bioRxiv : the preprint server for biology最新文献

Risky or maladaptive decision making is thought to be central to the etiology of both drug and gambling addiction. Salient audiovisual cues paired with rewarding outcomes, such as the jackpot sound on a win, can enhance disadvantageous, risky choice in both rats and humans, yet it is unclear which aspects of the cue-reward contingencies drive this effect. Here, we implemented six variants of the rat Gambling Task (rGT), in which animals can maximise their total sugar pellet profits by avoiding options paired with higher per-trial gains but disproportionately longer and more frequent time-out penalties. When audiovisual cues were delivered concurrently with wins, and scaled in salience with reward size, significantly more rats preferred the risky options as compared to the uncued rGT. Similar results were observed when the relationship between reward size and cue complexity was inverted, and when cues were delivered concurrently with all outcomes. Conversely, risky choice did not increase when cues occurred randomly on 50% of trials, and decision making actually improved when cues were coincident with losses alone. As such, cues do not increase risky choice by simply elevating arousal, or amplifying the difference between wins and losses. It is instead important that the cues are reliably associated with wins; presenting the cues on losing outcomes as well as wins does not diminish their ability to drive risky choice. Computational analyses indicate reductions in the impact of losses on decision making in all rGT variants in which win-paired cues increased risky choice. These results may help us understand how sensory stimulation can increase the addictive nature of gambling and gaming products.

Innate lymphoid cells (ILCs) are rare, tissue-resident innate lymphocytes that functionally mirror CD4+ T helper cell lineages but lack antigen receptors. Type 3 ILCs (ILC3s) are enriched in the gut, airways, and mucosal lymphoid tissues, where they regulate inflammation and promote barrier integrity. To define the regulatory architecture of primary human ILC3s, we map promoter-anchored chromosomal contacts using high-resolution, low-input Promoter Capture Hi-C (PCHi-C) in these cells alongside CD4+ T cells. By combining statistical detection with a PCHi-C-adapted Activity-by-Contact approach, we link promoters to distal regulatory elements, identifying hundreds of ILC3-specific contacts. We use these maps to connect genome-wide association study (GWAS) risk variants for Crohn's disease to target genes using multiCOGS, a Bayesian framework that integrates PCHi-C with summary-statistic imputation and multivariate fine-mapping. This analysis highlights both known and unanticipated candidates, including CLN3, a causal gene for the neurodevelopmental Batten disease. Using a mouse ILC3-like cell line, we show that Cln3 is downregulated upon cytokine stimulation, and Cln3 overexpression alters stimulation-induced transcriptional programmes and cytokine secretion. Extending this approach, we generate a catalogue of ILC3-linked risk genes for five additional autoimmune conditions and show that they are enriched for regulators of the ILC3 inflammatory response identified in a CRISPR interference screen. Together, these findings illuminate long-range gene control in ILC3s and prioritise known and newly implicated autoimmune risk genes with potential roles in this clinically important cell type.

The genetic code is a formal principle that determines which proteins an organism can produce from only its genome sequence, without mechanistic modeling. Whether similar formal principles govern the relationship between genome sequence and phenotype across scales - from molecules to cells to tissues - is unknown. Here, we show that a single formal principle - structural correspondence - underlies the relationship between phenotype and genome sequence across scales. We represent phenotypes and the genome as graphs and find mappings between them using structure preservation as the sole constraint. Combinatorial richness in phenotypes more tightly constrains which mappings preserve that structure. Thus, phenotypic structure predicts genetic associations independently of covariation with genotype. This principle rediscovers the amino acid code without prior knowledge of translation or coding sequences, using just one protein and genome sequence as input. We benchmark this principle: applied to phenotypes at the cell, tissue and organ scales, the mappings correctly predict established associations and are driven by transcription factor motifs. Applied to cancer tissue images, we find regulators of spatial gene expression in immune cells. We thus offer a first-principles framework to relate genome sequence with phenotypic structure and guide mechanistic discovery across scales.

Calcium-sensitive fluorescent indicators enable monitoring of spiking activity in large neuronal populations in animal models. Despite the plethora of algorithms developed over the past decades, accurate spike-time inference methods for spike rates exceeding 20 Hz are lacking. More importantly, little attention has been devoted to the quantification of statistical uncertainties in spike time estimation, which is essential for assigning confidence levels to inferred spike patterns. To address these challenges, we introduce (1) a statistical model that accounts for bursting neuronal activity and baseline fluorescence modulation and (2) apply a Monte Carlo strategy (particle Gibbs with ancestor sampling) to estimate the joint posterior distribution of spike times and model parameters. Our method is competitive with state-of-the-art supervised and unsupervised algorithms, as evaluated on the CASCADE benchmark datasets. Analysis of fluorescence transients recorded with the ultrafast genetically encoded calcium indicator GCaMP8f demonstrates that our method can resolve interspike intervals as short as 5 ms. Overall, our study describes a Bayesian inference method for detecting neuronal spiking patterns and quantifying their uncertainty. The use of particle Gibbs samplers enables unbiased estimates of spike times and all model parameters, and provides a flexible statistical framework for testing more specific models of calcium indicators.

In most eukaryotes, the enzyme telomerase maintains the termini of linear chromosomes through the addition of repetitive telomeric sequences. It is widely assumed that the primary site of action for telomerase is the single-stranded G-rich overhang at the ends of linear chromosomes. We show here that a second substrate, created by spontaneous replication fork collapse during duplex telomeric DNA replication in wild type budding yeast, is elongated by telomerase at a much higher frequency (∼50%) than fully replicated chromosome termini. Furthermore, as much as ∼200 nucleotides can be added in a single cell division to these newly collapsed forks, indicating that spontaneous replication fork collapse and the subsequent response by telomerase is a major determinant of telomere length homeostasis. This challenges a long-standing model for telomere length regulation which posits a length-sensing mechanism that assesses individual telomeres to determine whether chromosome ends are in "telomerase-extendible" or "telomerase-non-extendible" states. We propose that these two states are instead structurally and temporally distinct substrates for telomerase, generated by two different processes (fork collapse vs . completion of DNA replication). We also show that replication fork collapse at telomeres is kept in check by a telomere-dedicated Cdc13/Stn1/Ten1 complex in collaboration with the canonical RPA complex, indicating that these two complexes bind single-stranded DNA exposed at the replication fork to facilitate replisome progression through duplex telomeric DNA. Although failures during DNA replication are often genotoxic events, this represents an opposing example in which fork collapse has been co-opted to promote genome stability.

Significance statement: In most eukaryotes, the termini of linear chromosomes are composed of arrays of short repeats that are continually replenished by the enzyme telomerase. If telomerase is unable to act, gradual loss of these terminal repeats results in an eventual block to cell division. Therefore, in cells that depend on continuous cell division, the mechanism(s) by which telomerase is directed to chromosome ends is tightly regulated. This study shows that in addition to the ends of fully replicated chromosomes, a second site of action for telomerase is generated when replication through duplex telomeric DNA is disrupted. These results suggest that the disparate response of telomerase to two temporally and structurally distinct substrates is a major determinant of telomere length homeostasis.

The mitotic spindle, a key structure to partition chromosomes during cell division, connects its poles to the chromosomes through microtubules. Their plus-ends, oriented towards the chromosomes, exhibit dynamic instability crucial for kinetochore correct attachments. Involved in this process, the poleward flux implicates the displacement of microtubules towards the spindle poles, coordinated with polymerisation at the plus ends. The mechanisms behind this are diverse. It includes treadmilling powered by microtubule depolymerisation at the spindle poles, sliding of spindle microtubules by molecular motors like Kinesin-5, and pushing microtubules away from the chromosomes by chromokinesins. Interestingly, no such flux was reported in the Caenorhabditis elegans zygote, although all proteins contributing to flux in mammals have homologs in the nematode. To explore this, we fluorescently labelled microtubules and conducted photobleaching. We found no global poleward flux; the bleached zone's edges moved inward. The centrosome-side front motion was caused by dynamic instability, while the chromosome-side front exhibited faster recovery, suggesting an additional mechanism. This larger slope was detected only near the chromosomes, indicating that only kinetochore microtubules undergo flux. Consistently, this flux depended on proteins ensuring the chromosome attachment and growth of the kinetochore microtubules, notably NDC-80, CLS-2 ^CLASP , and ZYG-9 ^XMAP215 . Furthermore, this flux decreased as metaphase progressed and attachments transitioned from side- to end-on; it was reduced by SKA-1 recruitment. Treadmilling was unlikely to account for these observations, as most kinetochore microtubules do not reach spindle poles in the zygote spindle. Conversely, the depletion of kinesin-12 KLP-18 ^KIF15 , which cross-links and focuses microtubules at meiosis, reduced the front rate. Ultimately, we propose that the sole kinetochore microtubules slide along spindle microtubules, likely powered by KLP-18, contrasting with solid displacement in other systems. It aligns with observations in human cells of decreasing flux with increasing chromosome distance.

Actin is a key cytoskeletal protein that forms filaments that bundle into linear structures in vivo, which are involved in motility, signaling, and cell division. Despite the rapid turnover of individual actin monomers, these structures are often maintained at a specific length, which is important for their function. Length control is commonly attributed to length-dependent assembly or disassembly of the structure, whereby a stable length is achieved when the two opposing processes are balanced. Here we show that regardless of the nature of the length-dependent feedback, such balance point models predict a Gaussian distribution of lengths with a variance that is proportional to the steady state length. Contrary to this prediction, a reexamination of experimental measurements on the lengths of stereocilia, microvilli, actin cables, and filopodia reveals that the variance scales with the square of the steady state length. We propose a model in which the individual filaments in bundles undergo independent assembly dynamics, and the length of the bundle is set by the length of the longest filament. This model predicts a non-Gaussian distribution of bundle lengths with a variance that scales with the square of the steady state length. Our theory underscores the importance of crosslinking filaments into networks for size control of cytoskeleton structures.

Addictive drugs cause long-lasting changes in connectivity from inputs onto ventral tegmental area dopamine cells (VTADA) that contribute to drug-induced behavioral adaptations. However, it is not known which inputs are altered. Here we used a rabies virus (RABV)-based mapping strategy to quantify RABV-labeled inputs to VTA cells after a single exposure to one of a variety of misused drugs - cocaine, amphetamine, methamphetamine, morphine, and nicotine - and compared the relative global input labeling across conditions. We observed that all tested addictive drugs elicited similar input changes onto VTADA cells, in particular onto DA cells projecting to the lateral shell of the nucleus accumbens and amygdala. In addition, repeated administration of ketamine/xylazine to induce anesthesia induces a change in inputs to VTADA cells that is similar to but different from those elicited by a single exposure to addictive drugs, suggesting that caution should be taken when using ketamine/xylazine-based anesthesia in rodents when assessing motivated behaviors. Furthermore, comparison of viral tracing data to an atlas of gene expression in the adult mouse brain showed that the basal expression patterns of several gene classes, especially calcium channels, were highly correlated with the extent of both addictive drug- or ketamine/xylazine-induced changes in RABV-labeled inputs to VTADA cells. Reducing expression levels of the voltage-gated calcium channel Cacna1e in cells in the nucleus accumbens lateral shell reduced RABV-mediated input labeling of these cells into VTADA cells. These results directly link genes controlling cellular excitability and the extent of input labeling by RABV.

Hippocampal neurons encoding memories discharge in sparsely-distributed patterns; they can be optogenetically tagged, then photostimulated to elicit conditioned behavior, potentially generating a synthetic memory trace, "engram". We investigated mouse hippocampal population responses to the photostimulation of memory-tagged neurons to determine if memory-associated discharge is mimicked in hippocampus, a network with non-linear and homeostatic interactions. Both memory-tagged and not-tagged CA1 cells adjusted firing during photostimulation without altering place cell firing fields. Cell-pair cofiring relationships also maintain during photostimulation, indicating a low-dimensional, dynamical structure-preserving, homeostatic network response instead of the photostimulated pattern. Photostimulating neurons that were tagged during place-avoidance memory elicits similar place-avoidance memory in control conditions. Thus artificial photostimulation elicits natural, stored, homeostatic neuronal network cofiring patterns to elicit memory, establishing mimicry evidence for the engram.

Millions of SARS-CoV-2 genome sequences were collected during the COVID-19 pandemic, forming a dataset of unprecedented richness. Estimated genealogies are fundamental to understanding this ocean of data and form the primary input to many downstream analyses. A basic assumption of methods to infer genealogies from viral genetic data is that recombination is negligible and the genealogy is a tree. However, recombinant lineages have risen to global prevalence, and simple tree representations are therefore incomplete and potentially misleading. We present sc2ts, a method to infer reticulate genealogies as an Ancestral Recombination Graph (ARG) in real time at pandemic scale. We infer an ARG for 2.48 million SARS-CoV-2 genomes, which leverages the widely used tskit software ecosystem to support further analyses and visualisation. This rich and validated resource clarifies the relationships among recombinant lineages, quantifies the rate of recombination over time, and provides a lower bound on detectable recombination.