bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic Design of Pulse Dosing to Eradicate Persister Bacteria
Authors: Singh Garima , Orman Mehmet A. , Conrad Jacinta C. , Nikolaou Michael
Published: May 2022

A small fraction of infectious bacteria use persistence as a strategy to survive exposure to antibiotics. Periodic pulse dosing of antibiotics has long been considered a potentially effective strategy towards eradication of persisters. Recent studies have demonstrated throughin vitroexperiments that it is indeed feasible to achieve such effectiveness. However, systematic design of periodic pulse dosing regimens to treat persisters is currently lacking. Here we rigorously develop a methodology for the systematic design of optimal periodic pulse dosing strategies for rapid eradication of persisters. A key outcome of the theoretical analysis, on which the proposed methodology is based, is that bactericidal effectiveness of periodic pulse dosing depends mainly on the ratio of durations of the corresponding on and off parts of the pulse. Simple formulas for critical and optimal values of this ratio are derived. The proposed methodology is supported by computer simulations andin vitroexperiments.

Author Summary

Administering antibiotics in periodic pulses that alternate between high and low concentration has long been known as a possible dosing strategy to treat stubborn infections caused by bacteria known aspersisters. Such bacteria use clever mechanisms to survive otherwise lethal temporary exposure to antibiotics and to resume normal activity upon antibiotic removal. Persisters pose a serious health problem. Recent studies have elucidated mechanisms of persistence and have confirmed that pulse dosing, if designed appropriately, can indeed be effective. However, effective pulse dosing design has been mainly handled by trial and error, requiring relatively extensive experimentation. Here we develop a method for rapid systematic design of effective pulse dosing. The method relies on a simple mathematical model and a minimal amount of standard experimental data. We derive corresponding design formulas that explicitly characterize the shape of generally effective or optimal periodic pulses. We tested our method through computer simulations andin vitroexperiments, as well as on prior literature data. In all cases, the outcomes on persister bacteria eradication predicted by our method were confirmed. These results pave the way for ultimately developing effective pulse dosing regimens in realistic situationsin vivo.
Fine-scale diversity of microbial communities due to satellite niches in boom-and-bust environments
Authors: Wang Zihan , Fridman Yulia , Maslov Sergei , Goyal Akshit
Published: May 2022

Recent observations have revealed that closely related strains of the same microbial species can stably coexist in natural and laboratory settings subject to boom-and-bust dynamics and serial dilutions, respectively. However, the possible mechanisms enabling the coexistence of only a handful of strains, but not more, have thus far remained unknown. Here, using a consumer-resource model of microbial ecosystems, we propose that by differentiating on Monod parameters characterizing microbial growth rates in high and low nutrient conditions, strains can coexist in patterns similar to those observed. In our model, boom-and-bust environments create satellite niches due to resource concentrations varying in time. These satellite niches can be occupied by closely related strains, thereby enabling their coexistence. We demonstrate that this result is valid even in complex environments consisting of multiple resources and species. In these complex communities, each species partitions resources differently and creates separate sets of satellite niches for their own strains. While there is no theoretical limit to the number of coexisting strains, in our simulations, we always find between 1 and 3 strains coexisting, consistent with experiments and observations.

Author summary

Recent genomic data has exposed to us the remarkable spectrum of microbial diversity in natural communities surrounding us, which harbor not only hundreds of species, but also a handful of closely related strains within each of those species (termed “oligo-colonization”). While the mechanisms behind species coexistence are much better studied, the mechanisms behind the coexistence of closely related strains have remained understudied. Here, using a simple consumer-resource model, we show that if strains differ on their Monod growth parameters, they can coexist even on a single limiting resource, provided that the environments vary with time in boom-and-bust cycles. The Monod growth parameters describe how a strain’s growth rate changes with resource concentration, namely the half-maximal concentration and maximal growth rate. Simulations of our model show that both in simple and complex environments, even though an arbitrary number of strains can coexist, typically it is between 1 and 3 strains of a species that coexist over several randomly assembled communities, consistent with some experimental observations. This is because the allowed parameter space for coexistence shrinks significantly with the number of strains that coexist.
coiaf: directly estimating complexity of infection with allele frequencies
Authors: Paschalidis Aris , Watson Oliver J. , Aydemir Ozkan , Verity Robert , Bailey Jeffrey A.
Published: May 2022

In malaria, individuals are often infected with different parasite strains; the complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current methods in the literature. Through a sensitivity analysis, we characterize how the bias and accuracy of our two methods are impacted by the distribution of parasite densities and the assumed sequencing depth and number of sampled loci. We further estimate the COI globally from Plasmodium falciparum sequencing data using our developed methods and compare the results against the literature. We show significant differences in estimated COI globally between continents and a weak relationship between malaria prevalence and COI.

Author summary

Computational models, used in conjunction with rapidly advancing sequencing technologies, are increasingly being used to help inform surveillance efforts and understand the epidemiological dynamics of malaria. One such important metric, the complexity of infection (COI), indirectly quantifies the level of transmission. Existing “gold-standard” COI measures rely on complex probabilistic likelihood and Bayesian models. As an alternative, we have developed the statistics and software package coiaf, which features two rapid, direct measures to estimate of the number of genetically distinct parasite strains in an individual (the COI). Our methods were evaluated using simulated data and subsequently compared to current “state-of-the-art” methods, yielding comparable results. Lastly, we examined the distribution of the COI in several locations across the world, identifying significant differences in COI between continents. coiaf, therefore, provides a new, promising framework for rapidly characterizing polyclonal infections.
Orientation control strategies and adaptation to a visuomotor perturbation in rotational hand movements
Authors: Zruya Or , Nisky Ilana
Published: May 2022

Computational approaches to biological motor control are used to discover the building blocks of human motor behavior. Models explaining features of human hand movements have been studied thoroughly, yet only a few studies attempted to explain the control of the orientation of the hand; instead, they mainly focus on the control of hand translation, predominantly in a single plane. In this study, we aimed to establish a basic understanding of the way humans control the orientation of their hands. We developed a quaternion-based score that quantifies the geodicity of rotational hand movements and evaluated it experimentally. In the first experiment participants performed a simple orientation-matching task with a robotic manipulator. We found that rotations are generally performed by following a geodesic in the quaternion hypersphere, which suggests that, similarly to translation, the orientation of the hand is centrally controlled. We also established a baseline for the study of human response to perturbed visual feedback of the orientation of the hand. In the subsequent second experiment we studied the adaptation of participants to visuomotor rotation that is applied on the hand’s rotation, and the transfer of the adaptation to a different initial orientation. We observed partial adaptation to the perturbation. The patterns of the transfer of the adaptation to a different initial orientation were consistent with the representation of the orientation in extrinsic coordinates. The results of the two experiments raise questions regarding the nature of central control of hand orientation. Discussion and intuitions from these results can be of benefit for many applications that involve fine manipulation of rigid bodies, such as teleoperation and neurorehabilitation.

Author summary

Daily motor actions, as simple as pouring a glass of wine or as complicated as playing a violin, require coordinated activation of multiple muscles that synchronize to produce a precise motion of the hand. Controlled by sensorimotor areas in the central nervous system, our muscles can translate and rotate our hand from one posture to another. Our study focused on the very basis of the control of orientation: we attempted to reveal which variables are centrally controlled when we rotate our hand. The discovery that simple rotations are generally performed along a geometrically optimal path established a baseline for studying the response to rotation-based perturbations. By visually remapping the orientation of the hand, we found that humans perceive their hand’s orientation in visual, rather than joint-based coordinates. These findings have implications for the design of human-centered control systems for teleoperation, where visual distortions may occur, and for the design of rehabilitation devices for people with motor impairments.
The evolution of manipulative cheating
Authors: Liu Ming , West Stuart A. , Wild Geoff
Published: May 2022

A social cheat is typically assumed to be an individual that does not perform a cooperative behaviour, or performs less of it, but can still exploit the cooperative behaviour of others. However, empirical data suggests that cheating can be more subtle, involving evolutionary arms races over the ability to both exploit and resist exploitation. These complications have not been captured by evolutionary theory, which lags behind empirical studies in this area. We bridge this gap with a mixture of game-theoretical models and individual-based simulations, examining what conditions favour more elaborate patterns of cheating. We found that as well as adjusting their own behaviour, individuals can be selected to manipulate the behaviour of others, which we term ‘manipulative cheating’. Further, we found that manipulative cheating can lead to dynamic oscillations (arms races), between selfishness, manipulation, and suppression of manipulation. Our results can help explain both variation in the level of cheating, and genetic variation in the extent to which individuals can be exploited by cheats.
Facilitation by a hERG blocker is induced by pore opening and operates by pore reopening
Authors: Furutani Kazuharu , Kawano Ryotaro , Ichiwara Minami , Adachi Ryo , Clancy Colleen E. , Sack Jon T. , Kita Satomi
Published: May 2022

A drug that blocks the cardiac myocyte voltage-gated K+channels encoded by the human Ether-à-go-go-Related Gene (hERG) carries a potential risk of long QT syndrome and life-threatening cardiac arrhythmia, includingTorsade de Points. Interestingly, certain hERG blockers can also facilitate hERG activation to increase hERG currents, which may reduce proarrhythmic potential. However, the molecular mechanism involved in the facilitation effect of hERG blockers remains unclear. The hallmark feature of the facilitation effect by hERG blockers is that a depolarizing preconditioning pulse shifts voltage-dependence of hERG activation to more negative voltages. Here we utilize a D540K hERG mutant to study the mechanism of the facilitation effect. D540K hERG is activated by not only depolarization but also hyperpolarization. This unusual gating property of the D540K hERG channel enables testing of hypotheses about the mechanism by which voltage induces facilitation of hERG by blockers. With D540K hERG, we find that nifekalant, a hERG blocker and Class III antiarrhythmic agent, facilitates not only current activation by depolarization but also current activation by hyperpolarization. Our results indicate that induction of facilitation is coupled to pore opening, not voltageper se. We propose that a gated-access mechanism is involved in the voltage-dependence of induction of facilitation. This study provides a molecular mechanism for modulation of hERG channels by nifekalant, a clinically important antiarrhythmic agent.

Significance statement

Nifekalant is a clinically important antiarrhythmic agent and a hERG blocker which can also facilitate voltage-dependent activation of hERG channels after a preconditioning pulse. Here we show that the mechanism of action of the preconditioning pulse is to open a conductance gate to enable drug access to a facilitation site. Moreover, we find that facilitation increases hERG currents by altering pore dynamics, rather than acting through voltage sensors.
Kidney tubular epithelial cell ferroptosis links glomerular injury to tubulointerstitial pathology in lupus nephritis
Authors: Alli Abdel A , Desai Dhruv , Elshika Ahmed , Morel Laurence , Conrad Marcus , Proneth Bettina , Clapp William , Atkinson Carl , Segal Mark , Searcy Louis A. , Denslow Nancy D. , Bolisetty Subhashini , Mehrad Borna , Scindia Yogesh
Published: May 2022

Objective

An appreciation of factors that lead to tubular injury in lupus nephritis is lacking. Iron accumulates in the kidney tubules of nephritic patients and lupus-prone nephritic mice. Ferroptosis is a druggable, iron-dependent form of cell death that has received little attention in lupus nephritis. This study investigated whether intra-renal ferroptosis is a target for intervention in lupus nephritis.

Methods

Kidneys of lupus nephritis patients and two spontaneous murine models of lupus nephritis were characterized for ferroptosis using protein, RNA, and lipidomics-based approaches. Susceptibility of heavy chain ferritin (FtH1; an essential iron sequestration protein) deficient proximal tubular epithelial cells (PTECs) was studied using nephrotoxic serum nephritis and FtH1 knockdown human PTECs. The benefit of Liproxstatin-2, a novel second-generation ferroptosis, was evaluated using human PTECs exposed to lupus nephritis patients’ serum.

Results

Human and murine nephritic kidneys have the characteristic markers of ferroptosis, such as 4-hydroxynonenal and acyl-CoA synthetase long-chain family member 4, mainly in the tubular segments. Murine kidneys showed impairment in the glutathione synthesis pathway, decreased expression of glutathione peroxidase 4, a glutathione-dependent ferroptosis inhibitor, and characteristic ferroptotic lipid signature. Loss of FtH1 increased PTEC pathology independent of glomerular injury. These findings were recapitulated in human PTECs. Of translational relevance, Liproxstatin-2 demonstrated a prophylactic and therapeutic benefit in mitigating lupus nephritis patient serum-induced PTEC ferroptosis.

Conclusion

Our findings highlight tubular cell ferroptosis as a pathological feature in human and murine lupus nephritis and identify ferroptosis inhibitors as potential novel adjunct therapeutics to treat lupus nephritis.
Hippocampal Concentrations Drive Seizures in a Rat Model for Cefepime-induced Neurotoxicity
Authors: Lesnicki Emily , Pais Gwendolyn M. , Marianski Sylwia , Valdez Kimberly , Gibson Zoe , Christopher Jeffri , Scheetz Marc H.
Published: May 2022

Background

In high dose, cefepime causes neurotoxicity in patients with kidney injury; however, the relationship between exposure and observed neurotoxicity is not clear, and no animal model presently recapitulates the human condition.

Objectives

This study sought to describe plasma and tissue pharmacokinetics and pharmacodynamics (PK/PD) of cefepime in rats experiencing neurotoxicity.

Methods

Male Sprague-Dawley rats (n=21) received escalating cefepime total daily doses ranging from 531-1593 mg/kg body weight/day administered as a short infusion (0.5 mL/min) every 24h for 5 days. Cefepime was quantified in plasma, cerebral cortex and hippocampus via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Multiple PK/PD models of cefepime transit between plasma and brain compartments (i.e. cerebral cortex and hippocampus) and neurotoxic response were explored using Monolix 2021R1 (LixoftPK).

Results

Exposure estimation of cerebral cortex demonstrated a median (IQR) AUC0 –24 and Cmax 0 –24 of 181.8 (85.2-661.3) mg · 24 h/liter and 13.9 (1.0-30.1) mg/L, respectively. The median cerebral cortex/blood percentage of penetration was 1.7%. Exposure estimation of hippocampus demonstrated a median (IQR) AUC0 –24 and Cmax 0 –24 of 291.4 (126.6-1091.6) mg · 24 h/liter and 8.8 (3.4-33.4) mg/L, respectively. The median hippocampus/blood percentage of penetration was 4.5%. Rats that reached a cefepime Cmax of □17 mg/L in the hippocampus exhibited signs of neurotoxicity. A hippocampal cefepime concentration of 4.1 µg/100 mg brain tissue best described seizure stages >1 for cefepime-induced neurotoxicty.

Conclusions

A cefepime plasma AUC0 –24 of 28,000 mg•24h/L and hippocampal concentrations of 4.1 µg/100 mg brain tissue may be a threshold for cefepime-induced neurotoxicity. This model provides a methodology for future interrogation of the relationship between plasma concentrations, brain tissue concentrations, and neurotoxicity.
Signal Transformations and New Timing Rules of Hippocampal CA3 to CA1 Synapses
Authors: Gattas Sandra , Le Aliza A. , Abadchi Javad Karimi , Pruess Ben , Shen Yanning , Swindlehurst A. , Yassa Michael A. , Lynch Gary S.
Published: May 2022

The synapse is the fundamental unit of communication in the nervous system. Determining how information is transferred across the synaptic interface is one of the most complex endeavors in neuroscience, owing to the large number of contributing factors and events. An approach to solving this problem involves collapsing across these complexities to derive concise mathematical formulas that fully capture the governing dynamics of synaptic transmission. We investigated the feasibility of deriving such a formula – an input-output transformation function for the CA3 to CA1 node of the hippocampus -- using the Volterra expansion technique for nonlinear system identification. The entirety of the field EPSP in the apical dendrites of mouse brain slices was described with >94% accuracy by a 2nd order equation that captured the linear and nonlinear influence of past inputs on current outputs. This function generalized to cases not included in its derivation and uncovered previously undetected timing rules. The basal dendrites expressed a substantially different transfer function and evidence was obtained that, unlike the apical system, a 3rd order system or higher will be needed for complete characterization. Collectively, these results describe a readily implemented and unusually sensitive means for evaluating the effects of pharmacological treatments and disease related conditions on synaptic dynamics. At scale, the approach will also provide information needed for the construction of biologically realistic models of brain networks.
Hippocampal place cell remapping occurs with memory storage of aversive experiences
Authors: Blair Garrett J. , Guo Changliang , Wang Shiyun , Fanselow Michael S. , Golshani Peyman , Aharoni Daniel , Blair Hugh T.
Published: May 2022

Aversive stimuli can cause hippocampal place cells to remap their firing fields, but it is not known whether remapping plays a role in storing memories of aversive experiences. Here we addressed this question by performingin-vivocalcium imaging of CA1 place cells in freely behaving rats (n=14). Rats were first trained to prefer a short path over a long path for obtaining food reward, then trained to avoid the short path by delivering a mild footshock. Remapping was assessed by comparing place cell population vector similarity before acquisition versus after extinction of avoidance. Some rats received shock after systemic injections of the amnestic drug scopolamine at a dose (1 mg/kg) that impaired avoidance learning but spared spatial tuning and shock-evoked responses of CA1 neurons. Place cells remapped significantly more following remembered than forgotten shocks (drug-free versus scopolamine conditions); shock-induced remapping did not cause place fields to migrate toward or away from the shocked location and was similarly prevalent in cells that were responsive versus non-responsive to shocks. When rats were exposed to a neutral barrier rather than aversive shock, place cells remapped significantly less in response to the barrier. We conclude that place cell remapping occurs in response to events that are remembered rather than merely perceived and forgotten, suggesting that reorganization of hippocampal population codes may play a role in storing memories for aversive events.
Seeing social: A neural signature for conscious perception of social interactions
Authors: Varrier Rekha S. , Finn Emily S.
Published: May 2022

Percepts of ambiguous information are subjective and depend on observers’ traits and mental states. Social information is some of the most ambiguous content we encounter in our daily lives, yet in experimental contexts, percepts of social interactions—i.e., whether an interaction is present and if so, the nature of that interaction—are often dichotomized as correct or incorrect based on experimenter-assigned labels. Here, we investigated the behavioral and neural correlates of conscious social perception using a large dataset in which neurotypical individuals viewed animations of geometric shapes during fMRI and indicated whether they perceived a social interaction or random motion. Critically, rather than experimenter-assigned labels, we used observers’ own reports of “Social” or “Non-social” to classify percepts and characterize brain activity, including leveraging a particularly ambiguous animation perceived as “Social” by some observers but “Non-social” by others to control for visual input. Observers were biased toward perceiving information as social (versus non-social), and activity across much of the brain was higher during animations ultimately perceived as social. Using “Unsure” reports, we identified several regions that responded parametrically to perceived socialness. Neural responses to social versus nonsocial content diverged early both in time and in the cortical hierarchy. Lastly, individuals with higher internalizing trait scores showed both a higher response bias towards social and an inverse relationship with activity in default-mode and limbic regions while scanning for social information. Findings underscore the subjective nature of social perception and the importance of using observer reports to study percepts of social interactions.

Significance Statement

Simple animations involving two or more geometric shapes have been used as a gold standard to understand social cognition and impairments thereof. Yet experimenter-assigned labels of what is social versus non-social are frequently used as a ground truth, despite the fact that percepts of such ambiguous social stimuli are highly subjective. Here, we used behavioral and fMRI data from a large sample of neurotypical individuals to show that participants’ responses reveal subtle behavioral biases, help us study neural responses to social content more precisely, and covary with internalizing trait scores. Our findings underscore the subjective nature of social perception and the importance of considering observer reports in studying its behavioral and neural dynamics.
Development and validation of an expanded antibody toolset that captures alpha-synuclein pathological diversity in Lewy body diseases
Authors: Altay Melek Firat , Kumar Senthil T. , Burtscher Johannes , Jagannath Somanath , Strand Catherine , Miki Yasuo , Parkkinen Laura , Holton Janice L. , Lashuel Hilal A.
Published: May 2022

The abnormal aggregation and accumulation of alpha-synuclein (aSyn) in the brain is a defining hallmark of synucleinopathies. Different aSyn conformations and post-translationally modified forms accumulate in pathological inclusions and vary in abundance across synucleinopathies. Relying on antibodies that have not been assessed for their ability to capture the diversity of aSyn species may not provide an accurate estimation of aSyn pathology in human brains or disease models. To address this challenge, we developed and characterised an expanded antibody panel that targets different sequences and post-translational modifications along the length of aSyn and recognises all three aSyn conformations (monomeric, oligomeric, fibrillar). Next, we profiled aSyn pathology across sporadic and familial Lewy body diseases (LBDs) and reveal heterogeneously modified aSyn pathologies rich in Serine 129 phosphorylation but also in Tyrosine 39 nitration and N- and C-terminal tyrosine phosphorylations, scattered to neurons and glia. We also show that aSyn may become hyperphosphorylated during the aggregation and inclusion maturation processes in neuronal and animal models of aSyn aggregation and spreading. The antibody validation pipeline we describe here paves the way for more systematic investigations of aSyn pathological diversity in the human brain and peripheral tissues, and in cellular and animal models of synucleinopathies.
Lighting Up Mechanosensation: dyeing to see PIEZO2
Authors: Villarino Nicholas W. , Dubin Adrienne E. , Patapoutian Ardem , Marshall Kara L.
Published: May 2022

Sensory neurons gather information about mechanical forces from both the environment and internal organs to regulate physiology. PIEZO2 is a mechanosensory ion channel critical for touch, proprioception and bladder stretch sensation, yet its broad expression in sensory neurons and elsewhere suggests it may have undiscovered physiological roles. To fully understand mechanosensory physiology, we must know where and when PIEZO2-expressing neurons detect force. The fluorescent styryl dye FM 1-43 was shown to permeate several ion channels in cell culture and label sensory neurons. Surprisingly, we find that the vast majority of FM 1-43 somatosensory neuron labeling in vivo is dependent on PIEZO2-activity within nerve endings. We illustrate the potential of FM 1-43 by using it to identify novel Piezo2-expressing urethral neurons that are engaged by urination. These data reveal that FM 1-43 is a functional probe for mechanosensitivity via PIEZO2 activation in vivo and will facilitate the characterization of known and novel mechanosensory processes.
The encoding of touch by somatotopically aligned dorsal column subdivisions
Authors: Turecek Josef , Lehnert Brendan P. , Ginty David D.
Published: May 2022

The somatosensory system decodes a range of tactile stimuli to generate a coherent sense of touch. Discriminative touch of the body depends on signals conveyed from peripheral mechanoreceptors to the brain via the spinal cord dorsal column and its brainstem target the dorsal column nuclei (DCN)1, 2. Models of somatosensation emphasize that fast-conducting low- threshold mechanoreceptors (LTMRs) innervating the skin drive the DCN3, 4. However, post- synaptic dorsal column neurons (PSDCs) within the spinal cord dorsal horn also collect mechanoreceptor signals and form a second major input to the DCN5–7. The significance of PSDCs and their contributions to the coding of touch have remained unclear since their discovery. Here, we show that direct LTMR inputs to the DCN convey vibrotactile stimuli with high temporal precision, whereas PSDCs primarily encode touch onset and the intensity of sustained contact into the high force range. LTMR and PSDC signals topographically re-align in the DCN to preserve precise spatial detail. Different DCN neuron subtypes have specialized responses that are generated by unique combinations of LTMR and PSDC inputs. Thus, LTMR and PSDC subdivisions of the dorsal column encode different tactile features and differentially converge in the DCN to generate unique ascending sensory processing streams.
ICAT: A Novel Algorithm to Robustly Identify Cell States Following Perturbations in Single Cell Transcriptomes
Authors: Hawkins Dakota Y. , Zuch Daniel T. , Huth James , Rodriguez-Sastre Nahomie , McCutcheon Kelley R. , Glick Abigail , Lion Alexandra T. , Thomas Christopher F. , Descoteaux Abigail E. , Johnson W. Evan , Bradham Cynthia A.
Published: May 2022

Motivation

The detection of distinct cellular identities is central to the analysis of single-cell RNA sequencing experiments. However, in perturbation experiments, current methods typically fail to correctly match cell states between conditions or erroneously remove population substructure. Here we present the novel, unsupervised algorithm ICAT that employs self-supervised feature weighting and control-guided clustering to accurately resolve cell states across heterogeneous conditions.

Results

Using simulated and real datasets, we show ICAT is superior in identifying and resolving cell states compared to current integration workflows. While requiring no a priori knowledge of extant cell states or discriminatory marker genes, ICAT is robust to low signal strength, high perturbation severity, and disparate cell type proportions. We empirically validate ICAT in a developmental model and find that only ICAT identifies a perturbation-unique cellular response. Taken together, our results demonstrate that ICAT offers a significant improvement in defining cellular responses to perturbation in single-cell RNA sequencing data.

Availability and implementation

https://github.com/BradhamLab/icat

Supplemental Methods, Tables and Figures are available online.
Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress
Authors: Naama Maria , Telpaz Shahar , Awad Aya , Ben-Simon Shira , Harshuk-Shabso Sarina , Modilevsky Sonia , Rubin Elad , Sawaed Jasmin , Zelik Lilach , Zigdon Mor , Fadida Nofar , Turjeman Sondra , Werbner Michal , Wongkuna Supapit , Schroeder Bjoern O , Nyska Abraham , Nuriel-Ohayon Meital , Bel Shai
Published: May 2022

Colonic goblet cells are specialized epithelial cells that secrete mucus to form a barrier between the host and its microbiota, thus preventing bacterial invasion and inflammation. How goblet cells control the amount of mucus they secrete is unclear. We found that constitutive activation of autophagy in mice via Beclin 1 led to production of a thicker and less penetrable mucus layer by reducing endoplasmic reticulum (ER) stress. Accordingly, inhibiting Beclin 1-induced autophagy via Bcl-2 impaired mucus secretion. Furthermore, alleviating intestinal ER stress with a bile acid, or activating the unfolded protein response (UPR) pharmacologically via eIF2α phosphorylation, led to excessive mucus production. Over-production of mucus altered the gut microbiome, with expansion of mucus-utilizing bacteria, and protected from intestinal inflammation. Thus, ER stress is a cell-intrinsic switch that limits mucus secretion, while autophagy maintains proper mucus secretion and intestinal homeostasis by relieving ER stress.
Kinematics of individual muscle units in natural contractions measured in vivo using ultrafast ultrasound
Authors: Lubel Emma , Sgambato Bruno Grandi , Barsakcioglu Deren Y. , Ibáñez Jaime , Tang Meng-Xing , Farina Dario
Published: May 2022

Objective

The study of human neuromechanical control at the motor unit (MU) level has predominantly focussed on electrical activity and force generation, whilst the link between these, the muscle deformation, has not been widely studied. An important example of this is excitation-contraction coupling (E-C coupling) – the process by which electrical excitation is converted into contraction in the muscle fibres. Despite this being a clear marker for progression of certain diseases, it cannot be measured in vivo in natural contractions. To address this, we analyse the kinematics of muscle units in natural contractions.

Approach

We combine high density surface electromyography (HDsEMG) and ultrafast ultrasound (US) recordings of a mildly contracted muscle (tibialis anterior) to measure the deformation of the muscular tissue caused by individual MU twitches (decomposed from the HDsEMG). With a novel analysis on the US images we identified, with high spatio-temporal precision, the velocity maps associated with single muscle unit movements. From the individual MU profiles obtained from the velocity maps the region of movement, the duration of the mechanical twitch, the total and active contraction times, and the activation time (equivalent to E-C coupling) were computed.

Main results

The E-C coupling was 3.8 ± 3.0 ms (n = 390), providing the first measurement of this value in for single MUs in non-stimulated contractions. Furthermore, the experimental measures provided the first evidence of single muscle unit twisting during voluntary contractions and showed the presence of MUs with territories with multiple distinct split regions across the muscle region.

Significance

We show that the combined use of HDsEMG and ultrafast US can allow for the study of kinematics of individual MU twitches, including measurement of the excitation-contraction coupling time under natural neural control conditions. These measurements and characterisations open new avenues for study of neuromechanics in healthy and pathological conditions.
An essential experimental control for functional connectivity mapping with optogenetics
Authors: Tadres David , Shiozaki Hiroshi M. , Tastekin Ibrahim , Stern David L. , Louis Matthieu
Published: May 2022

To establish functional connectivity between two candidate neurons that might form a circuit element, a common approach is to activate an optogenetic tool such as Chrimson in the candidate pre-synaptic neuron and monitor fluorescence of the calcium-sensitive indicator GCaMP in a candidate post-synaptic neuron. While performing such experiments, we found that low levels of leaky Chrimson expression can lead to strong artifactual GCaMP signals in presumptive postsynaptic neurons even when Chrimson is not intentionally expressed in any particular neurons. Withholding all-trans retinal, the chromophore required as a co-factor for Chrimson response to light, eliminates GCaMP signal but does not provide an experimental control for leaky Chrimson expression. Leaky Chrimson expression appears to be an inherent feature of current Chrimson transgenes, since artifactual connectivity was detected with Chrimson transgenes integrated into three different genomic locations (two insertions tested in larvae; a third insertion tested in the adult fly). These false-positive signals may complicate the interpretation of functional connectivity experiments. We illustrate how a no-Gal4 negative control improves interpretability of functional connectivity assays. We also propose a simple but effective procedure to identify experimental conditions that minimize potentially incorrect interpretations caused by leaky Chrimson expression.
50 shades of greenbeard: Robust evolution of altruism based on similarity of complex phenotypes
Authors: Båvik Linnéa M , Mehta Rohan S , Weissman Daniel B
Published: May 2022

We study the evolution of altruistic behavior under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently similar to themselves in a multidimensional phenotype space. We find the generic maintenance of robust altruism when phenotypes are multidimensional. Selection for altruism is driven by the coevolution of individual strategy and phenotype; altruism levels shape the distribution of individuals in phenotype space. Low donation rates induce a phenotype distribution that renders the population vulnerable to the invasion of altruists, whereas high donation rates prime a population for cheater invasion, resulting in cyclic dynamics that maintain substantial levels of altruism. Altruism is therefore robust to invasion by cheaters in the long term in this model. Furthermore, the shape of the phenotype distribution in high phenotype dimension—which is potentially more biologically relevant than low phenotype dimension—allows altruists to better resist the invasion by cheaters, and as a result the amount of donation increases with increasing phenotype dimension. We also generalize previous results in the regime of weak selection to two competing strategies in continuous phenotype space, and show that success under weak selection is crucial to success under strong selection in our model. Our results support the viability of a simple similarity-based mechanism for altruism in a well-mixed population.
Leucine-Rich Repeat Kinase 2 limits dopamine D1 receptor signaling in striatum and biases against heavy persistent alcohol drinking
Authors: da Silva e Silva Daniel , Matsui Aya , Murray Erin M. , Mamais Adamantios , Shaw Marlisa , Ron Dorit , Cookson Mark R. , Alvarez Veronica A.
Published: May 2022

The transition from hedonic alcohol drinking to problematic drinking is a hallmark of alcohol use disorder that occurs only in a subset of drinkers. This transition is known to require long-lasting changes in the synaptic drive and the activity of striatal neurons expressing dopamine D1 receptor (D1R). The molecular mechanisms that generate vulnerability in some individuals to undergo the transition are less understood. Here, we report that the Parkinson’s-related protein leucine-rich repeat kinase 2 (LRRK2) modulates striatal D1R function to affect the behavioral response to alcohol and the likelihood that mice transition to heavy, persistent alcohol drinking. Deletion of theLrrk2gene specifically from D1R-expressing neurons potentiates D1R signaling at the cellular and synaptic level, enhancing alcohol-related behaviors and drinking. Mice with cell-specific deletion ofLrrk2are more prone to heavy alcohol drinking and consumption is insensitive to punishment. These findings identify a novel role for LRRK2 function in the striatum in promoting resilience against heavy and persistent alcohol drinking.
High frequency DBS-like optogenetic stimulation of nucleus accumbens dopamine D2 receptor-containing neurons attenuates cocaine reinstatement in male rats
Authors: Swinford-Jackson Sarah E. , Huffman Phillip J. , Knouse Melissa C. , Thomas Arthur S. , Mankame Sharvari , Worobey Samantha J. , Sarmiento Mateo , Coleman Ayanna , Pierce R. Christopher
Published: May 2022

Background

Previous work indicated that deep brain stimulation (DBS) of the nucleus accumbens shell in male rats attenuated reinstatement of cocaine seeking, an animal model of craving. However, the potential differential impact of DBS on specific populations of neurons to drive the suppression of cocaine seeking is unknown. Medium spiny neurons in the nucleus accumbens are differentiated by expression of dopamine D1 receptors (D1DRs) or D2DRs, activation of which promotes or inhibits cocaine-related behaviors, respectively. The advent of transgenic rat lines expressing Cre recombinase selectively in D1DR-containing or D2DR-containing neurons, when coupled with Cre-dependent virally mediated gene transfer of channelrhodopsin (ChR2), enabled mimicry of DBS in a selective subpopulation of neurons during complex tasks.

Hypothesis

We tested the hypothesis that high frequency DBS-like optogenetic stimulation of D1DR-containing neurons in the accumbens shell would potentiate, whereas stimulation of D2DR-containing neurons in the accumbens shell would attenuate, cocaine-primed reinstatement of cocaine seeking.

Results

Results indicated that high frequency, DBS-like optogenetic stimulation of D2DR-containing neurons attenuated reinstatement of cocaine seeking in male rats, whereas DBS-like optogenetic stimulation of D1DR-containing neurons did not alter cocaine-primed reinstatement. Surprisingly, DBS-like optogenetic stimulation did not alter reinstatement of cocaine seeking in female rats. In rats which only expressed eYFP, intra-accumbens optogenetic stimulation did not alter cocaine reinstatement relative to sham stimulation, indicating that the effect of DBS-like stimulation to attenuate cocaine reinstatement is mediated specifically by ChR2 rather than consequent to prolonged light delivery.

Conclusions

These results suggest that DBS of the accumbens attenuates cocaine-primed reinstatement in male rats through the selective manipulation of D2DR-containing neurons.
The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution
Authors: Nair Surag , Barrett Arjun , Li Daofeng , Raney Brian J , Lee Brian T , Kerpedjiev Peter , Ramalingam Vivekanandan , Pampari Anusri , Lekschas Fritz , Wang Ting , Haeussler Maximilian , Kundaje Anshul
Published: May 2022

We introduce the dynseq genome browser track, which displays DNA nucleotide characters scaled by user-specified, base-resolution scores provided in the BigWig file format. The dynseq track enables visualization of context-specific, informative genomic sequence features. We demonstrate its utility in three popular genome browsers for interpreting cis-regulatory sequence syntax and regulatory variant interpretation by visualizing nucleotide importance scores derived from machine learning models of regulatory DNA trained on protein-DNA binding and chromatin accessibility experiments.
A proton pump enhancing photosynthesis links phagocytosis to marine algae symbiogenesis
Authors: Yee Daniel P. , Samo Ty J. , Abbriano Raffaela M. , Shimasaki Bethany , Vernet Maria , Mayali Xavier , Weber Peter K. , Mitchell B. Greg , Hildebrand Mark , Tresguerres Martin
Published: May 2022

Diatoms, dinoflagellates, and coccolithophorids are the dominant groups of marine eukaryotic phytoplankton collectively responsible for the majority of primary production in the ocean1. These phytoplankton contain additional intracellular membranes around their chloroplasts derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary endosymbiosis2. This symbiogenesis hypothesis for the origin of modern secondary endosymbiotic phytoplankton is supported by a wealth of palaeontologic, morphologic, and genomic evidence3–6. However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton are unknown. We report that the proton-pumping enzyme V-type H+-ATPase (VHA), ubiquitously used in eukaryotic intercellular digestion, is localized around the chloroplasts of centric diatoms and that VHA-activity significantly enhances photosynthesis over a wide range of oceanic irradiances. Similar results in pennate diatoms, dinoflagellates, and coccolithophorids, but not green or red microalgae, imply a mechanism resulting from the co-option of phagocytic VHA activity into a carbon concentrating mechanism that is common to secondary endosymbiotic phytoplankton. Furthermore, analogous VHA-dependent mechanisms in extant photosymbiotic marine invertebrates7–9 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Our results suggest that VHA-dependent enhancement of photosynthesis contributes at least 7% of primary production in the ocean, providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.
Clavis: an open and versatile identification key format
Authors: Koch Wouter , Elven Hallvard , Finstad Anders G.
Published: May 2022

The skills and knowledge needed to recognize and classify taxa are becoming increasingly scarce in the scientific community. At the same time, it is clear that these skills are strongly needed in biodiversity monitoring for management and conservation, especially when carried out by citizen scientists. Formalizing the required knowledge in the form of digital identification keys is one way of making such knowledge more available for professional and amateur observers of biodiversity. In this paper we describe Clavis, an open and versatile data format for capturing the knowledge required for taxon identification through digital keys, allowing for a level of detail beyond that of any current key format. We present the format independently from any particular implementation, as our aim is for Clavis to serve as a basis for interoperable tools and interfaces serving different needs and actors.
Experimental effects of within-brood genetic variation on parasite resistance in a wild bird host
Authors: Gutiérrez Jessica , Taff Conor C. , Tupy Suzannah , Goncalves Catherine , Knutie Sarah A.
Published: May 2022

Hosts can differ in parasite susceptibility across individuals, populations, and species. Genetic variation can influence parasite susceptibility by affecting host resistance to parasitism. For example, genetic variation among related individuals, such as within broods of offspring, might be a key factor influencing within-brood resistance to ectoparasitism. The goal of this study was to determine if within-brood variation of eastern bluebirds (Sialia sialis) affects susceptibility to ectoparasitic blowflies (Protocalliphora sialia). To address the goal, we conducted a partial cross-fostering study for which half of the nestlings were cross-fostered (experimental) or not (control). Nestling physiology (i.e., glucose, hemoglobin, and parasite-specific IgY antibody levels), morphometrics (i.e., mass, tarsus length, bill length, and first primary feather), survival, nestling status (resident versus fostered), and sex were characterized. We also quantified parasite abundance, life stage, and pupal size. We found that experimental nests had fewer parasites and more larvae than pupae compared to control nests, which suggest that within-brood genetic variation affects parasite abundance. However, this effect was driven by the sex ratio with the experimental nests, with female-biased nests having fewer parasites than male-biased nests. Treatment did not affect nestling morphometrics, physiology, or survival at the nest level. Within experimental nests, resident females had significantly higher hemoglobin levels when compared to fostered females. Resident and fostered males and fostered females had significantly higher glucose levels than resident females. Together, these results suggest that resident females were fed upon less than fostered females and may have been less stressed than males and fostered females. Overall, our study demonstrates the importance of considering within-brood variation and nestling sex in understanding host-parasite interactions.