bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoacoustic imaging reveals mechanisms of rapid-acting insulin formulations dynamics at the injection site
Authors: Khadria Anjul , Paavola Chad D. , Maslov Konstantin , Valenzuela Francisco A. , Sperry Andrea E. , Cox Amy L. , Cao Rui , Shi Junhui , Brown-Augsburger Patricia L. , Lozano Emmanuel , Blankenship Ross L. , Majumdar Ranajoy , Bradley Scott A. , Beals John M. , Oladipupo Sunday S. , Wang Lihong V.
Published: March 2022

Objective

Ultra-rapid insulin formulations control postprandial hyperglycemia; however, inadequate understanding of injection site absorption mechanisms is limiting further advancement. We used photoacoustic imaging to investigate the injection site dynamics of dye-labeled insulin lispro in the Humalog® and Lyumjev® formulations using the murine ear cutaneous model and correlated it with results from unlabeled insulin lispro in pig subcutaneous injection model.

Methods

We employed dual-wavelength optical-resolution photoacoustic microscopy to study the absorption and diffusion of the near-infrared dye-labeled insulin lispro in the Humalog and Lyumjev formulations in mouse ears. We mathematically modeled the experimental data to calculate the absorption rate constants and diffusion coefficients. We studied the pharmacokinetics of the unlabeled insulin lispro in both the Humalog and Lyumjev formulations as well as a formulation lacking both the zinc and phenolic preservative in pigs. The association state of insulin lispro in each of the formulations was characterized using SV-AUC and NMR spectroscopy.

Results

Through experiments using murine and swine models, we show that the hexamer dissociation rate of insulin lispro is not the absorption rate-limiting step. We demonstrated that the excipients in the Lyumjev formulation produce local tissue expansion and speed both insulin diffusion and microvascular absorption. We also show that the diffusion of insulin lispro at the injection site drives its initial absorption; however, the rate at which the insulin lispro crosses the blood vessels is its overall absorption rate-limiting step.

Conclusions

This study provides insights into injection site dynamics of insulin lispro and the impact of formulation excipients. It also demonstrates photoacoustic microscopy as a promising tool for studying protein therapeutics. The results from this study address critical questions around the subcutaneous behavior of insulin lispro and the formulation excipients, which could be useful to make faster and better controlled insulin formulations in the future.

Highlights

Hexamer dissociation is not the absorption rate-limiting step for insulin lispro

Lyumjev excipients enhance insulin microvascular absorption and diffusion

Vascular endothelial transit determines the overall absorption for insulin lispr

Insulin diffusion studied for the first time at the injection site of live animals

In vivo imaging is a powerful tool to study injection site dynamics
Reliability of M1-P15 as a cortical marker for transcallosal inhibition: a preregistered TMS-EEG study
Authors: Zazio Agnese , Barchiesi Guido , Ferrari Clarissa , Marcantoni Eleonora , Bortoletto Marta
Published: March 2022

Background

In a recently published study combining transcranial magnetic stimulation and electroencephalography (TMS-EEG), we provided first evidence of M1-P15, an early component of TMS-evoked potentials, as a measure of transcallosal inhibition between motor cortices. However, considering the technical challenges of TMS-EEG recordings, further evidence is needed before M1-P15 can be considered a reliable index.

Objective

Here, we aimed at validating M1-P15 as a cortical index of transcallosal inhibition, by replicating previous findings on its relationship with the ipsilateral silent period (iSP) and with performance in bimanual coordination. Moreover, we aimed at inducing a task-dependent modulation of transcallosal inhibition.

Methods

A new sample of 32 healthy right-handed participants underwent behavioral motor tasks and TMS-EEG recording, in which left and right M1 were stimulated during bimanual tasks and during an iSP paradigm. Hypotheses and methods were preregistered before data collection.

Results

We successfully replicated our previous findings on the positive relationship between M1-P15 amplitude and the iSP normalized area. However, we did not confirm the relationship between M1-P15 latency and bimanual coordination. Finally, we show a task-dependent modulation of M1-P15 amplitude, which was affected by the characteristics of the bimanual task the participants were performing, but not by the contralateral hand activity during the iSP paradigm.

Conclusions

The present results corroborate our previous findings in validating the M1-P15 as a reliable cortical marker of transcallosal inhibition, and provide novel evidence of its task-dependent modulation. Importantly, we demonstrate the feasibility of a preregistration approach in the TMS-EEG field to increase methodological rigor and transparency.
Chondroitin Sulfate Proteoglycan 4,6 sulfation regulates sympathetic nerve regeneration after myocardial infarction
Authors: Blake MR , Parrish DC , Staffenson MA , Sueda S , Woodward W , Habecker BA
Published: March 2022

Sympathetic denervation of the heart following myocardial infarction (MI) is sustained by chondroitin sulfate proteoglycans (CSPGs) in the cardiac scar, and denervation predicts risk of sudden cardiac death. Blocking CSPG signaling restores sympathetic axon outgrowth into the cardiac scar, decreasing arrhythmia susceptibility. Axon growth inhibition by CSPGs is thought to depend on the sulfation status of the glycosaminoglycans (CS-GAGs) attached to the core protein. Tandem sulfation of CS-GAGs at the 4th (4S) and 6th (6S) positions of n-acetyl-galactosamine inhibits outgrowth in several types of neurons within the central nervous system, but it is not known if sulfation is similarly critical during peripheral nerve regeneration. We asked if CSPG sulfation prevented sympathetic axon outgrowth. Sympathetic neurite outgrowth across purified CSPGs is restored in vitro by reducing 4S with the 4-sulfatase enzyme Arylsulfatase-B (ARSB). Additionally, we co-cultured cardiac scar tissue with sympathetic ganglia ex vivo and found that reducing 4S with ARSB restored axon outgrowth to control levels. We examined levels of the enzymes responsible for adding and removing sulfation to CS-GAGs by western blot to determine if they were altered in the left ventricle after MI. We found that CHST15 (4S dependent 6-sulfotransferase) was upregulated, and ARSB was downregulated after MI. Increased CHST15 combined with decreased ARSB suggests a mechanism for production and maintenance of sulfated CSPGs in the cardiac scar. We altered tandem sulfated 4S,6S CS-GAGs in vivo by transient siRNA knockdown of Chst15 and found that reducing 4S,6S restored Tyrosine Hydroxylase (TH) positive sympathetic nerve fibers in the cardiac scar after MI and reduced arrhythmias. Overall, our results suggest that modulating CSPG-sulfation after MI may be a therapeutic target to promote sympathetic nerve regeneration in the cardiac scar and reduce post-MI cardiac arrhythmias.
sstar: A Python package for detecting archaic introgression from population genetic data with S*
Authors: Huang Xin , Kruisz Patricia , Kuhlwilm Martin
Published: March 2022

S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.
An immune-lncRNA risk model to predict prognosis for patients with head and neck squamous cell carcinoma
Authors: Jiang Xu , Qin Ying , Xia Wei , Li Jian , Shi Nan , Feng Qingyuan , Tang Anzhou , Yi Xiang
Published: March 2022

Background

long noncoding RNA (lncRNA) are closely correlated with the occurrence and development of tumors. The purpose of this research is to construct a risk model of immune-related lncRNAs that can be used for predicting the survival and prognosis of head and neck squamous cell carcinoma (HNSCC) patients and further exploring the immune function of immune-lncRNAs.

Methods

obtained detailed transcriptional data and clinical information for 545 cases of HNSCC from The Cancer Genome Atlas (TCGA). Combined lncRNAs and the immune gene sets from the Molecular Signatures Database (MSigDB) were employed to construct co□expression networks, the significant correlation of immune-lncRNAs obtained from the results of Cox regression analysis were used to build the model. Survival analysis and QRT-PCR were used to confirm the expression of immune-lncRNAs and optimize the risk model. Then single-cell RNA Sequencing (scRNA-seq) dataset analysis of laryngeal squamous cell carcinoma (LSCC), co-expression analysis, correlation analysis and immunohistochemistry were used to explore the immune function of immune-lncRNAs.

Results

A total of 13 immune-lncRNAs including AC104083.1、AC004148.2、AL357033.4、AC116914.2、AC024075.1、AC008115.3、PCED1B-AS1、RAB11B-AS1、AC004687.1、 AL450992.2、EP300-AS1、AC024075.2、AC136475.2 were identified to construct the risk model. In this model, low-risk patients had higher overall survival (OS, P=1.923e-12, hazard ratio=2.104, 95% CI: 1.622-2.730). AC004687.1 and PCED1B-AS1 were overexpressed in T cells and were closely related to the genes encoding major histocompatibility complex II (MHC II) molecules. And the results of QRT-PCR and immunohistochemistry showed the expression significant positively correlated with HLA-DR which is one of the MHC II classical molecules.

Conclusion

the immune-associated risk model constructed by 13 lncRNAs has good prognostic value for HNSCC. AC004687.1 and PCED1B-AS1 are significant correlating to clinical characteristics and MHC II, we provide a new insight into the immune function of lncRNAs.
Systems level analysis of time and stimuli specific signaling through PKA
Authors: Plank Michael , Carmiol Nicole , Mitri Bassam , Capaldi Andrew P.
Published: March 2022

Eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, how PKA responds to different concentrations of cAMP is unclear. Here, to address this question, we examine PKA signaling in S. cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1 using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
Empirical study on software and process quality in bioinformatics tools
Authors: Ferenc Katalin , Otto Konrad , de Oliveira Neto Francisco Gomes , López Marcela Dávila , Horkoff Jennifer , Schliep Alexander
Published: March 2022

Software quality in computational tools impacts research output in a variety of scientific disciplines. Biology is one of these fields, especially for High Throughput Sequencing (HTS) data, such tools play an important role. This study therefore characterises the overall quality of a selection of tools which are frequently part of HTS pipelines, as well as analyses the maintainability and process quality of a selection of HTS alignment tools. Our findings highlight the most pressing issues, and point to software engineering best practices developed for the improvement of maintenance and process quality. To help future research, we share the tooling for the static code analysis with SonarCloud which we used to collect data on the maintainability of different alignment tools. The results of the analysis show that the maintainability level is generally high but trends towards increasing technical debt over time. We also observed that the development activities on alignment tools are generally driven by very few developers and are not utilising modern tooling to their advantage. Based on these observations, we recommend actions to improve both maintainability and process quality in open source alignment tools. Those actions include improvements in tooling like the use of linters as well as better documentation of architecture and features. We encourage developers to use these tools in order to ease future maintenance efforts, increase user experience, support reproducibility, and ultimately increase the quality of research through increasing the quality of research software tools.
Predation increases prey fitness via transgenerational priming
Authors: Kost Silvia , Muhsal Linea Katharina , Kost Christian
Published: March 2022

Preparing your offspring for future challenges via priming can directly enhance its fitness. However, evidence for transgenerational priming has been limited to eukaryotic organisms. Here we test the hypothesis that predation primes bacteria such that their future generations respond with a more effective defence induction. In an evolution experiment, Escherichia coli was cultivated either in monoculture or in coculture with the predatory ciliate Tetrahymena thermophila. After 18 days, fitness and defensive clustering capabilities of derived bacterial populations were determined. Our results reveal that (i) predation can prime E.coli to induce their defensive cluster formation across generations and that (ii) three days of predation are sufficient to increase the fitness of predator-exposed over that of predator-free populations. Thus, our study shows that predation can have priming effects in bacterial populations that operate across generations, which concurs with the emerging perception that bacteria feature mechanisms to actively shape their evolutionary fate.
Unsupervised clustering reveals phenotypes of AKI in ICU Covid19 patients
Authors: Sangla Frederic , Marchi Elisa , Assouline Benjamin , Leterrier Christophe , Sgardello Sebastian , Pugin Jérôme , Criton Gilles , Legouis David
Published: March 2022

Background

Acute Kidney Injury (AKI) is a very frequent condition, occurring in about one in three patients admitted to an intensive care unit (ICU). AKI is a syndrome defined as a sudden decrease in glomerular filtration rate. However, this unified definition does not reflect the various mechanisms involved in AKI pathophysiology, each with its own characteristics and sensitivity to therapy. In this study, we aimed at developing an innovative machine learning based method able to subphenotype AKI according to its pattern of risk factors.

Methods

We adopted a three-step pipeline of analyses. Firstly, we looked for factors associated with AKI using a generalized additive model. Secondly, we calculated the importance of each identified AKI related factor in the estimated AKI risk to find the main risk factor for AKI, at the single patient level. Lastly, we clusterized AKI patients according to their profile of risk factors and compared the clinical characteristics and outcome of every cluster. We applied this method to a cohort of severe Covid19 patients hospitalized in the ICU of Geneva University Hospitals.

Results

Among the 250 patients analyzed, we found ten factors associated with AKI development. Using the individual expression of these factors, we identified three groups of AKI patients, based on the use of Lopinavir/Ritonavir, a prior history of diabetes mellitus and baseline eGFR and ventilation. The three clusters expressed distinct characteristic in terms of AKI severity and recovery, metabolic patterns and ICU mortality.

Conclusion

We propose here a new method to phenotype AKI patients according to their most important individual risk factors for AKI development. When applied to an ICU cohort of Covid19 patients, we were able to differentiate three groups of patients. Each expressed specific AKI characteristics and outcomes, which probably reflects a distinct pathophysiology.
Portable, Low-Field Magnetic Resonance Imaging Sensitively Detects and Accurately Quantifies Multiple Sclerosis Lesions
Authors: Arnold T. Campbell , Tu Danni , Okar Serhat V. , Nair Govind , By Samantha , Kawatra Karan , Robert-Fitzgerald Timothy E. , Desiderio Lisa M. , Schindler Matthew K. , Shinohara Russell T. , Reich Daniel S. , Stein Joel M.
Published: March 2022

Magnetic resonance imaging is a fundamental tool in the diagnosis and management of neurological diseases such as multiple sclerosis (MS). New portable, low-field MRI scanners could potentially lower financial and technical barriers to neuroimaging and reach underserved or disabled populations. However, the sensitivity of low-field MRI for MS lesions is unknown. We sought to determine if white matter lesions can be detected on a 64mT low-field MRI, compare automated lesion segmentations and total lesion burden between paired 3T and 64mT scans, and identify features that contribute to lesion detection accuracy. In this prospective, cross-sectional study, same-day brain MRI (FLAIR, T1, and T2) scans were collected from 36 adults (32 women; mean age, 50 ± 14 years) with known or suspected MS using 3T (Siemens) and 64mT (Hyperfine) scanners at two centers. Images were reviewed by neuroradiologists. MS lesions were measured manually and segmented using an automated algorithm. Statistical analyses assessed accuracy and variability of segmentations across scanners and systematic scanner biases in automated volumetric measurements. Lesions were identified on 64mT scans in 94% (31/33) of patients with confirmed MS. The smallest lesions manually detected were 5.7 ± 1.3 mm in maximum diameter at 64mT vs 2.1 ± 0.6 mm at 3T. Automated lesion burden estimates were highly correlated between 3T and 64mT scans (r = 0.89, p < 0.001). Bland-Altman analysis identified bias in 64mT segmentations (mean = 1.6 ml, standard error = 5.2 ml, limits of agreement = -19.0–15.9 ml), which over-estimated low lesion burden and under-estimated high burden (r = 0.74, p < 0.001). Visual inspection revealed over-segmentation was driven by flow-related hyperintensities in veins on 64mT FLAIR. Lesion size drove segmentation accuracy, with 93% of lesions >1.0 ml and all lesions >1.5 ml being detected. These results demonstrate that in established MS, a portable 64mT MRI scanner can identify white matter lesions, and disease burden estimates are consistent with 3T scans.

Highlights

Paired, same-day 3T and 64mT MRI studies were collected in 36 patients

64mT MRI showed 94% sensitivity for detecting any lesions in established MS cases

The diameter of the smallest detected lesion was larger at 64mT compared to 3T

Disease burden estimates were strongly correlated between 3T and 64mT scans

Low-field MRI can detect white matter lesions, though smaller lesions may be missed
Optimal dosing of cefotaxime and desacetylcefotaxime for critically ill paediatric patients. Can we use microsampling?
Authors: Guerra Valero Yarmarly C. , Dorofaeff Tavey , Coulthard Mark G , Sparkes Louise , Lipman Jeffrey , Wallis Steven C. , Roberts Jason A. , Parker Suzanne L.
Published: March 2022

Synopsis

Objectives

This study aimed to describe the population pharmacokinetics of cefotaxime and desacetylcefotaxime in critically ill paediatric patients and provide dosing recommendations. We also sought to evaluate the use of capillary microsampling to facilitate data-rich blood sampling.

Methods

Patients were recruited into a pharmacokinetic study, with cefotaxime and desacetylcefotaxime concentrations from plasma samples collected at 0, 0.5, 2, 4 and 6 h used to develop a population pharmacokinetic model using Pmetrics. Monte Carlo dosing simulations were tested using a range of estimated glomerular filtration rates (60, 100, 170 and 200 mL/min/1.73 m2) and body weights (4, 10, 15, 20 and 40 kg) to achieve PK/PD targets, including 100% ƒT>MIC with an MIC breakpoint of 1 mg/L.

Results

36 patients (0.2 – 12 y) provided 160 conventional samples for inclusion in the model. The pharmacokinetics of cefotaxime and desacetylcefotaxime were best described using one-compartmental model with first-order elimination. The clearance and volume of distribution for cefotaxime were 12.8 L and 39.4 L/h, respectively. The clearance for desacetylcefotaxime was 10.5 L/h. Standard dosing of 50 mg/kg Q6h was only able to achieve the PK/PD target of 100% ƒT>MIC in patients > 10 kg and with impaired renal function or patients of 40 kg with normal renal function.

Conclusions

Dosing recommendations support the use of extended or continuous infusion to achieve cefotaxime exposure suitable for bacterial killing in critically ill paediatric patients, including those with severe or deep-seated infection. An external validation of capillary microsampling demonstrated skin-prick sampling can facilitate data-rich pharmacokinetic studies.
Dimensionality reduction of calcium-imaged neuronal population activity
Authors: Koh Tze Hui , Bishop William E. , Kawashima Takashi , Jeon Brian B. , Srinivasan Ranjani , Kuhlman Sandra J. , Ahrens Misha B. , Chase Steven M. , Yu Byron M.
Published: March 2022

Calcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear if the dimensionality reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality reduction methods. We also developed a novel method to perform deconvolution and dimensionality reduction simultaneously (termed CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from calcium imaging that would have been recovered from spiking activity. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.
Dynamics of brain-fluid circulation are altered in the mature-onset Tet-off APP mouse model of amyloidosis
Authors: Ben-Nejma Inès R.H. , Keliris Aneta J. , Vanreusel Verdi , Ponsaerts Peter , Van der Linden Annemie , Keliris Georgios A.
Published: March 2022

Alzheimer’s disease (AD), the most common type of dementia, is an incurable brain disorder characterised by the progressive build-up of toxic amyloid-beta (Aβ) and tau protein aggregates. AD gradually inflicts cognitive functions of an individual such as memory, thinking, reasoning, and language by degrading synaptic function and the integrity of neuronal networks. It has been recently suggested that the efficacy of different brain-clearance systems like the glymphatic system (GS), involved in the removal of toxic waste and homeostatic balance, plays a key role in the pathology of AD. Moreover, the observed coupling between brain fluid movement and global brain activity implies that an alteration of the neuronal network integrity can impact brain fluid circulation throughout the brain and thereby the efficacy of the GS. Here, we investigated the dynamics of brain fluid circulation in Tet-Off APP (AD) mice, a mature-onset model of amyloidosis in which we have recently shown a deterioration of neuronal network integrity by resting-state fMRI. By utilizing dynamic contrast enhanced-MRI and gadoteric acid (Gd-DOTA) T1 contrast agent injected into the cisterna magna, we demonstrated that brain fluid exchange was significantly altered in 14-month-old AD mice compared to control littermates. More specifically, AD mice showed higher Gd-DOTA accumulation in areas proximal to the injection cite and computational modeling of time courses demonstrated significantly lower inflow time constants relative to the controls. Immunohistochemistry demonstrated abundant amyloid plaque burden in the forebrain of the AD group coinciding with extensive astrogliosis and microgliosis. The neuroinflammatory responses were also found in plaque-devoid regions, potentially impacting brain fluid circulation.
E-cigarette vapour from base components propylene glycol and vegetable glycerine inhibits the inflammatory response in macrophages and epithelial cells
Authors: Bell Rachael L. , McAuley Danny F. , Shyamsundar Murali , O’Kane Cecila M. , Dombrowski Yvonne
Published: March 2022

E-cigarettes are a highly popular nicotine replacement therapy in the process of smoking cessation. Despite this, research on the effects of E-vapours to human health remains limited. The popularity of vaping and mass production of cheap E-liquids has led to compromised safety regulations, with contaminants such as heavy metals and alkaloids detected in multiple liquids. Vaporised E-liquids increase cellular ROS generation and inflammatory cytokine release from pulmonary macrophages. This suggests that E-cigarette usage might activate inflammasomes. Common food additives vegetable glycerine (VG) and propylene glycol (PG) form the base of all E-liquids, but little is known about their inflammatory potential once inhaled. Here, the effect of base components PG and VG on inflammasome activation and cytokine release was investigated in macrophages and epithelial cells exposed to E-liquids and vaporised E-liquid extract (E-vapour). Base E-liquid and E-vapour did not induce cellular cytotoxicity and non-vapourised E-liquid had no effect on IL-8 release. However, basic PG/VG E-vapour inhibited both IL-8 release and conventional inflammasome activation by known inflammatory activators in macrophages and epithelial cells. These results propose a novel inhibitory effect of basic E-vapour components to inflammatory challenges.
Ecology and evolution of chlamydial symbionts of arthropods
Authors: Halter Tamara , Köstlbacher Stephan , Collingro Astrid , Sixt Barbara S. , Tönshoff Elena R. , Hendrickx Frederik , Kostanjšek Rok , Horn Matthias
Published: March 2022

The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of ‘Candidatus R. oedothoracis’ associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.
Urbanization and green corridors influence reproductive success and pollinators of common milkweed
Authors: Breitbart Sophie , Tomchyshyn Albert , Wagner Helene , Johnson Marc
Published: March 2022

Urbanization exerts many pressures on species, yet little is known about how these pressures impact species interactions. Studies of urban plant-pollinator systems provide mounting evidence that urbanization impairs pollinator movement in fragmented urban landscapes, yet the consequences for pollinator-mediated plant reproduction remains unclear. In non-urban areas, habitat corridors can facilitate the movement of organisms including pollinators, but whether these corridors facilitate plant-pollinator interactions in urban areas remains understudied. To examine how urban environments and green corridors influence plant-pollinator interactions, we measured reproductive success in the native plant common milkweed (Asclepias syriaca), and the community structure of its pollinators, for two years along two urban-rural transects in the Greater Toronto Area, Canada, one of which followed a green corridor. We found that urbanization decreased male fitness (i.e., pollen removal), increased fruit set (i.e., mean no. of follicles per inflorescence), and inconsistently affected female fitness (i.e., no. of follicles) in A. syriaca. Urbanization simultaneously decreased pollinator abundance but increased pollinator richness. Proximity to a green corridor inconsistently affected male fitness but increased reproductive effort (i.e., no. of inflorescences) in A. syriaca, while pollinator diversity and richness was lower in corridors. Notably, there were no consistent relationships between pollinator community structure and reproductive success in A. syriaca in both the presence, and absence, of a green corridor. These results demonstrate the complexity with which urbanization, green corridors, and pollinator communities can shape the reproductive investment and fitness of native plant populations.
GRAPE: Genomic Relatedness Detection Pipeline
Authors: Medvedev Aleksandr , Lebedev Mikhail , Ponomarev Andrew , Kosaretskiy Mikhail , Osipenko Dmitriy , Tischenko Alexander , Kosaretskiy Egor , Wang Hui , Kolobkov Dmitry , Chamberlain-Evans Vitalina , Vakhitov Ruslan , Nikonorov Pavel
Published: March 2022

Classifying the degree of relatedness between pairs of individuals has both scientific and commercial applications. As an example, GWAS may suffer from high rates of false positive results due to unrecognized population structure. This problem becomes especially relevant with recent increases in large-cohort studies. Accurate relationship classification is also required for genetic linkage analysis to identify disease-associated loci. Additionally, DNA relatives matching service is one of the leading drivers for the direct-to-consumer genetic testing market. Despite the availability of scientific and research information on the methods for determining kinship and the accessibility of relevant tools, the assembly of the pipeline, that stably operates on a real-world genotypic data, requires significant research and development resources. Currently, there is no open-source end-to-end solution for relatedness detection in genomic data, that is fast, reliable and accurate for both close and distant degrees of kinship, combines all the necessary processing steps to work on real data, and is ready for production integration. To address this, we developed GRAPE: Genomic RelAtedness detection PipelinE. It combines data preprocessing, identity-by-descent (IBD) segments detection, and accurate relationship estimation. The project uses software development best practices, as well as GA4GH standards and tools. Pipeline efficiency is demonstrated on both simulated and real-world datasets.
Deletion of can1/cat1 genes and expression of a dominant any1 mutation establish an effective canavanine selection in fission yeast
Authors: Saada Anissia Ait , Costa Alex B. , Lobachev Kirill S.
Published: March 2022

Positive and counter-selectable markers have been successfully integrated as a part of numerous genetic assays in many model organisms. In this study, we investigate the mechanism of resistance to arginine analog canavanine and its applicability for genetic selection inSchizosaccharomyces pombe. Deletion of both arginine permease genescat1andcan1provides strong drug resistance, while the singlecan1deletion does not have impact on canavanine resistance. Surprisingly, the widely usedcan1-1allele does not match to thecan1gene but rather corresponds to theany1-523C>Tallele. The strong canavanine-resistance conferred by this allele arises from an inability to deposit basic amino acid transporters on the cellular membrane.any1-523C>Tleads to reduced post-translational modifications of Any1 regulated by the Tor2 kinase. We also demonstrate thatany1-523C>Tis a dominate allele. Our results uncover the mechanisms of canavanine-resistance in fission yeast and open the opportunity of usingcat1, can1andany1mutant alleles in genetic assays.
MUC5B mobilizes and MUC5AC spatially aligns mucociliary transport on human airway epithelium
Authors: Song Daniel , Iverson Ethan , Kaler Logan , Scull Margaret A. , Duncan Gregg A.
Published: March 2022

Airway mucus acts as a protective barrier and vehicle for clearance of pathogens, providing the lungs with a defense mechanism called mucociliary clearance (MCC). Airway mucus is composed of two mucins, mucin 5B (MUC5B) and 5AC (MUC5AC) that form a hydrogel that enables functional clearance in health. However, abnormalities in mucin expression, specifically increases in MUC5AC is observed in chronic respiratory diseases and leading to defective MCC. Our current understanding of MCC impairment focuses on mucin concentration, while the impact of mucin composition remains unclear. Here, we use MUC5AC/B-knock out (KO) human airway epithelial (HAE) tissue cultures to understand the role and contribution of individual secreted mucins on MCC mechanisms. We find that KO cultures result in impaired or discoordinated mucociliary transport demonstrating the importance of each of these mucins to effective MCC and shedding light on a new mechanism of mucin composition-dependent airway clearance.
Strength-mass scaling law governs mass distribution inside honey bee swarms
Authors: Shishkov Olga , Chen Claudia , Madonna Claire Allison , Jayaram Kaushik , Peleg Orit
Published: March 2022

To survive during colony reproduction, bees create dense clusters of thousands of suspended individuals. How can this swarm, which is orders of magnitude larger than the size of an individual, maintain mechanical stability? We hypothesize that the internal structure in the bulk of the swarm, about which there is little prior information, plays a key role in mechanical stability and thermoregulation. Here, we provide the first-ever 3D reconstructions of the positions of the bees in the bulk of the swarm using x-ray computed tomography. We find that the mass of bees in a layer decreases with distance from the attachment surface. By quantifying the distribution of bees within swarms varying in size (made up of 4000-10000 bees), we find that the same power law governs the smallest and largest swarms, with the weight supported by each layer scaling with the mass of each layer to the ≈ 1.5 power. This arrangement ensures that each layer exerts the same fraction of its total strength, and on average a bee supports a lower weight than its maximum grip strength. This illustrates the extension of the scaling law relating weight to strength of single organisms to the weight distribution within a superorganism made up of thousands of individuals.
Circuit Analysis of the Drosophila Brain using Connectivity-based Neuronal Classification Reveals Organization of Key Communication Pathways
Authors: Mehta Ketan , Goldin Rebecca F. , Ascoli Giorgio A.
Published: March 2022

We present a functionally relevant, quantitative characterization of the neural circuitry of Drosophila melanogaster at the mesoscopic level of neuron types as classified exclusively based on potential network connectivity. Starting from a large neuron-to-neuron brain-wide connectome of the fruit fly, we use stochastic block modeling and spectral graph clustering to group neurons together into a common “cell class” if they connect to neurons of other classes according to the same probability distributions. We then characterize the connectivity-based cell classes with standard neuronal biomarkers, including neurotransmitters, developmental birthtimes, morphological features, spatial embedding, and functional anatomy. Mutual information indicates that connectivity-based classification reveals aspects of neurons that are not adequately captured by traditional classification schemes. Next, using graph-theoretic and random walk analyses to identify neuron classes as hubs, sources, or destinations, we detect pathways and patterns of directional connectivity that potentially underpin specific functional interactions in the Drosophila brain. We uncover a core of highly interconnected dopaminergic cell classes functioning as the backbone communication pathway for multisensory integration. Additional predicted pathways pertain to the facilitation of circadian rhythmic activity, spatial orientation, fight-or-flight response, and olfactory learning. Our analysis provides experimentally testable hypotheses critically deconstructing complex brain function from organized connectomic architecture.

AUTHOR SUMMARY

The potential synaptic circuitry of a neural system constitutes the fundamental architectural underpinning of its in vivo dynamics, plasticity, and functions. The fruit fly neural circuit presented here captures the latent stochastic patterns of network connectivity and provides a fundamental parts list for reverse-engineering brain computation. Mapping the interactions among connectivity-based neuronal classes to development, morphology, physiology, and transcriptomics result in testable hypotheses on the relationship between whole-brain neural architecture and behavior.
High axial-resolution optical stimulation of neurons in vivo via two-photon optogenetics with speckle-free beaded-ring pattern
Authors: Jin Cheng , Liu Chi , Kong Lingjie
Published: March 2022

Two-photon optogenetics has become an indispensable technology in neuroscience, due to its capability in precise and specific manipulation of neural activities. Scanless holographic approach is generally adopted to meet the requirement of stimulating neural emsembles simultaneously. However, the commonly used disk patterns fail in achieving single-neuron resolution, especially in axial dimension, and its inherent speckles decrease the stimulation efficiency. Here, we propose a novel speckle-free, beaded-ring pattern for high axial-resolution optical stimulation of neurons in vivo. Using a dye pool and a fluorescent thin-film as samples, we verify that, compared to those with disk patterns, higher axial resolution and better localization ability can be achieved with beaded-ring patterns. Furthermore, we perform two-photon based all-optical physiology with neurons in mouse S1 cortex in vivo, and demonstrate that the axial resolution obtained by beaded-ring patterns can be improved by 24% when stimulating multiple neurons, compared with that of disk patterns.
Minor differences in peptide presentation between chicken MHC class I molecules can explain differences in disease susceptibility
Authors: Han Lingxia , Wu Shaolian , Peng Weiyu , Zhao Min , Yue Can , Wen Wanxin , Cai Wenbo , Zhang Ting , Wallny Hans-Joachim , Avila David W. , Mwangi William , Nair Venugopal , Ternette Nicola , Guo Yaxin , Zhao Yingze , Chai Yan , Qi Jianxun , Liang Hao , Gao George F. , Kaufman Jim , Liu William J.
Published: March 2022

The highly polymorphic classical major histocompatibility complexes (MHCs) can confer resistance or susceptibility to diseases. The chicken MHC is known to confer decisive resistance or susceptibility to various economically-important pathogens, including the iconic oncogenic herpesvirus that causes Marek’s disease (MD). Only one classical class I gene, BF2, is expressed at a high level in chickens, so it was relatively easy to discern a hierarchy from well-expressed thermostable fastidious specialist alleles to promiscuous generalist alleles that are less stable and expressed less on the cell surface. The BF2*1901 is more highly expressed and more thermostable than the closely-related BF2*1501, but the data for peptide repertoire available did not obviously correlate as expected. Here, we confirm for newly-developed chicken lines that the chicken haplotype B15 confers resistance to MD compared to B19. Using gas phase sequencing of peptide pools, and using immunopeptidomics involving mass spectroscopy, we find that the BF2*1901 binds a greater variety of amino acids in some anchor positions than BF2*1501. However, by X-ray crystallography, we find that the peptide-binding groove of BF2*1901 is narrower and shallower. Though the self-peptides bound to BF2*1901 may appear more various than those of BF2*1501, the structures show that the wider and deeper peptide-binding groove of BF2*1501 allows it to tightly accept many more peptides overall, correlating with the expected hierarchies for expression level, thermostability and MD resistance. Moreover, the α2 helix of BF2*1901 is higher than BF2*1501, potentially reducing the number of T cell clones that can recognize this fastidious class I molecule.

IMPORTANCE

Disease susceptibility mechanism is complicated, but chicken infection of Marek’s disease (MD) is one of ideal models, considering the only one highly expressed classical MHC class I, BF2. The different susceptibility of the two close alleles BF2*1901 and BF2*1501 with minor difference of expression and thermostability is still unfathomed. Here, we confirm B15 chicken confers resistance to MD compared to B19. But the BF2*1901 binds a broader variety of anchoring peptides than BF2*1501. This mystery was solved by the structural determination of the two molecules with one similar peptide. The wider and deeper peptide-binding groove of BF2*1501 allows it to tightly accept many more peptides overall, which is concordant to the expected hierarchies for expression level, thermostability and MD resistance.
Did COVID-19 Vaccines Go to the Whitest Neighborhoods First? Racial Inequities in Six Million Phase 1 Doses Shipped to Pennsylvania
Authors: Holtzman Geoffrey S. , Yang Yukun , Louis Pierce
Published: March 2022

Research on racial disparities in COVID-19 vaccination rates has focused primarily on vaccine hesitancy. However, vaccine hesitancy research is increasingly unable to account for racial disparities in vaccination rates in the U.S., which have shrunk rapidly over the past year. This and other evidence suggests that inequities in vaccine allocation and access may have contributed to vaccination rate disparities in the U.S. But to our knowledge, no previously published research has examined whether the geographic distribution of COVID-19 vaccines has led to greater access for White Americans than for Black Americans.

Here, we link neighborhood-level data on vaccine allocation to data on racial demographics to show that in the first 17 weeks of Pennsylvania’s COVID-19 vaccine rollout (Phase 1), White people were 25% more likely than Black people to live in neighborhoods (census tracts) that received vaccine shipments. In the 17 weeks of Pennsylvania’s de jure restrictions on vaccine eligibility, de facto geographic restrictions on vaccine access disproportionately disadvantaged Black people and favored White people. In revealing these vaccine inequities, our work builds on prior work to develop a theory-driven, evidence-based, reproducible framework for studying racial inequities in the distribution of COVID-19 vaccines.
Homologous recombination deficiency (HRD) can predict the therapeutic outcomes of immuno-neoadjuvant therapy in NSCLC patients
Authors: Zhou Zhen , Ding Zhengping , Yuan Jie , Shen Shengping , Jian Hong , Tan Qiang , Yang Yunhai , Chen Zhiwei , Luo Qingquan , Cheng Xinghua , Yu Yongfeng , Niu Xiaomin , Qian Liqiang , Chen Xiaoke , Gu Linping , Liu Ruijun , Ma Shenglin , Huang Jia , Chen Tianxiang , Li Ziming , Ji Wenxiang , Song Liwei , Shen Lan , Jiang Long , Yu Zicheng , Zhang Chao , Tai Zaixian , Wang Changxi , Chen Rongrong , Lu Shun
Published: March 2022

Background

Neoadjuvant immunotherapy is emerging as novel effective intervention in lung cancer but the study to prioritize effective surrogates indicating its therapeutic outcomes is limited. We investigated the genetic changes between patients with distinct response to neoadjuvant immunotherapy in non-small-cell lung cancer (NSCLC) for the derive of biomarkers with indicative capability in predicting outcomes.

Methods

In this study, 3 adenocarcinoma and 11 squamous cell carcinoma NSCLC patients were treated by neoadjuvant immunotherapy with variated regimen followed by surgical resection. Pre-therapy FFPE or fresh tissues and blood samples were analyzed by whole-exome sequencing (WES). Genetic alternation comparisons were conducted between differently-responded patients. Multiple public cohorts were selected for validation.

Results

DNA damage repair (DDR)-related InDel signatures and DDR-related gene mutations were enriched in better-responded patients, i.e. major pathological response (MPR) group. Besides, MPR patients exhibited provoked genome instability and unique homologous recombination deficiency (HRD) events. By further inspecting alternation status of homology-dependent recombination (HR) pathway genes, the clonal alternations were exclusively enriched in MPR group. Additionally, associations between HR gene alternations, percent of viable tumor cells and HRD event were identified, which orchestrated tumor mutational burden (TMB), mutational intratumor heterogeneity (ITH), somatic copy number alteration (SCNA) ITH and clonal neoantigen load in patients. Validations in public cohorts further supported the generality of our findings.

Conclusions

We innovatively associated the HRD event with enhanced neoadjuvant immunotherapy response in lung cancer. The power of HRD event in patient therapeutic stratification persisted in multi-facet public cohorts. We propose the inspection of HR pathway gene status could serve as novel and additional indicators directing immune-neoadjuvant and immunotherapy treatment decisions for NSCLC patients.