bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive therapy for ovarian cancer: An integrated approach to PARP inhibitor scheduling
Authors: Strobl Maximilian , Martin Alexandra L. , West Jeffrey , Gallaher Jill , Robertson-Tessi Mark , Gatenby Robert , Wenham Robert , Maini Philip , Damaghi Mehdi , Anderson Alexander
Published: March 2023

Toxicity and emerging drug resistance are important challenges in PARP inhibitor (PARPi) treatment of ovarian cancer. Recent research has shown that evolutionary-inspired treatment algorithms which adapt treatment to the tumor’s treatment response (adaptive therapy) can help to mitigate both. Here, we present a first step in developing an adaptive therapy protocol for PARPi treatment by combining mathematical modelling and wet-lab experiments to characterize the cell population dynamics under different PARPi schedules. Using data fromin vitroIncucyte Zoom time-lapse microscopy experiments and a step-wise model selection process we derive a calibrated and validated ordinary differential equation model, which we then use to test different plausible adaptive treatment schedules. Our model can accurately predict thein vitrotreatment dynamics, even to new schedules, and suggests that treatment modifications need to be carefully timed, or one risks losing control over tumour growth, even in the absence of any resistance. This is because our model predicts that multiple rounds of cell division are required for cells to acquire sufficient DNA damage to induce apoptosis. As a result, adaptive therapy algorithms that modulate treatment but never completely withdraw it are predicted to perform better in this setting than strategies based on treatment interruptions. Pilot experimentsin vivoconfirm this conclusion. Overall, this study contributes to a better understanding of the impact of scheduling on treatment outcome for PARPis and showcases some of the challenges involved in developing adaptive therapies for new treatment settings.
An allocentric human odometer for perceiving distances on the ground plane
Authors: Zhou Liu , Wei Wei , Ooi Teng Leng , He Zijiang J.
Published: March 2023

We reliably judge locations of static objects when we walk despite the retinal images of these objects moving with every step we take. Here, we showed our brains solve this optical illusion by adopting an allocentric spatial reference frame. We measured perceived target location after the observer walked a short distance from the home base. Supporting the allocentric coding scheme, we found the intrinsic bias1, 2, which acts as a spatial reference frame for perceiving location of a dimly lit target in the dark, remained grounded at the home base rather than traveled along with the observer. The path-integration mechanism responsible for this can utilize both active and passive (vestibular) translational motion signals, but only along the horizontal direction. This anisotropic path-integration finding in human visual space perception is reminiscent of the anisotropic spatial memory finding in desert ants3, pointing to nature’s wondrous and logically simple design for terrestrial creatures.
Nigral Transcriptomic Profiles in Engrailed-1 Hemizygous Mouse Models of Parkinson’s Disease Reveal Upregulation of Oxidative Phosphorylation-Related Genes Associated with Resistance to Dopaminergic Neurodegeneration
Authors: Belfiori Lautaro , DueñasRey Alfredo , Ralbovszki Dorottya Mária , Jimenez-Ferrer Itzia , Bäckström Filip , Balikai Sagar Shivayogi , Ahrén Dag , Brolin Kajsa , Swanberg Maria
Published: March 2023

1.

Engrailed 1 (EN1) is a conserved transcription factor essential for programming, survival, and maintenance of midbrain dopaminergic neurons.En1-hemizygosity (En1+/-) leads to a spontaneous Parkinson’s disease-like (PD-like) progressive nigrostriatal degeneration as well as motor impairment and depressive-like behavior in SwissOF1 (OF1-En1+/-) mice. This phenotype is absent in C57Bl/6j (C57-En1+/-) mice. Here we studied PD-like phenotypes and early transcriptome profiles in OF1 wild-type (WT) and OF1-En1+/-male mice and compare to that of C57 WT and C57-En1+/-male mice. To detect transcriptional changes prior to dopaminergic cell loss, we performed RNA-seq of 1-week old mice substantia nigra pars compacta (SNpc). Histology and stereology were used to assess dopaminergic nigrostriatal pathology in 4 and 16 weeks old mice. OF1-En1+/-mice showed an increase (±79%) in dopaminergic striatal axonal swellings from 4 to 16 weeks and a loss (±23%) of dopaminergic neurons in the SNpc at 16 weeks compared to OF1 WT. Axonal swellings were also present in C57-En1+/-mice but did not increase over time. 52 differentially expressed genes (DEGs) were observed between the C57-WT and the C57-En1+/-mice, while 198 DEGs were observed in the OF1 strain. Enrichment analysis revealed that the neuroprotective phenotype of C57-En1+/-mice was associated with an upregulation of oxidative phosphorylation-related genes compared to both C57 WT and to OF1-En1+/-mice.

These results highlight the importance of considering genetic background in PD models and provide valuable insight on how expression of mitochondrial proteins before the onset of neurodegeneration is associated to vulnerability of nigrostriatal dopaminergic neurons.

2.

Significance statement

Most PD cases are idiopathic and caused by a complex interplay between genetic variants and environmental risk factors. However, the underlying mechanisms remain elusive. Here we show thatEn1hemizygosity leads to progressive nigrostriatal degeneration with a loss of dopaminergic neurons in OF1-En1+/-but that C57-En1+/-mice only exhibit early signs of nigrostriatal pathology and do not progress to a PD-like phenotype over time. We identified differences in gene expression related to oxidative phosphorylation before the onset of neurodegeneration to be associated to the differential susceptibility toEn1+/-induced PD-like pathology. Our work shows how gene expression changes modulate vulnerability to dopaminergic neurodegeneration in theEn1+/-mouse and reveals putative molecular mechanisms behind the onset and progression of PD.
Estimation of a treatment effect based on a modified covariates method withL0norm
Authors: Tanioka Kensuke , Okuda Kaoru , Hiwa Satoru , Hiroyasu Tomoyuki
Published: March 2023

Abstract

In randomized clinical trials, we assumed the situation that the new treatment is not adequate compared to the control treatment as result. However, it is unknown if the new treatment is ineffective for all patients or if it is effective for only a subgroup of patients with specific characteristics. If such a subgroup exists and can be detected, the patients can receive effective therapy. To detect subgroups, we need to estimate treatment effects. To achieve this, various treatment effect estimation methods have been proposed based on the sparse regression method. However, these methods are affected by noise. Therefore, we propose new treatment effect estimation approaches based on the modified covariate method, one using lasso regression and the other ridge regression, using theL0norm. The proposed approach was evaluated through numerical simulation and real data examples.
Precision of the Integrated Cognitive Assessment for the assessment of neurocognitive performance in athletes
Authors: Glassbrook Daniel J. , Chazot Paul L. , Hind Karen
Published: March 2023

Choice reaction time tests are commonly used for the assessment of cognitive function, and may be useful to assess the effect of sport participation. This study investigated the precision of the Integrated Cognitive Assessment (ICA; Cognetivity Neurosciences Ltd., Vancouver, Canada) test for the assessment of cognitive function in athletes. Thirty-one participants volunteered to take part in this study, from both contact (n= 22) and non-contact sports (n= 9). Participants performed the ICA test consecutively both before and after normal training session to simulate resting and post-sport conditions. Precision errors, relationships (Pearson’s r), and internal consistency (Cronbach’s Alpha) were calculated for three variables, ICA Index (overall information processing ability), ICA Speed (information processing speed) and ICA Accuracy (information processing accuracy). ICA precision errors [root mean squared-standard deviation, RMS-SD (coefficient of variation, %CV)] pre-sport were ICA Index: 5.18 (7.14%), ICA Speed: 3.98 (4.64%), and ICA Accuracy: 3.64 (5.00%); and post-sport were ICA Index: 3.96 (4.94%), ICA Speed: 2.14 (2.32%), and ICA Accuracy 3.40 (4.25%). The ICA test demonstrates high in-vivo precision with all variables except ICA Index (7.14%) demonstrating an acceptable precision error of ≤5% %CV. All variables demonstrated strong relationships between consecutive tests pre- and post-sport (r ≥ 0.8) except for the ICA Index post-sport which demonstrated a moderate (r ≥ 0.5) relationship. The ICA Index demonstrated good internal consistency (α ≥ 0.8) for both pre-and post-sport. The ICA Speed and ICA Accuracy variables demonstrated excellent internal consistency (α ≥ 0.9) for both pre-and post-sport. The ICA test is suitable for the assessment of cognitive function pre- and post-sport.
Basement membrane diversification relies on two competitive secretory routes defined by Rab10 and Rab8 and modulated by dystrophin and the exocyst complex
Authors: Dennis Cynthia , Pouchin Pierre , Richard Graziella , Mirouse Vincent
Published: March 2023

The basement membrane (BM) is an essential structural element of tissues, and its diversification participates in organ morphogenesis. However, the traffic routes associated with BM formation and the mechanistic modulations explaining its diversification are still poorly understood.Drosophila melanogasterfollicular epithelium relies on a BM composed of oriented BM fibrils and a more homogenous matrix. Here, we determined the specific molecular identity and cell exit sites of BM protein secretory routes. First, we found that Rab10 and Rab8 define two parallel routes for BM protein secretion. When both routes were abolished, BM production was fully blocked; however, genetic interactions revealed that these two routes competed. Rab10 promoted lateral and planar-polarized secretion, whereas Rab8 promoted basal secretion, leading to the formation of BM fibrils and homogenous BM, respectively. We also found that the dystrophin-associated protein complex (DAPC) and Rab10 were both present in a planar-polarized tubular compartment containing BM proteins. DAPC was essential for fibril formation and sufficient to reorient secretion towards the Rab10 route. Moreover, we identified a dual function for the exocyst complex in this context. First, the Exo70 subunit directly interacted with dystrophin to limit its planar polarization. Second, the exocyst complex was also required for the Rab8 route. Altogether, these results highlight important mechanistic aspects of BM protein secretion and illustrate how BM diversity can emerge from the spatial control of distinct traffic routes.
Self-loops in Evolutionary Graph Theory: Friends or Foes?
Authors: Sharma Nikhil , Yagoobi Sedigheh , Traulsen Arne
Published: March 2023

Evolutionary dynamics in spatially structured populations has been studied for a long time. More recently, the focus has been to construct structures that speeds up evolution – so called amplifiers of selection. It has been shown that for a structure to amplify selection, self-loops are necessary when mutants appear predominately in nodes that change often. As a result, for low mutation rates, self-looped amplifiers attain higher steady-state average fitness in the mutation-selection than well-mixed populations. But, what happens when the mutation rate increases such that fixation probabilities alone no longer describe the dynamics? We show that self-loops effects are detrimental outside the low mutation rate regime. In the intermediate and high mutation rate regime, amplifiers of selection attain lower steady-state average fitness than the complete graph and the suppressor of selection. We also provide an estimate of mutation rate beyond which the mutation-selection dynamics on a graph deviates from the weak mutation rate approximation. This involves computing how the average fixation time scales with the population size for several graphs.
Temporal progression of anaerobic fungal communities in dairy calves from birth to maturity
Authors: Jones Adrienne L. , Clayburn Jordan , Pribil Elizabeth , Foote Andrew P. , Montogomery Dagan , Elshahed Mostafa S. , Youssef Noha H.
Published: March 2023

Abstract

Establishment of microbial communities in neonatal calves is vital for their growth and overall health. Feed type and associated gastrointestinal tract morphophysiological changes occurring during the pre-weaning, weaning, and post-weaning phases are known to induce shifts in microbial community diversity, structure, and function. However, while the process has received considerable attention for bacteria, our knowledge on temporal progression of anaerobic gut fungi (AGF) in calves is lacking. Here, we examined AGF communities in fecal samples from six dairy cattle collected at 24 different time points during the pre-weaning (day 1-48), weaning (day 49-60), and post-weaning (3-12 months) stages. Quantitative PCR (qPCR) indicated that AGF colonize the calves GIT within 24 hours after birth, with AGF loads slowly increasing during pre-weaning/weaning phases and drastically increasing post-weaning. Culture- independent amplicon surveys identified higher AGF alpha diversity during pre-weaning/ weaning phases, compared to post-weaning. Further, the AGF community structure underwent a drastic shift post-weaning, from a community enriched in the generaKhoyollomyces, Orpinomyces, AL3, and NY8 (some of which commonly encountered in hindgut fermenters) to one enriched in the generaCaecomyces, Piromyces, Pecoramyces, and Cyllamyces, commonly encountered in adult ruminants. Inter-calf community variability was low in the pre- weaning/weaning phases but increased post-weaning. Finally, pairwise comparison of AGF community between calves day 1 post-birth and their mothers suggest a major role for maternal transmission, with additional input from cohabitating subjects. The distinct pattern of AGF progression in calves could best be understood in-light of their narrower niche preferences, metabolic specialization, and physiological optima when compared to bacteria, hence eliciting a unique response to changes in feeding pattern and associated structural development in the GIT of calves during maturation.
A multiplex PCR assay for the detection ofCryptosporidiumspecies and simultaneous differentiation ofCryptosporidium hominis, Cryptosporidium parvumin clinical stool samples
Authors: Katiyar Manish , Padukone Shashiraja , Gulati Reena , Singh Rakesh
Published: March 2023

Cryptosporidium hominisandCryptosporidium parvumare responsible for more than 90% of the global cryptosporidiosis. Species identification is done by amplification of small subunit ribosomal ribonucleic acid (SSU rRNA) gene, followed by sequencing. We have developed a multiplex polymerase chain reaction (mPCR) assay which detectCryptosporidiumspp. and differentiatesC. hominisandC. parvumfrom stool samples without the need of post amplification sequencing. Nine new set of primers for mPCR assay were designed and the mPCR assay was standardized with known positiveCryptosporidiumDNA template. Best result with three sets of primers that amplifies 436 bp for allCryptosporidiumspp., 577 bp forC. hominisand 287 bp forC. parvum. In addition, thirty-five positive and thirty-five negativeCryptosporidiumstool samples identified by the gold standard nested 18S rRNA PCR-sequencing assay were tested by mPCR. The sensitivity of the mPCR are 100%, 92.9%, and 87.5% forCryptosporidiumspp.,C. hominis, andC. parvumrespectively while specificity is 100% for all the three primers. No cross-reactivity was observed by the new mPCR assay when tested with five known DNA sample ofCystoisospora belliand two known DNA sample ofCyclospora cayetanensis, available in our laboratory from the clinical stool samples. A single species-specific mPCR product ofC. hominisandC. parvumwere sequenced and deposited in GenBank database with the accession noMT862538andMT875168respectively. The mPCR assay is developed which differentiatesC. hominis, andC. parvumin a single test run of amplification and without the need for RFLP or sequencing. Although it less sensitive than 18S rRNA PCR-sequencing assay, but 100% specific, rapid, cost-effective and suitable for making diagnosis of cryptosporidiosis especially in developing countries.

Highlights

Novel mPCR assay can detect allCryptosporidiumspecies

The sensitivity of the mPCR were 100%, 92.9%, and 87.5% for the primers designed to detectCryptosporidiumgenus,C. hominisandC. parvumspecies respectively.

No cross reactivity detected with newly developed mPCR assuring 100% specificity.

The developed mPCR assay is a robust, specific, reproducible, rapid and cost-effective molecular assay for the diagnosis of cryptosporidiosis.

Assay is useful in molecular diagnosis of cryptosporidiosis, especially in developing countries.
Distribution of nematocytes differs in two types of gonophores in hydrozoanSarsia lovenii
Authors: Vetrova Alexandra A. , Prudkovsky Andrey A. , Kremnyov Stanislav V.
Published: March 2023

Hydrozoan cnidarians are widely known for a diversity of life cycles. While some hydrozoan polyps produce medusae, in most species the gonophore remains attached to the polyp. Little is known about the mechanisms behind the loss of the medusal stage in hydrozoans. HydrozoanSarsia loveniiis a promising model for studying this issue. It is a polymorphic species with several haplogroups. One haplogroup produces attached eumedusoids and the other one buds free-swimming medusae. Here, we compared patterns of cell proliferation and distribution of nematocytes in medusoids, medusa buds and medusae ofS. lovenii.

Cell proliferation is absent from exumbrella of late medusa buds and medusae, but presumably i-cells proliferate in exumbrella of medusoids. In exumbrella of medusoids, we also observed evenly distributed nematocytes with capsules and expression of late nematogenesis-associated gene,Nowa. Nematocyte capsules andNowaexpression were also observed in exumbrella of medusa bud, but we did not detect prominentNowasignal in the bell of developed medusa. It is also known that abundance of exumbrellar nematocysts signs immaturity in medusae ofSarsiagenus. Our data demonstrate that nematocyte distribution and associated gene expression in medusoids resemble medusa buds rather than developed medusae. Thus, sexually mature medusoids exhibit juvenile somatic characters, demonstrating signs of neoteny.

Research highlights

HydrozoanSarsia loveniihas attached eumedusoids and free-swimming medusae. The distribution of nematocytes in eumedusoids resembles that in medusa buds. This may indicate neoteny of eumedusoids.
Mechanism of tension propagation in cell membranes
Authors: Barnoy Avishai , Tsaturyan Andrey K. , Kozlov Michael M.
Published: March 2023

The propagation of the membrane tension perturbations is a, potentially, essential mechanism of the mechanical signal transduction along surfaces of live cells. The efficiency of this process is determined by the propagation speed, which turned to be a hot and a controversial topic of the Cell Biophysics. In a stark contrast to the earlier results and expectations, the recent studies in several cell types revealed a wide range of the tension propagation speeds beginning from the strikingly low ones challenging the significance of the process and up to relatively high biologically relevant rates. The previously suggested models of the tension propagation have been based on assuming an unrealistic softness of the membranes for the stretching-compression deformations, which challenges the model ability to account for the observations. Here, we consider a different physics of the generation and the propagation of tension perturbations in cell membranes. We propose the tension to be controlled by an intra-cellular pressure and the propagation of the tension perturbations to be mediated by a membrane area redistribution between compartments, to which cell membranes are divided by the proteinic barriers, according to the picket-fence model. Using the established elastic features of cell membranes including their effective non-stretchability, this mechanism quantitatively accounts for the slowness of the propagation process and gives a natural explanation of the wide range of the observed propagation speeds. The model predictions are amenable to a direct experimental verification by controlled osmotic pressure variations.
Evolving antibody evasion and receptor affinity of the Omicron BA.2.75 sublineage of SARS-CoV-2
Authors: Wang Qian , Li Zhiteng , Guo Yicheng , Mellis Ian A. , Iketani Sho , Liu Michael , Yu Jian , Valdez Riccardo , Lauring Adam S. , Sheng Zizhang , Gordon Aubree , Liu Lihong , Ho David D.
Published: March 2023

SARS-CoV-2 Omicron BA.2.75 has diversified into multiple subvariants with additional spike mutations, and several are expanding in prevalence, particularly CH.1.1 and BN.1. Here, we investigated the viral receptor affinities and neutralization evasion properties of major BA.2.75 subvariants actively circulating in different regions worldwide. We found two distinct evolutionary pathways and three newly identified mutations that shaped the virological features of these subvariants. One phenotypic group exhibited a discernible decrease in viral receptor affinities, but a noteworthy increase in resistance to antibody neutralization, as exemplified by CH.1.1, which is apparently as resistant as XBB.1.5. In contrast, a second group demonstrated a substantial increase in viral receptor affinity but only a moderate increase in antibody evasion, as exemplified by BN.1. We also observed that all prevalent SARS-CoV-2 variants in the circulation presently, except for BN.1, exhibit profound levels of antibody evasion, suggesting this is the dominant determinant of virus transmissibility today.
Environmental selection overrides host selection in a horizontally acquired microbiota
Authors: Obeng Nancy , Schulenburg Hinrich
Published: March 2023

Horizontally acquired symbionts need to succeed both within hosts and the free-living environment. Microbes might invest differentially in these habitats, thus shaping fitness within host-associated microbiota communities. In this study, we investigated how host and environmental selection affect microbiota composition in a two-member model community ofPseudomonas luridaMYb11 andOchrobactrum vermisMYb71 from the natural microbiota ofCaenorhabditis elegans. Fitness characterizations in the host and non-host environment revealed distinct ecological strategies: while MYb11 dominated free-living by rapidly growing, it was quickly outcompeted within worms by MYb71. Using mathematical modeling and experimental evolution, we assessed how these distinct strategies affect microbiota composition over time. We found that MYb11 enriches in the host via its advantage in the environment and additionally adapts to the host. This community shift was mirrored in host fitness. Overall, this highlights the importance of the symbiont pool and shows that environmental selection can overwhelm host adaptation.
Validation of a Commercial Radioimmunoassay for Measurement of Human Peripheral Oxytocin
Authors: Gerred Keenan , Kapoor Amita
Published: March 2023

Oxytocin (OT) is a peptide hormone synthesized in the hypothalamus and released into systemic circulation or other areas of the brain. It has a variety of physiological roles such as stimulation of uterine contractions, involvement in social behaviors, and regulation of mood. Its small size and low levels within biological matrices make it challenging to accurately measure. The goal of this study was to demonstrate the specificity of the antibody, sensitivity, and reproducibility of the Phoenix Pharmaceuticals (PP) OT radioimmunoassay (RIA) for use in human urine, serum, and saliva. Specificity of the antibody was assessed by high pressure liquid chromatography with ultraviolet (HPLC-UV) separation and assay of the fractions. Immunoreactivity was evaluated using the percent OT bound, and the fraction retention times were compared to the retention time of an intact OT standard to determine which fractions contained OT in the extracted samples. Reproducibility was assessed by running replicates of pools of each biomatrix over several assays. Sensitivity was assessed by repeated measurement of physiologically relevant low-concentration specimens. In all tested specimens the greatest reactivity in assay corresponded to the same fraction(s) as the OT standard. Only minimal reactivity was found in the other fractions, suggesting that in an unfractionated sample the antibody reacts mostly with intact OT. Reproducibility was acceptable for all specimens and the coefficient of variation (CV) ranged from 3.72-8.04% and 5.89-12.8%, for intra and inter-assay, respectively. The limits of quantitation (LOQ) were sufficient for measurement of normal values in urine (0.643 & 1.43 pg/mL), serum (1.90 pg/mL), and saliva pools (0.485 & 4.42 pg/mL). In conclusion, the PP OT RIA is specific and sensitive enough for reproducible measurement of intact OT in human peripheral biological matrices.

HIGHLIGHTS

The oxytocin radioimmunoassay kit from Phoenix Pharmaceuticals is specific for intact oxytocin measured in human urine, serum, and saliva.

Basal levels of oxytocin are low in peripheral biomatrices, and the sensitivity of the assay is sufficient for reproducible measurement.
Visual working memory models of delayed estimation do not generalize to whole-report tasks
Authors: Cuthbert Benjamin , Standage Dominic , Paré Martin , Blohm Gunnar
Published: March 2023

Whole-report working memory tasks provide a measure of recall for all stimuli in a trial, and afford single-trial analyses that are not possible with single-report delayed estimation tasks. However, most whole-report studies assume that trial stimuli are encoded and reported independently, and do not consider the relationships between stimuli presented and reported within the same trial. Here, we present the results of two independently conducted whole-report experiments. The first dataset was recorded by Adam, Vogel, and Awh, 2017, and required participants to report color and orientation stimuli using a continuous response wheel. We recorded the second dataset, which required participants to report color stimuli using a set of discrete buttons. We find that participants often group their reports by color similarity, contradicting the assumption of independence implicit in most encoding models of working memory. Next, we show that this behavior is consistent across participants and experiments when reporting color but not orientation, two circular variables often assumed to be equivalent. Finally, we implement an alternative to independent encoding where stimuli are encoded as a hierarchical Bayesian ensemble, and show that this model predicts biases that are not present in either dataset. Our results suggest that assumptions made by both independent and hierarchical ensemble encoding models—which were developed in the context of single-report delayed estimation tasks—do not hold for the whole-report task. This failure to generalize highlights the need to consider variations in task structure when inferring fundamental principles of visual working memory.
Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axons
Authors: Liu Wei , Shrestha Rupendra , Lowe Albert , Zhang Xusheng , Spaeth Ludovic
Published: March 2023

The telencephalon and eye in mammals are originated from adjacent fields at the anterior neural plate. Morphogenesis of these fields generates telencephalon, optic-stalk, optic-disc, and neuroretina along a spatial axis. How these telencephalic and ocular tissues are specified coordinately to ensure directional retinal ganglion cell (RGC) axon growth is unclear. Here, we report the self-formation of human telencephalon-eye organoids comprising concentric zones of telencephalic, optic-stalk, optic-disc, and neuroretinal tissues along the center-periphery axis. Initially-differentiated RGCs grew axons towards and then along a path defined by adjacent PAX2+ optic-disc cells. Single-cell RNA sequencing of CONCEPT organoids not only confirmed telencephalic and ocular identities but also identified expression signatures of early optic-disc, optic-stalk, and RGCs. These signatures were similar to those in human fetal retinas. Optic-disc cells in CONCEPT organoids differentially expressedFGF8andFGF9; FGFR inhibitions drastically decreased RGC differentiation and directional axon growth. Through the identified RGC-specific cell-surface marker CNTN2, electrophysiologically-excitable RGCs were isolated under a native condition. Our findings provide insight into the coordinated specification of early telencephalic and ocular tissues in humans and establish resources for studying RGC-related diseases such as glaucoma.

Impact statement

A human telencephalon-eye organoid model that exhibited axon growth and pathfinding from retinal ganglion cell (RGC) axons is reported; via cell surface marker CNTN2 identified using scRNA-seq, early RGCs were isolated under a native condition.
Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors
Authors: Meller Artur , de Oliveira Saulo , Davtyan Aram , Abramyan Tigran , Bowman Gregory R. , van den Bedem Henry
Published: March 2023

Virtual screening is a widely used tool for drug discovery, but its predictive power can vary dramatically depending on how much structural data is available. In the best case, crystal structures of a ligand-bound protein can help find more potent ligands. However, virtual screens tend to be less predictive when only ligand-free crystal structures are available, and even less predictive if a homology model or other predicted structure must be used. Here, we explore the possibility that this situation can be improved by better accounting for protein dynamics, as simulations started from a single structure have a reasonable chance of sampling nearby structures that are more compatible with ligand binding. As a specific example, we consider the cancer drug target PPM1D/Wip1 phosphatase, a protein that lacks crystal structures. High-throughput screens have led to the discovery of several allosteric inhibitors of PPM1D, but their binding mode remains unknown. To enable further drug discovery efforts, we assessed the predictive power of an AlphaFold-predicted structure of PPM1D and a Markov state model (MSM) built from molecular dynamics simulations initiated from that structure. Our simulations reveal a cryptic pocket at the interface between two important structural elements, the flap and hinge regions. Using deep learning to predict the pose quality of each docked compound for the active site and cryptic pocket suggests that the inhibitors strongly prefer binding to the cryptic pocket, consistent with their allosteric effect. The predicted affinities for the dynamically uncovered cryptic pocket also recapitulate the relative potencies of the compounds (τb=0.70) better than the predicted affinities for the static AlphaFold-predicted structure (τb=0.42). Taken together, these results suggest that targeting the cryptic pocket is a good strategy for drugging PPM1D and, more generally, that conformations selected from simulation can improve virtual screening when limited structural data is available.
ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes
Authors: Nixon-Abell Jonathon , Ruggeri Francesco S. , Qamar Seema , Herling Therese W. , Czekalska Magdalena A. , Shen Yi , Wang Guozhen , King Christopher , Fernandopulle Michael S. , Sneideris Tomas , Watson Joseph L. , Pillai Visakh V.S. , Meadows William , Henderson James W. , Chambers Joseph E. , Wagstaff Jane L. , Williams Sioned H. , Coyle Helena , Lu Yuqian , Zhang Shuyuan , Marciniak Stefan J. , Freund Stefan M.V. , Derivery Emmanuel , Ward Michael E. , Vendruscolo Michele , Knowles Tuomas P.J. , St George-Hyslop Peter
Published: March 2023

Phase transitions of cellular proteins and lipids play a key role in governing the organisation and coordination of intracellular biology. The frequent juxtaposition of proteinaceous biomolecular condensates to cellular membranes raises the intriguing prospect that phase transitions in proteins and lipids could be co-regulated. Here we investigate this possibility in the ribonucleoprotein (RNP) granule-ANXA11-lysosome ensemble, where ANXA11 tethers RNP granule condensates to lysosomal membranes to enable their co-trafficking. We show that changes to the protein phase state within this system, driven by the low complexity ANXA11 N-terminus, induce a coupled phase state change in the lipids of the underlying membrane. We identify the ANXA11 interacting proteins ALG2 and CALC as potent regulators of ANXA11-based phase coupling and demonstrate their influence on the nanomechanical properties of the ANXA11-lysosome ensemble and its capacity to engage RNP granules. The phenomenon of protein-lipid phase coupling we observe within this system offers an important template to understand the numerous other examples across the cell whereby biomolecular condensates closely juxtapose cell membranes.

GRAPHICAL ABSTRACT
Microbial short-chain fatty acids regulate drug seeking and transcriptional control in a model of cocaine seeking
Authors: Meckel Katherine R. , Simpson Sierra S. , Godino Arthur , Peck Emily G. , George Olivier , Calipari Erin S. , Hofford Rebecca S. , Kiraly Drew D.
Published: March 2023

Cocaine use disorder represents a public health crisis with no FDA-approved medications for its treatment. A growing body of research has detailed the important connections between the brain and the resident population of bacteria in the gut, the gut microbiome in psychiatric disease models. Acute depletion of gut bacteria results in enhanced reward in a mouse cocaine place preference model, and repletion of bacterially-derived short-chain fatty acid (SCFA) metabolites reverses this effect. However, the role of the gut microbiome and its metabolites in modulating cocaine-seeking behavior after prolonged abstinence is unknown. Given that relapse prevention is the most clinically challenging issue in treating substance use disorders, studies examining the effects of microbiome manipulations in relapse-relevant models are critical. Here, Sprague-Dawley rats received either untreated water or antibiotics to deplete the gut microbiome and its metabolites. Rats were trained to self-administer cocaine and subjected to either within-session threshold testing to evaluate motivation for cocaine or 21 days of abstinence followed by a cue-induced cocaine-seeking task to model relapse behavior. Microbiome depletion did not affect cocaine acquisition on an FR1 schedule. However, microbiome-depleted subjects exhibited significantly enhanced motivation for low dose cocaine on a within-session threshold task. Similarly, microbiome depletion increased cue-induced cocaine-seeking following prolonged abstinence. In the absence of a normal microbiome, repletion of bacterially-derived SCFA metabolites reversed the behavioral and transcriptional changes associated with microbiome depletion. These findings suggest that gut bacteria, via their metabolites, are key regulators of drug-seeking behaviors, positioning the microbiome as a potential translational research target.
Germination responses to changing rainfall timing reveal potential climate vulnerability in a clade of wildflowers
Authors: Worthy Samantha J. , Miller Arquel , Ashlock Sarah R. , Ceviker Eda , Maloof Julin N. , Strauss Sharon Y. , Schmitt Johanna , Gremer Jennifer R.
Published: March 2023

The timing of germination, driven by seasonal cues, is critical for the life cycle of plants. Variation among species in germination responses can reflect evolutionary processes and adaptation to local climate and can affect vulnerability to changing conditions. Indeed, climate change is altering the timing of precipitation and associated temperatures, which may interact with germination cueing to affect the timing, quantity, and speed of germination. Germination responses to change can then have consequences for individual fitness, population dynamics, and species distributions. Here, we assessed responses to the timing of germination-triggering rains and corresponding temperatures for 11 species spanning theStreptanthus(s.l.) clade (Brassicaceae). To do so, we experimentally manipulated the onset date of rainfall events, measured effects on germination fraction and rate, and evaluated whether responses were constrained by evolutionary relationships across the phylogeny. We then explored the possible consequences of these responses to contemporary shifts in precipitation timing. Later onset rains and cooler temperatures significantly reduced germination rates for all species. Germination fractions decreased with later rains and cooler temperatures for all but threeCaulanthusspecies. Species’ germination responses to the timing of rainfall and seasonal temperatures were phylogenetically constrained, withCaulanthusspecies appearing less sensitive. Further, six species are likely already experiencing significant decreases in germination fractions or rates (or both) with observed climate change, which has shifted the timing of rainfall towards the cooler, winter months in California. Overall, our findings highlight the importance of the germination responses to seasonal timing, how they have evolved across the clade, and their implications under climate change.
Rapid systemic responses of Arabidopsis to waterlogging stress
Authors: Peláez-Vico María Ángeles , Tukuli Adama , Singh Pallav , Mendoza-Cózatl David G , Joshi Trupti , Mittler Ron
Published: March 2023

Waterlogging stress (WLS) negatively impacts the growth and yield of crops resulting in heavy losses to agricultural production. Previous studies revealed that WLS induces a systemic response in shoots that is partially dependent on the plant hormones ethylene and abscisic acid. However, the role of rapid cell-to-cell signaling pathways, such as the reactive oxygen species (ROS) and calcium waves, in systemic responses of plants to WLS is unknown at present. Here we reveal that an abrupt WLS treatment ofArabidopsis thalianaplants growing in peat moss triggers systemic ROS and calcium wave responses, and that the WLS-triggered ROS wave response of Arabidopsis is dependent on the ROS generating RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD), calcium-permeable channels GLUTAMATE-LIKE RECEPTOR 3.3 and 3.6 (GLR3.3 and GLR3.6), and aquaporin PLASMA MEMBRANE INTRINSIC PROTEIN 2;1 (PIP2;1) proteins. We further show that WLS is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation, includes many hypoxia-response transcripts, and is partially dependent on RBOHD. Interestingly, the abrupt WLS of Arabidopsis resulted in the triggering of a rapid hydraulic wave response and the transient opening of stomata on leaves. Taken together, our findings reveal that the initiation of WLS in plants is accompanied by rapid systemic physiological and transcriptomic responses that involve the ROS, calcium, and hydraulic waves. These findings reveal that systemic plant responses to WLS are rapid and at least partially dependent on cell-to-cell signaling mechanisms.
Differential effects of the stress peptides PACAP and CRF on sleep architecture in mice
Authors: Foilb Allison R. , Taylor-Yeremeeva Elisa M. , Fritsch Emma L. , Ravichandran Caitlin , Lezak Kimberly R. , Missig Galen , McCullough Kenneth M. , Carlezon William A.
Published: March 2023

Stress produces profound effects on behavior, including persistent alterations in sleep patterns. Here we examined the effects of two prototypical stress peptides, pituitary adenylate cyclase-activating polypeptide (PACAP) and corticotropin-releasing factor (CRF), on sleep architecture and other translationally-relevant endpoints. Male and female mice were implanted with subcutaneous transmitters enabling continuous measurement of electroencephalography (EEG) and electromyography (EMG), as well as body temperature and locomotor activity, without tethering that restricts free movement, body posture, or head orientation during sleep. At baseline, females spent more time awake (AW) and less time in slow wave sleep (SWS) than males. Mice then received intracerebral infusions of PACAP or CRF at doses producing equivalent increases in anxiety-like behavior. The effects of PACAP on sleep architecture were similar in both sexes and resembled those reported in male mice after chronic stress exposure. Compared to vehicle infusions, PACAP infusions decreased time in AW, increased time in SWS, and increased rapid eye movement sleep (REM) time and bouts on the day following treatment. In addition, PACAP effects on REM time remained detectable a week after treatment. PACAP infusions also reduced body temperature and locomotor activity. Under the same experimental conditions, CRF infusions had minimal effects on sleep architecture in either sex, causing only transient increases in SWS during the dark phase, with no effects on temperature or activity. These findings suggest that PACAP and CRF have fundamentally different effects on sleep-related metrics, and provide new insights into the mechanisms by which stress disrupts sleep.
HCC-1 accelerates atherosclerosis by inducing endothelial cells and macrophages pyroptosis and serves as an early diagnostic biomarker
Authors: Bu Fan , Wang Junhui , Zhang Qi , Lin Xiaomin , Zhang Ruyi , Bai Huanlan , Chen Juanjiang , Hua Yuneng , Wang Haifang , Huang Mei , Huang Yiyi , Hu Xiumei , Zheng Lei , Wang Qian
Published: March 2023

BACKGROUND

HCC-1 (Hemofiltrate CC chemokine-1), a CC-type chemokine, exerts function to change intracellular calcium concentration, induce leukocyte and manipulate enzyme release especially in monocytes. It has been reported that HCC-1 could predict the persistent acute kidney injury (AKI) or suppress hepatocellular carcinoma (HCC) by modulating cell cycle and promoting apoptosis, but the effect of HCC-1 on atherosclerosis is poorly understood. Here, we aimed to clarify the function and mechanism of HCC-1 in atherosclerosis and whether it could serve as a novel biomarker for the diagnosis of atherosclerosis.

METHODS

HCC-1 expression in serum, atherosclerotic plaques and normal arterial tissue from patients with atherosclerosis and control group was assessed by enzyme-linked immunosorbent assay, immunohistochemistry and con-focal microscope. The atherosclerotic model of HCC-1 overexpressing mice and control mice were generated by infection of AAV9-HCC-1 on an ApoE−/−background. Cell adhesion, polarization and pyroptosis were evaluated in vitro. The relationship between HCC-1 concentration in serum and atherosclerosis was analyzed in patients with atherosclerosis.

RESULTS

HCC-1 expression increased in patients with atherosclerosis both in serum and atherosclerotic plaque. HCC-1 overexpression mice had an enhancement in macrophage accumulation in plaque, higher levels of inflammatory factors, increased pyroptotic rate in ECs and Macrophages in plaque and decreased atherosclerotic plaque stability. In vitro, HCC-1 promoted monocytes to adhere to endothelial cells and M1 polarization, induced inflammation and pyroptosis both in ECs and Macrophages.

CONCLUSIONS

HCC-1 expression markedly increased in patients with atherosclerosis and HCC-1 overexpression accelerated atherosclerotic burden via an enhancement in monocytes recruitment, M1 polarization and pyroptosis both in ECs and Macrophages. Our findings suggested that HCC-1 may serve as an early biomarker for the diagnosis of atherosclerosis, with the capacity to reflect the degree of stenosis.

GRAPHIC ABSTRACT

A graphic abstract is available for this article.
Enterococcus faecalisOG1RF Evolution at Low pH Selects Fusidate-sensitive Mutants in Elongation Factor G and at High pH Selects Defects in Phosphate Transport
Authors: Fitzgerald Bailey A. , Wadud Ayman , Slimak Zachary , Slonczewski Joan L.
Published: March 2023

Enterococcusbacteria inhabit human and soil environments that show a wide range of pH. Strains include commensals as well as antibiotic-resistant pathogens. We investigated adaptation to pH stress inE. faecalisOG1RF by conducting experimental evolution in acid (pH 4.8), neutral pH (pH 7.0), and base (pH 9.0). Serial planktonic culture was performed for 500 generations, and in high-pH biofilm culture for four serial bead transfers. Nearly all mutations led to nonsynonomous codons, indicating adaptive selection. All acid-adapted clones from planktonic culture showed a mutation infusA(encoding elongation factor G). The acid-adaptedfusAmutants had a tradeoff of decreased resistance to fusidic acid (fusidate). All base-adapted clones from planktonic cultures, and some from biofilm-adapted cultures, showed mutations affecting the Pst phosphate ABC transporter (pstA, pstB, pstB2, pstC) andpyrR(pyrimidine biosynthesis regulator/uracil phosphoribosyltransferase). Biofilm culture produced small-size colonies on brain-heart infusion agar; these variants each contained a single mutation inpstB2,pstC, orpyrR. ThepstandpyrRmutants outgrew the ancestral strain at pH 9.2, with a tradeoff of lower growth at pH 4.8. Additional genes that had a mutation in multiple clones evolved at high pH (but not at low pH) includeoppBCDF(oligopeptide ABC transporter),ccpA(catabolite control protein A), andftsZ(septation protein). Overall, experimental evolution ofE. faecalisshowed strong pH dependence, favoring fusidate-sensitive elongation factor G modification at low pH and loss of phosphate transport genes at high pH.

IMPORTANCE

E. faecalisbacteria are found in dental biofilms where they experience low pH as a result of fermentative metabolism. Thus the effect of pH on antibiotic resistance has clinical importance. In endodontal infections, enterococci can resist calcium hydroxide therapy that generates extreme high pH. In other environments such as soil and plant rhizosphere, enterococci experience acidification associated with climate change. Thus the pH modulation of natural selection in enterococci is important for human health as well as for understanding soil environments.
The alternative sigma factor SigN ofBacillus subtilisis intrinsically toxic
Authors: Burton Aisha T. , Kálalová Debora , Snider Elizabeth V. , Burrage Andrew M. , Krásný Libor , Kearns Daniel B.
Published: March 2023

Sigma factors bind and direct the RNA polymerase core to specific promoter sequences and alternative sigma factors direct transcription of different regulons of genes. Here, we study the pBS32 plasmid-encoded sigma factor SigN ofBacillus subtilisto determine how it contributes to DNA damage-induced cell death. We find that SigN causes cell death when expressed at high level and does so in the absence of its regulon suggesting it is intrinsically toxic. One way toxicity was relieved was by curing the pBS32 plasmid, which eliminated a positive feedback loop that lead to SigN hyper-accumulation. Another way toxicity was relieved was through mutating the chromosomally-encoded transcriptional repressor protein AbrB and derepressing a potent antisense transcript that antagonized SigN expression. We note that SigN exhibits a relatively high affinity for the RNA polymerase core, efficiently competing with the vegetative sigma factor SigA, suggesting that toxicity was due to the competitive inhibition of one or more essential transcripts. WhyB. subtilisencodes a potentially toxic sigma factor is unclear but SigN may be related to phage-like genes also encoded on pBS32.

SIGNIFICANCE

Alternative sigma factors activate entire regulons of genes to improve viability in response to environmental stimuli. The pBS32 plasmid-encoded SigN ofBacillus subtilisis activated by the DNA damage response and leads to cellular demise. Here we find that SigN impairs viability by hyper-accumulating and outcompeting the vegetative sigma factor for the RNA polymerase core. WhyB. subtilisretains a plasmid with a deleterious alternative sigma factor is unknown.