bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning directed organoid morphogenesis uncovers an excitable system driving human axial elongation
Authors: Anand Giridhar M. , Megale Heitor C. , Murphy Sean H. , Weis Theresa , Lin Zuwan , He Yichun , Wang Xiao , Liu Jia , Ramanathan Sharad 
Published: May 2022

SummaryThe human embryo breaks symmetry to form the anterior-posterior axis of the body. As the embryo elongates along this axis, progenitors in the tailbud give rise to axial tissues that generate the spinal cord, skeleton, and musculature. The mechanisms underlying human axial elongation are unknown. While ethics necessitate in vitro studies, the variability of human organoid systems has hindered mechanistic insights. Here we developed a bioengineering and machine learning framework that optimizes symmetry breaking by tuning the spatial coupling between human pluripotent stem cell-derived organoids. This framework enabled the reproducible generation of hundreds of axially elongating organoids, each possessing a tailbud and an epithelial neural tube with a single lumen. We discovered that an excitable system composed of WNT and FGF signaling drives axial elongation through the induction of a signaling center in the form of neuromesodermal progenitor (NMP)-like cells. The ability of NMP-like cells to function as a signaling center and drive elongation is independent of their potency to generate mesodermal cell types. We further discovered that the instability of the underlying excitable system is suppressed by secreted WNT inhibitors of the secreted frizzled-related protein (SFRP) family. Absence of these inhibitors led to the formation of ectopic tailbuds and branches. Our results identify mechanisms governing stable human axial elongation to achieve robust morphogenesis.
Bcl-xL is a key mediator of apoptosis following KRASG12C inhibition in KRASG12C mutant colorectal cancer
Authors: Khawaja Hajrah , Briggs Rebecca , Latimer Cheryl , Rassel Md A.M.B. , Griffin Daryl , Hanson Lyndsey , Bardelli Alberto , Di Nicolantonio Frederica , McDade Simon , Scott Christopher J. , Lambe Shauna , Maurya Manisha , Lindner Andreas , Prehn Jochen H.M. , Sousa Jose , Winnington Chris , LaBonte Melissa J. , Ross Sarah , Van Schaeybroeck Sandra 
Published: May 2022

ABSTRACTPurposeNovel covalent inhibitors of KRASG12C have shown limited response rates in KRASG12C mutant (MT) colorectal cancer (CRC) patients. Thus, novel KRASG12C inhibitor combination strategies that can achieve deep and durable responses are needed.Experimental designSmall molecule KRASG12C inhibitors AZ’1569 and AZ’8037 were employed. To identify novel candidate combination strategies for AZ’1569, we performed RNA sequencing, siRNA and high-throughput drug screening. Top hits were validated in a panel of KRASG12CMT CRC cells and in vivo. AZ’1569-resistant CRC cells were generated and characterised.ResultsResponse to AZ’1569 was heterogeneous across the KRASG12CMT models. AZ’1569 was ineffective at inducing apoptosis when used as single-agent or combined with chemotherapy or agents targeting the EGFR/KRAS/AKT axis. Using a systems biology approach, we identified the anti-apoptotic BH3-family member BCL2L1/Bcl-xL as a top hit mediating resistance to AZ’1569. Further analyses identified acute increases in the pro-apoptotic protein BIM following AZ’1569 treatment. ABT-263 (Navitoclax), a pharmacological Bcl-2 family-inhibitor that blocks the ability of Bcl-xL to bind and inhibit BIM, led to dramatic and universal apoptosis when combined with AZ’1569. Furthermore, this combination also resulted in dramatically attenuated tumour growth in KRASG12CMT xenografts. Finally, AZ’1569-resistant cells showed amplification of KRASG12C, EphA2/c-MET activation, increased pro-inflammatory chemokine profile and cross-resistance to several targeted agents. Importantly, KRAS amplification and AZ’1569-resistance were reversible upon drug withdrawal, arguing strongly for the use of drug holidays in the case of KRAS amplification.ConclusionsCombinatorial targeting of Bcl-xL and KRASG12C is highly effective, suggesting a novel therapeutic strategy for KRASG12CMT CRC patients.
The statistical power of three monkeys
Authors: Laurens Jean 
Published: May 2022

AbstractNeuroscience studies in non-human primates (NHP) often follow the rule of thumb that results observed in one animal must be replicated in at least one other. However, we lack a statistical justification for this rule of thumb, or an analysis of whether including three or more animals is better than including two. Yet, a formal statistical framework for experiments with few subjects would be crucial for experimental design, ethical justification, and data analysis. Also, including three or four animals in a study creates the possibility that the results observed in one animal will differ from those observed in the others: we need a statistically justified rule to resolve such situations. Here, I present a statistical framework to address these issues. This framework assumes that conducting an experiment will produce a similar result for a large proportion of the population (termed ‘representative’), but will produce spurious results for a substantial proportion of animals (termed ‘outliers’); the fractions of ‘representative’ and ‘outliers’ animals being defined by a prior distribution. I propose a procedure in which experimenters collect results from M animals and accept results that are observed in at least N of them (‘N-out-of-M’ procedure). I show how to compute the risks α (of reaching an incorrect conclusion) and β (of failing to reach a conclusion) for any prior distribution, and as a function of N and M. Strikingly, I find that the N-out-of-M model leads to a similar conclusion across a wide range of prior distributions: recordings from two animals lowers the risk α and therefore ensures reliable result, but leaves a large risk β; and recordings from three animals and accepting results observed in two of them strikes an efficient balance between acceptable risks α and β. This framework gives a formal justification for the rule of thumb of using at least two animals in NHP studies, suggests that recording from three animals when possible markedly improves statistical power, provides a statistical solution for situations where results are not consistent between all animals, and may apply to other types of studies involving few animals.
Inferring Density-Dependent Population Dynamics Mechanisms through Rate Disambiguation for Logistic Birth-Death Processes
Authors: Huynh Linh , Scott Jacob G. , Thomas Peter J. 
Published: May 2022

ABSTRACTDensity dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can manifest in birth processes, death processes, or both. Therefore, we utilize the mean and variance of cell number fluctuations to separately identify birth and death rates from time series that follow stochastic birth-death processes with logistic growth. Our method provides a novel perspective on stochastic parameter identifiability, which we validate by analyzing the accuracy in terms of the discretization bin size. We apply our method to the scenario where a homogeneous cell population goes through three stages: (1) grows naturally to its carrying capacity, (2) is treated with a drug that reduces its carrying capacity, and (3) overcomes the drug effect to restore its original carrying capacity. In each stage, we disambiguate whether it happens through the birth process, death process, or some combination of the two, which contributes to understanding drug resistance mechanisms. In the case of limited data sets, we provide an alternative method based on maximum likelihood and solve a constrained nonlinear optimization problem to identify the most likely density dependence parameter for a given cell number time series. Our methods can be applied to other biological systems at different scales to disambiguate density-dependent mechanisms underlying the same net growth rate.Mathematics Subject Classifications60J27 · 92D25 · 62M10 · 60J25
Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system
Authors: Fung Herman K.H. , Grimes Shelley , Huet Alexis , Duda Robert L. , Chechik Maria , Gault Joseph , Robinson Carol V. , Hendrix Roger W. , Jardine Paul J. , Conway James F. , Baumann Christoph G. , Antson Alfred A. 
Published: May 2022

ABSTRACTMany essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and herpes viruses, use a homomeric ring ATPase to processively translocate viral genomic DNA into procapsids during assembly. Our current understanding of viral DNA packaging comes from three archetypal bacteriophage systems: cos, pac and phi29. Detailed mechanistic understanding exists for pac and phi29, but not for cos. Here we reconstituted in vitro a cos packaging system based on bacteriophage HK97 and provided a detailed biochemical and structural description. We used a photobleaching-based, single-molecule assay to determine the stoichiometry of the DNA-translocating ATPase large terminase. Crystal structures of the large terminase and DNA-recruiting small terminase, a first for both this phage and a cos system, reveal unexpected mechanistic similarities between cos and pac systems. At the same time, mutational and biochemical analyses indicate a new regulatory mechanism for ATPase multimerization and coordination in the HK97 system. This work therefore establishes a framework for studying the evolutionary relationships between ATP-dependent DNA translocation machineries in double-stranded DNA viruses.
Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection
Authors: Aracena Katherine A , Lin Yen-Lung , Luo Kaixuan , Pacis Alain , Gona Saideep , Mu Zepeng , Yotova Vania , Sindeaux Renata , Pramatarova Albena , Simon Marie-Michelle , Chen Xun , Groza Cristian , Lougheed David , Gregoire Romain , Brownlee David , Li Yang , He Xin , Bujold David , Pastinen Tomi , Bourque Guillaume , Barreiro Luis B 
Published: May 2022

SummaryHumans display remarkable inter-individual variation in immune response when exposed to identical immune challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we carried out in-depth genetic, epigenetic, and transcriptional profiling on primary macrophages derived from a panel of European and African-ancestry individuals before and after infection with influenza A virus (IAV). We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to IAV across individuals, and that ancestry-associated differences in gene expression are tightly coupled with variation in enhancer activity. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape are genetically controlled, even more so than variation in gene expression. Lastly, we show that among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, the remaining corresponding to genetic variants that impact one or more epigenetic marks, which stresses the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
Single molecule microscopy to profile the effect of zinc status of transcription factor dynamics
Authors: Damon Leah J. , Aaron Jesse , Palmer Amy E. 
Published: May 2022

AbstractTranscription factors (TFs) are DNA binding proteins that control the expression of genes. The regulation of transcription is a complex process that involves binding of TFs to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and ultimately the recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for visualizing and tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. In this work, we employ multifocus microscopy and highly inclined and laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. While it is widely appreciated that TFs need zinc to bind DNA, whether zinc occupancy and hence TF function are sensitive to changes in cellular zinc remain open questions. We utilized fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that the biophysical dynamics of both TFs are susceptible to changes in zinc, but in subtly different ways. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.
A versatile, chemically-controlled DNA binding switch enables temporal modulation of Cas9-based effectors
Authors: Wei Cindy T. , Peleg Omri , Borenstein Elhanan , Maly Dustin J. , Fowler Douglas M. 
Published: May 2022

AbstractCRISPR-Cas9’s RNA-guided genome targeting ability has been leveraged to develop a plethora of effectors including targeted transcriptional activators, DNA base editors, and DNA prime editors. Although systems for inducibly modulating Cas9 activity have been developed, current approaches for conferring temporal control require extensive screening of functional protein components. A simpler and general strategy for conferring temporal control over diverse Cas9-based effector activities is needed. Here we describe a versatile chemically-controlled and rapidly-activated DNA binding Cas9 module (ciCas9) that is able to confer temporal control over a variety of Cas9-based effectors. Using the ciCas9 module, we engineer temporally-controlled cytidine and adenine DNA base editors. We employ the ciCas9 base editors to reveal that in vivo bystander editing kinetics occurs via a dependent process where editing at a preferred nucleotide position increases the frequency of edits at a second nucleotide within a target site. Finally, we demonstrate the versatility of the ciCas9 module by creating a temporally-controlled transcriptional activator, a dual cytidine and adenine base editor, and a prime editor.
Macroscale Thalamic Functional Organization Disturbances and Underlying Core Cytoarchitecture in Early-Onset Schizophrenia
Authors: Fan Yun-Shuang , Xu Yong , Bayrak Şeyma , Shine James M. , Wan Bin , Li Haoru , Li Liang , Yang Siqi , Meng Yao , Valk Sofie Louise , Chen Huafu 
Published: May 2022

AbstractSchizophrenia is a polygenetic mental disorder with heterogeneous positive and negative symptom constellations, and is associated with abnormal cortical connectivity. The thalamus has a coordinative role in cortical function and is key to the development of the cerebral cortex. Conversely, altered functional organization of the thalamus might relate to overarching cortical disruptions in schizophrenia, anchored in development. Here, we contrasted resting-state fMRI in 99 antipsychotic-naive first-episode early-onset schizophrenia (EOS) patients and 100 typically developing controls to study whether macroscale thalamic organization is altered in EOS. Employing dimensional reduction techniques on thalamocortical functional connectome, we derived lateral-medial and anterior-posterior thalamic functional axes. We observed increased segregation of macroscale thalamic functional organization in EOS patients, which was related to altered thalamocortical interactions both in unimodal and transmodal networks. Using anex vivoapproximation of core-matrix cell distribution, we found that core cells particularly underlie the macroscale abnormalities in EOS patients. Moreover, the disruptions were associated with schizophrenia-related gene expression maps. Behavioral and disorder decoding analyses indicated that the macroscale hierarchy disturbances might perturb both perceptual and abstract cognitive functions and contribute to negative syndromes in schizophrenia, suggesting a unitary pathophysiological framework of schizophrenia.
A honey authenticity test by interphase emulsion reveals biosurfactant activity and biotechnology in the stingless bee nest ofScaptotrigonasp. ‘Catiana’ from Ecuador
Authors: Vit Patricia 
Published: May 2022

ABSTRACTBees are valuable pollinators of fruit trees and grasses. Honey is a medicinal food of plant and animal origin, with social impact for the wellbeing of bee keepers. The Neotropical apifauna has about 500 species of stingless bees (Meliponini). Commercial beekeeping withApis melliferaunderestimates the cultural legacy of meliponiculture, and both are affected by the presence of fake honeys in the market. Three alternative techniques (interphase emulsion, sensory analysis, and pollen residue) to nuclear magnetic resonance (NMR) were investigated to detect false honeys. One technique was based on an interphase emulsion test, which can be performed by beekeepers, farmers, housekeepers, professionals and consumers of honey in general. Another technique was sensory analysis by a tasting panel, and the third consisted on a palynological preparation with a simplified observation. Five genuine honeys produced byApis mellifera, Geotrigona leucogastra, Melipona mimetica, Scaptotrigonasp.,Tetragonisca angustulaand a fake honey from Ecuador were analyzed. The honey authenticity test by interphase emulsion was fast and effective to detect fake honey (two phases), and genuine honeys (one and three phases). A further screening of was done in 51 Asian, Australia, European and Latinamerican honeys. Additionally the HATIE generated a new application as a test to detect unique biosurfactants in honey (HBT) ofScaptotrigonasp. ‘Catiana’ (one phase) with potential microbial origin, and its entomological origin in this set of honeys. ‘Catiana’ nests smell like Roquefort cheese, indicating a fungus association with this rural stingless bee highlighted by its distribution, productivity and the peculiarities described in this research, 80 years after its description as a new genusScaptotrigonaMoure, 1942. Paradoxically, this communication without microbiological analysis, infers the fungal presence in the nest ofScaptotrigonasp. by sensory observations different from the classic sensory evaluation of honey.
Clones on the run - the genomics of a recently expanded facultative asexual species
Authors: Pereyra Ricardo T. , Rafajlović Marina , De Wit Pierre , Pinder Matthew , Kinnby Alexandra , Töpel Mats , Johannesson Kerstin 
Published: May 2022

AbstractWhy, in facultative asexual species, marginal populations are often richer in clones than are core populations, remains unclear. Cloning freezes genotypes but hampers recombination and local adaptation. During expansion, clones are favoured over non-selfing sexuals by uniparental reproduction. To better understand the dynamics of clones and sexual lineage, we used genome-wide sequencing to analyse a recently expanded seaweed. We found large clones and sexual populations mixed close to range margins. Clones had evolved repeatedly from sexual populations but were unexpectedly low in genetic variation. Modelling suggested clones form from sexual populations after repeated bottlenecks at the expansion front. A clonal wave of depauperate genotypes thereafter spread ahead of the sexual population. As we observed, these early formed clones may survive side-by-side sexual individuals, which suggests they lost their sexual capacity. Our study illustrates how range expansion can result in complex and dynamic patterns of genetic variation in facultative asexual species.TeaserWe use genome data and modelling to find out why large clones are only found at range margins in a recently expanded seaweed
A spatial map of antennal-expressed olfactory ionotropic receptors in the malaria mosquito
Authors: Raji Joshua I. , Potter Christopher J. 
Published: May 2022

AbstractThe malaria mosquito Anopheles coluzzii uses odors to guide various behaviors such as host-seeking. The detection of behaviorally relevant odors is mediated by a diverse family of receptors including the olfactory Ionotropic Receptors (IRs). Olfactory receptors are expressed on olfactory neurons, with the mosquito antennae representing the main olfactory appendage for detecting volatile chemical cues from the environment. It is currently unknown how many neurons across the antenna express a certain IR, or how these IR-expressing neurons are spatially arranged. Here, we performed whole mount fluorescent in situ hybridization of all IRs expressed in the antennae. The organization of IR-positive cells within an antennal segment (flagellomere) appeared stereotyped across multiple antennae. The spatial map of IR-expressing neurons revealed that the antenna might be organized into proximal and distal functional domains. Highly expressed tuning (odor-binding) IRs exhibit distinct co-localization patterns with cognate IR co-receptor(s) in a combinatorial fashion that might predict their functional properties. These findings reveal organizing principles of Anopheles IR-expressing neurons in the mosquito which might underlie their functional contribution to the detection of behaviorally relevant odors.