bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional and Psychosocial Outcomes following Innervated Breast Reconstruction: A Systematic Review
Authors: Abbas Fuad , Klomparens Kara , Simman Richard
Published: September 2022

Background:

With the incidence of breast cancer, breast cancer survival rates, and prophylactic mastectomies all increasing, efforts to optimize breast reconstruction and improve quality of life are becoming increasingly important. Nerve coaptation has been investigated for its potential to remedy the clinical and psychosocial deficits in newly reconstructed breasts. The purpose of this review is to gauge the efficacy of nerve coaptation during breast reconstruction in creating worthwhile benefits in both objective and subjective dimensions of sensation.

Methods:

A Prospero registered systematic review was conducted. Databases including PubMed, SCOPUS, and ScienceDirect were screened using search terms “innervation," “breast reconstruction," and “neurotization” and relevant inclusion criteria.

Results:

Twenty-three studies were found that met parameters for inclusion. We identified studies that assessed DIEP-based reconstruction (7), TRAM-based reconstruction (9), implant-based reconstruction (2), and five studies that looked at a variety of reconstructive modalities. Monofilament testing was the most common modality used to assess sensation, while pain, temperature, and pressure thresholds were assessed more infrequently. Various tools were used to measure psychosocial impacts, including the BREAST-Q. While the methods for evaluation of both aspects of sensation were heterogenous, there was a trend towards improved outcomes with neurotization.

Conclusions:

The results of this review show promising improvements in clinical and psychosocial outcomes in innervated breasts compared to non-innervated breasts. However, the heterogeneity of studies in the literature indicates that more multi-center studies with standardized methodology including the BREAST-Q, sensory testing and complication analysis are needed to adequately demonstrate the value of neurotization in breast reconstruction.
Targeting Cellular Senescence with Senotherapeutics: Development of New Approaches for Skin Care
Authors: Thompson Elizabeth L. , Pitcher Louise E. , Niedernhofer Laura J. , Robbins Paul D.
Published: September 2022

Aging of the skin is evidenced by increased wrinkles, age spots, dryness, and thinning with decreased elasticity. Extrinsic and intrinsic factors including UV, pollution, and inflammation lead to an increase in senescent cells (SnCs) in skin with age that contribute to these observed pathological changes. Cellular senescence is induced by multiple types of damage and stress and is characterized by the irreversible exit from the cell cycle with upregulation of cell cycle-dependent kinase inhibitors p16INK4aand p21CIP1. Most SnCs also developed an inflammatory senescence-associated secretory phenotype (SASP) that drives further pathology through paracrine effects on neighboring cells and endocrine effects on cells at a distance. Recently, compounds able to kill senescent cells specifically, termed senolytics, or suppress the SASP, termed senomorphics, have been developed that have the potential to improve skin aging as well as systemic aging in general. Here, we provide a summary of the evidence for a key role in cellular senescence in driving skin aging. In addition, the evidence for the potential application of senotherapeutics for skin treatments is presented. Overall, topical, and possibly oral senotherapeutic treatments have tremendous potential to eventually become a standard of care for skin aging and related skin disorders.
Management of a Gluteal Noninvoluting Hemangioma With Glue Embolization and Excision
Authors: Shah Nikhil D. , Reddy Narainsai K. , Bricker Jonathan , Rajeswaran Shankar , Yamada Akira
Published: September 2022

Noninvoluting congenital hemangiomas (NICHs) persist in a high-flow state into childhood and often require surgical excision. The inherent vascular nature of these tumors make effective surgical treatment challenging. Here we report on a patient that underwent intraoperative glue embolization and complete excision of a large gluteal NICH. Concurrent glue embolization followed by complete excision allows for decreased intraoperative blood loss and easier discrimination between the tumor and surrounding structures. Treating difficult vascular tumors with a multidisciplinary approach and subsequent intraoperative glue embolization with surgical excision allows for an effective, single-stage approach to NICHs.
Forecasting the publication and citation outcomes of COVID-19 preprints
Authors: Gordon Michael , Bishop Michael , Chen Yiling , Dreber Anna , Goldfedder Brandon , Holzmeister Felix , Johannesson Magnus , Liu Yang , Tran Louisa , Twardy Charles , Wang Juntao , Pfeiffer Thomas
Published: September 2022

Many publications on COVID-19 were released on preprint servers such as
medRxiv
and
bioRxiv.
It is unknown how reliable these preprints are, and which ones will eventually be published in scientific journals. In this study, we use crowdsourced human forecasts to predict publication outcomes and future citation counts for a sample of 400 preprints with high
Altmetric
score. Most of these preprints were published within 1 year of upload on a preprint server (70%), with a considerable fraction (45%) appearing in a high-impact journal with a journal impact factor of at least 10. On average, the preprints received 162 citations within the first year. We found that forecasters can predict if preprints will be published after 1 year and if the publishing journal has high impact. Forecasts are also informative with respect to
Google Scholar
citations within 1 year of upload on a preprint server. For both types of assessment, we found statistically significant positive correlations between forecasts and observed outcomes. While the forecasts can help to provide a preliminary assessment of preprints at a faster pace than traditional peer-review, it remains to be investigated if such an assessment is suited to identify methodological problems in preprints.
Spectroscopic strategies for quantitation of varenicline in pharmaceutical preparations and content uniformity testing
Authors: Ibrahim Fawzia , Aboshabana Rasha , Elmansi Heba
Published: September 2022

Herein, two new facile methods were examined for varenicline determination using erythrosine. The latter is a food additive that has been recently investigated as a fluorescent dye for the determination of drugs. In the first method, the fluorescence of erythrosine B was quenched quantitatively by increasing the concentration of varenicline through ion-pair complex formation. This linear response was a basis for the spectrofluorimetric method used for varenicline quantitation in pure and dosage forms. The quenching is correlated with the concentration linearly over the range of 0.4–4.0 µg ml
−1
at 550 nm after excitation at 528 nm with a correlation coefficient of 0.9993. Different parameters were investigated to reach the optimal conditions with the highest sensitivity and repeatability. The second method is depending on measuring the formed complex by spectrophotometry at 550 nm over the range of 1.0–10.0 µg ml
−1
with an excellent correlation coefficient of 0.9999. The suggested methods were validated consistently with ICH guidelines, with acceptable results. The procedures were used to test the uniformity of content of Champix tablets. By comparing with the previous spectroscopic method, there was no significant difference as revealed from the calculated Student
t
-test and variance ratio
F
-test values.
Syntactic modulation of rhythm in Australian pied butcherbird song
Authors: Xing Jeffrey , Sainburg Tim , Taylor Hollis , Gentner Timothy Q.
Published: September 2022

The acoustic structure of birdsong is spectrally and temporally complex. Temporal complexity is often investigated in a syntactic framework focusing on the statistical features of symbolic song sequences. Alternatively, temporal patterns can be investigated in a rhythmic framework that focuses on the relative timing between song elements. Here, we investigate the merits of combining both frameworks by integrating syntactic and rhythmic analyses of Australian pied butcherbird (Cracticus nigrogularis) songs, which exhibit organized syntax and diverse rhythms. We show that rhythms of the pied butcherbird song bouts in our sample are categorically organized and predictable by the song’s first-order sequential syntax. These song rhythms remain categorically distributed and strongly associated with the first-order sequential syntax even after controlling for variance in note length, suggesting that the silent intervals between notes induce a rhythmic structure on note sequences. We discuss the implication of syntactic–rhythmic relations as a relevant feature of song complexity with respect to signals such as human speech and music, and advocate for a broader conception of song complexity that takes into account syntax, rhythm, and their interaction with other acoustic and perceptual features.
Evolution of competitive traits changes species diversity in a natural field
Authors: Fukano Yuya , Tachiki Yuuya , Kasada Minoru , Uchida Kei
Published: September 2022

Studying the interaction between evolutionary and ecological processes (i.e. eco-evolutionary dynamics) has great potential to improve our understanding of biological processes such as species interactions, community assembly and ecosystem functions. However, most experimental studies have been conducted under controlled laboratory or mesocosm conditions, and the importance of these interactions in natural field communities has not been evaluated. In this study, we focused on the contemporary divergence of a competitive trait (the height–width ratio) of an annual grass
Eleusine indica
between urban and farmland populations and investigated how trait evolution affects ecological processes by transplanting
E. indica
individuals from lineages with different trait values into semi-natural grassland. The competitive trait of the transplanted individuals not only affected their own growth and fitness, but also affected the vegetative growth of the competing species and the species diversity. These results indicate that the evolution of competitive traits, even in a single species, can influence the community species diversity through changes in interspecific interactions. Eco-evolutionary interactions therefore play a crucial role in natural field environments. Our results suggest that understanding intraspecific variation in competitive traits driven by rapid evolution is essential for understanding interspecific competitive interactions, community assembly and species diversity.
Evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude
Authors: Wearing Oliver H. , Scott Graham R.
Published: September 2022

The evolution of endothermy was instrumental to the diversification of birds and mammals, but the energetic demands of maintaining high body temperature could offset the advantages of endothermy in some environments. We hypothesized that reductions in body temperature help high-altitude natives overcome the metabolic challenges of cold and hypoxia in their native environment. Deer mice (Peromyscus maniculatus) from high-altitude and low-altitude populations were bred in captivity to the second generation and were acclimated as adults to warm normoxia or cold hypoxia. Subcutaneous temperature (Tsub, used as a proxy for body temperature) and cardiovascular function were then measured throughout the diel cycle using biotelemetry. Cold hypoxia increased metabolic demands, as reflected by increased food consumption and heart rate (associated with reduced vagal tone). These increased metabolic demands were offset by plastic reductions inTsub(approx. 2°C) in response to cold hypoxia, and highlanders had lowerTsub(approx. 1°C) than lowlanders in both environmental treatments. Empirical and theoretical evidence suggested that these reductions could together reduce metabolic demands by approximately 10–30%. Therefore, plastic and evolved reductions in body temperature can help mammals overcome the metabolic challenges at high altitude and may be a valuable energy-saving strategy in some non-hibernating endotherms in extreme environments.
Diversity, Equity, and Inclusion in the Melanoma Research Community
Authors: Portuallo Marie E. , Lu David Y. , Alicea Gretchen M. , Bolling Joel , Lee Rebecca , McQuade Jennifer , Warner Allison Betof , Davies Michael , Weeraratna Ashani , Villanueva Jessie , Rebecca Vito W.
Published: September 2022

Last October, within the 2021 SMR congress, we held the inaugural Diversity in Science Session. The goal of the session was to discuss diversity, equity, and inclusion in the melanoma research community and strategies to promote the advancement of underrepresented melanoma researchers. An international survey was conducted to assess the diversity, equity, and inclusion (DEI) climate among researchers and clinicians within the Society for Melanoma Research (SMR). The findings suggest there are feelings and experiences of inequity, bias, and harassment within the melanoma community that correlate with one’s gender, ethnic/racial group, and/or geographic location. Notably, significant reports of inequity in opportunity, discrimination, and sexual harassment demonstrate there is much work remaining to ensure all scientists in our community experience an academic workplace culture built on mutual respect, fair access, inclusion, and equitable opportunity.
Nature of epigenetic aging from a single-cell perspective
Authors: Tarkhov Andrei E. , Lindstrom-Vautrin Thomas , Zhang Sirui , Ying Kejun , Moqri Mahdi , Zhang Bohan , Tyshkovskiy Alexander , Levy Orr , Gladyshev Vadim N.
Published: September 2022

Age-related changes in DNA methylation (DNAm) form the basis for the development of most robust predictors of age, epigenetic clocks, but a clear mechanistic basis for exactly what part of the aging process they quantify is lacking. Here, to clarify the nature of epigenetic aging, we juxtapose the aging dynamics of tissue and single-cell DNAm (scDNAm) with scDNAm changes during early development, and corroborate our analyses with a single-cell RNAseq analysis within the same multi-omics dataset. We show that epigenetic aging involves co-regulated changes, but it is dominated by the stochastic component, and this agrees with transcriptional coordination patterns. We further support the finding of stochastic epigenetic aging by direct tissue and single-cell DNAm analyses and modeling of aging DNAm trajectories with a stochastic process akin to radiocarbon decay. Finally, we describe a single-cell algorithm for the identification of co-regulated and stochastic CpG clusters showing consistent transcriptomic coordination patterns, providing new opportunities for targeting aging and evaluating longevity interventions.
Can genomics and meteorology predict outbreaks of legionellosis in urban settings?
Authors: Timms Verlaine J , Sim Eby , Pey Keenan , Sintchenko Vitali
Published: September 2022

Legionella pneumophila is ubiquitous and sporadically infects humans causing Legionnaires disease (LD). Globally, reported cases of LD has risen four-fold from 2000-2014. In 2016, Sydney, Australia was the epicentre of an outbreak caused by L. pneumophila serogroup 1 (Lpsg1). Whole genome sequencing was instrumental in identifying the causal clone which was found in multiple locations across the city. This study examined the epidemiology of Lpsg1 in an urban environment, assessed typing schemes to classify resident clones and investigated the association between local climate variables and LD outbreaks. Of 223 local Lpsg1 isolates, we identified dominant clones with one clone isolated from patients in high frequency during outbreak investigations. The cgMLST scheme was the most reliable in identifying this Lpsg1 clone. While an increase in humidity and rainfall was found to coincide with a rise in LD cases, the incidence of the major L. pneumophila outbreak clone did not link to weather phenomena. These findings demonstrated the role of high resolution typing and weather context assessment in determining source attribution for LD outbreaks in urban settings, particularly when clinical isolates remain scarce.

Importance

We investigated the genomic and meteorological influences of infections caused by Legionella pneumophila in Sydney, Australia. Our study contributes to a knowledge gap of factors that drive outbreaks of legionellosis compared to sporadic infections in urban settings. In such cases, clinical isolates can be rare and other data is then relied upon to inform decision making around control measures. We found that cgMLST typing offered a robust and scalable approach for high-resolution investigation of Lpsg1 outbreaks. The genomic landscape of Lpsg1 in Sydney was dominated by a single clone which was responsible for multiple clusters of community cases over four decades. While legionellosis incidence peaked in Autumn, this was not linked to the dominant outbreak clone. The synthesis of meteorological data with Lpsg1 genomics can be a part of the risk assessment for legionellosis in urban settings and is relevant for other densely populated areas around the world.
Phenome-wide genetic correlation analysis and genetically-informed causal inference of amyotrophic lateral sclerosis
Authors: D’Antona Salvatore , Pathak Gita A , Koller Dora , Porro Danilo , Cava Claudia , Polimanti Renato
Published: September 2022

Leveraging genome-wide association statistics generated from a large study of amyotrophic lateral sclerosis (ALS; 29,612 cases and 122,656 controls) and UK Biobank (UKB; 4,024 phenotypes, up to 361,194 participants), we conducted a phenome-wide genetic correlation analysis of ALS and identified 46 genetically-correlated traits, such as fluid intelligence score (rg = −0.21, p = 1.74×10−6), “spending time in pub or social club” (rg = 0.24, p = 2.77×10−6), non-work related walking (rg = −0.25, p = 1.95×10−6), college education (rg = −0.15, p = 7.08×10−5), “ever diagnosed with panic attacks (rg = 0.39, p = 4.24×10−5), and “self-reported other gastritis including duodenitis” (rg = 0.28, p = 1.4×10−3). To assess the putative directionality of these genetic correlations, we conducted a latent causal variable analysis, identifying significant genetic causality proportions (gĉp) linking ALS to seven traits. While the genetic component of “self-reported other gastritis including duodenitis” showed a positive causal effect on ALS (gĉp = 0.50, p = 1.26×10−29), the genetic liability to ALS is potentially causal for multiple traits, also including a positive effect on “ever being diagnosed with panic attacks” (gĉp = 0.79, p = 5.011×10−15) and inverse effects on “other leisure/social group activities” (gĉp = 0.66, p = 1×10−4) and prospective memory result (gĉp = 0.35, p = 0.005). Our subsequent Mendelian randomization analysis indicated that some of these associations may be due to bi-directional effects. In conclusion, this is the first phenome-wide investigation of ALS polygenic architecture, highlighting the complex pleiotropy linking this disorder with different health domains.
The fitness of an introgressing haplotype
Authors: Dagilis Andrius J. , Matute Daniel R.
Published: September 2022

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge, or as the size of the introgressing haplotype changes. In a simple model, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. The buildup of incompatibilities between diverging species in the form of deleterious epistasis eventually favors the introgression of small haplotypes as the number of diverged alleles increases, and eventually even single alleles with positive direct effects can be selected against. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome, however it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will always be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in D. melanogaster, with some support for both.
Enhanced Complex Stability and Optimal JAK Geometry are Pivotal for a Potent Type III Interferon Response
Authors: Aung Theint , Horvath Curt M. , Mendoza Juan L.
Published: September 2022

Type I and III Interferons (IFN) constitute the host system’s first line of defense against viral infections. Although the two families use distinct extracellular receptor complexes, an identical pair of Janus kinases (JAK) activates a similar set of signal transducer and activator of transcription (STATs) through a conserved pathway. Consequently, type I and III IFNs are presumed to activate a largely overlapping set of IFN-stimulated genes (ISGs) and elicit similar biological responses. Therapeutically, type III IFNs are attractive alternatives to type I IFNs due to their innate tissue specificity and lower systemic toxicity. However, a major limitation of type III IFNs is the significantly lower potency of their physiological activities compared to type I IFNs. To evaluate the role of receptor geometry in IFN signaling, we engineered cell lines that express wild-type and mutant IFNλ receptors (IFNλR1) with rotated intracellular registers with respect to the associated JAK1. Evaluation of downstream signaling and biological activity of type III IFNs in cells with varied JAK-JAK geometries uncovered variant receptors that result in potentiation of type III IFN signaling and all downstream activities. With the combined use of a high-affinity ligand to stabilize the extracellular receptor complex, we found that the optimization of the intracellular JAK-JAK geometry enhances the type III IFN antiviral and anti-proliferative activities by 2- and 3-logs, respectively. In addition to providing a molecular basis for the observed differences in potency between type I and III IFNs, this work provides deeper insights into broader cytokine signaling mechanisms and novel blueprints for modulating cytokine functions to develop next generation antiviral and anticancer therapeutics.
Spatiotemporally resolved transcriptomics reveals subcellular RNA kinetic landscape
Authors: Ren Jingyi , Zhou Haowen , Zeng Hu , Wang Connie Kangni , Huang Jiahao , Qiu Xiaojie , Maher Kamal , Lin Zuwan , He Yichun , Tang Xin , Li Brian , Liu Jia , Wang Xiao
Published: September 2022

Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function1. However, the intricate subcellular dynamics of RNA synthesis, decay, export, and translocation remain obscured due to the limitations of existing transcriptomics methods2–8. Here, we report a spatiotemporally resolved RNA mapping method (TEMPOmap) to uncover subcellular RNA profiles across time and space at the single-cell level in heterogeneous cell populations. TEMPOmap integrates pulse-chase metabolic labeling of the transcriptome with highly multiplexed three-dimensional (3D) in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape of 991 genes in human HeLa cells from upstream transcription to downstream subcellular translocation. Clustering analysis of critical RNA kinetic parameters across single cells revealed kinetic gene clusters whose expression patterns were shaped by multi-step kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated to serve molecular and cellular functions in cell-cycle dependent manner. Together, these single-cell spatiotemporally resolved transcriptomics measurements provide us the gateway to uncover new gene regulation principles and understand how kinetic strategies enable precise RNA expression in time and space.
Metabolic Stability of the Demyelination PET Tracer [18F]3F4AP and Identification of its Metabolites
Authors: Sun Yang , Ramos-Torres Karla , Brugarolas Pedro
Published: September 2022

[18F]3-fluoro-4-aminopyridine ([18F]3F4AP) is a PET tracer for imaging demyelination based on the multiple sclerosis drug 4-aminopyridine (4AP, dalfampridine). This radiotracer was found to be stable in rodents and nonhuman primates imaged under isoflurane anesthesia. However, recent findings indicate that its stability is greatly decreased in awake humans and mice. Since both 4AP and isoflurane are metabolized primarily by cytochrome P450 enzymes, particularly CYP2E1, we postulated that this enzyme may be responsible for the metabolism of 3F4AP. Here, we investigated the metabolism of [18F]3F4AP by CYP2E1 and identified its metabolites. We also investigated whether deuteration, a common approach to increase the stability of drugs, could improve its stability. Our results demonstrate that CYP2E1 readily metabolizes 3F4AP and its deuterated analogues and that the primary metabolites are 5-hydroxy-3-fluoro-4-aminopyridine and 3-fluoro-4-aminopyridine N-oxide. Although deuteration did not decrease the rate of the CYP2E1 mediated oxidation, our findings explain the diminished in vivo stability of 3F4AP compared to 4AP and further our understanding of when deuteration may improve the metabolic stability of drugs and PET ligands.

Significance Statement

Understanding the metabolic stability of PET tracers is paramount to its application in humans as metabolism, which varies from person to person, can affect the target-to-background signal. This study identified the predominant enzyme that metabolizes the demyelination PET tracer [18F]3F4AP and its metabolites. These findings may allow assessment of whether the radiometabolites can get into the brain and potentially lead to tracers with enhanced stability. Furthermore, this study furthers our understanding of when deuteration can improve metabolic stability.
Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics
Authors: Vuckovic Ziva , Wang Jinan , Pham Vi , Mobbs Jesse I. , Belousoff Matthew J. , Bhattarai Apurba , Burger Wessel A.C. , Thompson Geoff , Yeasmin Mahmuda , Leach Katie , van der Westhuizen Emma T. , Khajehali Elham , Liang Yi-Lynn , Glukhova Alisa , Wootten Denise , Lindsley Craig W. , Tobin Andrew B. , Sexton Patrick M. , Danev Radostin , Valant Celine , Miao Yinglong , Christopoulos Arthur , Thal David M.
Published: September 2022

Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular level understanding of the general principals that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4muscarinic acetylcholine receptor (M4mAChR) is a well-validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. Here, we present high-resolution cryo-electron microscopy structures of the M4mAChR bound to a cognate Gi1protein and the high affinity agonist, iperoxo, in the absence and presence of two different positive allosteric modulators, LY2033298 or VU0467154. We have also determined the structure of the M4mAChR-Gi1complex bound to its endogenous agonist, acetylcholine (ACh). Structural comparisons, together with molecular dynamics, mutagenesis, and pharmacological validations, have provided in-depth insights into the role of structure and dynamics in orthosteric and allosteric ligand binding, global mechanisms of receptor activation, cooperativity, probe-dependence, and species variability; all key hallmarks underpinning contemporary GPCR drug discovery.
SARS-CoV-2 variants show temperature-dependent enhanced polymerase activity in the upper respiratory tract and high transmissibility
Authors: Kim Se-Mi , Kim Eun-Ha , Casel Mark Anthony B. , Kim Young-Il , Sun Rong , Kwack Mi-Jeong , Yoo Ji-Seung , Yu Min-Ah , Yu Kwang-Min , Jang Seung-Gyu , Rollon Rare , Choi Jeong Ho , Gil JuRyeon , Eun Kiyoung , Kim Hyunggee , Ensser Armin , Hwang Jungwon , Song Min-Suk , Kim Myung Hee , Jung Jae U , Choi Young Ki
Published: September 2022

With the convergent global emergence of SARS-CoV-2 variants of concern (VOC), a precise comparison study of viral fitness and transmission characteristics is necessary for the prediction of dominant VOCs and the development of suitable countermeasures. While airway temperature plays important roles in the fitness and transmissibility of respiratory tract viruses, it has not been well studied with SARS-CoV-2. Here we demonstrate that natural temperature differences between the upper (33°C) and lower (37°C) respiratory tract have profound effects on SARS-CoV-2 replication and transmission. Specifically, SARS-COV-2 variants containing the P323L or P323L/G671S mutation in the NSP12 RNA-dependent RNA polymerase (RdRp) exhibited enhanced RdRp enzymatic activity at 33°C compared to 37°C and high transmissibility in ferrets. MicroScale Thermophoresis demonstrated that the NSP12 P323L or P323L/G671S mutation stabilized the NSP12-NSP7-NSP8 complex interaction. Furthermore, reverse genetics-derived SARS-CoV-2 variants containing the NSP12 P323L or P323L/G671S mutation displayed enhanced replication at 33°C, and high transmission in ferrets. This suggests that the evolutionarily forced NSP12 P323L and P323L/G671S mutations of recent SARS-CoV-2 VOC strains are associated with increases of the RdRp complex stability and enzymatic activity, promoting the high transmissibility.
An automated microscopy workflow to study Shigella-neutrophil interactions and antibiotic efficacy in vivo
Authors: Lensen Arthur , Gomes Margarida C. , López-Jiménez Ana Teresa , Mostowy Serge
Published: September 2022

Shigella are Gram-negative bacterial pathogens responsible for bacillary dysentery (also called shigellosis). The absence of a licensed vaccine and widespread emergence of antibiotic resistance has recently led the WHO to highlight Shigella as a priority pathogen requiring urgent attention. Several infection models have been useful to explore the Shigella infection process, yet we still lack information regarding events taking place in vivo. Here, using a Shigella-zebrafish infection model and high-content microscopy, we develop an automated microscopy workflow to non-invasively study fluorescently labelled bacteria and neutrophils in vivo. We apply our workflow to antibiotic-treated zebrafish and demonstrate that neutrophil recruitment is independent of bacterial burden. Strikingly, we discover that nalidixic acid (a bactericidal antibiotic) can restrict Shigella dissemination from the hindbrain ventricle. We envision that our automated microscopy workflow, applied here to study Shigella-neutrophil interactions and antibiotic efficacy in zebrafish, can be useful to innovate treatments for infection control in humans.

SUMMARY STATEMENT

We develop an automated image analysis workflow to enable fast and reliant immune cell counting in Shigella-infected zebrafish larvae, and reveal how antibiotics impact Shigella-neutrophil interactions in vivo.
An analysis of laboratory variability and thresholds for human in vitro ADME/PK methods
Authors: Fagerholm Urban
Published: September 2022

Abstract

Introduction

Various in vitro methods are used to measure absorption, distribution, metabolism and excretion/pharmacokinetics (ADME/PK) of candidate drugs and predict and decide whether properties are clinically adequate.

Methods

Objectives were to evaluate variability within and between laboratories for commonly used human in vitro ADME/PK methods and to explore whether reliable thresholds may be defined. The literature was searched for in vitro data for intrinsic metabolic clearance (hepatocyte CLint), apparent intestinal permeability (Caco-2 Papp), efflux ratio (Caco-2 ER), solubility (S) and BCS-class, and corresponding clinical estimates. In vitro ADME/PK data for three example drugs (atenolol, diclofenac and gemfibrozil) were used to predict human in vivo ADME/PK and investigate whether these would pass a compound selection process.

Results and Conclusions

Interlaboratory variability is considerable, especially for fu, S, ER and BCS-classification, and on average about twice as high as intralaboratory variability. Approximate mean interlaboratory variability for CLint, Papp, ER and fu (3- to 3.5-fold) appears to be about 2- to 3-fold higher than corresponding interlaboratory variability. Mean and maximum interlaboratory range for CLint, Papp, ER, fu and S are approximately 5- to 100-fold and 50- to 4500-fold, respectively, with second largest range for fu and largest range for S. For one drug, laboratories produced almost 1000-fold different CLint • fu-values. It appears difficult/impossible to set clear clinically useful thresholds, especially for CLint, ER and S. Poor in vitro-in vivo consistency for S and BCS-classification and large portions of compounds out of reach for Caco-2 and conventional hepatocyte assays are evident. Predictions for reference compounds are consistent with inadequate in vivo ADME/PK. Ways to improve predictions and compound selection are suggested.
Goal-directed vocal planning in a songbird
Authors: Zai Anja T. , Stepien Anna E. , Giret Nicolas , Hahnloser Richard H.R.
Published: September 2022

Songbirds’ vocal mastery is impressive, but to what extent is it a result of practice? Can they, based on experienced mismatch with a known target, plan the necessary changes to recover the target in a practice-free manner without intermittently singing? In adult zebra finches, we drive the pitch of a song syllable away from its stable (baseline) variant acquired from a tutor, then we withdraw reinforcement and subsequently deprive them of singing experience by muting or deafening. In this deprived state, birds do not recover their baseline song. However, they revert their songs towards the target by about one standard deviation of their recent practice, provided the sensory feedback during the latter signaled a pitch mismatch with the target. Thus, targeted vocal plasticity does not require immediate sensory experience, showing that zebra finches are capable of goal-directed vocal planning.
Cones and Cone Pathways Remain Functional in Advanced Retinal Degeneration
Authors: Ellis Erika M. , Paniagua Antonio E. , Scalabrino Miranda L. , Thapa Mishek , Rathinavelu Jay , Jiao Yuekan , Williams David S. , Field Greg D. , Fain Gordon L. , Sampath Alapakkam P.
Published: September 2022

Most defects causing retinal degeneration in retinitis pigmentosa (RP) are rod-specific mutations, but the subsequent degeneration of cones, which produces loss of daylight vision and high-acuity perception, is the most debilitating feature of the disease. To understand better why cones degenerate and how cone vision might be restored, we have made the first single-cell recordings of light responses from degenerating cones and retinal interneurons after most rods have died and cones have lost their outer-segment disk membranes and synaptic pedicles. We show that degenerating cones have functional cyclic-nucleotide-gated channels and can continue to give light responses, apparently produced by opsin localized either to small areas of organized membrane near the ciliary axoneme or distributed throughout the inner segment. Light responses of second-order horizontal and bipolar cells are smaller and less sensitive but surprisingly similar to those of normal retina. Furthermore, retinal output as reflected in responses of ganglion cells is largely intact at cone-mediated light levels. Together, these findings show that cones and their retinal pathways can remain functional even as degeneration is progressing, an encouraging result for future research aimed at enhancing the light sensitivity of residual cones to restore vision in patients with genetically inherited retinal degeneration.
Distinct Activation Mechanisms Regulate Subtype Selectivity of Cannabinoid Receptors
Authors: Dutta Soumajit , Shukla Diwakar
Published: September 2022

Cannabinoid receptors (CB1 and CB2) are important drug targets for inflammation, obesity, and other central nervous system disorders. However, due to sequence and structural similarities of the ligand binding pockets of these receptors, most of the ligands lack subtype selectivity and cause off-target side effects. CB2 selective agonists can potentially treat pain and inflammation without the psychoactive effects of CB1 agonism. We hypothesize that the subtype selectivity of designed selective ligands can be explained by ligand binding to the conformationally distinct states between CB1 and CB2. To find these conformationally distinct states, we perform ∼ 700μs of unbiased simulations to study the activation mechanism of both the receptors in absence of ligands. The simulation datasets of two receptors were analyzed using Markov state models to identify similarities and distinctions of the major conformational changes associated with activation and allosteric communication between them. Specifically, toggle switch residue movement and its effect on receptor activation differ greatly between CB1 and CB2. Upon further analysis, we discretize the conformational ensembles of both receptors into metastable states using the neural network-based VAMPnets. Structural and dynamic comparisons of these metastable states allow us to decipher a coarse-grained view of protein activation by revealing sequential conversion between these states. Specifically, we observe the difference in the binding pocket volume of different metastable states of CB1, whereas there are minimal changes observed in the CB2. Docking analysis reveals that differential binding pocket volume leads to distinct binding poses and docking affinities of CB2 selective agonists in CB1. Only a few of the intermediate metastable states of CB1 shows high affinity towards CB2 selective agonists. On the other hand, all the CB2 metastable states show a similar affinity for CB2 selective agonists, explaining these ligands’ overall higher affinity towards CB2. Overall, this computational study mechanistically explains the subtype selectivity of CB2 selective ligands by deciphering the activation mechanism of cannabinoid receptors.
The phylogenetic placement of an enigmatic moth Egybolis vaillantina based on museomics
Authors: Zahiri Reza , Holloway Jeremy D. , Ghanavi Hamid Reza , Aarvik Leif , Wahlberg Niklas
Published: September 2022

Here, we present multi-locus sequencing results from the enigmatic Afrotropical monotypic genus Egybolis Boisduval (occurring in East- and South Africa – previously placed in the subfamily Catocalinae, Noctuidae). Model-based phylogenetic analysis places Egybolis within a strongly supported clade comprising four Old World Tropical genera Cocytia Boisduval, Avatha Walker, Anereuthina Hübner and Serrodes Guenée from the family Erebidae, subfamily Erebinae. Hence, we propose to formally assign the monotypic genus Egybolis to the subfamily Erebinae, and the tribe Cocytiini. Timing of divergence analysis reveals the late Oligocene origin around 25 million years ago (mya) for the tribe Cocytiini, an early Miocene i.e., about 21 mya for the split between Cocytia and Egybolis.
Spatial control of ARGONAUTE-mediated RNA silencing in anther development
Authors: Tamotsu Hinako , Koizumi Koji , Briones Alejandro Villar , Komiya Reina
Published: September 2022

Argonaute protein (AGO) in association with small RNAs is the core machinery of RNA silencing, an essential mechanism for precise development and defense against pathogens in many organisms. Here, we identified two AGOs in rice anthers, AGO1b and AGO1d, that interact with phased small interfering RNAs (phasiRNAs) derived from numerous long non-coding RNAs. Moreover, 3D-immunoimaging and mutant analysis demonstrated that rice AGO1b and AGO1d redundantly and cell type-specifically regulate anther development by acting as mobile carriers of these phasiRNAs from the somatic cell layers to the germ cells in anthers. Our study also highlights a new mode of reproductive RNA silencing via the specific nuclear and cytoplasmic localization of three AGOs, AGO1b, AGO1d, and MEL1, in rice pollen mother cells.
FOXP1 orchestrates neurogenesis in human cortical basal radial glial cells
Authors: Park Seon Hye E. , Kulkarni Ashwinikumar , Konopka Genevieve
Published: September 2022

During cortical development, human basal radial glial cells (bRGCs) are highly capable of sustained self-renewal and neurogenesis. Selective pressures on this cell type may have contributed to the evolution of the human neocortex, leading to an increase in cortical size. bRGCs have enriched expression for Forkhead Box P1 (FOXP1), a transcription factor implicated in neurodevelopmental disorders such as autism spectrum disorder. However, the cell type-specific roles of FOXP1 in bRGCs during cortical development remain unexplored. Here, we examine the requirement for FOXP1 gene expression regulation underlying the production of bRGCs using human brain organoids. We examine a developmental time point when FOXP1 expression is highest in the cortical progenitors, and the bRGCs, in particular, begin to actively produce neurons. With the loss of FOXP1, we show a reduction in the number of bRGCs, as well as reduced proliferation and differentiation of the remaining bRGCs, all of which lead to reduced numbers of excitatory cortical neurons over time. Using single-nuclei RNA sequencing and cell trajectory analysis, we uncover a role for FOXP1 in directing cortical progenitor proliferation and differentiation by regulating key signaling pathways related to neurogenesis and neurodevelopmental disorders. Together, these results demonstrate that FOXP1 regulates human-specific features in early cortical development.
Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance
Authors: Ren Luyao , Duan Xiaoke , Dong Lianghua , Zhang Rui , Yang Jingcheng , Gao Yuechen , Peng Rongxue , Hou Wanwan , Liu Yaqing , Li Jingjing , Yu Ying , Zhang Naixin , Shang Jun , Liang Fan , Wang Depeng , Chen Hui , Sun Lele , Hao Lingtong ,   The Quartet Project Team, Scherer Andreas , Nordlund Jessica , Xiao Wenming , Xu Joshua , Tong Weida , Hu Xin , Jia Peng , Ye Kai , Li Jinming , Jin Li , Shi Leming , Hong Huixiao , Wang Jing , Fan Shaohua , Fang Xiang , Zheng Yuanting
Published: September 2022

Current methods for evaluating the accuracy of germline variant calls are restricted to easy-to-detect high-confidence regions, thus ignoring a substantial portion of difficult variants beyond the benchmark regions. We established four DNA reference materials from immortalized cell lines derived from a Chinese Quartet including parents and monozygotic twins. We integrated benchmark calls of 4.2 million small variants and 15,000 structural variants from multiple platforms and bioinformatic pipelines for evaluating the reliability of germline variant calls inside the benchmark regions. The genetic built-in-truth of the Quartet family design not only improved sensitivity of benchmark calls by removing additional false positive variants with apparently high quality, but also enabled estimation of the precision of variants calls outside the benchmark regions. Batch effects of variant calling in large-scale DNA sequencing efforts can be effectively identified with the concurrent use of the Quartet DNA reference materials along with study samples, and can be alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Matched RNA and protein reference materials were also established in the Quartet project, thereby enabling benchmark calls constructed from DNA reference materials for evaluation of variants calling performance on RNA and protein data. The Quartet DNA reference materials from this study are a resource for objective and comprehensive assessment of the accuracy of germline variant calls throughout the whole-genome regions.
Domain Auto Finder (DAFi) program: the analysis of single-crystal X-ray diffraction data from polycrystalline samples
Authors: Aslandukov Andrey , Aslandukov Matvii , Dubrovinskaia Natalia , Dubrovinsky Leonid
Published: September 2022

This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single-crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X-ray diffraction data sets obtained from real samples: a multi-mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser-heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC-XRD data online during experiments at synchrotron facilities.
Analytic modeling of inhomogeneous-resolution maps in cryo-electron microscopy and crystallography
Authors: Urzhumtsev Alexandre , Lunin Vladimir Y.
Published: September 2022

Refinement of macromolecular atomic models versus experimental maps in crystallography and cryo-electron microscopy is a critical step in structure solution. For an appropriate comparison, model maps should mimic the imperfections in the experimental maps, mainly atomic disorder and limited resolution, which are often inhomogeneous over the molecular region. In the suggested method, these model maps are calculated as the sum of atomic contributions expressed through a specifically designed function describing a solitary spherical wave. Thanks to this function, atomic contributions are analytically expressed through their atomic displacement parameter and local resolution, a value now associated with each atom. Such a full analytic dependence of inhomogeneous-resolution map values on model parameters permits the refinement of all of these parameters together.