The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species.

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.

Combined exercise intervention in a mouse model of high-risk neuroblastoma: effects on physical, immune, tumor and clinical outcomes.

Background: Exercise might exert anti-tumoral effects in adult cancers but this question remains open in pediatric tumors, which frequently show a different biology compared to adult malignancies. We studied the effects of an exercise intervention on physical function, immune variables and tumoral response in a preclinical model of a highly aggressive pediatric cancer, high-risk neuroblastoma (HR-NB). Methods: 6-8-week-old male mice with orthotopically-induced HR-NB were assigned to a control (N = 13) or exercise (5-week combined [aerobic+resistance]) group (N = 17). Outcomes included physical function (cardiorespiratory fitness [CRF] and muscle strength), as well as related muscle molecular indicators, blood and tumor immune cell and molecular variables, tumor progression, clinical severity, and survival. Results: Exercise attenuated CRF decline (p=0.029 for the group-by-time interaction effect), which was accompanied by higher muscle levels of oxidative capacity (citrate synthase and respiratory chain complexes III, IV and V) and an indicator of antioxidant defense (glutathione reductase) in the intervention arm (all p≤0.001), as well as by higher levels of apoptosis (caspase-3, p=0.029) and angiogenesis (vascular endothelial growth factor receptor-2, p=0.012). The proportion of 'hot-like' (i.e., with viable immune infiltrates in flow cytometry analyses) tumors tended to be higher (p=0.0789) in the exercise group (76.9%, vs. 33.3% in control mice). Exercise also promoted greater total immune (p=0.045) and myeloid cell (p=0.049) infiltration within the 'hot' tumors, with a higher proportion of two myeloid cell subsets (CD11C+ [dendritic] cells [p=0.049] and M2-like tumor-associated macrophages [p=0.028]), yet with no significant changes in lymphoid infiltrates or in cirulating immune cells or chemokines/cytokines. No training effect was found either for muscle strength or anabolic status, cancer progression (tumor weight and metastasis, tumor microenvironment), clinical severity, or survival. Conclusions: Combined exercise appears as an effective strategy for attenuating physical function decline in a mouse model of HR-NB, also exerting some potential immune benefits within the tumor, which seem overall different from those previously reported in adult cancers.

Genomic insights into rapid speciation within the world's largest tree genus Syzygium.

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.

Effects of Exercise on the Immune Function of Pediatric Patients With Solid Tumors: Insights From the PAPEC Randomized Trial.

The purpose of this study was to assess the effects of an in-hospital exercise intervention during neoadjuvant chemotherapy on the inflammatory profile and immune cell subpopulation in 20 children with solid tumors (control [n = 11] and exercise group [n = 9]). Although no significant interaction (group × time) effect was found with an analysis of variance test, we found a trend toward an interaction effect for natural killer cells expressing the immunoglobulin-like receptor KIR2DS4, with their numbers remaining stable in the exercise group but increasing in controls. Our data support that exercise interventions are safe in pediatric cancer patients with solid tumors during chemotherapy treatment despite its aggressive, immunosuppressive nature.

Exercise Intervention in Pediatric Patients with Solid Tumors: The Physical Activity in Pediatric Cancer Trial.

INTRODUCTION: The randomized controlled trial "Physical Activity in Pediatric Cancer" determined the effects of an inhospital exercise intervention combining aerobic and muscle strength training on pediatric cancer patients with solid tumors undergoing neoadjuvant chemotherapy. METHODS: Participants were allocated to an exercise (n = 24, 17 boys; mean ± SEM age, 10 ± 1 yr) or control group (n = 25, 18 boys; 11 ± 1 yr). Training included three sessions per week for 19 ± 2 wk. Participants were assessed at treatment initiation, termination, and 2 months after end treatment. The primary endpoint was muscle strength (as assessed by upper and lower-body five-repetition-maximum tests). Secondary endpoints included cardiorespiratory fitness, functional capacity during daily life activities, physical activity, body mass and body mass index, and quality of life. RESULTS: Most sessions were performed in the hospital's gymnasium. Adherence to the program averaged 68% ± 4% and no major adverse events or health issues were noted. A significant interaction (group-time) effect was found for all five-repetition maximum tests (leg/bench press and lateral row; all P < 0.001). Performance significantly increased after training (leg press: 40% [95% confidence interval [CI], 15-41 kg); bench press: 24% [95% CI, 6-14 kg]; lateral row 25% [95% CI, 6-15 kg]), whereas an opposite trend was found in controls. Two-month post values tended to be higher than baseline for leg (P = 0.017) and bench press (P = 0.014). In contrast, no significant interaction effect was found for any of the secondary endpoints. CONCLUSION: An inhospital exercise program for pediatric cancer patients with solid tumors undergoing neoadjuvant treatment increases muscle strength despite the aggressiveness of such therapy.

Benefits of combining inspiratory muscle with 'whole muscle' training in children with cystic fibrosis: a randomised controlled trial.

BACKGROUND: The purpose of this study (randomised controlled trial) was to assess the effects of an 8-week combined 'whole muscle' (resistance+aerobic) and inspiratory muscle training (IMT) on lung volume, inspiratory muscle strength (PImax) and cardiorespiratory fitness (VO2 peak) (primary outcomes), and dynamic muscle strength, body composition and quality of life in paediatric outpatients with CF (cystic fibrosis, secondary outcomes). We also determined the effects of a detraining period. METHODS: Participants were randomly allocated with a block on gender to a control (standard therapy) or intervention group (initial n=10 (6 boys) in each group; age 10±1 and 11±1 years). The latter group performed a combined programme (IMT (2 sessions/day) and aerobic+strength exercises (3 days/week, in-hospital)) that was followed by a 4-week detraining period. All participants were evaluated at baseline, post-training and detraining. RESULTS: Adherence to the training programme averaged 97.5%±1.7%. There was a significant interaction (group×time) effect for PImax, VO2peak and five-repetition maximum strength (leg-press, bench-press, seated-row) (all (p<0.001), and also for %fat (p<0.023) and %fat-free mass (p=0.001), with training exerting a significant beneficial effect only in the intervention group, which was maintained after detraining for PImax and leg-press. CONCLUSION: The relatively short-term (8-week) training programme used here induced significant benefits in important health phenotypes of paediatric patients with CF. IMT is an easily applicable intervention that could be included, together with supervised exercise training in the standard care of these patients.

Intrahospital weight and aerobic training in children with cystic fibrosis: a randomized controlled trial.

PURPOSE: The purpose of our study was to assess the effects of an 8-wk intrahospital combined circuit weight and aerobic training program performed by children with cystic fibrosis (of low-moderate severity and stable clinical condition) on the following outcomes: cardiorespiratory fitness (VO2peak) and muscle strength (five-repetition maximum (5RM) bench press, 5RM leg press, and 5RM seated row) (primary outcomes) and pulmonary function (forced vital capacity, forced expiratory volume in 1 s), weight, body composition, functional mobility (Timed Up and Down Stairs and 3-m Timed Up and Go tests), and quality of life (secondary outcomes). We also determined the effects of a detraining period (4 wk) on the aforementioned outcomes. METHODS: We performed a randomized controlled trial design. Eleven participants in each group (controls: 7 boys, age = 11 ± 3 yr, body mass index = 17.2 ± 0.8 kg · m(-2) (mean ± SEM); intervention: 6 boys, age = 10 ± 2 yr, body mass index = 18.4 ± 1.0 kg · m(-2)) started the study. RESULTS: Adherence to training averaged 95.1% ± 7.4%. We observed a significant group × time interaction effect (P = 0.036) for VO2peak. In the intervention group, VO2peak significantly increased with training by 3.9 mL · kg(-1) · min(-1) (95% confidence interval = 1.8-6.1 mL · kg(-1) · min(-1), P = 0.002), whereas it decreased during the detraining period (-3.4 mL · kg(-1) · min(-1), 95% confidence interval = -5.7 to -1.7 mL · kg(-1) · min(-1), P = 0.001). In contrast, no significant changes were observed during the study period within the control group. Although significant improvements were also observed after training for all 5RM strength tests (P < 0.001 for the interaction effect), the training improvements were not significantly decreased after the detraining period in the intervention group (all P > 0.1 for after training vs detraining). We found no significant training benefits in any of the secondary outcomes. CONCLUSIONS: A short-term combined circuit weight and aerobic training program performed in a hospital setting induces significant benefits in the cardiorespiratory fitness and muscle strength of children with cystic fibrosis.

Preliminary findings of a 4-month intrahospital exercise training intervention on IGFs and IGFBPs in children with leukemia.

The aim of this study was to determine the effect of a 16-week intrahospital supervised, conditioning program including both resistance and aerobic type training on insulin-like growth factors 1 and 2 (IGF-1, IGF-2), several IGF-binding proteins (IGFBPs), and growth hormone (GH) in children receiving treatment against acute lymphoblastic leukemia (ALL). We also analyzed the effects of a 20-week detraining period on these hormones. Seven children (3 girls and 4 boys) aged 4-7 years in the maintenance phase of treatment against ALL performed 3 training sessions per week for 16 weeks of resistance (1 set of 8-15 repetitions of 11 exercises) and aerobic training (30 minutes at >or=50% heart rate max) followed by 20 weeks of detraining where no structured exercise program was performed. Levels of IFG-1 and IFG-2 did not significantly change after the intervention period or after the detraining phase. Likewise, levels of GH, IGFBP-2, and IGFBP-3 remained stable pre and posttraining and after the detraining period. IGFBP-1 levels significantly decreased after training (-43.8%, p = 0.014), whereas there were no significant differences between pretraining vs. detraining (-17.8%, p = 0.108) nor between posttraining vs. detraining (17.7%, p = 0.251). Exercise training did not have major effects on the IGFs, IGFBPs, and GH in children with ALL. Although the importance of these findings to long-term cancer prognosis and/or recurrence remains to be determined, the present data (particularly those on IGF-1 and IGFBP-3) support the idea that exercise training can be safely undergone during treatment against ALL with no major adverse effect.

Exercise during hematopoietic stem cell transplant hospitalization in children.

PURPOSE: The purpose of this controlled trial was to assess the effect of an approximately 3-wk intrahospital exercise intervention performed during inpatient hospitalization for pediatric allogeneic hematopoietic stem cell transplant (HSCT) on (i) immune cell recovery and (ii) body composition. METHODS: Immune (i.e., blood counts of leukocytes, monocytes, lymphocytes, and lymphocyte subpopulations) and anthropometric variables (i.e., body mass, body mass index, and estimated fat-free mass) were measured before and after (+15 and 30 d) HSCT. Seven children (5 boys and 2 girls; age (mean +/- SD) = 8 +/- 4 yr) with high-risk cancer performed an individualized training program (aerobic + resistance exercises) in their isolated hospital rooms. We also assessed a control group (n = 13; 9 boys and 4 girls; age = 7 +/- 3 yr) with similar medical conditions and following the same transplant protocol. RESULTS: In both groups, the dendritic cell count decreased from pre-HSCT to +15 d post-HSCT and thereafter (up to +30 d) remained stabile; however, the posttransplant decrease was more abrupt in the control group than that in the intervention group (-87% vs -63%, respectively, from pre-HSCT to +15 d). The rest of the immune cell parameters measured showed a similar response from pre-HSCT to post-HSCT in both groups. We found a significant effect of the interaction group x time for all anthropometric variables (weight, body mass index, body fat, and fat-free mass), indicating an increase over the hospitalization period only in the intervention group, for example, body mass increased from 32.9 +/- 18.7 kg pre-HSCT to 35.4 +/- 18.6 kg at +30 d in the intervention group versus a decrease from 30.2 +/- 16.6 to 29.3 +/- 6.3 kg in the control group. CONCLUSION: Our findings support the feasibility of exercise training interventions during hospitalization, including immunocompromised children.

Early-phase adaptations to intrahospital training in strength and functional mobility of children with leukemia.

Improvements in chemotherapy and radiotherapy have contributed to the high survival rate (approximately 70%) of childhood acute lymphoblastic leukemia (ALL). However, during treatment, lack of physical activity and treatment cause various short- to long-term side effects, such as muscle atrophy and physical deconditioning. The purpose of this study was to determine the effects of an intrahospital, short-duration (8 weeks) exercise training program on muscle strength and endurance and functional mobility of children with ALL. Seven children (4 boys and 3 girls; 4-7 years of age) who were in the maintenance phase of treatment for ALL were selected as subjects. Three training sessions of 90- to 120-minute duration were performed each week. Each session included 11 different strength exercises engaging the major muscle groups and aerobic training. Gains in strength and endurance were assessed with a 6 repetition maximum test for upper (seated bench press and seated lateral row) and lower extremities (leg press). Gains in functional mobility were assessed with the time up and go test (TUG) and the timed up and down stairs test (TUDS). Performance was significantly improved after the training program in all strength tests (p < 0.01 for seated bench press and p < 0.05 for both seated lateral row and seated leg press) and in the TUG test (p < 0.05). In summary, a period of time as short as 8 weeks is enough to produce clinically relevant early-phase adaptations in children receiving treatment against ALL (i.e., improved functional mobility and muscle strength). Although more research is needed in the area of exercise training and pediatric cancer, exercise sciences can play a beneficial role in assisting both oncologists in treating cancer and improving children's quality of life during and after treatment.

Effects of an intrahospital exercise program intervention for children with leukemia.

PURPOSE: The purpose was to investigate the effect of a 16-wk intrahospital supervised conditioning program including both resistance and aerobic training and a 20-wk detraining period on measures of aerobic fitness, muscular strength, functional mobility, ankle range of motion, and quality of life (QOL) in children receiving treatment for acute lymphoblastic leukemia (ALL). METHODS: Seven children (four boys, three girls; age: 5.1 +/- 1.2 yr, body mass: 24.0 +/- 5.8 kg, height: 114.6 +/- 7.7 cm) in the maintenance phase of treatment against ALL performed three sessions per week for 16 wk of resistance (one set of 8-15 repetitions of 11 exercises) and aerobic training (30 min at > 70% HRmax) followed by 20 wk of detraining where no structured exercise program was performed. Before training, after training, and after detraining, a treadmill test determining .VO2peak and ventilator threshold (VT), muscular strength (6RM), functional mobility (timed up and down stairs test, time up and go 3-m and 10-m tests), passive and dynamic ankle range of motion, and self-reported quality of living were determined. RESULTS: After training, significant increases in .VO2peak, VT, upper- and lower-body muscular strength, and all measures of functional mobility were shown (P < 0.05). Muscular strength was well maintained (significantly greater than before training and no significant decrease from after training) during detraining, whereas .VO2peak, VT, and functional mobility (not significantly different from before training but no significant decrease from after training) were only partially retained. CONCLUSION: Young children in the maintenance phase of treatment against ALL can safely perform both aerobic and resistance training. Training results in significant increases in measures of aerobic fitness, strength, and functional mobility. During detraining, strength and functional mobility are well maintained, whereas .VO2peak and VT are partially maintained.

Is cardiorespiratory fitness related to quality of life in survivors of breast cancer?

The purpose of this study was to investigate whether indices of cardiorespiratory fitness are related to quality of life (QOL) in women survivors of breast cancer. Using the European Organization for Research and Treatment of Cancer QLQ-30 questionnaire, we assessed the QOL of 16 participants (age, 50 +/- 9 years; body mass, 66.6 +/- 9.6 kg). All participants performed incremental cycle ergometer exercise to determine several indices of cardiorespiratory fitness (e.g., peak oxygen uptake [.V(O2)peak, in L.min(-1), ml.kg(-1).min(-1)]), peak power output (PPO, in W), PPO/ body mass (W.kg(-1), peak heart rate (HRpeak, b.min(-1), peak ventilation (VEpeak), and .V(O2) and heart rate (HR) at the ventilatory (VT) and respiratory compensation (RCT) thresholds. Relationships between QOL and variables were assessed using Spearman rank-difference correlation tests. A significant inverse relationship (p < 0.05) was found for QOL scores and values for age (years) and body mass (kg) ( = -0.53), %HRpeak@VT ( = -0.59) and %VEpeak@VT ( = -0.61). A significant positive relationship (p < 0.05) was found for QOL and PPO/body mass ( = 0.59) and HRpeak ( = 0.78), .V(O2)@RCT (ml.kg(-1.min(-1) ( = 0.51), power output (PO, expressed as either W or W.kg(-1) at RCT, and HR at RCT ( = 0.54). No other significant relationship was found between QOL and variables obtained from the tests. In conclusion, these findings highlight possible relationships between cardiorespiratory fitness and well-being in survivors of breast cancer. From a practical point of view, our data emphasize the need for this population to engage in programmed cardiorespiratory exercise training, mainly designed to improve VT and RCT. The improvement of both submaximal indices can have a beneficial effect on QOL.

Androgen receptor content following heavy resistance exercise in men.

The purpose of the present investigation was to examine androgen receptor (AR) content in the vastus lateralis following two resistance exercise protocols of different volume. Nine resistance-trained men (age=24.3+/-4.4 years) performed the squat exercise for 1 (SS) and 6 sets (MS) of 10 repetitions in a random, counter-balanced order. Muscle biopsies were performed at baseline, and 1h following each protocol. Blood was collected prior to, immediately following (IP), and every 15 min after each protocol for 1h. No acute elevations in serum total testosterone were observed following SS, whereas significant 16-23% elevations were observed at IP, 15, and 30 min post-exercise following MS. No acute elevations in plasma cortisol were observed following SS, whereas significant 31-49% elevations were observed for MS at IP, 15, and 30 min post-exercise. Androgen receptor content did not change 1h following SS but significantly decreased by 46% following MS. These results demonstrated that a higher volume of resistance exercise resulted in down-regulation of AR content 1h post-exercise. This may have been due to greater protein catabolism associated with the higher level of stress following higher-volume resistance exercise.

Efeito da suplementaçäo de creatina em sprints no pedalar e na prfomance de sprints repetitivos no pedalar / Creatine supplementation's effect on sprint cycling and repeated sprint cycling perfomance

[1] Fleck S.J., Volek, J.S.,and Kraemer W.J., Efeito da Suplementaçäo de creatina em sprints no pedalar e na perfomance de sprints repetitivos no pedalar. Rev.Bras. Ciên.e Mov. 8 (3):25-32,2000. Um número suficiente de estudos em Ciências do Esporte, têm sido completados, considerando os efeitos da suplementaçäo de creatina na habilidade de realizar sprints, pedalando em curta duraçäo e alta intensidade, que buscam apresentar conclusöes da efetividade da suplementaçäo, nestas atividades. Estudos recentes indicam que um regime típico de suplementaçäo de, aproximadamente, 20 gramas de creatina por dia, por 5 ou sete dias, näo apresentou nenhum impacto na habilidade no tempo de sprints do pedalar, em curta duraçäo e alta intensidade, quando os sprints duraram entre 5 e 30 segundos. Enquanto o efeito da suplementaçäo de creatina em protocolos, com períodos mais longos, comparados com suplementaçäo única na habilidade do sprints no pedalar, em eventos de curta duraçäo e alta intensidade para ambos os protocolos ainda é equívoco. Embora a maioria dos estudos näo sejam conclusivos, em relaçäo ao efeito do regime de suplementaçäo de cargas de creatina em protocolos mais longos que 28 dias de duraçäo, aumento na habilidade de sprint em curta duraçäo e alta intensidade säo observadas. Isto parece ser especialmente verdadeiro quando do esforço para o período de repouso, quando houver pelo menos dois sprints. A perfomance em protocolos de sprints repetidos apresentaram no primeiro, como também nos diversos sprints seguintes, aumentos. A suplementaçäo de creatina parece näo ter efeito nas medidas clássicas de endurance cardiovascular, tais como consumo máximo de oxigênio e consumo de oxigênio em cargas submáximas; sprints após endurance cardiovascular, em perfomance na bicicleta, com duraçäo entre 30 minutos e 2,5 horas, poderia ser aumentada com uma suplementaçäo regular de creatina