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Bowen, M.

Publications and source records attributed to Bowen, M..

8 recordsLinked to original sources

Evaluating a structured expert elicitation approach for adaptive conservation: Lessons from five years in practice

Threatened species management relies on Ex ante estimates of species responses to different interventions to generate meaningful predictions. Structured expert elicitation is often used to generate these estimates, but comparisons of these expert-predicted outcomes with observed results are rare. This study aims to evaluate the utility of expert elicitation for adaptive management in the New South Wales Saving our Species (SoS) program in Australia by revisiting six species management plans that were generated from bespoke structured elicitation guidelines five years prior. Each species management plan included a defined scope, conceptual model, monitoring indicators and estimated response to management curves under different scenarios. Experts reviewed the conceptual models after five years of management and monitoring and compared the predicted response to management with observed monitoring data. In three of the six case studies, observed outcomes closely matched predictions. Where predictions diverged, factors such as unanticipated new threats and unexpected responses to interventions contributed to discrepancies. However, in all cases, the structured approach provided a clear logic for planning, enabling managers to systematically refine their understanding. The conceptual models and response curves proved valuable for collaboration, communication, and generating hypotheses for unexpected results. This work demonstrates the value of the bespoke guidelines in supporting adaptive management processes, strengthening the knowledge base for threatened species conservation while improving alignment between predictions and real-world outcomes.

ecology↗

RACLET: the Ramp Above Critical Level Endurance Test to evaluate critical force in isometric task.

The Ramp Above Critical Level Endurance Test (RACLET) is a novel submaximal test designed to evaluate the parameters of the critical force model without strenuous exercise. This study aimed to validate the RACLET in healthy and pathological populations and to assess its reliability, concurrent validity, and predictive capacity. Sixteen healthy volunteers and ten patients with respiratory pathologies participated in this study. The RACLET consisted of a decreasing ramp force starting at 60% and ending at 15% of the maximum force for a total duration of 425 s with brief regular maximal voluntary contractions. The goodness of fit for the RACLET model on the maximal contraction force was excellent in both populations (median r2{approx} 0.95). In patients, RACLET parameters demonstrated excellent reliability (ICC > 0.90). The concurrent validity of the critical force estimate compared with the all-out method was high (error: -0.3{+/-}7.4%). The models predictive capacity for time-to-exhaustion and fatigue during constant-intensity exercise was excellent (r2 = 0.910 and 0.907, respectively). The RACLET provides a reliable and valid estimate of critical force model parameters opening up numerous practical applications in vulnerable populations, individualised physical activity programs, and longitudinal monitoring. The feasibility and performance of the test make it a promising tool for assessing muscle function in various contexts.

biophysics↗

RACLET: the Ramp Above Critical Level Endurance Test to evaluate critical power in cycling.

This study introduces the Ramp Above Critical Level Endurance Test (RACLET), a novel method for evaluating critical power model parameters, and tests its reliability and concurrent validity. Twenty-three participants completed several RACLET and time-to-exhaustion tests (TTE). The RACLET involves a decreasing power ramp with intermittent maximal sprints, inducing moderate fatigue without exhaustion. The test demonstrated excellent reliability for the initial power (Pi) and critical power (Pc) (ICC > 0.97), with acceptable reliability for the time constant ({tau}) (ICC = 0.70). The concurrent validity against TTE was excellent for Pi and Pc (systematic errors: 1.7% and 3.0%, respectively), but moderate for{tau} and maximum work above the critical power (systematic errors {approx} 10%). The RACLET showed excellent predictive capacity for time-to-exhaustion (systematic error = -0.6%; random error = 10.3%). These results suggest that the RACLET is a reliable, valid, and efficient alternative to traditional critical power testing methods, offering comparable accuracy with a single test without inducing exhaustion. This approach could be particularly beneficial for populations in which exhaustive testing is challenging or impractical.

biophysics↗

RACLET: the Ramp Above Critical Level Endurance Test to evaluate critical velocity in running.

Critical velocity (Vc) is an important fatigability threshold in running, but only strenuous methods exist to assess it (e.g. time-trials). Based on a novel mathematical model of fatigability, the Ramp Above Critical Level Endurance Test (RACLET), a simple, non-exhaustive, 5-min test to evaluate Vc was developed. This study aimed to test the reliability and validity of the RACLET. Thirty-eight participants performed two RACLET (session 1) and three time-trials (sessions 2-4). For the RACLET, velocity target tracking was guaranteed by either a pacing bike or cones and whistle signals. GPS was used to measure the participants running velocities. Vc,{tau} , and [Formula] were determined by adjusting the fatigability model on the measured Vmax. The RACLET test-retest and RACLET vs. time-trials parameters were compared for reliability and validity testing, respectively. The RACLET Vc is reliable and valid (mean difference=-1.7{+/-}1.9% and 6.2{+/-}6.5%, respectively). Although{tau} and [Formula] presented important variability (s.d. difference ~30%), the combination of the RACLET parameters enabled an excellent prediction of time-trials performance (mean error=-8.9{+/-}5.1%, 0.9{+/-}7.4%, -2.0{+/-}5.2% for 400, 1500, and 3000 m, respectively). RACLET is a novel non-exhausting test that enables a reliable and valid assessment of the velocity-time relationship parameters.

biophysics↗

A single decreasing ramp friction sprint for torque-cadence relationship assessment during cycling

This study aimed to introduce and validate a novel method for assessing dynamic fatigue components through a single-sprint test, addressing the limitations of traditional multi-sprint evaluations. We tested this method on twenty-one participants by computing torque-cadence relationships from two iso-friction sprints at varying friction levels (3% and 9% of body mass), the traditional combination of these iso-friction sprints and a novel decreasing ramp friction sprint (FrD). The accuracy of this new method through fatigue was also tested with ten 6-s FrD sprints interspersed with a 24-s passive rest. FrD outperformed single iso-friction sprints and provided accurate and valid torque-cadence relationships parameters estimates (T0, C0, and Pmax) with systematic bias < 3%, typical error of estimate < 6% and very high r2 (median of 0.962). The quality of the input data from this method was also high, as evidenced by the well-distributed and wide-range cadence spectrum (51.3% of C0; skewness = -0.51, p < 0.05) and was maintained throughout the fatiguing exercise. Our novel method not only allows the dynamic fatigue components evaluation with only one sprint but also maintains accuracy and validity across varying fatigue states, offering significant advantages for both research and practical applications.

physiology↗

Strategic engineering unlocks in vitro type II polyketide biosynthesis

Microbial polyketides represent a structurally diverse class of secondary metabolites with medicinally relevant properties and are synthesized by polyketide synthases (PKS). While Type I PKSs are large biosynthetic machineries composed of a single polypeptide chain, type II PKSs are minimally composed of a ketosynthase-chain length factor (KS-CLF) and a phosphopantetheinylated acyl carrier protein (holo-ACP) expressed separately. Although type II PKSs are found throughout the bacterial kingdom, and despite their importance to strategic bioengineering, type II PKSs have not been well-studied in vitro: In cases where the KS-CLF can be accessed via E. coli heterologous expression, the cognate ACPs are not activatable by the broad specificity Bacillus subtilis surfactin-producing phosphopantetheinyl transferase (PPTase) Sfp and, conversely, in systems where the ACP can be activated by Sfp, the corresponding KS-CLF is typically not readily obtained. Here, we report the high-yield heterologous expression of both cyanobacterial Gloeocapsa sp. PCC 7428 minimal type II PKS (gloPKS) components in E. coli, which allowed us to functionally reconstitute this minimal type II PKS in vitro. Initially, neither the cognate PPTase nor Sfp converted gloACP to its active holo state. However, by examining sequence differences between Sfp-compatible and -incompatible ACPs, we identified two conserved residues in gloACP that, when mutated, enabled high-yield phosphopantetheinylation of gloACP by Sfp. Using analogous mutations, other previously Sfp-incompatible type II PKS ACPs from different bacterial phyla were also rendered activatable by Sfp. This demonstrates the generalizability of our approach and breaks down a longstanding barrier to type II PKS studies and the exploration of complex biosynthetic pathways.

biochemistry↗

Integrated K+ channel and K+-Cl- cotransporter functions regulate fin proportionality in zebrafish

The coordination of growth during development establishes proportionality within and among the different anatomic structures of organisms. Innate memory of this proportionality is preserved, as shown in the ability of regenerating structures to return to their original size. Although the regulation of this coordination is incompletely understood, mutant analyses of zebrafish with long-finned phenotypes have uncovered important roles for bioelectric signaling in modulating growth and size of the fins and barbs. To date, long-finned mutants identified are caused by hypermorphic mutations, leaving unresolved whether such signaling is required for normal development. We isolated a new zebrafish mutant, schleier, with proportional overgrowth phenotypes caused by a missense mutation and loss of function in the K+-Cl- cotransporter Kcc4a. Genetic depletion of Kcc4a in wild-type fish leads to a dose-dependent loss of growth restriction in fins and barbs, supporting a requirement for Kcc4a in regulation of proportion. Epistasis experiments suggest that Kcc4a and the two-pore potassium channel Kcnk5b both contribute to a common bioelectrical signaling response in the fin. These data suggest that an integrated bioelectric signaling pathway is required for the coordination of size and proportion during development.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC=\"FIGDIR/small/621243v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@2ba7b0org.highwire.dtl.DTLVardef@e3df5org.highwire.dtl.DTLVardef@105b878org.highwire.dtl.DTLVardef@920b54_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements

A high quality genome annotation greatly facilitates successful cell line engineering. Standard draft genome annotation pipelines are based largely on de novo gene prediction, homology, and RNA-Seq data. However, draft annotations can suffer from incorrectly predictions of translated sequence, incorrect splice isoforms and missing genes. Here we generated a draft annotation for the newly assembled Chinese hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally annotate the genome. We identified 4,333 new proteins compared to the hamster RefSeq protein annotation and 2,503 novel translational events (e.g., alternative splices, mutations, novel splices). Finally, we used this pipeline to identify the source of translated retroviruses contaminating recombinant products from Chinese hamster ovary (CHO) cell lines, including 131 type-C retroviruses, thus enabling future efforts to eliminate retroviruses by reducing the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate platform for guiding CHO cell line engineering, including facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.

bioinformatics↗