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1.
PLoS Genet ; 18(10): e1010396, 2022 10.
Article in English | MEDLINE | ID: mdl-36197938

ABSTRACT

Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.


Subject(s)
Drosophila Proteins , Drosophila , Animals , Chromatin/genetics , Chromatin/metabolism , DNA/metabolism , Drosophila/genetics , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Histones/genetics , Histones/metabolism , Insulator Elements/genetics , Microtubule-Associated Proteins/genetics , Nuclear Proteins/genetics , Phosphoric Monoester Hydrolases/genetics , Polytene Chromosomes/genetics
2.
BMC Genomics ; 25(1): 519, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38802751

ABSTRACT

BACKGROUND: Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype. RESULTS: In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases. CONCLUSIONS: Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.


Subject(s)
Breast Neoplasms , Class I Phosphatidylinositol 3-Kinases , Genomics , Mutation , Class I Phosphatidylinositol 3-Kinases/genetics , Humans , Breast Neoplasms/genetics , Genomics/methods , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic
3.
J Strength Cond Res ; 38(2): 283-289, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-37884002

ABSTRACT

ABSTRACT: Horsley, BJ, Tofari, PJ, Halson, SL, Kemp, JG, Johnston, RD, and Cormack, SJ. Thoracic-worn accelerometers detect fatigue-related changes in vertical stiffness during sprinting. J Strength Cond Res 38(2): 283-289, 2024-Thoracic-mounted accelerometers are valid and reliable for analyzing gait characteristics and may provide the opportunity to assess running-related neuromuscular fatigue (NMF) during training and competition without the need for additional tests, such as a countermovement jump (CMJ). However, their sensitivity for detecting fatigue-related changes in gait across different speeds is unclear. We, therefore, assessed the changes in accelerometer-derived gait characteristics, including vertical stiffness (K vert ), following a repeated sprint protocol (RSP). Sixteen recreationally active subjects performed single and repeated CMJs on a force plate and 40 m run throughs overground at 3-4, 5-6, and 7-8 m·s -1 pre-post a 12 × 40 m RSP. Gait characteristics (contact time, step frequency, step length, K vert , etc.) were derived from an accelerometer contained within a global navigation satellite system unit on the thoracic spine using a validated algorithm. Changes in running gait and CMJ performance were assessed using a linear mixed-effects model (95% confidence interval [95% CI]; effect size [ES]). Significance was set at p < 0.05. A significant reduction in K vert occurred at 7-8 m·s -1 following the RSP (-8.51 kN·m -1 [-13.9, -3.11]; p = 0.007; ES [95% CI] = -0.39 [-0.62, -0.15]) which coincided with a decreased jump height (-0.03 m [-0.04, -0.01]; p = 0.002; ES [95% CI] = -0.87 [-1.41, -0.30]). However, all other gait characteristics were not significantly different irrespective of speed. Thoracic-worn accelerometers can detect changes in K vert at 7-8 m·s -1 which may be useful for monitoring NMF during sprinting. However, a RSP does not result in altered gait mechanics in subsequent running at lower speeds.


Subject(s)
Athletic Performance , Running , Humans , Gait , Algorithms , Accelerometry
4.
J Strength Cond Res ; 38(2): 274-282, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-37884006

ABSTRACT

ABSTRACT: Horsley, BJ, Tofari, PJ, Halson, SL, Kemp, JG, Chalkley, D, Cole, MH, Johnston, RD, and Cormack, SJ. Validity and reliability of thoracic-mounted inertial measurement units to derive gait characteristics during running. J Strength Cond Res 38(2): 274-282, 2024-Inertial measurement units (IMUs) attached to the tibia or lumbar spine can be used to analyze running gait but, with team-sports, are often contained in global navigation satellite system (GNSS) units worn on the thoracic spine. We assessed the validity and reliability of thoracic-mounted IMUs to derive gait characteristics, including peak vertical ground reaction force (vGRF peak ) and vertical stiffness (K vert ). Sixteen recreationally active subjects performed 40 m run throughs at 3-4, 5-6, and 7-8 m·s -1 . Inertial measurement units were attached to the tibia, lumbar, and thoracic spine, whereas 2 GNSS units were also worn on the thoracic spine. Initial contact (IC) from a validated algorithm was evaluated with F1 score and agreement (mean difference ± SD ) of gait data with the tibia and lumbar spine using nonparametric limits of agreement (LoA). Test-retest error {coefficient of variation, CV (95% confidence interval [CI])} established reliability. Thoracic IMUs detected a nearly perfect proportion (F1 ≥ 0.95) of IC events compared with tibia and lumbar sites. Step length had the strongest agreement (0 ± 0.04 m) at 3-4 m·s -1 , whereas contact time improved from 3 to 4 (-0.028 ± 0.018 second) to 7-8 m·s -1 (-0.004 ± 0.013 second). All values for K vert fell within the LoA at 7-8 m·s -1 . Test-retest error was ≤12.8% for all gait characteristics obtained from GNSS units, where K vert was most reliable at 3-4 m·s -1 (6.8% [5.2, 9.6]) and vGRF peak at 7-8 m·s -1 (3.7% [2.5, 5.2]). The thoracic-spine site is suitable to derive gait characteristics, including K vert , from IMUs within GNSS units, eliminating the need for additional sensors to analyze running gait.


Subject(s)
Gait , Running , Humans , Reproducibility of Results , Algorithms , Team Sports , Biomechanical Phenomena
5.
J Strength Cond Res ; 36(12): 3390-3397, 2022 Dec 01.
Article in English | MEDLINE | ID: mdl-34334772

ABSTRACT

ABSTRACT: Conlan, G, McLean, B, Kemp, J, and Duffield, R. Effect of training/competition load and scheduling on sleep characteristics in professional rugby league athletes. J Strength Cond Res 36(12): 3390-3397, 2022-This study examined the effect of training/competition load, scheduling, and associated factors on sleep behavior in professional rugby league athletes. Sleep characteristics were assessed in 26 professional rugby league athletes using wrist-mounted actigraphy and nightly sleep diaries. Sleep actigraphy assessed the time into and out of bed, the duration in bed, sleep duration, efficiency, latency, wake after sleep onset, number of awakenings, and the awakening length. Sleep was measured during 3 different weeks: (a) preseason low training load (TL) (2,356 ± 322 AU), (b) preseason high TL (3,542 ± 445 AU), and (c) in-season match week (1,526 ± 409 AU). The influences of internal TL (session rating of perceived exertion load), training schedule, age, and training location on sleep behavior were analyzed. Repeated-measures 2-way analysis of variance and effect size analyses (d) compared sleep variables between training weeks. The mean weekly sleep duration was significantly lower during high TL week (5 hours 53minutes ± 14 min/night; p = 0.015, d = 0.59) compared with the low TL (6 hours 25minutes ± 8 min·night -1 ) or match weeks (6 hours 26minutes ± 10 min·night -1 ; p = 0.02, d = 2.04). Reduced sleep duration in the high TL week occurred alongside earlier out-of-bed times compared with the low TL ( p = 0.003, d = 1.46) and match weeks ( p = 0.001, d = 5.99). Regardless, the lowest sleep duration was on match night ( p = 0.0001, d = 1.22). Earlier training start times resulted in earlier wake times ( p = 0.003, d = 4.84), shorter in-bed durations ( p = 0.0001, d = 0.62), and shorter sleep durations ( p = 0.002, d = 0.32). Younger athletes slept for longer durations ( p = 0.029, d = 1.70) and perceived their sleep quality to be superior ( p = 0.006, d = 14.94) compared with older athletes. Sleep attained by rugby league athletes is influenced by training and competition schedules, with early training start times and late-night matches being primary drivers of sleep behavior. Coaching staff should have awareness surrounding the implications of training and playing schedules on athlete sleeping patterns.


Subject(s)
Football , Humans , Rugby , Athletes , Sleep , Actigraphy
6.
Res Sports Med ; 30(5): 529-539, 2022.
Article in English | MEDLINE | ID: mdl-33870812

ABSTRACT

The aim was to determine the effects of repeated-sprint training in hypoxia on haematocrit and haemoglobin in different sporting modalities. Seventy-two participants were randomly allocated to Active-Repeated sprint in hypoxia (A-RSH, n= 8); Active-Repeated sprint in normoxia (A-RSN, n= 8); Active-Control (A-CON, n= 8); Team Sports-RSH (T-RSH, n= 8); Team Sports-RSN (T-RSN, n= 8); Team Sports-Control (T-CON, n= 8); Endurance-RSH (E-RSH, n= 8); Endurance-RSN (E-RSN, n= 8); Endurance-Control (E-CON, n= 8). Sessions consisted of two sets of five sprints of 10 swith recovery of 20 sbetween sprints and 10 min between sets. Blood samples for haematocrit and haemoglobin concentrations were obtained before and after, and 2 weeks after cessation. Haematocrit and haemoglobin were lower for the E-RSN group following 2 weeks of cessation of protocol compared with E-RSH (p = 0.035) and E-CON (p = 0.045). Haematocrit of the A-RSH group was higher compared with baseline (p = 0.05) and Post (p = 0.05). Similarly, the T-RSH group demonstrated increases in haematocrit following 2 weeks of cessation compared with Post (p = 0.04). Repeated Sprint Training in Hypoxia had different haematological effects depending on sporting modality.


Subject(s)
Athletic Performance , Running , Athletic Performance/physiology , Hemoglobins , Humans , Hypoxia , Running/physiology
7.
J Strength Cond Res ; 32(12): 3552-3563, 2018 Dec.
Article in English | MEDLINE | ID: mdl-28240711

ABSTRACT

Tofari, PJ, Kemp, JG, and Cormack, SJ. Self-paced team-sport match-simulation results in reductions in voluntary activation and modifications to biological, perceptual, and performance measures at halftime and for up to 96 hours postmatch. J Strength Cond Res 32(12): 3561-3572, 2018-Assessing responses to soccer match play is limited by match variability or unrealistic simulations. To address this, the biological, perceptual, and performance responses were assessed using a self-paced, simulated soccer match protocol using a nonmotorized treadmill. Twelve male team-sport athletes performed the 90-minute simulation. Match activity, quadriceps twitch interpolation (voluntary activation [%VA] and potentiated twitch [POT]), biochemical markers, strength and power performance, rating of perceived exertion (RPE), and self-report wellness were collected prematch, halftime, postmatch, and 2, 24, 48, 72, and 96-hour postmatch. Change compared with prematch was calculated using effect size ±90% confidence limit, and relationships were assessed using regression analysis. Subjects covered 12,445.8 ± 768.7 m at 87.1 ± 3.2% maximal heart rate (mean ± SD). Reductions in %VA and POT was present at halftime (-0.38 ± 0.46 and -0.79 ± 0.30, respectively) and persisted postmatch. Squat jump height decreased at halftime (-0.42 ± 0.31) and was decreased until Post96. Perceptual fatigue, soreness (-0.92 ± 0.88 and -1.49 ± 0.76, respectively), and creatine kinase (CK) (1.11 ± 0.43) peaked at Post24. Pretest strength (N·kg) correlated with changes in CK (r = -0.58 to -0.81), peak oxygen consumption (V[Combining Dot Above]O2peak) correlated with reduced perceived wellness at Post24 (r = 0.44-0.58) and RPE post (r = -0.71 ± 0.28). High-speed running correlated with soreness (r = 0.42) and very high-speed running with reduced POT (r = 0.61). Previously, unreported half-time reductions in %VA and POT plateaued by postmatch, suggesting a role in regulating second-half performance. Perceptual and neuromuscular responses seem related to running intensity. Greater lower-body strength and V[Combining Dot Above]O2peak were associated with less CK (i.e., muscle damage) and perceptual responses postmatch, respectively, suggesting a training focus should be placed on these capacities.


Subject(s)
Athletic Performance/physiology , Muscle Fatigue , Muscle, Skeletal/physiology , Soccer/physiology , Adult , Athletes , Creatine Kinase , Exercise Test , Fatigue , Humans , Male , Myalgia , Oxygen Consumption , Running/physiology , Young Adult
8.
J Sports Sci ; 35(19): 1947-1953, 2017 Oct.
Article in English | MEDLINE | ID: mdl-27779439

ABSTRACT

Talent identification (TID) and talent development (TDE) programmes in track sprint cycling use ergometer- and track-based tests to select junior athletes and assess their development. The purpose of this study was to assess which tests are best at monitoring TID and TDE. Ten male participants (16.2 ± 1.1 year; 178.5 ± 6.0 cm and 73.6 ± 7.6 kg) were selected into the national TID squad based on initial testing. These tests consisted of two 6-s maximal sprints on a custom-built ergometer and 4 maximal track-based tests (2 rolling and 2 standing starts) using 2 gear ratios. Magnitude-based inferences and correlation coefficients assessed changes following a 3-month TDE programme. Training elicited meaningful improvements (80-100% likely) in all ergometer parameters. The standing and rolling small gear, track-based effort times were likely and very likely (3.2 ± 2.4% and 3.3 ± 1.9%, respectively) improved by training. Stronger correlations between ergometer- and track-based measures were very likely following training. Ergometer-based testing provides a more sensitive tool than track-based testing to monitor changes in neuromuscular function during the early stages of TDE. However, track-based testing can indicate skill-based improvements in performance when interpreted with ergometer testing. In combination, these tests provide information on overall talent development.


Subject(s)
Aptitude , Athletic Performance , Bicycling , Ergometry , Exercise Test/methods , Adolescent , Humans , Male
9.
Muscle Nerve ; 53(5): 770-8, 2016 May.
Article in English | MEDLINE | ID: mdl-26427047

ABSTRACT

INTRODUCTION: Magnetic stimulation can be used to assess muscle function by calculating voluntary activation using an interpolated twitch during maximal voluntary contractions (MVCs) and control twitches to potentiated muscle. In this study we assessed the reliability of torque, electromyography (EMG), and voluntary activation variables. METHODS: Fifteen men completed 5 testing sessions (2 familiarization and 3 reliability trials) to assess quadriceps femoris muscle function. Intra- and interday reliability levels of torque and EMG variables were estimated using typical error ± 90% confidence limits, expressed as percentage [coefficient of variation (CV)] and intraclass correlation coefficient. The smallest worthwhile change was calculated as 0.2 × between-participant standard deviation. RESULTS: Intra- and interday torque variables for MVC were reliable (CV < 4%, ICC 0.98, and CV < 5%, ICC 0.99, respectively). EMG variables were less reliable than torque variables, with CVs ranging from 7% to 18%. CONCLUSION: Magnetic stimulation of the femoral nerve is a reliable method for assessing muscle function.


Subject(s)
Femoral Nerve , Magnetic Fields , Muscle Contraction/physiology , Quadriceps Muscle/physiology , Torque , Adult , Electromyography , Humans , Male , Reproducibility of Results , Young Adult
10.
J Strength Cond Res ; 29(11): 3206-15, 2015 Nov.
Article in English | MEDLINE | ID: mdl-25944456

ABSTRACT

There is a paucity of data examining the impact of high-intensity interval hypoxic training (IHT) on intermittent running performance. This study assessed the effects of IHT on 17 amateur Australian Footballers, who completed 8 interval treadmill running sessions (IHT [FIO2 = 15.1%] or PLACEBO) over 4 weeks, in addition to normoxic football (2 per week) and resistance (2 per week) training sessions. To match relative training intensity, absolute IHT intensity reduced by 6% of normoxic vV[Combining Dot Above]O2peak compared with PLACEBO. Before and after the intervention, performance was assessed by Yo-Yo intermittent recovery test level 2 (Yo-Yo IR2) and a self-paced team sport running protocol. Standardized effect size statistics were calculated using Cohen's d to compare between the interventions. Compared with PLACEBO, IHT subjects experienced (a) smaller improvements in Yo-Yo IR2 performance (Cohen's d = -0.42 [-0.82 to -0.02; 90% confidence interval]); (b) similar increases in high-intensity running distance during the team sport protocol (d = 0.17 [-0.50 to 0.84]); and (c) greater improvements in total distance (d = 0.72 [0.33-1.10]) and distance covered during low-intensity activity (d = 0.59 [-0.07 to 1.11]) during the team sport protocol. The lower absolute training intensity of IHT may explain the smaller improvements in Yo-Yo IR2 performance in the hypoxic group. Conversely, the data from the self-paced protocol suggest that IHT may positively influence pacing strategies in team sport athletes. In conclusion, IHT alters pacing strategies in team sport athletes (i.e., increased distance covered during low-intensity activity). However, IHT leads to smaller improvements in externally paced high-intensity intermittent running performance (i.e., Yo-Yo IR2), which may be related to a reduced absolute training intensity during IHT sessions.


Subject(s)
Athletic Performance/physiology , Hypoxia/physiopathology , Physical Conditioning, Human/methods , Running/physiology , Adolescent , Adult , Australia , Exercise Test , Football/physiology , Humans , Male , Oxygen Consumption/physiology , Physical Endurance/physiology , Single-Blind Method , Young Adult
11.
Ergonomics ; 58(5): 770-80, 2015.
Article in English | MEDLINE | ID: mdl-25428772

ABSTRACT

The aim of this study was to simultaneously assess the changes in physiology, and kinematic and spatiotemporal features of gait, during prolonged load carriage in individuals without load carriage experience. Eleven males, representative of new military recruits, walked for 120 min at 5.5 km h(- 1), 0% grade, on a motorised treadmill while carrying a 22 kg load. The load ( ≤ 30% body mass) was distributed over a weighted vest, combat webbing and replica model firearm, to reflect a patrol order load. Oxygen consumption and heart rate increased throughout the trial; however, apart from a minor increase in step length, there were no changes in the kinematic or spatiotemporal parameters, despite an increase in perceived exertion and discomfort. These data suggest that individuals with no experience in load carriage are able to maintain normal gait during 2 h of fixed speed walking, while carrying a patrol order load ≤ 30% body mass.


Subject(s)
Gait/physiology , Heart Rate , Lower Extremity/physiology , Military Personnel , Oxygen Consumption , Weight-Bearing/physiology , Adolescent , Adult , Biomechanical Phenomena , Exercise Test , Humans , Male , Young Adult
12.
J Sports Sci Med ; 14(1): 62-8, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25729291

ABSTRACT

This study assessed the reliability of a 'self-paced' 30-min, team-sport running protocol on a Woodway Curve 3.0 non-motorised treadmill (NMT). Ten male team-sport athletes (20.3 ± 1.2 y, 74.4 ± 9.7 kg, VO2peak 57.1 ± 4.5 ml·kg(-1)·min(-1)) attended five sessions (VO2peak testing + familiarisation; four reliability trials). The 30-min protocol consisted of three identical 10-min activity blocks, with visual and audible commands directing locomotor activity; however, actual speeds were self-selected by participants. Reliability of variables was estimated using typical error ± 90% confidence limits expressed as a percentage [coefficient of variation (CV)] and intraclass correlation coefficient. The smallest worthwhile change (SWC) was calculated as 0.2 × between participant standard deviation. Peak/mean speed and distance variables assessed across the 30-min protocol exhibited a CV < 5%, and < 6% for each 10-min activity block. All power variables exhibited a CV < 7.5%, except walking (CV 8.3-10.1%). The most reliable variables were maximum and mean sprint speed (CV < 2%). All variables produced a CV% greater than the SWC. A self-paced, team-sport running protocol performed on a NMT produces reliable speed/distance and power data. Importantly, a single familiarisation session allowed for adequate test-retest reliability. The self-paced design provides an ecologically-valid alternative to externally-paced team-sport running simulations. Key pointsSelf-paced team-sport running protocols on a curved NMT that closely match the locomotor demands of competition deliver reliable test-retest measures of speed, distance and power.Such protocols may be sensitive to changes in running profile following an intervention that may not be detectable during externally-paced protocols.One familiarisation session is adequate to ensure test-retest reliability.

13.
Sports Biomech ; 13(3): 241-58, 2014 Sep.
Article in English | MEDLINE | ID: mdl-25325769

ABSTRACT

Eccentric contractions that provide spring energy can also cause muscle damage. The aim of this study was to explore leg and vertical stiffness following muscle damage induced by an eccentric exercise protocol. Twenty active males completed 60 minutes of backward-walking on a treadmill at 0.67 m/s and a gradient of - 8.5° to induce muscle damage. Tests were performed immediately before; immediately post; and 24, 48, and 168 hours post eccentric exercise. Tests included running at 3.35 m/s and hopping at 2.2 Hz using single- and double-legged actions. Leg and vertical stiffness were measured from kinetic and kinematic data, and electromyography (EMG) of five muscles of the preferred limb were recorded during hopping. Increases in pain scores (over 37%) occurred post-exercise and 24 and 48 hours later (p < 0.001). A 7% decrease in maximal voluntary contraction occurred immediately post-exercise (p = 0.019). Changes in knee kinematics during single-legged hopping were observed 168 hours post (p < 0.05). No significant changes were observed in EMG, creatine kinase activity, leg, or vertical stiffness. Results indicate that knee mechanics may be altered to maintain consistent levels of leg and vertical stiffness when eccentric exercise-induced muscle damage is present in the lower legs.


Subject(s)
Leg/physiology , Locomotion/physiology , Muscle, Skeletal/injuries , Muscle, Skeletal/physiology , Running/physiology , Walking/physiology , Ankle Joint/physiology , Biomechanical Phenomena , Electromyography , Humans , Male , Muscle Contraction/physiology , Time and Motion Studies , Young Adult
14.
bioRxiv ; 2024 Jan 04.
Article in English | MEDLINE | ID: mdl-38260414

ABSTRACT

Background: Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype. Results: In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases. Conclusions: Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.

15.
Commun Biol ; 7(1): 441, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38600351

ABSTRACT

ABTRACT: Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.


Subject(s)
Cell-Free Nucleic Acids , Cell-Free Nucleic Acids/genetics , Clustered Regularly Interspaced Short Palindromic Repeats , Apoptosis/genetics , DNA/genetics , Cell Line
16.
Br J Sports Med ; 47 Suppl 1: i51-8, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24282208

ABSTRACT

AIM: To quantify the year-to-year variability of altitude-induced changes in haemoglobin mass (Hb(mass)) in elite team-sport athletes. METHODS: 12 Australian-Footballers completed a 19-day (ALT1) and 18-day (ALT2) moderate altitude (∼2100 m), training camp separated by 12 months. An additional 20 participants completed only one of the two training camps (ALT1 additional n=9, ALT2 additional n=11). Total Hb(mass) was assessed using carbon monoxide rebreathing before (PRE), after (POST1) and 4 weeks after each camp. The typical error of Hb(mass) for the pooled data of all 32 participants was 2.6%. A contemporary statistics analysis was used with the smallest worthwhile change set to 2% for Hb(mass). RESULTS: POST1 Hb(mass) was very likely increased in ALT1 (3.6 ± 1.6%, n=19; mean ± ∼90 CL) as well as ALT2 (4.4 ± 1.3%, n=23) with an individual responsiveness of 1.3% and 2.2%, respectively. There was a small correlation between ALT1 and ALT2 (R=0.21, p=0.59) for a change in Hb(mass), but a moderately inverse relationship between the change in Hb(mass) and initial relative Hb(mass) (g/kg (R=-0.51, p=0.04)). CONCLUSIONS: Two preseason moderate altitude camps 1 year apart yielded a similar (4%) mean increase in Hb(mass) of elite footballers, with an individual responsiveness of approximately half the group mean effect, indicating that most players gained benefit. Nevertheless, the same individuals generally did not change their Hb(mass) consistently from year to year. Thus, a 'responder' or 'non-responder' to altitude for Hb(mass) does not appear to be a fixed trait.


Subject(s)
Altitude , Football/physiology , Hemoglobins/metabolism , Australia , Body Mass Index , Erythropoietin/metabolism , Humans , Resistance Training , Reticulocytes/physiology , Time Factors
17.
J Sports Sci ; 31(3): 238-47, 2013.
Article in English | MEDLINE | ID: mdl-23046418

ABSTRACT

We examined the influence of instructions on decision-making accuracy using video simulations of game-specific scenarios in Australian football. Skilled performers (average age of 23.4 ± 4.2 years) differing in experience (range 0 to 339 Australian Football League (AFL) matches) assumed the role of the key attacker and verbally indicated their kicking decision. Participants were randomly stratified into three groups: (1) LOOSE (n = 15)--instructed to "keep the ball away from the loose defender"; (2) TTF (n = 15) - instructed to "take the first option"; and (3) NI (control) (n = 16)--given no instructions. Gaze behaviour for a subset of participants (n = 20) was recorded. In the scenarios with an even number of attacking and defensive players, the decision-making accuracy of LOOSE was greater than TTF. This difference was most evident for lesser experienced performers, highlighting that lesser experienced performers are more affected by instructional foci than experienced performers. Gaze behaviour was not affected by instructional foci, but visual search rate was greater in scenarios of greater player number and complexity.


Subject(s)
Athletic Performance , Communication , Decision Making , Movement , Soccer , Adult , Australia , Football , Humans , Videotape Recording , Young Adult
18.
J Strength Cond Res ; 27(6): 1539-45, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23037614

ABSTRACT

Previous investigators have reported significant relationships between tests of physical qualities and physical match performance in high-intensity, intermittent team sport (e.g., soccer) players. Although rugby league requires competitors to perform high-intensity running, unlike most other high-intensity intermittent team sports, the physical demands are significantly increased through the large amounts of tackling, wrestling, and grappling that players are required to perform during match play. This study investigated the relationship between tests of physical qualities and match performance in professional rugby league players and determined whether running capacities were associated with the collision and repeated high-intensity effort demands of match play. Thirty-eight elite rugby league players (mean ± SD, age, 23.1 ± 2.7 years) performed tests of repeated sprint ability (12 × 20-m sprints on a 20-second cycle), prolonged high-intensity intermittent running ability (8 × 12-second shuttle sprints on a 48-second cycle), and estimated maximal aerobic power (VO2max) (multistage fitness test). Global positioning system data were collected during 16 professional rugby league matches. Players with better, prolonged, high-intensity intermittent running ability covered greater total distance and greater distance in high-speed running during match play. However, inconsistent relationships were found between tests of running abilities and other match performance variables, with prolonged high-intensity running ability (negative), VO2max (positive), and repeated-sprint ability (no relationship) differentially associated with the total number of collisions and repeated high-intensity effort bouts performed in competition. These findings demonstrate the importance of prolonged high-intensity running ability to the match running performance of elite rugby league players but also highlight the need for game-specific conditioning to prepare players for the high-intensity collision and repeated-effort demands of the game.


Subject(s)
Athletic Performance/physiology , Exercise Test , Football/physiology , Physical Fitness/physiology , Running/physiology , Adult , Humans , Oxygen Consumption , Physical Conditioning, Human/physiology , Young Adult
19.
J Appl Biomech ; 29(4): 386-94, 2013 Aug.
Article in English | MEDLINE | ID: mdl-22923423

ABSTRACT

A number of methods are used to measure lower extremity musculoskeletal stiffness, but there is a paucity of research examining the reliability of these techniques. Therefore, we investigated the reliability of vertical, leg, knee, and ankle stiffness during overground running and hopping in 20 active men. Participants were required to run on a 10 m overground runway at 3.83 m/s (actual; 3.35 ± 0.12 m/s) and to hop in place at 2.2 Hz (actual; 2.37 ± 0.03 Hz), and at a self-selected frequency (actual; 2.05 ± 0.12 Hz) and at 2.2 Hz (actual; 2.39 ± 0.04 Hz). Reliability was determined using the intraclass correlation coefficient, coefficient of variation, mean differences, and Cohen's effect sizes. There was good reliability for vertical stiffness, moderate reliability for leg stiffness, and poor reliability for knee and ankle stiffness during the running task. Similar results were observed during the 2.2 Hz hopping tasks, with good reliability displayed for vertical stiffness and poor reliability for ankle and knee stiffness. In conclusion, our results suggest that vertical stiffness is a reliable measure when running at 3.83 m/s and hopping at 2.2 Hz.


Subject(s)
Ankle Joint/physiology , Gait/physiology , Knee Joint/physiology , Leg/physiology , Models, Biological , Running/physiology , Computer Simulation , Elastic Modulus/physiology , Humans , Male , Reproducibility of Results , Sensitivity and Specificity , Young Adult
20.
Int J Sports Physiol Perform ; 16(10): 1490-1501, 2021 10 01.
Article in English | MEDLINE | ID: mdl-33831844

ABSTRACT

PURPOSE: To determine the impact of the quality and quantity of sleep during an international flight on subsequent objective sleep characteristics, training and match-day load, self-reported well-being, and perceptions of jet lag of elite female cricketers during an International Cricket Council Women's T20 World Cup. METHODS: In-flight and tournament objective sleep characteristics of 11 elite female cricketers were assessed using activity monitors. Seated in business class, players traveled west from Melbourne, Australia, to Chennai, India. The outbound flight departed Melbourne at 3:30 AM with a stopover in Dubai for 2 hours. The arrival time in Chennai was 8:10 PM local time (1:40 AM in Melbourne). The total travel time was 19 hours 35 minutes. Perceptual ratings of jet lag, well-being, and training and competition load were collected. To determine the impact of in-flight sleep on tournament measures, a median split was used to create subsamples based on (1) in-flight sleep quantity and (2) in-flight sleep quality (2 groups: higher vs lower). Spearman correlation coefficients were calculated to assess the bivariate associations between sleep measures, self-reported well-being, perceptual measures of jet lag, and internal training and match-day load. RESULTS: Mean duration and efficiency of in-flight sleep bouts were 4.72 hours and 87.45%, respectively. Aggregated in-flight sleep duration was 14.64 + 3.56 hours. Players with higher in-flight sleep efficiency reported higher ratings for fatigue (ie, lower perceived fatigue) during the tournament period. Tournament sleep duration was longer, and bed and wake times were earlier compared with habitual. Compared with other nights during the tournament, sleep duration was shorter following matches. CONCLUSIONS: Maximizing in-flight sleep quality and quantity appears to have implications for recovery and sleep exhibited during competition. Sleep duration was longer than habitual except for the night of a match, which suggests that T20 matches may disrupt sleep duration.


Subject(s)
Athletic Performance , Soccer , Female , Humans , India , Jet Lag Syndrome/prevention & control , Sleep , Sleep Quality , Travel
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