Biology subjects

Peters, J. M.

Publications and source records attributed to Peters, J. M..

5 recordsLinked to original sources

bioRxiv2018

Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria

Introductory paragraphThe vast majority of bacteria, including human pathogens and microbiome species, lack genetic tools needed to systematically associate genes with phenotypes. This is the major impediment to understanding the fundamental contributions of genes and gene networks to bacterial physiology and human health. CRISPRi, a versatile method of blocking gene expression using a catalytically inactive Cas9 protein (dCas9) and programmable single guide RNAs (sgRNAs), has emerged as a powerful genetic tool to dissect the functions of essential and non-essential genes in species ranging from bacteria to human. However, the difficulty of establishing effective CRISPRi systems in non-model bacteria is a major barrier to its widespread use to dissect bacterial gene function. Here, we establish \"Mobile-CRISPRi\", a suite of CRISPRi systems that combine modularity, stable genomic integration and ease of transfer to diverse bacteria by conjugation. Focusing predominantly on human pathogens associated with antibiotic resistance, we demonstrate the efficacy of Mobile-CRISPRi in Proteobacteria and Firmicutes at the individual gene scale by examining drug-gene synergies and at the library scale by systematically phenotyping conditionally essential genes involved in amino acid biosynthesis. Mobile-CRISPRi enables genetic dissection of non-model bacteria, facilitating analyses of microbiome function, antibiotic resistances and sensitivities, and comprehensive screens for host-microbe interactions.

microbiology↗

bioRxiv2018

Presurgical language fMRI: Current technical practices in epilepsy surgical planning

Little is known about how language functional MRI (fMRI) is executed in clinical practice in spite of its widespread use. Here we comprehensively documented its execution in surgical planning in epilepsy. A questionnaire focusing on cognitive design, imaging acquisition, analysis and interpretation and practical considerations was developed. Individuals responsible for collecting, analyzing, and interpreting clinical language fMRI data at 63 epilepsy surgical programs responded. The central finding was of marked heterogeneity in all aspects of fMRI. Most programs use multiple tasks, with a fifth routinely using 2, 3, 4 or 5 tasks with a modal run duration of five minutes. Variants of over fifteen protocols are in routine use with forms of noun-verb generation, verbal fluency, and semantic decision-making used most often. Nearly all aspects of data acquisition and analysis vary markedly. Neither of the two best-validated protocols were used by more than 10% of respondents. Preprocessing steps are broadly consistent across sites, language-related blood flow is most often identified using general linear modeling (76% of respondents), and statistical thresholding typically varies by patient (79%). The software SPM is most often used. fMRI programs inconsistently include input from experts with all required skills (imaging, cognitive assessment, MR physics, statistical analysis, brain-behavior relationships). These data highlight marked gaps between the evidence supporting fMRI and its clinical application. Teams performing language fMRI may benefit from evaluating practice with reference to the best-validated protocols to date and ensuring individuals trained in all aspects of fMRI are involved to optimize patient care.

neuroscience↗

bioRxiv2017

Fluid mediated self-organization of ventilation in honeybee nests

European honey bees (Apis mellifera) live in large congested nest cavities with a single opening that limits passive ventilation. These nests are actively ventilated by individual bees which fan their wings at the nest entrance when the local air temperature exceeds a threshold. Here we show that colonies with relatively large nest entrances use an emergent ventilation strategy where fanning bees self-organize to form fanning groups, separating regions of continuous inflow and outflow. The observed spatio-temporal patterns correlate the air velocity and air temperature along the entrances to the distribution of fanning bees. A mathematical model that couples these variables to known fanning behavior of individuals recapitulates their collective dynamics. Additionally, the model makes predictions about the temporal stability of the fanning group as a function of the temperature difference between the environment and the nest. Consistent with these predictions, we observe that the fanning groups drift, cling to the entrance boundaries, break-up and reform as the ambient temperature varies over a period of days. Overall, our study shows how honeybees use flow-mediated communication to self-organize into a steady-state in fluctuating environments.

animal behavior and cognition↗

bioRxiv2017

Collective mechanical adaptation of honeybee swarms

Honeybee Apis mellifera swarms form clusters made solely of bees attached to each other, forming pendant structures on tree branches (1). These clusters can be hundreds of times the size of a single organism. How these structures are stably maintained under the influence of static gravity and dynamic stimuli (e.g. wind) is unknown. To address this, we created pendant conical clusters attached to a board that was shaken with varying amplitude, frequency and total duration. Our observations show that horizontally shaken clusters spread out to form wider, flatter cones, i.e. the cluster adapts to the dynamic loading conditions, but in a reversible manner - when the loading is removed, the cluster recovers its original shape, slowly. Measuring the response of a cluster to a sharp pendular excitation before and after it adapted shows that the flattened cones deform less and relax faster than the elongated ones, i.e. they are more stable mechanically. We use particle-based simulations of a passive assemblage to suggest a behavioral hypothesis that individual bees respond to local variations in strain. This behavioral response improves the collective stability of the cluster as a whole at the expense of increasing the average mechanical burden experienced by the individual. Simulations using this rule explain our observations of adaptation to horizontal shaking. The simulations also suggest that vertical shaking will not lead to significant differential strains and thus no adaptation. To test this, we shake the cluster vertically and find that indeed there is no response to this stimulus. Altogether, our results show how an active, functional super-organism structure can respond adaptively to dynamic mechanical loading by changing its morphology to achieve better load sharing.

animal behavior and cognition↗

bioRxiv2017

Presurgical language fMRI: Current practices and patient outcomes in epilepsy surgical planning

The goal of this study was to document current clinical practice and report patient outcomes in presurgical language functional MRI (fMRI) for epilepsy surgery. Epilepsy surgical programs worldwide were surveyed as to the utility, implementation, and efficacy of language fMRI in the clinic; 82 programs responded between July 2015 and January 2016. Respondents were predominantly from the US (61%), were academic programs (85%), and predominantly evaluated adults (44%), both adults and children (40%), or children only (16%). Nearly all (96%) respondents reported using language fMRI. fMRI is used for language lateralization (100%) and for localizing (44%) language cortex to guide surgical margins. While typically considered useful, programs often reported at least one instance of disagreement with other measures (56%). When used to localize language cortex, direct brain stimulation typically confirmed fMRI findings (74%) but instances of unpredicted decline were reported by 17% of programs and unexpected preservation of function were reported by 54%. Programs reporting unexpected decline did not clearly differ from those which did not. Clinicians using fMRI to guide surgical margins typically map Brocas and Wernickes areas but not other known language areas. Language fMRI is widely used for lateralizing language cortex in patients with medically intractable epilepsy. It is also frequently used to localize language cortex though it is not yet well validated for this purpose. Many centers report cases of unexpected language preservation when fMRI activation is resected, and cases of language decline when it is not. Care will almost certainly be improved by standardizing protocols and accurately detailing the relationship between fMRI-positive areas and post-surgical language decline.

neuroscience↗