MetaCompass: Reference-guided Assembly of Metagenomes.

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here we describe the first effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.

Reinforcement feedback impairs locomotor adaptation and retention.

Introduction: Locomotor adaptation is a motor learning process used to alter spatiotemporal elements of walking that are driven by prediction errors, a discrepancy between the expected and actual outcomes of our actions. Sensory and reward prediction errors are two different types of prediction errors that can facilitate locomotor adaptation. Reward and punishment feedback generate reward prediction errors but have demonstrated mixed effects on upper extremity motor learning, with punishment enhancing adaptation, and reward supporting motor memory. However, an in-depth behavioral analysis of these distinct forms of feedback is sparse in locomotor tasks. Methods: For this study, three groups of healthy young adults were divided into distinct feedback groups [Supervised, Reward, Punishment] and performed a novel locomotor adaptation task where each participant adapted their knee flexion to 30 degrees greater than baseline, guided by visual supervised or reinforcement feedback (Adaptation). Participants were then asked to recall the new walking pattern without feedback (Retention) and after a washout period with feedback restored (Savings). Results: We found that all groups learned the adaptation task with external feedback. However, contrary to our initial hypothesis, enhancing sensory feedback with a visual representation of the knee angle (Supervised) accelerated the rate of learning and short-term retention in comparison to monetary reinforcement feedback. Reward and Punishment displayed similar rates of adaptation, short-term retention, and savings, suggesting both types of reinforcement feedback work similarly in locomotor adaptation. Moreover, all feedback enhanced the aftereffect of locomotor task indicating changes to implicit learning. Discussion: These results demonstrate the multi-faceted nature of reinforcement feedback on locomotor adaptation and demonstrate the possible different neural substrates that underly reward and sensory prediction errors during different motor tasks.

The effect of lower back and lower-extremity kinesiology taping on static balance and physical function performance in people with multiple sclerosis: A pilot study.

INTRODUCTION: Multiple sclerosis (MS) can lead to numerous deficits in body functions, including balance and mobility impairment. This study examined the effect of lower back and lower extremity kinesiology tape (KT) application on static balance and physical functioning performance in people with MS (pwMS) and compared that to a non-elastic tape. METHODS: This pilot randomized study recruited and enrolled 10 participants with MS that were allocated into two groups: kinesio (n = 6) and non-elastic (n = 4) tape. Participants were assessed with and without the respective tape on static balance with eyes open and closed and various physical function tests. RESULTS: Effect sizes for the Kinesio tape intervention were found to be small, while effect sizes for the sham tape/place condition varied from small to high. For both groups, the tendency was to reduce or maintain performance on the tests comparing tape and no tape. A subsequent, mixed-factor ANOVA revealed no significant difference between KT or sham tape/placebo. CONCLUSION: Our findings suggest that KT applied on lower back and lower extremity muscles does not seem to improve static balance and physical function performance in pwMS.

Quick on Your Feet: Modifying the Star Excursion Balance Test with a Cognitive Motor Response Time Task.

The Star Excursion Balance Test (SEBT) is a common assessment used across clinical and research settings to test dynamic standing balance. The primary measure of this test is maximal reaching distance performed by the non-stance limb. Response time (RT) is a critical cognitive component of dynamic balance control and the faster the RT, the better the postural control and recovery from a postural perturbation. However, the measure of RT has not been done in conjunction with SEBT, especially with musculoskeletal fatigue. The purpose of this study is to examine RT during a SEBT, creating a modified SEBT (mSEBT), with a secondary goal to examine the effects of muscular fatigue on RT during SEBT. Sixteen healthy young male and female adults [age: 20 ± 1 years; height: 169.48 ± 8.2 cm; weight: 67.93 ± 12.7 kg] performed the mSEBT in five directions for three trials, after which the same was repeated with a response time task using Blazepod™ with a random stimulus. Participants then performed a low-intensity musculoskeletal fatigue task and completed the above measures again. A 2 × 2 × 3 repeated measures ANOVA was performed to test for differences in mean response time across trials, fatigue states, and leg reach as within-subjects factors. All statistical analyses were conducted in JASP at an alpha level of 0.05. RT was significantly faster over the course of testing regardless of reach leg or fatigue state (p = 0.023). Trial 3 demonstrated significantly lower RT compared to Trial 1 (p = 0.021). No significant differences were found between fatigue states or leg reach. These results indicate that response times during the mSEBT with RT is a learned skill that can improve over time. Future research should include an extended familiarization period to remove learning effects and a greater fatigue state to test for differences in RT during the mSEBT.

Relative Contributions of Handgrip and Individual Finger Strength on Climbing Performance in a Bouldering Competition.

PURPOSE: To determine the relative contributions of handgrip and individual finger strength for the prediction of climbing performance in a bouldering competition. A secondary aim was to examine the influence of body size, bouldering experience, and training habits. METHODS: Sixty-seven boulderers (mean [SD], age = 21.1 [4.0] y; body mass = 69.5 [9.8] kg) volunteered for this study. Data collection occurred immediately before an indoor bouldering competition and involved the assessment of handgrip and individual finger maximal force production using an electronic handheld dynamometer. The bouldering competition consisted of 70 routes graded V0 to V8, with higher point values awarded for completing more difficult routes. Stepwise multiple regression analysis was used to examine the relative contributions of handgrip and individual finger strengths, body mass, height, bouldering experience, and bouldering frequency to the prediction of performance scores in the competition. RESULTS: Ring finger pinch strength, bouldering experience, and bouldering frequency significantly (P < .05) contributed to the model (R2 = .373), whereas body mass; height; full handgrip strength, as well as index, middle, and little finger pinch strengths did not. The ß weights showed that ring finger pinch strength (ß = .430) was the most significant contributor, followed by bouldering experience (ß = .331) and bouldering frequency (ß = .244). CONCLUSIONS: The current findings indicated that trainable factors contributed to the prediction of bouldering performance. These results suggest greater bouldering frequency and experience likely contribute to greater isolated individual finger strength, thereby optimizing preparation for the diverse handholds in competitive rock climbing.

Cortical preparatory activity during motor learning reflects visuomotor retention deficits after punishment feedback.

Previous studies have shown that reinforcement-based motor learning requires the brain to process feedback-related information after movement execution. However, whether reinforcement feedback changes how the brain processes motor preparation before movement execution is unclear. By using electroencephalography (EEG), this study investigates whether reinforcement feedback changes cortical preparatory activity to modulate motor learning and memory. Human subjects were divided in three groups [reward, punishment, control] to perform a visuomotor rotation task under different conditions that assess adaptation (learning) and retention (memory) during the task. Reinforcement feedback was provided in the form of points after each trial that signaled monetary gains (reward) or losses (punishment). EEG was utilized to evaluate the amplitude of movement readiness potentials (MRPs) at the beginning of each trial for each group during the adaptation and retention conditions of the task. The results show that punishment feedback significantly decreased MRPs amplitude during both task conditions compared to Reward and Control groups. Moreover, the punishment-related decrease in MRPs amplitude paralleled decreases in motor performance during the retention but not the adaptation condition. No changes in MRPs or motor performance were observed in the Reward group. These results support the idea that reinforcement feedback modulates motor preparation and suggest that changes in cortical preparatory activity contribute to the visuomotor retention deficits observed after punishment feedback.

Comparison of Countermovement and Squat Jumps Performance in Recreationally Trained Males.

The vertical jump has been shown to be an effective tool in assessing neuromuscular fatigue. The two most common iterations of the vertical jump are the countermovement and squat jumps. This investigation sought to identify if differences exist between the two jumping strategies with regard to electromyography (EMG) and kinetics in a group of recreationally trained males. Twenty-two participants completed one experimental session, where three countermovement (CMJ) and three squat jumps (SJ) were performed using a counterbalanced within-subject design. Jump performance was evaluated with data obtained using a force platform. Additionally, EMG was collected on the vastus lateralis (VL), vastus medialis (VM), semitendinosus (ST) and medial gastrocnemius (MG). Greater EMG values were seen in the CMJ for ST as well as percentage of activation in the MG (p < 0.05). Increased values of mean force and mean power were observed in the SJ, while the CMJ showed greater peak and mean velocity. Greater jump heights in the CMJ were present as well (p < 0.05). These findings suggest that the increase in CMJ jump height due to the increase in propulsive velocity is not due to increases in knee extensors muscle activation.

Impact of Hydration Status on Jump Performance in Recreationally Trained Males.

The vertical jump is commonly used as a means of evaluating athlete readiness. Athletes have been shown to arrive to training and competition in a hypohydrated state. Thus, this investigation sought to examine the impact of hydration status on both countermovement (CMJ) and squat jump (SJ) performance. Twenty-five recreationally trained males completed three CMJ and SJ in a euhydrated, hypohydrated and control condition. Conditions were separated by a minimum of 24 hours. Hydration status was assessed using urine specific gravity. Jump performance was evaluated using both kinematic and kinetic data obtained from a force platform. A repeated-measures ANOVA was performed for each variable of interest in both the CMJ and SJ. CMJ peak and mean force values were significantly greater in the euhydrated condition compared to the hypohydrated condition (p < 0.05), with no differences between the control condition and either experimental condition. SJ showed reductions in jump height, peak and mean velocity, peak and mean power and impulse from control and euhydrated conditions (p < 0.05). The findings of this investigation show that when performing jump testing, specifically SJ, that hydration status of the individual may impact commonly used variables to assess the readiness of the individual for a given day.

Punishment Feedback Impairs Memory and Changes Cortical Feedback-Related Potentials During Motor Learning.

Reward and punishment have demonstrated dissociable effects on motor learning and memory, which suggests that these reinforcers are differently processed by the brain. To test this possibility, we use electroencephalography to record cortical neural activity after the presentation of reward and punishment feedback during a visuomotor rotation task. Participants were randomly placed into Reward, Punishment, or Control groups and performed the task under different conditions to assess the adaptation (learning) and retention (memory) of the motor task. These conditions featured an incongruent position between the cursor and the target, with the cursor trajectory, rotated 30° counterclockwise, requiring the participant to adapt their movement to hit the target. Feedback based on error magnitude was provided during the Adaptation condition in the form of a positive number (Reward) or negative number (Punishment), each representing a monetary gain or loss, respectively. No reinforcement or visual feedback was provided during the No Vision condition (retention). Performance error and event-related potentials (ERPs) time-locked to feedback presentation were calculated for each participant during both conditions. Punishment feedback reduced performance error and promoted faster learning during the Adaptation condition. In contrast, punishment feedback increased performance error during the No Vision condition compared to Control and Reward groups, which suggests a diminished motor memory. Moreover, the Punishment group showed a significant decrease in the amplitude of ERPs during the No Vision condition compared to the Adaptation condition. The amplitude of ERPs did not change in the other two groups. These results suggest that punishment feedback impairs motor retention by altering the neural processing involved in memory encoding. This study provides a neurophysiological underpinning for the dissociative effects of punishment feedback on motor learning.

Virtual-Reality-Induced Visual Perturbations Impact Postural Control System Behavior.

BACKGROUND: Virtual reality (VR) is becoming a widespread tool in rehabilitation, especially for postural stability. However, the impact of using VR in a "moving wall paradigm" (visual perturbation), specifically without and with anticipation of the perturbation, is unknown. METHODS: Nineteen healthy subjects performed three trials of static balance testing on a force plate under three different conditions: baseline (no perturbation), unexpected VR perturbation, and expected VR perturbation. The statistical analysis consisted of a 1 × 3 repeated-measures ANOVA to test for differences in the center of pressure (COP) displacement, 95% ellipsoid area, and COP sway velocity. RESULTS: The expected perturbation rendered significantly lower (p < 0.05) COP displacements and 95% ellipsoid area compared to the unexpected condition. A significantly higher (p < 0.05) sway velocity was also observed in the expected condition compared to the unexpected condition. CONCLUSIONS: Postural stability was lowered during unexpected visual perturbations compared to both during baseline and during expected visual perturbations, suggesting that conflicting visual feedback induced postural instability due to compensatory postural responses. However, during expected visual perturbations, significantly lowered postural sway displacement and area were achieved by increasing the sway velocity, suggesting the occurrence of postural behavior due to anticipatory postural responses. Finally, the study also concluded that VR could be used to induce different postural responses by providing visual perturbations to the postural control system, which can subsequently be used as an effective and low-cost tool for postural stability training and rehabilitation.

The Interaction of Cognitive Interference, Standing Surface, and Fatigue on Lower Extremity Muscle Activity.

BACKGROUND: Performing cognitive tasks and muscular fatigue have been shown to increase muscle activity of the lower extremity during quiet standing. A common intervention to reduce muscular fatigue is to provide a softer shoe-surface interface. However, little is known regarding how muscle activity is affected by softer shoe-surface interfaces during static standing. The purpose of this study was to assess lower extremity muscular activity during erect standing on three different standing surfaces, before and after an acute workload and during cognitive tasks. METHODS: Surface electromyography was collected on ankle dorsiflexors and plantarflexors, and knee flexors and extensors of fifteen male participants. Dependent electromyography variables of mean, peak, root mean square, and cocontraction index were calculated and analyzed with a 2 × 2 × 3 within-subject repeated measures analysis of variance. RESULTS: Pre-workload muscle activity did not differ between surfaces and cognitive task conditions. However, greater muscle activity during post-workload balance assessment was found, specifically during the cognitive task. Cognitive task errors did not differ between surface and workload. CONCLUSIONS: The cognitive task after workload increased lower extremity muscular activity compared to quite standing, irrespective of the surface condition, suggesting an increased demand was placed on the postural control system as the result of both fatigue and cognitive task.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.

High-resolution comparative analysis of great ape genomes.

Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

Motor adaption during repeated motor control testing: Attenuated muscle activation without changes in response latencies.

With repeated exposure to postural perturbations the human postural control system can adapt and create efficient strategies to counteract these perturbations. The Motor Control Test (MCT) is commonly used to elicit reactionary postural movements. Though this device has been assessed for possible learning effects and reliability of composite scores, yet no study has evaluated possible neuromuscular alterations repeated bouts might elicit. Twenty participants (age: 25 ±â€¯4.73 years; height: 183.8 ±â€¯8.5 cm; mass: 85.2 ±â€¯15.6 kg) volunteered and, following familiarization, performed five full-randomized MCTs over six testing sessions. The first five sessions occurred on consecutive days, with the sixth occurring two days later. Electromyography (EMG) was recorded on right lower extremity knee flexors and extensors, and ankle plantarflexors and dorsiflexors. Response latencies and Mean and RMS muscle activity were calculated and analyzed using 1 × 5 (within days) and 1 × 6 (across days) RM ANOVA. Decreases in muscle activation of proximal musculature were noted between days and trials within days, however these changes were not maintained after the two-day retention period. No differences were detected for MCT scores. These results suggest repeated MCT exposure modifies neuromuscular responses to maintain similar reaction time through a postural control strategy shift.

The Influence of an Acute Bout of Whole Body Vibration on Human Postural Control Responses.

The use of vibrating platforms has become increasingly available, and popular at sports and rehabilitation institutes. Given the discrepancies in the literature regarding whole body vibration (WBV) and human reflexive responses, the purpose of this study was to examine the acute effects of WBV on postural response latencies, as well as associated electromyography measures of the lower extremities during balance perturbations. Reflexive responses during backward and forward balance perturbations were examined before, after, and 10 min after a bout of WBV. The findings suggest that following an acute bout of whole body vibration, muscle activity of the lower extremities is decreased during a reflexive response to an unexpected perturbation, and may be associated with faster reaction time.

SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms.

Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies.

The highly anticipated transition from next generation sequencing (NGS) to third generation sequencing (3GS) has been difficult primarily due to high error rates and excessive sequencing cost. The high error rates make the assembly of long erroneous reads of large genomes challenging because existing software solutions are often overwhelmed by error correction tasks. Here we report a hybrid assembly approach that simultaneously utilizes NGS and 3GS data to address both issues. We gain advantages from three general and basic design principles: (i) Compact representation of the long reads leads to efficient alignments. (ii) Base-level errors can be skipped; structural errors need to be detected and corrected. (iii) Structurally correct 3GS reads are assembled and polished. In our implementation, preassembled NGS contigs are used to derive the compact representation of the long reads, motivating an algorithmic conversion from a de Bruijn graph to an overlap graph, the two major assembly paradigms. Moreover, since NGS and 3GS data can compensate for each other, our hybrid assembly approach reduces both of their sequencing requirements. Experiments show that our software is able to assemble mammalian-sized genomes orders of magnitude more quickly than existing methods without consuming a lot of memory, while saving about half of the sequencing cost.

Long-read sequence assembly of the gorilla genome.

Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.

Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli.

Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of diarrhea worldwide. Among the 25 different ETEC adhesins, 22 are known as "colonization factors" (CFs), of which 17 are assembled by the chaperone-usher (CU) mechanism. Currently, there is no preventive therapy against ETEC, and CFs have been proposed as components for vaccine development. However, studies of diarrhea-causing ETEC strains worldwide indicate that between 15 and 50% of these are negative for known CFs, hindering the selection of the most widespread structures and suggesting that unknown adhesins remain to be identified. Here, we report the result of a comprehensive analysis of 35 draft genomes of ETEC strains which do not carry known adhesin genes; our goal was to find new CU pili loci. The phylogenetic profiles and serogroups of these strains were highly diverse, a majority of which produced only the heat-labile toxin. We identified 10 pili loci belonging to CU families ß (1 locus), γ2 (7 loci), κ (1 locus), and π (1 locus), all of which contained the required number of open reading frames (ORFs) to encode functional structures. Three loci were variants of previously-known clusters, three had been only-partially described, and four are novel loci. Intra-loci genetic variability identified would allow the synthesis of up to 14 different structures. Clusters of putative γ2-CU pili were most common (23 strains), followed by putative ß-CU pili (12 strains), which have not yet been fully characterized. Overall, our findings significantly increase the number of ETEC adhesion genes associated with human infections.

Automated ensemble assembly and validation of microbial genomes.

BACKGROUND: The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. RESULTS: To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. CONCLUSIONS: Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.