Biology subjects

Willis, J.

Publications and source records attributed to Willis, J..

8 recordsLinked to original sources

bioRxiv2023

How do conservationists choose where to publish?

Conservation literature addresses a broad spectrum of interdisciplinary questions and benefits most by representing a diverse range of authors, particularly those from countries where much conservation work is focused. In other disciplines, it is well known that barriers and biases exist in the academic publishing sphere, which can impact research dissemination and an authors career development. Here, we used a Discrete Choice Experiment to determine how different journal attributes impact authors choices of where to publish in conservation. We identified three demographic groups across 1038 respondents who have previously published in conservation journals, each exhibiting different publishing preferences. Only two attributes showed a consistent response across groups: cost to publish negatively impacted journal choice, including for those in high-income countries, and authors had a consistent preference for double-blind review. Authors from middle-income countries were willing to pay more for society-owned journals, unlike authors from higher-income countries. Journals with a broad geographical scope, which were Open Access, and which had higher impact factors were preferable to two of the three demographic groups. However, we found journal scope and Open Access were more important in dictating journal choice than impact factor. Overall, our findings demonstrate that different demographics experience different preferences or limitations depending on attributes such as a journals Open Access policy. However, the scarcity of published authors from low-income countries highlights further, pervasive barriers to representation in conservation research. Based on our findings, we provide recommendations to conservation-related journals to reduce barriers to publishing and ultimately benefit conservation science.

scientific communication and education↗

bioRxiv2021

Liver Endothelium Microenvironment Promotes HER3-mediated Cell Survival in KRAS Wild-type and Mutant Colorectal Cancer

We previously showed that liver endothelial cells (ECs) secreted soluble factors in a paracrine fashion and activated human epidermal growth factor receptor 3 (HER3, also known as ERBB3) for promoting colorectal cancer (CRC) growth and chemoresistance. However, RAS proteins play a critical role in receptor tyrosine kinase signaling pathways, and KRAS mutations mediate CRC resistance to therapies targeting EGFR, another HER protein. Therefore, the role of KRAS mutation status in EC-induced HER3 activation and CRC survival was investigated as it has therapeutic implications. We used CRC cell lines and patient-derived xenografts harboring KRAS wild-type or mutant genes and demonstrated that liver EC-secreted factors promoted HER3-mediated CRC cell growth independent of KRAS mutation status. Also, blocking HER3 in CRC cells by siRNAs or a HER3 antibody seribantumab blocked EC-induced CRC survival. Our findings highlight the potential of utilizing HER3 targeted therapies for treating patients with mCRC independent of RAS mutational status.

cancer biology↗

bioRxiv2020

Sensei: How many samples to tell evolution in single-cell studies?

1AO_SCPLOWBSTRACTC_SCPLOWCellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific expression profiles and abundance across heterogeneous cancer samples obtained from clinical trials and preclinical studies. However, challenges remain in determining sample sizes needed for ascertaining changes in cell type abundances in a controlled study. To address this statistical challenge, we have developed a new approach, named Sensei, to determine the number of samples and the number of cells that are required to ascertain such changes between two groups of samples in single-cell studies. Sensei expands the t-test and models the cell abundances using a beta-binomial distribution. We evaluate the mathematical accuracy of Sensei and provide practical guidelines on over 20 cell types in over 30 cancer types based on knowledge acquired from the cancer cell atlas (TCGA) and prior single-cell studies. We provide a web application to enable user-friendly study design via https://kchen-lab.github.io/sensei/table_beta.html.

bioinformatics↗

bioRxiv2019

A new method for measuring fish swimming patterns in shallow water and a previously undescribed swimming gait

Hill stream loaches are fish which live their entire lives in close contact with rock. They have elaborate physical adaptations to fast flow, adherence to substrate, and movement in very shallow water. Here we describe a method for observing how they swim in detail. There are many similarly shaped rheophilic fish, insects, and amphibian larvae, which live in fast flowing water, and a method of observing their swimming modes has wide potential application. We measured the deflection of the water surface around a swimming fish by viewing a fixed pattern on the bottom of the tank through the water surface. This is a Schlieren method in which the movement or other physical properties of a medium are derived from the deflection of a pattern viewed through that medium. We used this method to describe a new type of swimming gait which is likely to be common among small rheophiles - pulse swimming mode - in which thrust is produced in a series of discrete impulses. The method of analysis described here is beneficial in that the fish is allowed to swim freely in relatively normal conditions without the use of intrusive equipment such as lasers, dyes, or additives to the water, and the pattern of thrust is viewed directly against the skin of the fish rather than being inferred from the wake pattern behind the fish. The method is also low cost and easily set up.

zoology↗

bioRxiv2019

Restoration, dispersal and settlement of native European oyster (Ostrea edulis) in energetic tidal areas

We modelled the pelagic larval phase of native European oyster (Ostrea edulis) in the Solent. The Solent is a complex and tidally energetic environment on the south coast of the UK. Until recently it was the largest self-sustaining fishery of the native oyster in Europe. We developed a new larval settlement behavioural model that is the simplest plausible model which remains consistent with all available data and evidence on larval behaviour. We used a hydrodynamic sub-model, a Lagrangian advection sub-model, and an individual agent based model. The results demonstrate how isolated oyster assemblages can re-populate larger areas of historical inhabitance. We predict the most likely patterns of redistribution from refugia or from fisheries seeding. We show that settlement swimming behaviour is as equally important as passive hydrodynamic transport for larval survival and adult distribution and that settlement swimming behaviour has a profound impact on settlement patterns. The models show that managed broodstock refugia have the potential to seed much larger oyster beds in contrast to broad-scale seeding. Such refugia have the advantage of maintaining a locally high and mature population with potential for reef features and their associated biodiversity. We show that such refugia may be best placed in the tidally dynamic and exposed areas rather than on sheltered coastal sites as they have been in the past. Our model is insensitive to parameter variation and could be an effective and practical management tool in the face of a paucity of field data on larval distribution and behaviour.

zoology↗

bioRxiv2019

The structure and function of the sucker systems of hill stream loaches

Hill stream loaches (family Balitoridae and Gastromyzontidae) are thumb-sized fish that effortlessly exploit environments where flow rates are so high that potential competitors would be washed away. To cope with these extreme flow rates hill stream loaches have evolved adaptations to stick to the bottom, equivalent to the downforce generating wings and skirts of F1 racing cars, and scale architecture reminiscent of the drag-reducing riblets of Mako sharks. Hill stream loaches exhibit far more diverse flow-modifying morphological features than fast pelagic predators, suggesting as yet unknown drag reducing systems remain to be discovered. Here we describe the skeletal structure of Sewellia lineolata and Gastromyzon punctulatus and contrast that with other fish that face similar hydrodynamic challenges. We identify a major structural variation within Balitoridae pelvic sucker attachment positions which may explain fundamental constraints on the parallel development of different genera and which has not been described before. We also use high speed video capture, CT scans and Frustrated Total Internal Reflection to image and measure the sucker system in live operation and describe how it functions on a familiar activity for hill stream loaches (climbing waterfalls). We show how they can drag 3 to 4 times their own bodyweight up a vertical glass waterfall. Adaptations to high flow rates are the inspiration for this study, because there are many engineering applications where the ability to deal with high flow rates are important - either by reducing drag, or by generating the forces needed to hold an animal in place.

zoology↗

bioRxiv2019

Teleost fish can accurately estimate distance travelled

Terrestrial animals compute shortcuts through their environment by integrating self-motion vectors containing distance and direction information. The sensory and neural mechanisms underlying this navigational feat have been extensively documented, but their evolutionary origins remain unexplored. Among extant vertebrates, the teleost fish make up one of the most diverse and earliest-branching phylogenetic groups, and provide a powerful system to study the origins of vertebrate spatial processing. However, how freely-swimming teleost fish collect and compute metric spatial information underwater are unknown. Using the Picasso triggerfish, Rhinecanthus aculeatus, we investigate the functional and mechanistic basis of distance estimation in teleost fish for the first time. We show that a fish can learn and remember distance travelled with remarkable accuracy. By analysing swimming trajectories, we form hypotheses about how distance is represented in the teleost brain, and propose that distance may be encoded by dedicated neural structures in a similar way to terrestrial vertebrates. Finally, we begin exploring the sensory mechanisms underlying distance estimation in fish. Many walking animals use a step counter for odometry. By quantifying finbeat use during our distance task, we show that a functionally equivalent finbeat counter is unlikely to provide reliable and precise distance information in an aquatic environment.

animal behavior and cognition↗

bioRxiv2017

nextPARS: Parallel probing of RNA structures in Illumina

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in-vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing.

genomics↗