bluuebunny/crossref_metadata_2025 huggingface dataset:
A neuromorphic model of active vision shows spatio-temporal encoding in lobula neurons can aid pattern recognition in bees
Authors: MaBouDi HaDi , Roper Mark , Guiraud Marie-Genevieve , Chittka Lars , Marshall James A.R.
Published: June 2023

Bees possess remarkable cognitive abilities in on-the-fly visual learning, making them an ideal model for studying active information acquisition and representation. In this study, we investigated the minimal circuitry required for active vision in bees by considering their flight behaviours during visual pattern scanning. By developing a neural network model inspired by the insect visual system, we examined the influence of scanning behaviour on optic lobe connectivity and neural activity. Through the incorporation of non-associative learning and exposure to diverse natural images, we obtained compelling results that align with neurobiological observations. Our findings reveal that active scanning and non-associative learning dynamically shape the connectivity within the visual lobe, resulting in an efficient representation of visual input. Interestingly, we observed self-organization in orientation-selective neurons in the lobula region, characterized by sparse responses to orthogonal bar movements. These dynamic orientation-selective cells cover various orientations, exhibiting a bias towards the speed and contrast of input sampling. To assess the effectiveness of this spatiotemporal coding for pattern recognition, we integrated our model with the mushroom body circuitry underlying associative learning. Notably, our model demonstrated impressive performance across several pattern recognition tasks, suggesting a similar coding system within the bee visual system. Overall, this study integrates behavioural experiments, neurobiological findings, and computational models to reveal how complex visual features can be condensed through spatiotemporal encoding in the lobula neurons, facilitating efficient sampling of visual cues for identifying rewarding foraging resources. Our findings have broader implications for understanding active vision in diverse animals, including humans, and offer valuable insights for the application of bio-inspired principles in the design of autonomous robots.
Mimicry in motion: A grasshopper species that looks like, and moves like, a sympatric butterfly
Authors: Loeffler-Henry Karl , Kang Changku , Dawson Jeff W. , Sherratt Thomas N.
Published: June 2023

Flash displays describe the sudden revealing of a conspicuous signal by an otherwise cryptic animal as it is fleeing from predators. One hypothesis for flash displays is that they have evolved to mislead predators into adopting an inappropriate search strategy following pursuit. Thus, if predators believe that the fleeing prey item will also be conspicuous when settled, then they will tend to give up searching sooner if they fail to find it. Naturally, if this hypothesis is correct then one might expect that the value of the flash display would cease once predators learn the flasher’s true resting appearance. However, even if predators are aware that the resting appearance of the signaller could be cryptic, flash displays will still be selected for if the flasher resembles another species that maintains its conspicuous appearance throughout. Motivated by this insight, we quantified the degree of chromatic and behavioral resemblance between the Carolina grasshopper (Dissosteira carolina) and mourning cloak butterfly (Nymphalis antiopa), a sympatric species with which it is commonly confused. The close similarity in both morphology and flight behavior (in the field and lab) between these distantly related species strongly suggests that they are in a mimetic relationship. It is unclear why this mimicry has evolved. One explanation is that mimicry has arisen through selection to maintain the efficacy of the flash display through search disruption even after predator learning. Another possibility is that the grasshopper has evolved to resemble the butterfly because the latter is harder to catch (evasive mimicry). However, we argue that pursuit and search disruption are entirely complementary explanations for the mimetic resemblance because they interfere with predation at two different stages of the attack sequence.
DesiRNA: structure-based design of RNA sequences with a Monte Carlo approach
Authors: Wirecki Tomasz , Lach Grzegorz , Jaryani Farhang , Badepally Nagendar Goud , Moafinejad S. Naeim , Klaudel Gaja , Bujnicki Janusz M.
Published: June 2023

RNA sequences underpin the formation of complex and diverse structures, subsequently governing their respective functional properties. Despite the pivotal role RNA sequences play in cellular mechanisms, creating optimized sequences that can predictably fold into desired structures remains a significant challenge. We have developed DesiRNA, a versatile Python-based software tool for RNA sequence design. This program considers a comprehensive array of constraints, ranging from secondary structures (including pseudoknots) and GC content, to the distribution of dinucleotides emulating natural RNAs. Additionally, it factors in the presence or absence of specific sequence motifs and prevents or promotes oligomerization, thereby ensuring a robust and flexible design process. DesiRNA utilizes the Monte Carlo algorithm for the selection and acceptance of mutation sites. In tests on the EteRNA benchmark, DesiRNA displayed high accuracy and computational efficiency, outperforming most existing RNA design programs.
Brain Templates for Chinese Babies from Newborn to Three Months of Age
Authors: Geng Xiujuan , Chen Peggy HY , Lam Hugh S , Chu Winnie CW , Wong Patrick CM
Published: June 2023

The infant brain develops rapidly and this area of research has great clinical implications. Neurodevelopmental disorders such as autism and developmental delay have their origins, potentially, in abnormal early brain maturation. Searching for potential early neural markers requiresa prioriknowledge about infant brain development and anatomy. One of the most common methods of characterizing brain features requires normalization of individual images into a standard stereotactic space and conduct of group-based analyses in this space. A population representative brain template is critical for these population-based studies. Little research is available on constructing brain templates for typical developing Chinese infants. In the present work, a total of 112 babies from 6 to 98 days of age were included with high resolution structural magnetic resonance imaging scans. T1-weighted and T2-weighted templates were constructed using an unbiased registration approach for babies from newborn to 3 months of age. Age-specific templates were also estimated for babies aged at 0, 1, 2 and 3 months old. Then we conducted a series of evaluations and statistical analyses over whole tissue segmentations and brain parcellations. Compared to the use of population mismatched templates, using our established templates resulted in lower deformation energy to transform individual images into the template space and produced a smaller registration error, i.e., smaller standard deviation of the registered images. Significant volumetric growth was observed across total brain tissues and most of the brain regions within the first three months of age. The total brain tissues exhibited larger volumes in baby boys compared to baby girls. To the best of our knowledge, this is the first study focusing on the construction of Chinese infant brain templates. These templates can be used for investigating birth related conditions such as preterm birth, detecting neural biomarkers for neurological and neurodevelopmental disorders in Chinese populations, and exploring genetic and cultural effects on the brain.
Dual mechanism of kinetochore microtubule detachment
Authors: Conway William , Ha Gloria , Needleman Daniel
Published: June 2023

During eukaryotic cell division, microtubules connect to chromosomes by attaching to the kinetochore via the NDC80 complex (NDC80c). The regulation of kinetochore microtubule (KMT) detachment is crucial for correcting mitotic errors. Here, we investigate the mechanism of KMT detachment by combining photoconversion measurements of KMT detachment rate, FLIM-FRET measurements of NCD80c/KMT binding, and mathematical modeling. Our results support a dual detachment mechanism in which KMTs detach from kinetochores when either 1) all NDC80c spontaneously unbind from the KMT or 2) following KMT catastrophe. We identify kinetochore components that selectively impact these two mechanisms and show that the affinity of NDC80c for KMTs is reduced at low-tension, non-bioriented kinetochores due to centromere-localized Aurora B phosphorylating the NDC80c, resulting in an elevated detachment rate for the associated KMTs. Taken together, this work leads to a biophysical model for the molecular basis of KMT detachments and their regulation during mitotic error correction.
Motion direction is represented as a bimodal probability distribution in the human visual cortex
Authors: Chetverikov Andrey , Jehee Janneke F.M.
Published: June 2023

How do humans infer motion direction from noisy sensory signals? We hypothesized that motion direction is computed not only from velocity but also spatial orientation signals – a ‘streak’ created by moving objects. We implemented this hypothesis in a Bayesian model, which quantifies knowledge with probability distributions, and tested its predictions using psychophysics and fMRI. Using a probabilistic pattern-based analysis, we decoded probability distributions of motion direction from trial-by-trial activity in the human visual cortex. Corroborating the predictions, the decoded distributions had a bimodal shape, with peaks that predicted the direction and magnitude of behavioral errors. Interestingly, we observed similar bimodality in the distribution of the observers’ behavioral responses across trials. Together, these results suggest that observers use spatial orientation signals when estimating motion direction. More broadly, our findings indicate that the cortical representation of low-level visual features, such as motion direction, can reflect a combination of several qualitatively distinct signals.
One thousand samples per day capillary-flow LC/MS/MS for high-speed, high-sensitivity and in-depth proteomics
Authors: Tomioka Ayana , Tomioka Ryota , Mori Issei , Isobe Yosuke , Arita Makoto , Imami Koshi , Kanao Eisuke , Ogata Kosuke , Ishihama Yasushi
Published: June 2023

We developed a capillary-flow LC/MS/MS system with ultrahigh speed, enabling a throughput of 1,000 samples per day while maintaining high sensitivity and depth of analysis. In targeted LC/MS mode, 36 endogenous phosphopeptides in HeLa cells, including EphA2- derived phosphopeptide isomers, were successfully quantified with high selectivity and linearity by combining ion mobility separation. When 500 ng of HeLa cell digest was measured 100 times repeatedly in data-dependent acquisition mode, the coefficient of variation of retention time, peak intensity and number of identified peptides were on average 3.4%, 19.8%, and 6.0%, respectively. In data-independent acquisition mode, this system achieved the identification and quantification of 3,139 protein groups from a 100 ng HeLa cell digest and 2,145 protein groups from a sample of only 10 ng. The coefficient of variation of protein commonly quantified in the triplicate analysis ranged from 12 to 24% for HeLa digest samples ranging from 10 to 1000 ng. Finally, we applied this high-speed system to the spatial proteomics of the mouse brain, and succeeded in capturing the proteome distribution along a 96-sectioned brain structure in 135 minutes. This is the first LC/MS/MS system to achieve both more than 500 samples per day and more than 3000 identified protein groups ID with less than 100 ng human cultured cells simultaneously.
Metabolomic analysis ofDrosophila melanogasterlarvae lacking Pyruvate kinase
Authors: Heidarian Yasaman , Tourigny Jason P. , Fasteen Tess D. , Mahmoudzadeh Nader H. , Hurlburt Alexander J. , Nemkov Travis , Reisz Julie A. , D’Alessandro Angelo , Tennessen Jason M.
Published: June 2023

Pyruvate kinase (Pyk) is a rate-limiting enzyme that catalyzes the final metabolic reaction in glycolysis. The importance of this enzyme, however, extends far beyond ATP production, as Pyk is also known to regulate tissue growth, cell proliferation, and development. Studies of this enzyme inDrosophila melanogaster, however, are complicated by the fact that the fly genome encodes six Pyk paralogs whose functions remain poorly defined. To address this issue, we used sequence distance and phylogenetic approaches to demonstrate that the genePykencodes the enzyme most similar to the mammalian Pyk orthologs, while the other fiveDrosophilaPyk paralogs have significantly diverged from the canonical enzyme. Consistent with this observation, metabolomic studies of two differentPykmutant backgrounds revealed that larvae lacking Pyk exhibit a severe block in glycolysis, with a buildup of glycolytic intermediates upstream of pyruvate. However, our analysis also unexpectedly reveals that steady state pyruvate levels are unchanged inPykmutants, indicating that larval metabolism maintains pyruvate pool size despite severe metabolic limitations. Consistent with our metabolomic findings, a complementary RNA-seq analysis revealed that genes involved in lipid metabolism and peptidase activity are elevated inPykmutants, again indicating that loss of this glycolytic enzyme induces compensatory changes in other aspects of metabolism. Overall, our study provides both insight into how Drosophila larval metabolism adapts to disruption of glycolytic metabolism as well as immediate clinical relevance, considering that Pyk deficiency is the most common congenital enzymatic defect in humans.
Dopamine alters the effect of brain stimulation on decision-making
Authors: Leow Li-Ann , Marcos Anjeli , Nielsen Esteban , Sewell David K , Ballard Tim , Dux Paul E. , Filmer Hannah L.
Published: June 2023

Non-invasive brain stimulation techniques, such as transcranial direct current stimulation (tDCS), show promise in treating cognitive and behavioural impairments in clinical conditions. However, optimisation of such clinical applications requires a better understanding of how tDCS alters cognition and behaviour. Existing evidence implicates dopamine in the way tDCS alters brain activity and plasticity, however, there is as yet no causal evidence for a role of dopamine in tDCS effects on cognition and behaviour. Here, in a preregistered, double-blinded study, we examined how pharmacologically manipulating dopamine altered the effect of tDCS on the speed-accuracy trade-off, which taps ubiquitous strategic cognitive processes. Cathodal tDCS was delivered over the left prefrontal cortex and the superior medial frontal cortex before participants completed a dot-motion task, deciding the direction of moving dots under instructions to emphasize speed, accuracy, or both. We leveraged computational modelling to uncover how our manipulations altered latent decisional processes driving the speed-accuracy tradeoff. We show that dopamine in combination with tDCS (but not tDCS alone, nor dopamine alone) not only impaired decision accuracy, but also impaired discriminability, which suggests that these manipulations altered the encoding or representation of discriminative evidence. This is, to the best of our knowledge, the first direct evidence implicating dopamine in the way tDCS affects cognition and behaviour.

Significance statement

Transcranial direct current stimulation (tDCS) can improve cognitive and behavioural impairments in clinical conditions, however better understanding of its mechanisms is required to optimise future clinical applications. Here, using a pharmacological approach to manipulate brain dopamine levels in healthy adults, we demonstrate a role for dopamine in the effects of tDCS in the speed-accuracy trade-off, a strategic cognitive process ubiquitous in many contexts. In doing so, we provide direct evidence implicating dopamine in the way tDCS affects cognition and behaviour.
Impaired cerebellar plasticity hypersensitizes sensory reflexes inSCN2A-associated ASD
Authors: Wang Chenyu , Derderian Kimberly D. , Hamada Elizabeth , Zhou Xujia , Nelson Andrew D. , Kyoung Henry , Ahituv Nadav , Bouvier Guy , Bender Kevin J
Published: June 2023

Children diagnosed with autism spectrum disorder (ASD) commonly present with sensory hypersensitivity, or abnormally strong reactions to sensory stimuli. Such hypersensitivity can be overwhelming, causing high levels of distress that contribute markedly to the negative aspects of the disorder. Here, we identify the mechanisms that underlie hypersensitivity in a sensorimotor reflex found to be altered in humans and in mice with loss-of-function in the ASD risk-factor geneSCN2A. The cerebellum-dependent vestibulo-ocular reflex (VOR), which helps maintain one’s gaze during movement, was hypersensitized due to deficits in cerebellar synaptic plasticity. Heterozygous loss ofSCN2A-encoded NaV1.2 sodium channels in granule cells impaired high-frequency transmission to Purkinje cells and long-term potentiation, a form of synaptic plasticity important for modulating VOR gain. VOR plasticity could be rescued in adolescent mice via a CRISPR-activator approach that increasesScn2aexpression, highlighting how evaluation of simple reflexes can be used as quantitative readout of therapeutic interventions.
Genetic factors explaining anthocyanin pigmentation differences
Authors: Recinos Maria F. Marin , Pucker Boas
Published: June 2023

Background

Anthocyanins represent one of the most abundant coloration factors found in plants. Biological functions of anthocyanins range from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins.

Results

A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties across flowering plant species was performed. Literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from previous studies were reanalyzed to determine the genes most likely to be responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the pigmentation differences was quantified. Gene expression differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are substantially more likely to explain pigmentation differences than bHLH or WD40 genes.

Conclusions

These findings support previous assumptions about the plasticity of transcriptional regulation and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent dominant role in the specificity of the MBW complex.
Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study
Authors: Monteiro Higor S. , Lima Neto Antonio S. , Kahn Rebecca , Sousa Geziel S. , Carmona Humberto A. , Andrade José S. , Castro Marcia C.
Published: June 2023

Background

Although CoronaVac was the only Covid-19 vaccine adopted in the first months of the Brazilian vaccination campaign, randomized clinical trials to evaluate its efficacy in elderly adults were limited. In this study, we use routinely collected surveillance and SARS-CoV-2 vaccination and testing data comprising the population of the fifth largest city of Brazil to evaluate the effectiveness of CoronaVac in adults 60+ years old against severe outcomes.

Methods

Using large observational databases on vaccination and surveillance data from the city of Fortaleza, Brazil, we defined a retrospective cohort including 324,302 eligible adults aged ≥ 60 years to evaluate the effectiveness of the CoronaVac vaccine. The cohort included individuals vaccinated between January 21, 2021, and August 31, 2021, who were matched with unvaccinated persons at the time of rollout following a 1:1 ratio according to baseline covariates of age, sex, and Human Development Index of the neighborhood of residence. Only Covid-19-related severe outcomes were included in the analysis: hospitalization, ICU admission, and death. Vaccine effectiveness for each outcome was calculated by using the risk ratio between the two groups, with the risk obtained by the Kaplan-Meier estimator.

Results

We obtained 62,643 matched pairs for assessing the effectiveness of the two-dose regimen of CoronaVac. The demographic profile of the matched population was statistically representative of the population of Fortaleza. Using the cumulative incidence as the risk associated with each group, starting at day 14 since the receipt of the second dose, we found an 82.3% (95% CI 66.3 - 93.9) effectiveness against Covid-19-related death, 68.4% (95% CI 42.3 - 86.4) against ICU admission, and 55.8% (95% CI 42.7 - 68.3) against hospital admission.

Conclusions

Our results show that, despite critical delays in vaccine delivery and limited evidence in efficacy trial estimates, CoronaVac contributed to preventing deaths and severe morbidity due to Covid-19 in elderly adults.
Quality of Systematic Reviews in Dental Journals Published from India: A Methodological Review
Authors: Mathew Rohan Thomas , Babu Anu
Published: June 2023

Background

Evidence-based medicine (EBM) is a crucial aspect of modern medical practice, emphasizing the use of the best available evidence to inform clinical decision-making. Systematic reviews (SRs) play a key role in EBM by integrating and evaluating findings from multiple studies. However, the methodological quality of SRs can vary, and assessing their quality is essential for accurate interpretation and application of the findings.

Methods

This study aims to analyze the methodological quality of SRs published in dentistry journals from India between 2015 and 2020. A comprehensive search was conducted, resulting in the inclusion of 130 SRs from 21 journals.

Results

The findings reveal several discrepancies in the methodological quality of the included SRs. Only a small percentage of SRs were registered in the PROSPERO registry, and adherence to PRISMA guidelines was limited. The majority of SRs did not assess scientific quality, such as risk of bias and publication bias, adequately. Furthermore, the study highlights a lack of awareness and support for conducting high-quality SRs, including limited funding and insufficient utilization of standardized guidelines.

Conclusion

The authors suggest that increasing awareness among researchers, editors, and funding agencies, as well as adopting standardized guidelines and protocols, can improve the quality and quantity of SRs produced in India. Overall, this study emphasizes the need to enhance the methodological rigor of SRs in dentistry to ensure reliable evidence for clinical decision-making.
Neural substrates of top-down processing during perceptual duration-based timing and beat-based timing
Authors: Niida Mitsuki , Haruki Yusuke , Imai Fumihito , Ogawa Kenji
Published: June 2023

Temporal context is a crucial factor in timing. Previous studies have revealed that the timing of regular stimuli, such as isochronous beats or rhythmic sequences (termed beat-based timing), activated the basal ganglia, whereas the timing of single intervals or irregular stimuli (termed duration-based timing) activated the cerebellum. We conducted a functional magnetic resonance imaging (fMRI) experiment to determine whether top-down processing of perceptual duration-based and beat-based timings affected brain activation patterns. Our participants listened to auditory sequences containing both single intervals and isochronous beats and judged either the duration of the intervals or the tempo of the beats. Whole-brain analysis revealed that both duration judgments and tempo judgments activated similar areas, including the basal ganglia and cerebellum, with no significant difference in the activated regions between the two conditions. In addition, an analysis of the regions of interest revealed no significant differences between the activation levels measured for the two tasks in the basal ganglia as well as the cerebellum. These results suggested that a set of common brain areas were involved in top-down processing of both duration judgments and tempo judgments. Our findings indicate that perceptual duration-based timing and beat-based timing are driven by stimulus regularity irrespective of top-down processing.
Humans Exploit the Trade-Off Between Lateral Stability and Manoeuvrability During Walking
Authors: Kulkarni Rucha , Grover Francis M. , Shafer Anna , Schmitz Xenia , Gordon Keith E.
Published: June 2023

People use the mechanical interplay between stability and manoeuvrability to successfully walk. During single limb support, body states (position and velocity) that increase lateral stability will inherently resist lateral manoeuvres, decrease medial stability, and facilitate medial manoeuvres. Although not well understood, people can make behavioural decisions exploiting this relationship in anticipation of perturbations or direction changes. To characterize the behavioural component of the stability-manoeuvrability relationship, twenty-four participants performed many repetitions of a discrete stepping task involving mid-trial reactive manoeuvres (medial or lateral direction) in a Baseline (no external perturbations) and Perturbed (random mediolateral perturbations applied to their pelvis) environment. We hypothesized people would make systematic changes in lateral stability dependent on both environment (increasing lateral stability in the Perturbed environment) and anticipated manoeuvre direction (reducing lateral stability to facilitate lateral manoeuvres). Participants increased lateral stability in the Perturbed environment, coinciding with an increase in manoeuvre reaction time for laterally but not medially directed manoeuvres. Moreover, we observed lower lateral stability in both environments when people anticipated making a lateral manoeuvre when compared to medial manoeuvres. These results support the hypothesis that people behaviourally exploit the mechanical relationship between lateral stability and manoeuvrability depending on walk task goals and external environment.
A Spatiotemporal Compartmentalization of Glucose Metabolism Guides Mammalian Gastrulation Progression
Authors: Cao Dominica , Zhong Liangwen , Hemalatha Anupama , Bergmann Jenna , Cox Andy L. , Greco Valentina , Sozen Berna
Published: June 2023

Gastrulation is considered thesine qua nonof embryogenesis, establishing a multidimensional structure and the spatial coordinates upon which all later developmental events transpire. At this time, the embryo adopts a heavy reliance on glucose metabolism to support rapidly accelerating changes in morphology, proliferation, and differentiation. However, it is currently unknown how this conserved metabolic shift maps onto the three-dimensional landscape of the growing embryo and whether it is spatially linked to the orchestrated cellular and molecular processes necessary for gastrulation. Here we identify that glucose is utilised during mouse gastrulation via distinct metabolic pathways to instruct local and global embryonic morphogenesis, in a cell type and stage-specific manner. Through detailed mechanistic studies and quantitative live imaging of mouse embryos, in parallel with tractablein vitrostem cell differentiation models and embryo-derived tissue explants, we discover that cell fate acquisition and the epithelial-to-mesenchymal transition (EMT) relies on the Hexosamine Biosynthetic Pathway (HBP) branch of glucose metabolism, while newly-formed mesoderm requires glycolysis for correct migration and lateral expansion. This regional and tissue-specific difference in glucose metabolism is coordinated with Fibroblast Growth Factor (FGF) activity, demonstrating that reciprocal crosstalk between metabolism and growth factor signalling is a prerequisite for gastrulation progression. We expect these studies to provide important insights into the function of metabolism in other developmental contexts and may help uncover mechanisms that underpin embryonic lethality, cancer, and congenital disease.
Continuous Measures of Decision-Difficulty Captured Remotely: II. Webcam eye-tracking reveals early decision processing
Authors: Bertrand Jennifer K. , Zuk Alexandra A. Ouellette , Chapman Craig S.
Published: June 2023

As decisions require the gathering of relevant information, eye-tracking measures that capture the way visual information is typically acquired offer powerful indices of the dynamic decision-making process. This study is the second of a pair of studies that explore continuous measures of decision-making using remote, online tools in naturalistic settings. While cursor-tracking, used in the companion paper (Ouellette Zuk et al., 2023), enabled access to dynamic decision processes expressed during movement, in the present study, we now employ webcam eye-tracking to examine the dynamics of information gathering during decision making prior to movement initiation. Using three previously published binary choice tasks, we explored indices of decision difficulty in the gaze dynamics that would complement the motor measures in our companion paper. We find that harder choices elicit more eye dwells and longer final dwells, reflecting a decision resolution process that Ouellette Zuk et al. index during the final choice movement. Beyond this, we identify distinct gaze patterns uniquely employed in each task, revealing the utility and sensitivity of gaze metrics in illuminating the early difficulty-independent information gathering processes at play. Together, this paper series demonstrates the power of remote, online methods as tools for deeply understanding the complete, dynamic and continuous decision process, from the first glance to the final response.
Role of Mce proteins inMycobacterium avium paratuberculosisinfection
Authors: Blake Rose , Jensen Kirsty , Alfituri Omar , Mabbott Neil , Hope Jayne , Stevens Jo
Published: June 2023

Mycobacterium aviumsubspeciesparatuberculosis(MAP) is the causative agent of Johne’s Disease, a chronic granulomatous enteritis of ruminants. MAP establishes an infection in the host via the small intestine. This requires the bacteria to adhere to and be internalised by cells of the intestinal tract. The effector molecules expressed by MAP for this remain to be fully identified and understood. The mammalian cell entry (Mce) proteins play an essential role for other Mycobacterial species to facilitate the attachment and invasion of host epithelial cells. Here, we have expressed Mce1A, Mce1D, Mce3C and Mce4A proteins derived from MAP on the surface of a non-invasiveE. colihost to characterise their role in the initial interaction between MAP and the host. To this end,mce1Awas found to significantly increase the ability of theE. colito attach and survive intracellularly in THP-1 cells, andmce1Dwas found to significantly increase attachment and invasion of MDBK cells. Both genes were implicated in the increased ability ofE. colito infect 3D bovine basal-out enteroids. Together, these results have identified two effector molecules used by MAP with a degree of cell-type specificity.
Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5
Authors: Hehl Laura A. , Horn-Ghetko Daniel , Prabu J. Rajan , Vollrath Ronnald , Vu D. Tung , Pérez Berrocal David A. , Mulder Monique P. C. , van der Heden van Noort Gerbrand J , Schulman Brenda A.
Published: June 2023

Ubiquitin chain formation by HECT catalytic domain-containing E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We employed chemistry and cryo-EM to visualize stable mimics of the intermediates along K48-linked ubiquitin chain formation by the human E3, UBR5. The structural data reveal a ≈620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly-tethered ubiquitin-binding UBA domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor ubiquitin, with its K48 lured into the active site by numerous interactions between the acceptor ubiquitin, manifold UBR5 elements, and the donor ubiquitin. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing ubiquitin transfer from E2 to E3, and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2, and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked ubiquitin chain forging machine.
The microbial derived bile acid lithocholate and its epimers inhibitClostridioides difficilegrowth and pathogenicity while sparing members of the gut microbiota
Authors: Kisthardt Samantha C , Thanissery Rajani , Pike Colleen M , Foley Matthew H , Theriot Casey M
Published: June 2023

C. difficileinfection (CDI) is associated with antibiotic usage, which disrupts the indigenous gut microbiota and causes the loss of microbial derived secondary bile acids that normally provide protection againstC. difficilecolonization. Previous work has shown that the secondary bile acid lithocholate (LCA) and its epimer isolithocholate (iLCA) have potent inhibitory activity against clinically relevantC. difficilestrains. To further characterize the mechanisms by which LCA and its epimers iLCA and isoallolithocholate (iaLCA) inhibitC. difficile,we tested their minimum inhibitory concentration (MIC) againstC. difficileR20291, and a commensal gut microbiota panel. We also performed a series of experiments to determine the mechanism of action by which LCA and its epimers inhibitC. difficilethrough bacterial killing and effects on toxin expression and activity. Here we show that epimers iLCA and iaLCA strongly inhibitC. difficilegrowthin vitrowhile sparing most commensal Gram-negative gut microbes. We also show that iLCA and iaLCA have bactericidal activity againstC. difficile,and these epimers cause significant bacterial membrane damage at subinhibitory concentrations. Finally, we observe that iLCA and iaLCA decrease the expression of the large cytotoxintcdAwhile LCA significantly reduces toxin activity. Although iLCA and iaLCA are both epimers of LCA, they have distinct mechanisms for inhibitingC. difficile. LCA epimers, iLCA and iaLCA, represent promising compounds that targetC. difficilewith minimal effects on members of the gut microbiota that are important for colonization resistance.

Importance

In the search for a novel therapeutic that targetsC. difficile, bile acids have become a viable solution. Epimers of bile acids are particularly attractive as they may provide protection againstC. difficilewhile leaving the indigenous gut microbiota largely unaltered. This study shows that iLCA and iaLCA specifically are potent inhibitors ofC. difficile, affecting key virulence factors including growth, toxin expression and activity. As we move toward the use of bile acids as therapeutics, further work will be required to determine how best to deliver these bile acids to a target site within the host intestinal tract.
Effects of growth feedback on adaptive gene circuits: A dynamical understanding
Authors: Kong Ling-Wei , Shi Wenjia , Tian Xiao-Jun , Lai Ying-Cheng
Published: June 2023

The successful integration of engineered gene circuits into host cells remains a significant challenge in synthetic biology due to circuit-host interactions, such as growth feedback, where the circuit influences cell growth and vice versa. Understanding the dynamics of circuit failures and identifying topologies resilient to growth feedback are crucial for both fundamental and applied research. Utilizing transcriptional regulation circuits with adaptation as a paradigm, we systematically study more than four hundred topological structures and uncover various categories of failures. Three dynamical mechanisms of circuit failures are identified: continuous deformation of the response curve, strengthened or induced oscillations, and sudden switching to coexisting attractors. Our extensive computations also uncover a scaling law between a circuit robustness measure and the strength of growth feedback. Despite the negative effects of growth feedback on the majority of circuit topologies, we identify several circuits that maintain optimal performance as designed, a feature important for applications.
Single cell RNA-seq analysis of spinal locomotor circuitry in larval zebrafish
Authors: Kelly Jimmy J. , Wen Hua , Brehm Paul
Published: June 2023

Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish. Electrophysiological studies have shown that additional to connectivity, understanding of circuitry requires identification of functional specializations among individual circuit components, such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNA sequencing (scRNAseq) to identify the molecular bases for functional distinctions between motoneuron types that are causal to their differential roles in swimming. The primary motoneuron (PMn) in particular, expresses high levels of a unique combination of voltage-dependent ion channel types and synaptic proteins termed functional ‘cassettes’. The ion channel types are specialized for promoting high frequency firing of action potentials and augmented transmitter release at the neuromuscular junction, both contributing to greater power generation. Our transcriptional profiling of spinal neurons further assigns expression of this cassette to specific interneuron types also involved in the central circuitry controlling high speed swimming and escape behaviors. Our analysis highlights the utility of scRNAseq in functional characterization of neuronal circuitry, in addition to providing a gene expression resource for studying cell type diversity.
High-throughput mRNA-seq atlas of human placenta shows vast transcriptome remodeling from first to third trimester
Authors: Gonzalez Tania L , Wertheimer Sahar , Flowers Amy E , Wang Yizhou , Santiskulvong Chintda , Clark Ekaterina L , Jefferies Caroline A , Lawrenson Kate , Chan Jessica L , Joshi Nikhil V , Zhu Yazhen , Tseng Hsian-Rong , Karumanchi S. Ananth , Williams John , Pisarska Margareta D
Published: June 2023

Background

The placenta, composed of chorionic villi, changes dramatically across gestation. Understanding differences in ongoing pregnancies are essential to identify the role of chorionic villi at specific times in gestation and develop biomarkers and prognostic indicators of maternal- fetal health.

Methods

The normative mRNA profile is established using next-generation sequencing of 124 first trimester and 43 third trimester human placentas from ongoing healthy pregnancies. Stably expressed genes not different between trimesters and with low variability are identified. Differential expression analysis of first versus third trimester adjusted for fetal sex is performed, followed by a subanalysis with 23 matched pregnancies to control for subject variability using the same genetic and environmental background.

Results

Placenta expresses 14,979 mRNAs above sequencing noise (TPM>0.66), with 1,545 stably expressed genes across gestation. Differentially expressed genes account for 86.7% of genes in the full cohort (FDR<0.05). Fold changes highly correlate between the full cohort and subanalysis (Pearson = 0.98). At stricter thresholds (FDR<0.001, fold change>1.5), there are 6,941 differentially expressed protein coding genes (3,206 upregulated in first and 3,735 upregulated in third trimester).

Conclusion

This is the largest mRNA atlas of healthy human placenta across gestation, controlling for genetic and environmental factors, demonstrating substantial changes from first to third trimester in chorionic villi. Specific differences and stably expressed genes may be used to understand the specific role of the chorionic villi throughout gestation and develop first trimester biomarkers of placental health that transpire across gestation, which can be used for future development of biomarkers in maternal-fetal disease.
TheCaulobacterNtrB-NtrC two-component system bridges nitrogen assimilation and cell development
Authors: North Hunter , McLaughlin Maeve , Fiebig Aretha , Crosson Sean
Published: June 2023

A suite of molecular sensory systems enablesCaulobacterto control growth, development, and reproduction in re-sponse to levels of essential elements. The bacterial enhancer binding protein (bEBP) NtrC, and its cognate sensor histidine kinase NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles inCaulobactermetab-olism and development are not well defined. Notably,CaulobacterNtrC is an unconventional bEBP that lacks the σ54- interacting loop commonly known as the GAFTGA motif. Here we show that deletion ofC. crescentus ntrCslows cell growth in complex medium, and thatntrBandntrCare essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect ofntrCmutant strains by restoring transcription of theglnBAoperon, revealing a possible role for IS3 transposition in shaping the evolution ofCaulobacterpopulations during nutri-ent limitation. We further identified dozens of direct NtrC binding sites on theC. crescentuschromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis inCaulobacter.

Importance

Bacteria balance cellular processes with the availability of nutrients in their environment. The NtrB-NtrC two-component signaling system is responsible for controlling nitrogen assimilation in many bacteria. We have characterized the effect ofntrBandntrCdeletion onCaulobactergrowth and development and uncovered a role for spontaneous IS element transposition in the rescue of transcriptional and nutritional deficiencies caused byntrCmutation. We further defined the regulon ofCaulobacterNtrC, a bacterial enhancer binding protein, and demonstrate that it shares specific binding sites with essential proteins involved in cell cycle regulation and chromosome organization. Our work provides a com-prehensive view of transcriptional regulation mediated by a distinctive NtrC protein, establishing its connection to nitro-gen assimilation and developmental processes inCaulobacter.
Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population
Authors: Birzu Gabriel , Muralidharan Harihara Subrahmaniam , Goudeau Danielle , Malmstrom Rex R. , Fisher Daniel S. , Bhaya Devaki
Published: June 2023

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.
Cholinergic input to mouse visual cortex signals a movement state and acutely enhances layer 5 responsiveness
Authors: Yogesh Baba , Keller Georg B.
Published: June 2023

Acetylcholine is released in visual cortex by axonal projections from the basal forebrain. The signals conveyed by these projections and their computational significance are still unclear. Using two-photon calcium imaging in behaving mice, we show that basal forebrain cholinergic axons in the mouse visual cortex provide a binary locomotion state signal. In these axons, we found no evidence of responses to visual stimuli or visuomotor prediction errors. While optogenetic activation of cholinergic axons in visual cortex in isolation did not drive local neuronal activity, when paired with visuomotor stimuli, it resulted in layer-specific increases of neuronal activity. Responses in layer 5 neurons to both top-down and bottom-up inputs were increased in amplitude and decreased in latency, whereas those in layer 2/3 neurons remained unchanged. Using opto- and chemogenetic manipulations of cholinergic activity, we found acetylcholine to underlie the locomotion-associated decorrelation of activity between neurons in both layer 2/3 and layer 5. Our results suggest that acetylcholine augments the responsiveness of layer 5 neurons to inputs from outside of the local network, possibly enabling faster switching between internal representations during locomotion.
Transforming descending input into behavior: The organization of premotor circuits in theDrosophilaMale Adult Nerve Cord connectome
Authors: Cheong H. S. J. , Eichler K. , Stürner T. , Asinof S. K. , Champion A. S. , Marin E. C. , Oram T. B. , Sumathipala M. , Venkatasubramanian L. , Namiki S. , Siwanowicz I. , Costa M. , Berg S. ,   Janelia FlyEM Project Team, Jefferis G. S. X. E. , Card G. M.
Published: June 2023

In most animals, a relatively small number of descending neurons (DNs) connect higher brain centers in the animal’s head to circuits and motor neurons (MNs) in the nerve cord of the animal’s body that effect movement of the limbs. To understand how brain signals generate behavior, it is critical to understand how these descending pathways are organized onto the body MNs. In the fly,Drosophila melanogaster, MNs controlling muscles in the leg, wing, and other motor systems reside in a ventral nerve cord (VNC), analogous to the mammalian spinal cord. In companion papers, we introduced a densely-reconstructed connectome of theDrosophilaMale Adult Nerve Cord (MANC, Takemura et al., 2023), including cell type and developmental lineage annotation (Marin et al., 2023), which provides complete VNC connectivity at synaptic resolution. Here, we present a first look at the organization of the VNC networks connecting DNs to MNs based on this new connectome information. We proofread and curated all DNs and MNs to ensure accuracy and reliability, then systematically matched DN axon terminals and MN dendrites with light microscopy data to link their VNC morphology with their brain inputs or muscle targets. We report both broad organizational patterns of the entire network and fine-scale analysis of selected circuits of interest. We discover that direct DN-MN connections are infrequent and identify communities of intrinsic neurons linked to control of different motor systems, including putative ventral circuits for walking, dorsal circuits for flight steering and power generation, and intermediate circuits in the lower tectulum for coordinated action of wings and legs. Our analysis generates hypotheses for future functional experiments and, together with the MANC connectome, empowers others to investigate these and other circuits of theDrosophilaventral nerve cord in richer mechanistic detail.