bluuebunny/crossref_metadata_2025 huggingface dataset:
Lidocaine hampers colorectal cancer process via circITFG2/miR-1204/SOCS2 axis
Authors: Wang Huashe , Zhang Xuexia , Li Yi , Li Yanan , Pang Ting
Published: January 2022

Colorectal cancer (CRC) is a deadly disease with a poor prognosis. Lidocaine is preferred by surgical procedures due to the excellent anesthesia. Circular RNA integrin alpha FG-GAP repeat containing 2 (circITFG2) has been recognized as a momentous participator in CRC progression. The specific role of circITFG2 was further studied in this research. Quantitative real-time PCR (qRT-PCR) was devoted to examining the expression of circITFG2, microRNA-1204 (miR-1204) and SOCS2 mRNA in CRC cells. Western blot was used to determine SOCS2 protein expression in CRC cells. Cell viability, colony formation and apoptosis were detected by cell counting kit-8 (CCK-8) assay, colony formation assay and flow cytometry assay respectively. Cell migration and invasion were tested by wound healing assay and transwell assay. Dual-luciferase reporter system, RNA pull down and RNA-binding protein immunoprecipitation (RIP) assays were applied to verify the combination between miR-1204 and circITFG2 or SOCS2. CircITFG2 was strikingly downregulated; however, lidocaine treatment induced a significant increase in the expression of circITFG2 and SOCS2 and a decrease in miR-1204 expression in CRC cells. Meanwhile, SOCS2 protein expression was upregulated by lidocaine treatment or miR-1204 silence in CRC cells and downregulated by circITFG2 knockdown or miR-1204 overexpression in lidocaine-treated CRC cells. CircITFG2 knockdown or miR-1204 overexpression abolished lidocaine-induced inhibition in proliferation, metastasis and promotion in apoptosis in CRC cells. CircITFG2 overexpression, SOCS3 overexpression or lidocaine treatment suppressed proliferation, metastasis and facilitated apoptosis in CRC cells. CircITFG2 sponged miR-1204 to regulate SOCS3 expression in lidocaine-treated CRC cells. Lidocaine hindered CRC progression by circITFG2/miR-1204/SOCS2 axis. This finding might beat a path in improving CRC therapy.
Growth arrest-specific 5 lncRNA as a valuable biomarker of chemoresistance in osteosarcoma
Authors: Polvani Simone , Martignano Filippo , Scoccianti Guido , Pasqui Adriano , Palomba Anna Rita , Conticello Silvo , Galli Andrea , Palchetti Ilaria , Caporalini Chiara , Antonuzzo Lorenzo , Campanacci Domenico Andrea , Pillozzi Serena
Published: January 2022

Osteosarcoma is the most common primary malignant bone tumour in children and teenagers, and it is characterised by drug resistance and high metastatic potential. Increasing studies have highlighted the critical roles of long noncoding RNAs (lncRNAs) as oncogenes or tumour suppressors as well as new biomarkers and therapeutic targets in osteosarcoma. The growth arrest-specific 5 (GAS5) lncRNA can function as a tumour suppressor in several cancers. The present study aimed to validate GAS5 and other chemoresistance-associated lncRNAs as biomarkers in a cohort of primary osteosarcoma samples, to obtain predictive information on resistance or sensitivity to treatment. The GAS5 and a panel of lncRNAs related to chemoresistance [SNGH1, FOXD2-AS1, deleted in lymphocytic leukemia (DLEU2) and LINC00963] were evaluated in a cohort of osteosarcoma patients enrolled at the Careggi University Hospital. Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue sections and the expression levels of the lncRNAs were quantified by qPCR. A bioinformatic analysis on deposited RNA-seq data was performed to validate the qPCR results. Clustering analysis shows that GAS5 could be linked to the expression of isoforms 02 and 04 of the lncRNA DLEU2, whereas the DLEU2 isoform 08 is linked to the lncRNA LINC00963. We found that GAS5 is significantly increased in patients with a good prognosis and is expressed differently between chemosensitive and chemoresistant osteosarcoma patients. However, the results obtained are not concordant with the in-silico analysis performed on the TARGET osteosarcoma dataset. In the future, we would enlarge the case series, including different disease settings.
Anterior Chamber Angle Changes in Primary Angle-closure Glaucoma Following Phacoemulsification Versus Phacotrabeculectomy: A Prospective Randomized Clinical Trial
Authors: Ghadamzadeh Mojtaba , Karimi Farshid , Ghasemi Moghaddam Somayeh , Daneshvar Ramin
Published: January 2022

Précis:

We used anterior segment optical coherence tomography to investigate anterior chamber angle in primary angle-closure glaucoma (PACG) eyes following phacoemulsification and phacotrabeculectomy. Angle widening was significantly greater after phacoemulsification up to 6 months after the surgery.

Purpose:

To compare anterior chamber angle following 2 common surgeries for PACG.

Methods:

One hundred ten glaucoma patients were evaluated in this single center, prospective, randomized clinical trial. Those with concomitant PACG and senile cataract and without a history of ocular surgery, trauma, or chronic miotic use were recruited. Monocular patients were also excluded. Finally, 52 eligible subjects were randomly assigned to phacoemulsification (“Phaco” group, 25 eyes) or phacotrabeculectomy (“Combined” group, 27 eyes) surgeries. A swept-source, anterior segment optical coherence tomography device (CASIA SS-1000 OCT) was used to image the anterior segment. Mask graders used the images to measure the following parameters before and 1 week, 1 month, and 6 months after surgery: angle opening distance at 500 µm, trabecular iris surface area at 500 µm, and trabecular iris angle at 500 µm.

Results:

There was no significant difference between study groups regarding best-corrected visual acuity, intraocular pressure (IOP), and the number of glaucoma medications in preoperative or postoperative visits (P>0.076). Also, the measured angle parameters were not statistically significantly different between the 2 groups before surgery (P>0.123). After surgery, all measured parameters were significantly increased in both groups (P<0.0001). At the 6-month follow-up, nasal angle opening distance at 500 µm was 0.383±0.027 vs. 0.349±0.017, trabecular iris surface area at 500 µm was 0.141±0.007 vs. 0.125±0.005, and trabecular iris angle at 500 µm was 40.1±12.9 vs. 34.6±3.1 in Phaco and Combined groups, respectively (P<0.0001 for all).

Conclusions:

Anterior chamber angle widening by anterior segment optical coherence tomography was observed in PACG patients following surgery and was significantly greater after phacoemulsification compared with combined phacotrabeculectomy at all time points. Similar IOP and medication burden were noted for up to 6 months as secondary outcomes. The contribution of angle changes to the IOP-lowering effect of phacoemulsification in PACG eyes needs further study.
A Guide to Establishing a Pediatric Neurogastroenterology and Motility Program
Authors: Patel Dhiren , Sood Vibha , Ambartsumyan Lusine , Wheeler Justin , Kaul Ajay , Khlevner Julie , Darbari Anil , Rodriguez Leonel
Published: January 2022

The purpose of this document is to provide guidance for establishing a pediatric neurogastroenterology and motility (PNGM) program, including considerations for personnel, equipment, and physical space requirements, and business planning, from members of the neurogastroenterology and motility (NGM) Committee of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) who have developed PNGM programs at various institutions. A business plan defining the needs for required personnel, dedicated physical space, procedures, clinical care, and equipment storage is a prerequisite. Thoughtful logistical planning should address provider schedules, clinical visits, procedure coordination, and prior authorization processes. A business‐plan outlining equipment purchase with projected costs, revenue generation, and goals for future growth is desirable for obtaining institutional support, which is imperative to building a successful PNGM program.
Emerging Trends in Smartphone Photo Documentation of Child Physical Abuse
Authors: Schulte Ansley G. , Ricci Lawrence R. , Melville John D. , Brown Jocelyn
Published: January 2022

Photo documentation of injuries on children is universally recommended in cases of suspected child physical abuse. As technology improves, the ability to document physical examination findings through smartphone photography is increasingly accessible and practical. The quality of images captured on smartphones now rivals traditional photography and the integration of photo capture within the electronic medical record has led to a variety of fields adopting smartphone photo documentation for diagnosis, consult, and follow-up. However, in cases of child physical abuse, practitioners have been hesitant to adopt smartphones as a primary means of photo documentation because of concerns around image quality, privacy, and security. In this article, we discuss the technology of available smartphone cameras and current evidence regarding their use for photo documentation, use existing guidelines to propose a workflow to improve the yield of smartphone photo documentation in child physical abuse, and discuss common medicolegal concerns.
Regulators of proteostasis are translationally repressed in fibroblasts from sporadic and LRRK2-G2019S Parkinson’s patients
Authors: Flinkman Dani , Hong Ye , Deshpande Prasannakumar , Peltonen Sirkku , Kaasinen Valtteri , James Peter , Coffey Eleanor T.
Published: January 2022

Parkinson’s disease (PD) is characterized by heterogeneous motor and non-motor symptoms. The majority of PD cases are sporadic, whereas the leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common monogenic cause of familial PD and symptomatically indistinguishable from the sporadic form. Deficits in protein synthesis have been reported in PD. However, it is not known which proteins are affected or if there are synthesis differences between patients with sporadic and LRRK2 G2019S PD. Here we used non-canonical amino acid labeling and mass-spectrometry based proteomics to perform a quantitative comparison of nascent proteins in fibroblasts from sporadic and G2019S mutation PD patients compared to healthy individuals. We found that several proteins were under-represented among nascent proteins in cells from PD patients. Among these were regulators endo-lysosomal sorting, mRNA processing and translation itself. We further validated which of these proteins were dysregulated at the static proteome level using targeted proteomics. Key downregulated proteins included the autophagy regulator ATG9A and translational stability regulator YTHDF3. Notably, 68% of the identified proteins were downregulated in both sporadic and LRRK2-G2019S forms of PD. We identify translational repression of key regulators of proteostasis in patient fibroblasts that are common to both sporadic and LRRK2-G2019S PD.
Higher aboveground carbon stocks in mixed-species planted forests than monocultures – a meta-analysis
Authors: Warner Emily , Cook-Patton Susan C. , Lewis Owen T. , Brown Nick , Koricheva Julia , Eisenhauer Nico , Ferlian Olga , Gravel Dominique , Hall Jefferson S. , Jactel Hervé , Mayoral Carolina , Meredieu Céline , Messier Christian , Paquette Alain , Parker William C. , Potvin Catherine , Reich Peter B. , Hector Andy
Published: January 2022

Natural forest is declining globally as the area of planted forest increases. Planted forests are often monocultures, despite results suggesting that higher species richness improves ecosystem functioning and stability. To test if this is generally the case, we performed a meta-analysis of available results. We assessed aboveground carbon stocks in mixed-species planted forests vs (a) the average of constituent species monocultures, (b) the best constituent species monoculture, and (c) commercial species monocultures. We investigated whether any advantage of mixtures over monocultures was positively related to species richness, as well as potential mechanisms driving differences in carbon stocks between mixtures and monocultures. The meta-analysis dataset included 79 comparisons from 21 sites. Carbon stocks in mixed planted forests were higher than the average of stocks in monocultures of their constituent species, containing on average 70% more carbon. Mixed planted forests also out-performed commercial monocultures, containing on average 77% more carbon. There was c.25% more carbon in mixed planted forests relative to the best performing monocultures, although this difference was not statistically significant. Overyielding was highest in four-species mixtures (richness range 2-6 species). More data providing better coverage of richness and age gradients (study sites aged 3.5-28 years) is needed to increase confidence in these results. None of the potential mechanisms we examined (nitrogen-fixer present vs absent; native vs non-native/mixed origin; tree diversity experiment vs forestry plantation) consistently explained variation in the diversity effects. This suggests that our findings are driven by a combination of small (statistically insignificant) effects from these sources or further unidentified mechanisms or some combination of the two. We conclude that increasing tree species richness in planted forests can increase carbon stocks while bringing other potential benefits associated with diversification. However, implementation will depend on the balance of these benefits relative to the operational challenges and costs of diversification.
ccnWheat: A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors
Authors: Li Zhongqiu , Hu Yiheng , Ma Xuelian , Da Lingling , She Jiajie , Liu Yue , Yi Xin , Cao Yaxin , Xu Wenying , Jiao Yuannian , Su Zhen
Published: January 2022

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named ccnWheat. ccnWheat is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathway, gene family, protein-protein interactions, microRNA (miRNA), and several lines of epigenome data are integrated in this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using ccnWheat, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CArG specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. ccnWheat is useful for investigating co-expression networks and conducting other associated analyses, and thus facilitates comparative and functional genomic studies in wheat. ccnWheat is freely available at http://bioinformatics.cau.edu.cn/ccnWheat.
Isolating perceptual biases caused by trial history during auditory categorization
Authors: Duque Daniel , de la Rocha Jaime
Published: January 2022

Just as most experiences have their origin in our perceptions, our perceptions can also be fundamentally shaped by our experiences. However, isolating which events in the recent past can impact perceptual judgments remains a difficult question, partly because post-perceptual processes can also introduce strong history dependencies. Two mechanisms have been hypothesized to specifically modulate perception: 1) the repulsive influence caused by previous stimuli and generally labeled as aftereffects, and 2) the modulation caused by stimulus predictions based on learned temporal regularities of the sensory environment, a key assumption in the predictive coding framework. Here, we ask whether these two mechanisms do indeed bias perception by training rats in an auditory task featuring serial correlations along the sequence of stimuli. We develop a detailed behavioral model that isolates the repulsive aftereffect generated by previous stimuli and shows that this repulsion cannot be explained from an interaction between past and current stimuli, and that it is still present in catch trials lacking the current stimulus. Moreover, the model describes that the bias caused by the animals’ expectation, as they leverage the predictability of the stimulus sequence, is present in a foraging task without the sensory component but with the same serial correlations in the sequence of rewards. These results indicate that the aftereffect and the prediction biases observed during an auditory task can all be revealed in the absence of a sensory stimulus, putting into question their perceptual nature.
Metastability, fractal scaling, and synergistic information processing: what phase relationships reveal about intrinsic brain activity
Authors: Hancock Fran , Cabral Joana , Luppi Andrea I. , Rosas Fernando E. , Mediano Pedro A.M. , Dipasquale Ottavia , Turkheimer Federico E.
Published: January 2022

Dynamic functional connectivity (dFC) in resting-state fMRI holds promise to deliver candidate biomarkers for clinical applications. However, the reliability and interpretability of dFC metrics remain contested. Despite a myriad of methodologies and resulting measures, few studies have combined metrics derived from different conceptualizations of brain functioning within the same analysis - perhaps missing an opportunity for improved interpretability. Using a complexity-science approach, we assessed the reliability and interrelationships of a battery of phase-based dFC metrics including tools originated from dynamical systems, stochastic processes, and information dynamics approaches. Our analysis revealed novel relationships between these metrics, which allowed us to build a predictive model for integrated information using metrics from dynamical systems and information theory. Furthermore, global metastability - a metric reflecting simultaneous tendencies for coupling and decoupling - was found to be the most representative and stable metric in brain parcellations that included cerebellar regions. Additionally, spatiotemporal patterns of phase-locking were found to change in a slow, non-random, continuous manner over time. Taken together, our findings show that the majority of characteristics of resting-state fMRI dynamics reflect an interrelated dynamical- and informational-complexity profile, which is unique to each acquisition. This finding challenges the interpretation of results from cross-sectional designs for brain neuromarker discovery, suggesting that individual life-trajectories may be more informative than sample means.

Highlights

Spatiotemporal patterns of phase-locking tend to be time-invariant

Global metastability is representative and stable in a cohort of heathy young adults

dFC characteristics are in general unique to any fMRI acquisition

Dynamical- and informational-complexity are interrelated

Complexity science contributes to a coherent description of brain dynamics
Balancing sensitivity and specificity in preclinical research
Authors: Danziger Meggie , Collazo Anja , Dirnagl Ulrich , Toelch Ulf
Published: January 2022

The success of scientific discovery in preclinical research is based on the different roles of exploration and confirmation. Exploration involves identifying potential effects (high sensitivity), which are then tested more rigorously during confirmation (high specificity). Here, we examine different experimental strategies and their ability to balance sensitivity and specificity to identify relevant effects. In simulations based on empirical data, we specifically compare a conventional p-value based approach with a method based on an a priori determined smallest effect size of interest (SESOI). Using a SESOI increases transition rates from exploration to confirmation and leads to higher detection rates across the trajectory. In particular, specificity in the SESOI trajectory increases if number of true effects are low. We conclude that employing a SESOI is superior to a p-value based approach in many contexts. Based on our findings, we propose a reconsideration of planning and conducting preclinical experiments, especially when the prior probability of true hypotheses is low.
Contractility-induced self-organization of smooth muscle cells: from multilayer cell sheets to dynamic three-dimensional clusters
Authors: Wang Xiuyu , Gonzalez-Rodriguez David , Vourc’h Thomas , Silberzan Pascal , Barakat Abdul I.
Published: January 2022

Smooth muscle cells (SMCs) are mural cells that play a vital contractile function in many tissues. Abnormalities in SMC organization are associated with many diseases including atherosclerosis, asthma, and uterine fibroids. Various studies have reported that SMCs cultured on flat surfaces can spontaneously form three-dimensional clusters whose organization resembles that encountered in some of these pathological settings. Remarkably, how these structures form remains unknown. Here we combine in vitro experiments and physical modeling to show that three-dimensional clusters initiate when cellular contractile forces induce a hole in a flat SMC sheet, a process that can be modeled as the brittle fracture of a viscoelastic material. The subsequent evolution of the nascent cluster can be modeled as an active dewetting process with cluster shape evolution driven by a balance between cluster surface tension, arising from both cell contractility and adhesion, and cluster viscous dissipation. The description of the physical mechanisms governing the spontaneous emergence of these intriguing three-dimensional clusters offers insight into SMC-related disorders.
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns
Authors: Mikheenko Alla , Prjibelski Andrey D , Joglekar Anoushka , Tilgner Hagen U
Published: January 2022

Long-read transcriptomics requires understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform comparison method that combined barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences and Oxford Nanopore. We compared these long reads pairs in terms of sequence content and splicing structure. Although individual read pairs show high similarity, we found differences in (i) aligned length, (ii) TSS and (iii) polyA-site assignment, and (iv) exon-intron structures. Overall 25% of read pairs disagreed on either TSS, polyA-site, or a splice site. Intron-chain disagreement typically arises from alignment errors of microexons and complicated splice sites. Our single-molecule technology comparison revealed that inconsistencies are often caused by sequencing-error induced inaccurate ONT alignments, especially to downstream GTNNGT donor motifs. However, annotation-disagreeing upstream shifts in NAGNAG acceptors in ONT are often confirmed by PacBio and thus likely real. In both barcoded and non-barcoded ONT reads, we found that intron number and proximity of other GT/AGs better predict inconsistency with the annotation than read quality alone. We summarized these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.
Region-specific CREB function regulates distinct forms of regret associated with resilience versus susceptibility to chronic stress
Authors: Cuttoli Romain Durand-de , Martínez-Rivera Freddyson J. , Li Long , Minier-Toribio Angélica , Cathomas Flurin , Holt Leanne M. , Yasmin Farzana , Elhassa Salma O. , Shaikh Jasmine F. , Ahmed Sanjana , Russo Scott J. , Nestler Eric J. , Sweis Brian M.
Published: January 2022

Regret describes recognizing that alternative actions could have led to better outcomes. This can transform into behavioral consequences, altering subsequent valuations, but remains unclear if regret derives from a generalized computation for mistake appraisal or instead is made up of dissociable action-specific processes. Using a novel neuroeconomic decision-making paradigm, we found mice were differentially sensitive to fundamentally distinct types of missed opportunities following exposure to chronic social defeat stress or manipulations of CREB, a key transcription factor implicated in chronic stress action. Bias to make compensatory decisions after rejecting high-value offers (regret type I) was unique to stress-susceptible mice. Bias following the converse operation, accepting low-value offers (regret type II), was enhanced in stress-resilient and absent in stress-susceptible mice. CREB function in either the medial prefrontal cortex or nucleus accumbens was required to suppress regret type I but differentially affected regret type II. We provide insight into how adaptive versus maladaptive stress-response traits may be related to fundamentally distinct forms of counterfactual thinking and could steer psychotherapy for mood disorders such as depression toward unveiling circuit-specific computations through a careful description of decision narrative.
Exploiting color space geometry for visual stimulus design across animals
Authors: Christenson Matthias P. , Mousavi S. Navid , Heath Sarah L. , Behnia Rudy
Published: January 2022

Color vision represents a vital aspect of perception that ultimately enables a wide variety of species to thrive in the natural world. However, unified methods for constructing chromatic visual stimuli in a laboratory setting are lacking. Here, we present stimulus design methods and an accompanying programming package to efficiently probe the color space of any species in which the photoreceptor spectral sensitivities are known. Our hardware-agnostic approach incorporates photoreceptor models within the framework of the principle of univariance. This enables experimenters to identify the most effective way to combine multiple light sources to create desired distributions of light, and thus easily construct relevant stimuli for mapping the color space of an organism. We include methodology to handle uncertainty of photoreceptor spectral sensitivity as well as to optimally reconstruct hyperspectral images given recent hardware advances. Our methods support broad applications in color vision science and provide a framework for uniform stimulus designs across experimental systems.
Nirmatrelvir, Molnupiravir, and Remdesivir maintain potent in vitro activity against the SARS-CoV-2 Omicron variant
Authors: Rosales Romel , McGovern Briana L. , Rodriguez M. Luis , Rai Devendra K. , Cardin Rhonda D. , Anderson Annaliesa S. ,   PSP study group, Sordillo Emilia Mia , van Bakel Harm , Simon Viviana , García-Sastre Adolfo , White Kris M.
Published: January 2022

Variants of SARS-CoV-2 have become a major public health concern due to increased transmissibility, and escape from natural immunity, vaccine protection, and monoclonal antibody therapeutics. The highly transmissible Omicron variant has up to 32 mutations within the spike protein, many more than previous variants, heightening these concerns of immune escape. There are now multiple antiviral therapeutics that have received approval for emergency use by the FDA and target both the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and the main protease (Mpro), which have accumulated fewer mutations in known SARS-CoV-2 variants. Here we test nirmatrelvir (PF-07321332), and other clinically relevant SARS-CoV-2 antivirals, against a panel of SARS-CoV-2 variants, including the novel Omicron variant, in live-virus antiviral assays. We confirm that nirmatrelvir and other clinically relevant antivirals all maintain activity against all variants tested, including Omicron.
Assessing the impact of roadkill on the persistence of wildlife populations: a case study on the giant anteater
Authors: Ascensão Fernando , Desbiez Arnaud L.J.
Published: January 2022

Human activity is depleting biodiversity, and road networks are directly contributing to this trend due to roadkill. Nevertheless, few studies empirically estimated the impact of roadkill on wildlife populations. We integrated information on roadkill rates, population abundance, and animal movement to estimate the survival rates and the proportion of the population likely to be extirpated due to roadkill, using giant anteater (Myrmecophaga tridactyla) as model species. We then assessed the consequent implications of roadkill on population persistence using population viability analysis (PVA). The yearly survival rate of resident anteaters inhabiting road vicinity areas (0.78; CI:0.62-0.97) was considerably lower than for those living far from roads (0.95; CI:0.86-1.00). The real number of anteaters being road-killed is considerably higher than the one recorded in previous studies (by a factor of 2.4), with ca. 20% of the population inhabiting road vicinity areas being road-killed every year. According to PVA results, roadkill can greatly affect the persistence of the giant anteater populations by reducing the growth rate down to null or negative values. This study confirms that roads have significant impacts on local population persistence. Such impacts are likely to be common to other large mammals, calling for effective mitigation to reduce roadkill rates.
Modified viral-genetic mapping reveals local and global connectivity relationships of ventral tegmental area dopamine cells
Authors: Beier Kevin T.
Published: January 2022

Dopamine cells in the ventral tegmental area (VTADA) are critical for a variety of motivated behaviors. These cells receive synaptic inputs from over 100 anatomically-defined brain regions, which enables control from a distributed set of inputs across the brain. Extensive efforts have been made to map inputs to VTA cells based on neurochemical phenotype and output site. However, all of these studies have the same fundamental limitation that inputs local to the VTA cannot be properly assessed due to non-Cre-dependent uptake of EnvA-pseudotyped virus. Therefore, the quantitative contribution of local inputs to the VTA, including GABAergic, DAergic, and serotonergic, is not known. Here, we used a modified viral-genetic strategy that enables examination of both local as well as long-range inputs to VTADAcells. We found that nearly half of the total inputs to VTADAcells are located locally, revealing a substantial portion of inputs that have been missed by previous analyses. The majority of inhibition to VTADAcells arises from the substantia nigra pars reticulata, with large contributions from the VTA and the substantia nigra pars compacta. In addition to receiving inputs from VTAGABAneurons, DA neurons are connected with other DA neurons within the VTA as well as the nearby retrorubal field. Lastly, we show that VTADAneurons receive inputs from distributed serotonergic neurons throughout the midbrain and hindbrain, with the majority arising from the dorsal raphe. Our study highlights the importance of using the appropriate combination of viral-genetic reagents to unmask the complexity of connectivity relationships to defined cells in the brain.
Resistor: an algorithm for predicting resistance mutations using Pareto optimization over multistate protein design and mutational signatures
Authors: Guerin Nathan , Feichtner Andreas , Stefan Eduard , Kaserer Teresa , Donald Bruce R.
Published: January 2022

Resistance to pharmacological treatments is a major public health challenge. Here we report Resistor—a novel structure- and sequence-based algorithm for drug design providing prospective prediction of resistance mutations. Resistor computes the Pareto frontier of four resistance-causing criteria: the change in binding affinity (ΔKa) of the (1) drug and (2) endogenous ligand upon a protein’s mutation; (3) the probability a mutation will occur based on empirically derived mutational signatures; and (4) the cardinality of mutations comprising a hotspot. To validate Resistor, we applied it to kinase inhibitors targeting EGFR and BRAF in lung adenocarcinoma and melanoma. Resistor correctly identified eight clinically significant EGFR resistance mutations, including the “gatekeeper” T790M mutation to erlotinib and gefitinib and five known resistance mutations to osimertinib. Furthermore, Resistor predictions are consistent with sensitivity data on BRAF inhibitors from both retrospective and prospective experiments using the KinCon biosensor technology. Resistor is available in the open-source protein design software OSPREY.
Event-related potential correlates of learning to produce novel foreign phonemes
Authors: Railo Henry , Varjonen Anni , Lehtonen Minna , Sikka Pilleriin
Published: January 2022

Learning to pronounce a foreign phoneme requires an individual to acquire a motor program that enables the reproduction of the new acoustic target sound. This process is largely based on the use of auditory feedback to detect pronunciation errors to adjust vocalization. While early auditory evoked neural activity underlies automatic detection and adaptation to vocalization errors, little is known about the neural correlates of acquiring novel speech targets. To investigate the neural processes that mediate the learning of foreign phoneme pronunciation, we recorded event-related potentials (ERP) when participants (N=19) pronounced native or foreign phonemes. Behavioral results indicated that the participants’ pronunciation of the foreign phoneme improved during the experiment. Early auditory responses (N1 and P2 waves, approx. 85–290 ms after the sound onset) revealed no differences between foreign and native phonemes. In contrast, the amplitude of the fronto-centrally distributed late slow wave (LSW, 320–440 ms) was modulated by the pronunciation of the foreign phonemes, and the effect changed during the experiment, paralleling the improvement in pronunciation. These results suggest that the LSW may reflect higher-order monitoring processes that signal successful pronunciation and help learn novel phonemes.
The accuracy of protein structures in solution determined by AlphaFold and NMR
Authors: Fowler Nicholas J. , Williamson Mike P.
Published: January 2022

In the recent CASP (Critical Assessment of Structure Prediction) competition, AlphaFold2 performed outstandingly. Its worst predictions were for NMR structures, which has two alternative explanations: either the NMR structures were poor, implying that AlphaFold may be more accurate than NMR; or there is a genuine difference between crystal and solution structures. Here, we use the program ANSURR, which measures the accuracy of solution structures, and show that one of the NMR structures was indeed poor. We then compare AlphaFold predictions to NMR structures, and show that AlphaFold tends to be more accurate than NMR ensembles, in particular correctly more rigid in loops. There are however some cases where the NMR ensembles are more accurate. These tend to be dynamic structures where AlphaFold had low confidence. We suggest that AlphaFold could be used as the model for NMR structure refinements, and that AlphaFold structures validated by ANSURR require no further refinement.
Proton-pumping rhodopsins in marine diatoms
Authors: Yoshizawa Susumu , Azuma Tomonori , Kojima Keiichi , Inomura Keisuke , Hasegawa Masumi , Nishimura Yosuke , Kikuchi Masuzu , Armin Gabrielle , Miyashita Hideaki , Ifuku Kentaro , Yamano Takashi , Marchetti Adrian , Fukuzawa Hideya , Sudo Yuki , Kamikawa Ryoma
Published: January 2022

Diatoms are a major phytoplankton group responsible for about 20% of Earth’s primary production. They carry out photosynthesis inside the plastid, an organelle obtained through eukaryote-eukaryote endosymbiosis. Recently, microbial rhodopsin, a photoreceptor distinct from chlorophyll-based photosystems, has been identified in certain diatoms. However, the physiological function of diatom rhodopsin is not well understood. Here we show that the diatom rhodopsin acts as a light-driven proton pump and localizes to the outermost membrane of the four membrane-bound complex plastids. Heterologous expression techniques were used to investigate the protein function and subcellular localization of diatom rhodopsin. Using model simulations, we further evaluated the physiological role of the acidic pool in the plastid produced by proton-transporting rhodopsin. Our results propose that the rhodopsin-derived acidic pool may be involved in a photosynthetic CO2-concentrating mechanism and assist CO2 fixation in diatom cells.
Massively parallel genomic perturbations with multi-target CRISPR reveal new insights on Cas9 activity and DNA damage responses at endogenous sites
Authors: Zou Roger S. , Marin-Gonzalez Alberto , Liu Yang , Liu Hans B. , Shen Leo , Dveirin Rachel , Luo Jay X. J. , Kalhor Reza , Ha Taekjip
Published: January 2022

We present an approach that combines a Cas9 that simultaneously targets hundreds of epigenetically diverse endogenous genomic sites with high-throughput sequencing technologies to measure Cas9 dynamics and cellular responses at scale. This massive multiplexing of CRISPR is enabled by means of novel multi-target gRNAs (mgRNAs), degenerate gRNAs that direct Cas9 to a pre-determined number of well-mapped sites. mgRNAs uncovered generalizable insights into Cas9 binding and cleavage, discovering rapid post-cleavage Cas9 departure and repair factor loading at PAM-proximal genomic DNA. Moreover, by bypassing confounding effects from gRNA sequence, mgRNAs unveiled that Cas9 binding is enhanced at chromatin-accessible regions, and Cas9 cleavage is more efficient near transcribed regions. Combined with light-mediated activation and deactivation of Cas9 activity, mgRNAs further enabled high-throughput study of the cellular response to double strand breaks with high temporal resolution, discovering the presence, extent (under 2 kb), and kinetics (~ 0.5 hr) of reversible DNA damage-induced chromatin decompaction. Altogether, this work establishes mgRNAs as a generalizable platform for multiplexing CRISPR and advances our understanding of intracellular Cas9 activity and the DNA damage response at endogenous loci.
RNF213 loss of function reshapes vascular transcriptome and spliceosome leading to disrupted angiogenesis and aggravated vascular inflammatory responses
Authors: Zhang Liyin , Rashad Sherif , Zhou Yuan , Niizuma Kuniyasu , Tominaga Teiji
Published: January 2022

Rationale

Moyamoya disease (MMD) is a rare cerebrovascular occlusive disease that affects Asian population more often. The pathogenesis of MMD is related to mutation in RNF213 gene. However, why, and how RNF213 mutation leads to MMD is still not fully understood.

Objective

Analyze the impact of RNF213 loss of function on vascular cells and the observed changes correlate with MMD.

Methods and results

RNF213 KD was conducted in HUVEC and vascular smooth muscle cells (vSMCs). First, HUVEC cells showed alteration of angiogenesis, migration under LPS stimulation, Leukocyte endothelial transmigration, and endothelial-to-vSMCs communication.

Transcriptome analysis revealed downregulation of genes regulating cell division and mitosis. Interestingly, Alternative splicing (AS) analysis revealed hundreds of AS events to occur after RNF213 KD in various types of AS. The alternatively spliced genes showed minimal overlap with transcriptome profiling. Pathway analysis revealed many processes and pathways to be regulated by AS events observed. Transcriptome profiling was also performed after LPS treatment and revealed the basis for increased sensitivity to LPS observed in our analysis. AS changes were also observed after LPS treatment in RNF213 KD HUVEC. Different types of AS showed different patterns of convergence or divergence in terms of the regulated pathways after LPS treatment. Finally, transcriptome and AS analysis was performed in vSMCs and showed various processes that impact vSMCs function and phenotype in RNF213 loss of function.

Conclusion

Our data provide a wealth of information on RNF213 gene function in vascular tissues and shed important light on different processes that contribute to MMD pathogenesis. Our results signify an immune-driven and hemodynamically linked process of MMD initiation and progression.
Environmental and taxonomic drivers of bacterial extracellular vesicle production in marine ecosystems
Authors: Biller Steven J. , Coe Allison , Arellano Aldo A. , Dooley Keven , Gong Jacqueline S. , Yeager Emily A. , Becker Jamie W. , Chisholm Sallie W.
Published: January 2022

Extracellular vesicles are small (∼50-250 nm diameter) membrane-bound structures released by cells into their surrounding environment. Vesicles are abundant in the global oceans and likely play a number of ecological roles in these microbially dominated ecosystems, yet we know nothing about what influences their production and distributions. Here we examine how vesicle production varies among different strains of cultivated marine microbes and explore the degree to which this is influenced by some key environmental variables. We show that vesicle production rates – the number of vesicles produced per cell per generation – vary across an order of magnitude in cultures of marine Proteobacteria, Cyanobacteria, and Bacteroidetes. Vesicle production rates further differ among strains of the cyanobacteriumProchlorococcus, and vary across temperature and light gradients. These data suggest that both community composition and local environmental conditions modulate the production and standing stock of vesicles in the oceans. Examining samples from the oligotrophic North Pacific Gyre, we show depth-dependent changes in the abundance of vesicle-like particles in the upper water column in a manner broadly consistent with culture observations: highest vesicle abundances are found near the surface, where light irradiances and temperatures are greatest, and then decrease with depth. This work represents the beginnings of a quantitative framework for describing extracellular vesicle dynamics in the oceans – essential as we begin to incorporate vesicles into our ecological and biogeochemical understanding of marine ecosystems.

Importance

Bacteria secrete extracellular vesicles containing a wide variety of cellular compounds, including lipids, proteins, nucleic acids, and small molecules, into their surrounding environment. These structures are found in diverse microbial habitats, including the oceans, where their distributions vary throughout the water column. Differences in vesicle abundances likely affect their functional impacts within microbial ecosystems, but the factors influencing vesicle distributions in the environment remain poorly understood. Using quantitative analysis of marine microbial cultures, we show that bacterial vesicle production in the oceans is shaped by a combination of biotic and abiotic factors. Our data indicate that different marine taxa release vesicles at rates varying across an order of magnitude, and that vesicle production can change dynamically as a function of environmental conditions. Taken together with direct measurements of vesicle concentrations in the oceans, these culture-based measurements further provide a window into estimating vesicle loss rates. These findings represent a step forward in our understanding of marine vesicle distributions and provide a basis for quantitatively exploring vesicle dynamics in natural ecosystems.
Psychological flexibility and the moderating role of the therapeutic working alliance in Acceptance and Commitment Therapy in Daily Life (ACT-DL) in an early psychosis sample
Authors: van Aubel Evelyne , Vaessen Thomas , van Winkel Ruud , Lafit Ginette , Beijer-Klippel Annelie , Viechtbauer Wolfgang , Batink Tim , van der Gaag Mark , van Amelsvoort Therese , Marcelis Machteld , Schirmbeck Frederike , de Haan Lieuwe , Reininghaus Ulrich , Myin-Germeys Inez
Published: January 2022

Background

We investigated treatment effects of Acceptance and Commitment Therapy in Daily Life (ACT-DL) on psychological flexibility (PF) and the moderating role of the therapeutic working alliance on these effects in patients with early psychosis.

Methods

ACT-DL is an ecological momentary intervention (EMI) combining face-to-face ACT with a smartphone app. In the multi-center INTERACT randomized controlled trial, n=148 early psychosis individuals were randomized to either treatment as usual (TAU as the control condition, n=77) or to ACT-DL in addition to TAU (ACT-DL + TAU as the experimental condition, n=71). We assessed global PF and the therapeutic alliance with self-report questionnaires. In addition, we used the experience sampling methodology (ESM) to assess PF with a momentary (in-the-moment and since-the-previous-beep openness) and an evening (daily PF) questionnaire. Assessments took place at baseline, post-intervention (POST), six (FU6), and twelve months (FU12) follow-up.

Results

Global (B=19.49 to 33.14; all P-values<.001) and daily PF (B=0.68; P-value<.001) improved equally in both conditions at each time point. Individuals in the ACT-DL condition improved more than those in TAU on momentary openness (in-the-moment openness at POST (B=0.32; P-value=0.007) and since-the-previous-beep openness at POST (B=0.33; P<.001) and FU6 (B=0.23; P-value=0.025). Client-perceived working alliance moderated in-the-moment openness such that larger improvements in openness at POST (B=0.05; P-value<.001) were found in ACT-DL in individuals with higher working alliance scores.

Conclusion

Our results provide partial support for the capability of ACT-DL to improve daily life measures of openness, and emphasize the importance of the therapeutic relationship in supporting processes of change.
Seeing sounds: Neural mechanisms underlying auditory contributions to visual detection
Authors: Pérez-Bellido Alexis , Spaak Eelke , de Lange Floris P.
Published: January 2022

Sounds enhance the detection of visual stimuli while concurrently biasing an observer’s decisions. To investigate the neural mechanisms that underlie such multisensory interactions, we decoded time-resolved signal detection theory (SDT) sensitivity and criterion parameters from neural activity using magnetoencalography, while participants performed a visual detection task. Using temporal generalization analysis, we found that sounds improve visual detection by enhancing the maintenance of the most informative perceptual samples over time. In parallel, criterion decoding analyses revealed that sounds evoke patterns of activity that resembled the patterns evoked by an actual visual stimulus. These two complementary mechanisms of audiovisual interaction differed in terms of their automaticity: Whereas the sound-induced enhancement in visual information maintenance depended on participants being actively engaged in a detection task, sounds evoked visual activity patterns in the visual cortex in a bottom-up fashion, challenging the classical assumption that sound- induced reductions in criterion correspond to decision-level biases.
SARS-CoV-2 Omicron efficiently infects human airway, but not alveolar epithelium
Authors: Lamers Mart M. , Mykytyn Anna Z. , Breugem Tim I. , Groen Nathalie , Knoops Kèvin , Schipper Debby , van Acker Romy , van den Doel Petra B. , Bestebroer Theo , Koopman Charlotte D. , Reusken Chantal , Muraro Mauro J. , GeurtsvanKessel Corine H. , van Royen Martin E. , Peters Peter J. , Zhang Jingshu , Haagmans Bart L.
Published: January 2022

In late 2021, the highly mutated SARS-CoV-2 Omicron variant emerged, raising concerns about its potential extensive immune evasion, increased transmissibility and pathogenicity. Here, we used organoids of the human airways and alveoli to investigate Omicron’s fitness and replicative potential in comparison with earlier SARS-CoV-2 variants. We report that Omicron replicates more rapidly in the airways and has an increased fitness compared to the early 614G variant and Delta. In contrast, Omicron did not replicate productively in human alveolar type 2 cells. Mechanistically, we show that Omicron does not efficiently use TMPRSS2 for entry or spread through cell-cell fusion. Altogether, our data show that Omicron has an altered tropism and protease usage, potentially explaining its higher transmissibility and decreased pathogenicity.