehabilitation in Norway with general population norms. DESIGN: Multicenter observational study. SETTING: Five specialist rehabilitation facilities participating in a national rehabilitation register between March 11, 2020, and April 20, 2022. PARTICIPANTS: 1167 inpatients admitted (N=1167), with a mean age of 56.1 (range, 18-91) years; 43% were female. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: EQ-5D-5L dimension, index, and EQ VAS scores. RESULTS: At admission, mean±SD EQ-5D-5L index scores were 0.48 (0.31) compared to 0.82 (0.19) for general population norms. EQ VAS scores were 51.29 (20.74) compared to 79.46 (17.53) for population norms. Together with those for the 5 dimensions, these differences were all statistically significant (P<.01). Compared to population norms, patients undergoing rehabilitation had more health states as assessed by the 5 dimensions (550 vs 156) and EQ VAS (98 vs 49). As hypothesized, EQ-5D-5L scores were associated with number of diagnoses, admission to/from secondary care, and help with completion. At discharge there were statistically significant improvements in all EQ-5D-5L scores that compare favorably with available estimates for minimal important differences. CONCLUSIONS: The large deviations in scores at admission and score changes at discharge lend support to EQ-5D-5L application in national quality measurement. Evidence for construct validity was found through associations with number of secondary diagnoses and help with completion.

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency.

Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.

Evaluation of Gas 6 as a Prognostic Marker in Papillary Renal Cell Carcinoma.

INTRODUCTION: Growth arrest-specific protein 6 (Gas 6) is a ligand that plays a role in proliferation and migration of cells. For several tumor entities, high levels of Gas 6 are associated with poorer survival. We examined the prognostic role of Gas 6 in renal cell carcinoma (RCC), especially in papillary RCC (pRCC), which is still unclear. METHODS: The patients' sample collection is a joint collaboration of the PANZAR consortium. Patients' medical history and tumor specimens were collected from n = 240 and n = 128 patients with type 1 and 2 pRCC, respectively. Expression of Gas 6 was determined by immunohistochemistry. RESULTS: In total, Gas 6 staining was evaluable in 180 of 240 type 1 and 110 of 128 type 2 pRCC cases. Kaplan-Meier analysis disclosed no significant difference in 5-year overall survival for all pRCC nor either subtype. Also, Gas+ and Gas- groups did not significantly differ in any tumor or patient characteristics. CONCLUSION: Gas 6 was not found to be an independent prognostic marker in pRCC. Future studies are warranted to determine if Gas 6 plays a role as prognostic marker or therapeutic target in pRCC.

Hepatic Global Transcriptomic Profiles of Holstein Cows According to Parity Reveal Age-Related Changes in Early Lactation.

Cows can live for over 20 years, but their productive lifespan averages only around 3 years after first calving. Liver dysfunction can reduce lifespan by increasing the risk of metabolic and infectious disease. This study investigated the changes in hepatic global transcriptomic profiles in early lactation Holstein cows in different lactations. Cows from five herds were grouped as primiparous (lactation number 1, PP, 534.7 ± 6.9 kg, n = 41), or multiparous with lactation numbers 2-3 (MP2-3, 634.5 ± 7.5 kg, n = 87) or 4-7 (MP4-7, 686.6 ± 11.4 kg, n = 40). Liver biopsies were collected at around 14 days after calving for RNA sequencing. Blood metabolites and milk yields were measured, and energy balance was calculated. There were extensive differences in hepatic gene expression between MP and PP cows, with 568 differentially expressed genes (DEGs) between MP2-3 and PP cows, and 719 DEGs between MP4-7 and PP cows, with downregulated DEGs predominating in MP cows. The differences between the two age groups of MP cows were moderate (82 DEGs). The gene expression differences suggested that MP cows had reduced immune functions compared with the PP cows. MP cows had increased gluconeogenesis but also evidence of impaired liver functionality. The MP cows had dysregulated protein synthesis and glycerophospholipid metabolism, and impaired genome and RNA stability and nutrient transport (22 differentially expressed solute carrier transporters). The genes associated with cell cycle arrest, apoptosis, and the production of antimicrobial peptides were upregulated. More surprisingly, evidence of hepatic inflammation leading to fibrosis was present in the primiparous cows as they started their first lactation. This study has therefore shown that the ageing process in the livers of dairy cows is accelerated by successive lactations and increasing milk yields. This was associated with evidence of metabolic and immune disorders together with hepatic dysfunction. These problems are likely to increase involuntary culling, thus reducing the average longevity in dairy herds.

Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map.

Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions and their putative trans-targets, we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.

The Prognostic Impact of PD-L2 in Papillary Renal-Cell Carcinoma.

INTRODUCTION: Programmed death-1 ligand (PD-L1) has been often studied in different types of renal-cell carcinoma (RCC). For example, in clear-cell renal carcinoma it is well established that programmed death-1 receptor and PD-L1 are important prognostic markers. In contrast, the role of programmed death-2 ligand (PD-L2) as prognostic marker remains unclear. The aim of this study was to evaluate if PD-L2 expression could play a role as a prognostic marker for papillary RCC (pRCC). METHODS: The patients' sample collection was a joint collaboration of the PANZAR consortium. Patients' medical history and tumor specimens were collected from n = 240 and n = 128 patients with type 1 and 2 pRCC, respectively. Expression of PD-L2 was determined by immunohistochemistry. In total, PD-L2 staining was evaluable in 185 of 240 type 1 and 99 of 128 type 2 pRCC cases. RESULTS: PD-L2 staining was positive in 67 (36.2%) of type 1 and in 31 (31.3%) of type 2 pRCC specimens. The prevalence of PD-L2+ cells was significantly higher in high-grade type 1 tumors (p = 0.019) and in type 2 patients with metastasis (p = 0.002). Kaplan-Meier analysis disclosed significant differences in 5-year overall survival (OS) for patients with PD-L2- compared to PD-L2+ in pRCC type 1 of 88.4% compared to 73.6% (p = 0.039) and type 2 of 78.8% compared to 39.1% % (p < 0.001). However, multivariate analysis did not identify the presence of PD-L2+ cells neither in type 1 nor type 2 pRCC as an independent predictor of poor OS. DISCUSSION/CONCLUSION: PD-L2 expression did not qualify as an independent prognostic marker in pRCC. Future studies will have to determine whether anti-PD-L2-targeted treatment may play a role in pRCC and expression can potentially serve as a predictive marker for these therapeutic approaches.

Effects of High-Intensity Interval Training After Stroke (The HIIT Stroke Study) on Physical and Cognitive Function: A Multicenter Randomized Controlled Trial.

OBJECTIVE: To assess the effects of high-intensity interval training (HIIT) on physical, mental, and cognitive functioning after stroke. DESIGN: The HIIT Stroke Study was a single-blind, multicenter, parallel-group randomized controlled trial. SETTING: Specialized rehabilitation units at 3 Norwegian hospitals. PARTICIPANTS: Adult stroke survivors (N=70) 3 months to 5 years after a first-ever stroke. Mean age was 57.6±9.2 years and 58.7±9.2 years in the intervention and control groups, respectively. INTERVENTIONS: Participants were randomized to standard care in combination with 4×4 minutes of treadmill HIIT at 85%-95% of peak heart rate or standard care only. OUTCOMES: Outcomes were measured using physical, mental, and cognitive tests and the FIM and Stroke Impact Scale. Linear mixed models were used to analyze differences between groups at posttest and 12-month follow-up. RESULTS: The intervention group showed a significant treatment effect (95% confidence interval [CI]) from baseline to posttest on a 6-minute walk test of 28.3 (CI, 2.80-53.77) meters (P=.030); Berg Balance Scale 1.27 (CI, 0.17-2.28) points (P=.025); and Trail Making Test Part B (TMT-B; -24.16 [CI, -46.35 to -1.98] s, P=.033). The intervention group showed significantly greater improvement on TMT-B at the 12-month follow-up (25.44 [CI, -49.01 to -1.87] s, P=.035). The control group showed significantly greater improvement in total Functional Independence Measure score with a treatment effect of -2.37 (CI, -4.30 to -0.44) points (P=.016) at 12-month follow-up. No significant differences were identified between groups on other outcomes at any time point. CONCLUSIONS: HIIT combined with standard care improved walking distance, balance, and executive function immediately after the intervention compared with standard care only. However, only TMT-B remained significant at the 12-month follow-up.

Changes in cardiorespiratory fitness and activity levels over the first year after discharge in ambulatory persons with recent incomplete spinal cord injury.

STUDY DESIGN: Secondary analysis of a clinical trial. OBJECTIVES: To investigate changes in cardiorespiratory fitness (CRF) and activity level in ambulatory persons with SCI during the first year after discharge from inpatient rehabilitation. SETTING: Sunnaas Rehabilitation Hospital, Nesoddtangen, Norway. METHODS: Thirty persons with incomplete SCI, all community walkers (25 males and 5 females, 18-69 years old) were recruited to a clinical trial of a 12 weeks home-based aerobic exercise program of either high or moderate intensity. During the last week of inpatient rehabilitation (baseline), participants performed a maximal exercise test on a treadmill (peak oxygen uptake; peak VO2) and a 6-min walking test (6MWT). Also, total daily energy expenditure (TDEE) and daily amount of steps were measured continuously during 7 days in the participants' homes. All tests were repeated after 3 and 12 months (post tests). RESULTS: Twenty of the 30 clinical trial participants performed baseline and both posttests and are included in this secondary analysis. We found no statistically significant between-group differences in the time course over the first year of either peak VO2, 6MWT, or physical activity outcomes. Therefore, data from both exercise groups and the control group were merged for secondary analyses, revealing statistically significant increase over time in peak VO2, 6MWT, and TDEE. The increase over time in the average daily steps did not reach statistical significance. CONCLUSIONS: Ambulatory persons with SCI were able to increase their CRF levels over the first year after discharge from inpatient rehabilitation, despite a minimal increase in activity levels.

Genome-Wide Association Mapping Reveals That Specific and Pleiotropic Regulatory Mechanisms Fine-Tune Central Metabolism and Growth in Arabidopsis.

Central metabolism is a coordinated network that is regulated at multiple levels by resource availability and by environmental and developmental cues. Its genetic architecture has been investigated by mapping metabolite quantitative trait loci (QTL). A more direct approach is to identify enzyme activity QTL, which distinguishes between cis-QTL in structural genes encoding enzymes and regulatory trans-QTL. Using genome-wide association studies, we mapped QTL for 24 enzyme activities, nine metabolites, three structural components, and biomass in Arabidopsis thaliana We detected strong cis-QTL for five enzyme activities. A cis-QTL for UDP-glucose pyrophosphorylase activity in the UGP1 promoter is maintained through balancing selection. Variation in acid invertase activity reflects multiple evolutionary events in the promoter and coding region of VAC-INVcis-QTL were also detected for ADP-glucose pyrophosphorylase, fumarase, and phosphoglucose isomerase activity. We detected many trans-QTL, including transcription factors, E3 ligases, protein targeting components, and protein kinases, and validated some by knockout analysis. trans-QTL are more frequent but tend to have smaller individual effects than cis-QTL. We detected many colocalized QTL, including a multitrait QTL on chromosome 4 that affects six enzyme activities, three metabolites, protein, and biomass. These traits are coordinately modified by different ACCELERATED CELL DEATH6 alleles, revealing a trade-off between metabolism and defense against biotic stress.

Effects of High-Intensity Interval Training After Stroke (the HIIT-Stroke Study): A Multicenter Randomized Controlled Trial.

OBJECTIVE: To examine if 8 weeks of high-intensity interval training (HIIT) in addition to standard care would increase and maintain peak oxygen uptake (Vo2peak) more than standard care alone in patients with stroke. DESIGN: This was a single-blind, multicenter, parallel group, randomized controlled trial. SETTING: Specialized rehabilitation units at 3 Norwegian hospitals. PARTICIPANTS: Participants (N=70), 3 months to 5 years after first-ever stroke, were randomly assigned to the intervention group (n=36) or the control group (n=34); 42% were women, mean age was 57.6±9.3 years, mean time post stroke was 26.4±14.5 months. INTERVENTION: The intervention was 8 weeks: 3 times a week with HIIT treadmill training with work periods of 4 × 4 minutes at 85%-95% of peak heart rate interspersed with 3 minutes of active recovery at 50%-70% of peak heart rate. The control group received standard care according to national guidelines. OUTCOMES: The primary outcome, analyzed by intention-to-treat, was Vo2peak measured as liters per minute 12 months after inclusion. Secondary outcome measures were blood pressure and blood profile. RESULTS: Mean baseline Vo2peak was 2.63±1.08 L·min-1 vs 2.87±0.71 L·min-1, while at 12 months Vo2peak was 2.70±1.00 L·min-1 vs 2.67±0.76 L·min-1 (P=.068) in the intervention and control groups, respectively. There was a significant and greater improvement in the intervention group compared with the control group at 12 months in 3 of 6 secondary outcomes from the peak test but no significant differences for blood pressure or blood profile. CONCLUSIONS: The HIIT intervention, which was well-tolerated in this sample of well-functioning survivors of stroke, was not superior to standard care in improving and maintaining Vo2peak at the 12-month follow-up. However, secondary results from the peak test showed a significant improvement from before to immediately after the intervention.

The effect of augmented speech-language therapy delivered by telerehabilitation on poststroke aphasia-a pilot randomized controlled trial.

OBJECTIVE: Pilot a definitive randomized controlled trial of speech-language telerehabilitation in poststroke aphasia in addition to usual care with regard to recruitment, drop-outs, and language effects. DESIGN: Pilot single-blinded randomized controlled trial. SETTING: Telerehabilitation delivered from tertiary rehabilitation center to participants at their home or admitted to secondary rehabilitation centers. SUBJECTS: People with naming impairment due to aphasia following stroke. INTERVENTION: Sixty-two participants randomly allocated to 5 hours of speech and language telerehabilitation by videoconference per week over four consecutive weeks together with usual care or usual care alone. The telerehabilitation targeted functional, expressive language. MAIN MEASURES: Norwegian Basic Aphasia Assessment: naming (primary outcome), repetition, and auditory comprehension subtests; Verb and Sentence Test sentence production subtest and the Communicative Effectiveness Index at baseline, four weeks, and four months postrandomization. Data were analyzed by intention to treat. RESULTS: No significant between-group differences were seen in naming or auditory comprehension in the Norwegian Basic Aphasia Assessment at four weeks and four months post randomization. The telerehabilitation group (n = 29) achieved a Norwegian Basic Aphasia Assessment repetition score of 8.9 points higher (P = 0.026) and a Verb and Sentence Test score 3 points higher (P = 0.002) than the control group (n = 27) four months postrandomization. Communicative Effectiveness Index was not significantly different between groups, but increased significantly within both groups. No adverse events were reported. CONCLUSION: Augmented telerehabilitation via videoconference may be a viable rehabilitation model for aphasia affecting language outcomes poststroke. A definitive trial with 230 participants is needed to confirm results.

Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana.

Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions.

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana.

For crops that are grown for their fruits or seeds, elevated temperatures that occur during flowering and seed or fruit set have a stronger effect on yield than high temperatures during the vegetative stage. Even short-term exposure to heat can have a large impact on yield. In this study, we used Arabidopsis thaliana to study the effect of short-term heat exposure on flower and seed development. The impact of a single hot day (35°C) was determined in more than 250 natural accessions by measuring the lengths of the siliques along the main inflorescence. Two sensitive developmental stages were identified, one before anthesis, during male and female meiosis, and one after anthesis, during fertilization and early embryo development. In addition, we observed a correlation between flowering time and heat tolerance. Genome-wide association mapping revealed four quantitative trait loci (QTLs) strongly associated with the heat response. These QTLs were developmental stage specific, as different QTLs were detected before and after anthesis. For a number of QTLs, T-DNA insertion knockout lines could validate assigned candidate genes. Our findings show that the regulation of complex traits can be highly dependent on the developmental timing.

Implication of transcriptome profiling of spermatozoa for stallion fertility.

Poor fertility of breeding stallions is a recognised problem in the equine industry. The aim of the present study was to detect molecular pathways using two groups of stallions that differed in pregnancy rates as well as in the proportion of normal and motile spermatozoa. RNA was isolated from spermatozoa of each stallion and microarray data were analysed to obtain a list of genes for which transcript abundance differed between the groups (P ≤0.05, fold change ≥1.2). In all, there were 437 differentially expressed (DE) genes between the two groups (P ≤ 0.05, fold change ≥1.2). Next, the DE genes were analysed using Database for Annotation, Visualisation, and Integrated Discovery (DAVID). Finally, ingenuity pathways analysis (IPA) was used to identify top biological functions and significant canonical pathways associated with the DE genes. Analysis using the DAVID database showed significant enrichment in the gene ontology (GO) term 'RNA binding' (P=0.05) and in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway cytokine-cytokine receptor interaction (P=0.02). Furthermore, IPA analysis showed interconnected biological functions and canonical pathways involved in the regulation of spermatogenesis and male fertility. In addition, significantly enriched metabolic pathways were identified. In conclusion, the present study has identified, for the first time, molecular processes in stallion spermatozoa that could be associated with stallion fertility.

Assessment of Nociception and Pain in Participants in an Unresponsive or Minimally Conscious State After Acquired Brain Injury: The Relation Between the Coma Recovery Scale-Revised and the Nociception Coma Scale-Revised.

OBJECTIVES: To investigate the relation between consciousness and nociceptive responsiveness (ie, Nociception Coma Scale-Revised [NCS-R]), to examine the suitability of the NCS-R for assessing nociception in participants with disorders of consciousness (DOC), and to replicate previous findings on psychometric properties of the scale. DESIGN: Specialized DOC program. SETTING: Specialized DOC program and university hospitals. PARTICIPANTS: Participants (N=85) diagnosed with DOC. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: We prospectively assessed consciousness with the Coma Recovery Scale-Revised (CRS-R). Responses during baseline, non-noxious, and noxious stimulations were scored with the NCS-R and CRS-R oromotor and motor subscales. RESULTS: CRS-R total scores correlated with NCS-R total scores and subscores. CRS-R motor subscores correlated with NCS-R total scores and motor subscores, and CRS-R oromotor subscores correlated with NCS-R total scores as well as verbal and facial expression subscores. There was a difference between unresponsive wakefulness syndrome and minimally conscious state in the proportion of grimacing and/or crying participants during noxious conditions. We replicated previous findings on psychometric properties of the scale but found a different score as the best threshold for nociception. CONCLUSIONS: We report a strong relation between the responsiveness to nociception and the level of consciousness. The NCS-R seems to be a valuable tool for assessing nociception in an efficient manner, but additional studies are needed to allow recommendations for clinical assessment of subjective pain experience.