Biology subjects

Keenan, T.

Publications and source records attributed to Keenan, T..

9 recordsLinked to original sources

bioRxiv2024

Thermal acclimation of stem respiration reduces global carbon burden

Stem respiration is a key driver of carbon flux from ecosystems to the atmosphere, yet its response to global warming remains poorly constrained. In particular it has been proposed that stem respiration acclimates to changing temperatures, which could have large implications for carbon cycling under climate change, but no theory exists to predict acclimated respiration rates. Here, we hypothesized that stem respiration is physiologically linked to transpiration in order to maintain hydraulic continuity. We then use that linkage, combined with Eco-evolutionary optimality theory, to develop a theoretical prediction of the temperature sensitivity of both acclimated and instantaneous stem respiration. Leveraging an extensive global dataset, we observe temperature sensitivities of stem respiration across geographical and seasonal variations that are consistent with this prediction. Our findings reveal that stem respiration contributes approximately a quarter of the global above-ground auto-trophic respiration, with an estimated annual emission of around 11.20 {+/-} 5.88 Pg C--comparable to total anthropogenic emissions. Importantly, incorporating thermal acclimation of stem respiration into projections significantly reduces predicted land ecosystem carbon emissions by 4.41 and 9.56 Pg C under the SSP126 and SSP585 scenarios, respectively, for the 21st century.

ecology↗

bioRxiv2023

Integrating Shear Flow and Trypsin Treatment to Assess Cell Adhesion Strength

Cell adhesion is of fundamental importance in cell and tissue organization, and for designing cell-laden constructs for tissue engineering. Prior methods to assess cell adhesion strength for strongly adherent cells using hydrodynamic shear flow either involved the use of specialized flow devices to generate high shear stress or used simpler implementations like larger height parallel plate chambers that enable multi-hour cell culture but generate low shear stress and are hence more applicable for weakly adherent cells. Here, we propose a shear flow assay for adhesion strength assessment of strongly adherent cells that employs off-the-shelf parallel plate chambers for shear flow as well as simultaneous trypsin treatment to tune down the adhesion strength of cells. We implement the assay with a strongly adherent cell type and show that shear stress in the 0.07 to 7 Pa range is sufficient to dislodge the cells with simultaneous trypsin treatment. Imaging of cells over a square centimeter area allows cell morphological analysis of hundreds of cells. We show that the cell area of cells that are dislodged, on average, does not monotonically increase with shear stress at the higher end of shear stresses used and suggest that this can be explained by the likely higher resistance of high circularity cells to trypsin digestion. The adhesion strength assay proposed can be easily adapted by labs to assess the adhesion strength of both weakly and strongly adherent cell types and has the potential to be adapted for substrate stiffness-dependent adhesion strength assessment in mechanobiology studies.

bioengineering↗

bioRxiv2023

Distribution of carbon monoxide (CO) in several tissues from Atlantic bottlenose dolphins (Tursiops truncatus)

Carbon monoxide (CO) is known as "The Silent Killer" due to its toxic effect at high concentrations, leading to an impairment in oxygen storage, delivery, and use. The cytotoxicity of CO is due to its high affinity for transition metals, such as iron, where CO outcompetes oxygen for the heme binding sites on hemoproteins in the body. CO is made in vivo in most organisms as a byproduct of heme degradation via heme oxygenase enzymes. Certain species of deep-diving marine mammals with high quantities of hemoproteins in blood and skeletal muscle have naturally elevated concentrations of CO in these tissues. To date, there exist few data on extravascular tissue CO content in wild animals. This study aims to characterize CO concentrations in nine different tissues from stranded Atlantic bottlenose dolphins (Tursiops truncatus). We found three tissues (liver, skeletal muscle, and spleen) have higher CO concentrations than other tissues. In a subset of samples from animals that tested positive for dolphin morbillivirus, the CO content in their kidney and liver was lower when compared to animals that tested negative. The mean CO concentration found in every tissue from dolphins was higher than those previously reported in healthy rodents. However, the skeletal muscle CO concentrations in dolphins from this study were much lower than those of deep-diving elephant seals. These results highlight the diversity and pattern of CO found in different tissues from bottlenose dolphins and continues to show that the heme oxygenase/carbon monoxide pathway appears to be critical for air-breathing divers.

physiology↗

bioRxiv2021

Cell-specific Bioorthogonal Tagging of Glycoproteins in Co-culture

Altered glycosylation is an undisputed corollary of cancer development. Understanding these alterations is paramount but hampered by limitations underlying cellular model systems. For instance, the intricate interactions between tumour and host cannot be adequately recapitulated in monoculture of tumour-derived cell lines. More complex co-culture models usually rely on sorting procedures for proteome analyses and rarely capture the details of protein glycosylation. Here, we report a strategy termed Bio-Orthogonal Cell line-specific Tagging of Glycoproteins (BOCTAG). Cells are equipped by transfection with an artificial biosynthetic pathway that transforms bioorthogonally tagged sugars into the corresponding nucleotide-sugars. Only transfected cells incorporate bioorthogonal tags into glycoproteins in the presence of non-transfected cells. We employ BOCTAG as an imaging technique and to annotate cell-specific glycosylation sites in mass spectrometry-glycoproteomics. We demonstrate application in co-culture and mouse models, allowing for profiling of the glycoproteome as an important modulator of cellular function.

synthetic biology↗

bioRxiv2020

Clinical interpretation of integrative molecular profiles to guide precision cancer medicine

Individual tumor molecular profiling is routinely used to detect single gene-variant ("first-order") genomic alterations that may inform therapeutic actions -- for instance, a tumor with a BRAF p.V600E variant might be considered for RAF/MEK inhibitor therapy. Interactions between such first-order events (e.g., somatic-germline) and global molecular features (e.g. mutational signatures) are increasingly associated with clinical outcomes, but these "second order" alterations are not yet generally accounted for in clinical interpretation algorithms and knowledge bases. Here, we introduce the Molecular Oncology Almanac (MOAlmanac), a clinical interpretation algorithm paired with a novel underlying knowledge base to enable integrative interpretation of genomic and transcriptional cancer data for point-of-care treatment decision-making and translational hypothesis generation. We compared MOAlmanac to first-order interpretation methodology in multiple retrospective patient cohorts and observed that the inclusion of preclinical and inferential evidence as well as second-order molecular features increased the number of nominated clinical hypotheses. MOAlmanac also performed matchmaking between patient molecular profiles and cancer cell lines to further expand individualized clinical actionability. When applied to a prospective precision oncology trial cohort, MOAlmanac nominated a median of two therapies per patient and identified therapeutic strategies administered in 46% of patient profiles. Overall, we present a novel computational method to perform integrative clinical interpretation of individualized molecular profiles. MOAlmanc increases clinical actionability over conventional approaches by considering second-order molecular features and additional evidence sources, and is available as an open-source framework.

cancer biology↗

bioRxiv2020

Utilizing Quantum Biological Techniques on a Rigetti QPUfor Improved Protein Binding Simulation

Iff Technologies has constructed a tool named Polar+ that can predict protein-to-protein binding that operates faster and at a higher quality than the prominent industry standards for protein binding, including Autodock Vina and SwissDock. The ability to provide this advantage over other market leaders comes from a new approach to biophysics, dubbed many-body biological quantum systems, that are modeled using quantum processing units and quantum algorithms provided by Rigetti. This paper provides both experimental and theoretical evidence behind the validity of the quantum biology approach to protein modeling, an overview of the first experimental work completed by Polar+, and a review of results obtained compared to other tools and data found in the lab.

bioinformatics↗

bioRxiv2020

A standardized head-fixation system for performing large-scale, in-vivo physiological recordings in mice

BACKGROUNDThe Allen Institute recently built a set of high-throughput experimental pipelines to collect comprehensive in vivo surveys of physiological activity in the visual cortex of awake, head-fixed mice. Developing these large-scale, industrial-like pipelines posed many scientific, operational, and engineering challenges. NEW METHODOur strategies for creating a cross-platform reference space to which all pipeline datasets were mapped required development of 1) a robust headframe, 2) a reproducible clamping system, and 3) data-collection systems that are built, and maintained, around precise alignment with a reference artifact. RESULTSWhen paired with our pipeline clamping system, our headframe exceeded deflection and reproducibility requirements. By leveraging our headframe and clamping system we were able to create a cross-platform reference space to which multi-modal imaging datasets could be mapped. COMPARISON WITH EXISTING METHODSTogether, the Allen Brain Observatory headframe, surgical tooling, clamping system, and system registration strategy create a unique system for collecting large amounts of standardized in vivo datasets over long periods of time. Moreover, the integrated approach to cross-platform registration allows for multi-modal datasets to be collected within a shared reference space. CONCLUSIONSHere we report the engineering strategies that we implemented when creating the Allen Brain Observatory physiology pipelines. All of the documentation related to headframe, surgical tooling, and clamp design has been made freely available and can be readily manufactured or procured. The engineering strategy, or components of the strategy, described in this report can be tailored and applied by external researchers to improve data standardization and stability.

neuroscience↗

bioRxiv2018

Thermal acclimation of leaf respiration consistent with optimal plant function

Main Main References Introduction Terrestrial plant respiration is a major component of the global carbon cycle, releasing ca. 60 Pg C yr-1 to the atmosphere: six times more than anthropogenic CO2 emissions from all sources combined (Ciais et al. 2014). About half this flux is leaf maintenance respiration in darkness (Rd) (Atkin et al. 2007). Rd is highly temperature-dependent, following a near-exponential relationship over short time-scales (Heskel et al. 2016). It has been predicted that global warming will increase Rd and accelerate future climate change via a carbon-climate feedback (Cox et al. 2000; Huntingford et al. 2013). However, large uncertainties in future ...

ecology↗

bioRxiv2018

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.

neuroscience↗