Biology subjects

Davis, C.

Publications and source records attributed to Davis, C..

5 recordsLinked to original sources

bioRxiv2018

Functional clustering of dendritic activity during decision-making

The active properties of dendrites support local nonlinear operations, but previous imaging and electrophysiological measurements have produced conflicting views regarding the prevalence of local nonlinearities in vivo. We imaged calcium signals in pyramidal cell dendrites in the motor cortex of mice performing a tactile decision task. A custom microscope allowed us to image the soma and up to 300 m of contiguous dendrite at 15 Hz, while resolving individual spines. New analysis methods were used to estimate the frequency and spatial scales of activity in dendritic branches and spines. The majority of dendritic calcium transients were coincident with global events. However, task-associated calcium signals in dendrites and spines were compartmentalized by dendritic branching and clustered within branches over approximately 10 m. Diverse behavior-related signals were intermingled and distributed throughout the dendritic arbor, potentially supporting a large computational repertoire and learning capacity in individual neurons.

neuroscience↗

bioRxiv2018

Engineered Microbes to Sense and Respond to Enterotoxigenic Escherichia coli

Every year, Enterotoxigenic Escherichia coli (ETEC), the most common form of travelers diarrhea, affects thousands of military personnel deployed overseas. The goal of this research was to engineer non-pathogenic E. coli to sense ETEC, respond to its presence, and package the non-pathogenic E. coli in a cellulose matrix to enable environmental detection of ETEC. Two plasmids were created: sense-respond; and packaging. The sense-respond plasmid detected autoinducer 2 (AI-2), a quorum sensing molecule created by most ETEC strains, by expressing LsrR which switches on the Lsr promoter. Activation of the Lsr promoter expresses superfolder green fluorescent protein (sfGFP), indicating the presence of ETEC. The packaging plasmid expresses a fusion protein consisting of curli fibers and cellulose binding domains. These modified surface proteins permit the bacteria to bind to cellulose, encapsulating the sense-response module. This genetically engineered machine could be deployed in both the internal and external environment to detect ETEC.

synthetic biology↗

bioRxiv2017

Reconstructing deep-time paleoclimate legacies unveil the demise and turnover of the ancient (boreo)tropical flora

AimSince the Late Cretaceous, the Earth has gone through periods of climate change similar in scale and pace to the warming trend observed today in the Anthropocene. The impact of these ancient climatic events on the evolutionary trajectories of organisms provides clues on the organismal response to climate change, including extinction, migration or persistence. Here, we examine the evolutionary response to climate cooling/warming events of the clusioid families Calophyllaceae, Podostemaceae and Hypericaceae (CPH), and the genus Hypericum as test cases.\n\nLocationHolarctic.\n\nTime periodLate Cretaceous-Cenozoic\n\nMajor taxa studiedangiosperms\n\nMethodsWe use paleoclimate simulations, species distribution models and phylogenetic comparative approaches calibrated with fossils.\n\nResultsAncestral CPH lineages could have been distributed in the Holarctic 100 Ma, occupying tropical subhumid assemblages, a finding supported by the fossil record. Expansion to closed-canopy tropical rain forests occurred after 60 Ma, in the Cenozoic, in agreement with earlier ideas of a post-Cretaceous origin of current tropical rain forest. Cooling during this period triggered diversification declines on CPH tropical lineages, and was associated with a climatic shift towards temperate affinities in Hypericum. Hypericum subsequently migrated to tropical mountains where it encountered different temperate conditions than in the Holarctic.\n\nMain conclusionsWe hypothesize that most clusioid CPH lineages failed to adapt to temperate regimes during periods of Cenozoic climate change, and thus went extinct in the Holarctic. In contrast, boreotropical descendants including Hypericum that underwent niche evolution demonstrated selective advantages as climates became colder. Our results points toward macroevolutionary trajectories involving the altering fates of closely related clades that adapt to periods of global climate change versus those that do not. Moreover, they suggest the hypothesis that potentially many clades, particularly inhabitants of boreotropical floras, were likely extirpated from the Holarctic and persist today (if at all) in more southern tropical locations.

evolutionary biology↗

bioRxiv2017

Mineral analysis of complete dog and cat foods in the UK and compliance with European guidelines

The mineral content of complete pet food is regulated to ensure health of the companion animal population. A comprehensive analysis of adherence to these regulatory guidelines has not been conducted. We measured mineral composition of a range of complete wet (n=97) and dry (n=80) canine and feline pet food sold in the UK to assess compliance with EU guidelines. While a majority of foods complied with [≥]8 of 11 guidelines (99% and 83% for dry and wet food, respectively), many failed to provide nutritional minimum (e.g. Cu, 20 % of wet food) or exceeded nutritional maximum (e.g. Se, 76% of wet food). Only 6% (6/97) of wet and 39% (34/80) of dry food were fully compliant. Some foods (20-30% of all analysed) had mineral imbalances such as not having the recommended balance of Ca:P (between 1:1 to 2:1). Foods with high fish content had high levels of undesirable metal elements such as arsenic. The study highlights broad non-compliance of a range of popular pet foods sold in the UK with EU guidelines (95% and 61% of wet and dry foods, respectively). If fed exclusively and over an extended period, a number of these pet foods could impact the general health of companion animals.

zoology↗

bioRxiv2017

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, reference gene collections remain incomplete: many gene models are fragmentary, while thousands more remain uncatalogued-particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third-generation long-read sequencing. We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574 / 561 gene loci, respectively. CLS approximately doubles the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enable us to definitively characterize the genomic features of lncRNAs, including promoter- and gene-structure, and protein-coding potential. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.\n\nAbbreviations

genomics↗