bluuebunny/crossref_metadata_2025 huggingface dataset:
Prenatal stress programs behavioral pattern separation in adult mice
Authors: Rajendran S , Kaci ML , Ladeveze E , Abrous DN , Koehl M
Published: January 2022

Stress is an unavoidable condition in human life. Stressful events experienced during development, including in utero, have been suggested as one major pathophysiological mechanism for developing vulnerability towards neuropsychiatric and neurodevelopmental disorders in adulthood. One cardinal feature of such disorders is impaired cognitive ability, which may in part rely on abnormal structure and function of the hippocampus. In the hippocampus, the dentate gyrus is a site of continuous neurogenesis, a process that has been recently implicated in spatial pattern separation, a cognitive phenomenon that serves to reduce the degree of overlap in the incoming information to facilitate its storage with minimal interference. We previously reported that adult neurogenesis is altered by prenatal stress allowing us to hypothesize that prenatal stress may possibly lead to impairment in pattern separation. To test this hypothesis, both control (C) and prenatally stressed (PS) adult mice were tested for metric and contextual discrimination abilities. We report for the first time that prenatal stress impairs pattern separation process, a deficit that may underlie their cognitive alterations and that may result in defective behaviors reminiscent of psychiatric illness such as post‐traumatic stress disorder.
Amniotic fluid stem cell extracellular vesicles promote fetal lung branching and cell differentiation in experimental congenital diaphragmatic hernia
Authors: Khalaj Kasra , Figueira Rebeca Lopes , Antounians Lina , Gandhi Sree , Wales Matthew , Montalva Louise , Biouss George , Zani Augusto
Published: January 2022

Pulmonary hypoplasia secondary to congenital diaphragmatic hernia (CDH) is characterized by impaired branching morphogenesis and differentiation. We have previously demonstrated that administration of extracellular vesicles derived from rat amniotic fluid stem cells (AFSC-EVs) rescues development of hypoplastic lungs at the pseudoglandular and alveolar stages in rodent models of CDH. Herein, we tested whether AFSC-EVs exert their regenerative effects at the canalicular and saccular stages, as these are translationally relevant for clinical intervention. To induce fetal pulmonary hypoplasia, we gavaged rat dams with nitrofen at embryonic day 9.5 and demonstrated that nitrofen-exposed lungs had impaired branching morphogenesis, dysregulated signaling pathways relevant to lung development (FGF10/FGFR2, ROBO/SLIT, Ephrin, Neuropilin 1, β-catenin) and impaired epithelial and mesenchymal cell marker expression at both stages. AFSC-EVs administered to nitrofen-exposed lung explants rescued airspace density and increased the expression levels of key factors responsible for branching morphogenesis. Moreover, AFSC-EVs rescued the expression of alveolar type 1 and 2 cell markers at both canalicular and saccular stages, and restored markers of club, ciliated epithelial, and pulmonary neuroendocrine cells at the saccular stage. AFSC-EV treated lungs also had restored markers of lipofibroblasts and PDGFRA+ cells to control levels at both stages. EV tracking showed uptake of AFSC-EV RNA cargo throughout the fetal lung and an mRNA-miRNA network analysis identified that several miRNAs responsible for regulating lung development processes were contained in the AFSC-EV cargo. These findings suggest that AFSC-EV based therapies hold potential for restoring fetal lung growth and maturation in babies with pulmonary hypoplasia secondary to CDH.

Graphical abstract

Babies with congenital diaphragmatic hernia have hypoplastic lungs characterized by impaired branching morphogenesis and undifferentiated epithelium and mesenchyme. The authors demonstrate that amniotic fluid stem cell extracellular vesicles (AFSC-EVs) administered to rat hypoplastic fetal lungs restore branching and exert regenerative effects on epithelial and mesenchymal cells, partly through miRNA cargo transfer. AFSC-EV beneficial effects were obtained at translationally relevant timepoints.
Highly efficient multiplex genome editing in dicots using improved CRISPR/Cas systems
Authors: Li Bingjie , shang Yun , Wang Lixianqiu , Lv Jing , Wang Fengjiao , Chao Jiangtao , Mao Jingjing , Ding Anming , Wu Xinru , Cui Mengmeng , Sun Yuhe , Dai Changbo
Published: January 2022

CRISPR/Cas9-mediated gene editing provides a powerful tool for dissecting gene function and improving important traits in crops. However, there are still persisting challenges to obtain high homozygous/bi-allelic (ho/bi) mutations in dicot plants. Here, we develop an improved CRISPR/Cas9 system harboring a calreticulin-like gene promoter, which can boost targeted mutations in dicots. Additionally, the pDC45_dsg construct, combining a 35Spro-tRNA_sgRNA-EU unit and PCE8pro-controlled Cas9, can achieve more than 80.0% ho/bi mutations at target sites in allotetraploid tobacco. We construct pDC45_Fast system that can simultaneously fulfill gene editing and shorten the life span of T0 generation tobacco and tomato. This study provides new tools for improving targeted gene mutagenesis in dicots, and makes manipulations of genes in Solanum more feasible.
36-year study reveals stability of a wild wheat population across microhabitats
Authors: Dahan-Meir Tal , Ellis Thomas James , Mafessoni Fabrizio , Sela Hanan , Rudich Ori , Manisterski Jacob , Avivi-Ragolsky Naomi , Raz Amir , Feldman Moshe , Anikster Yehoshua , Nordborg Magnus , Levy Avraham A.
Published: January 2022

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to explain this spatial and temporal stability using only limited dispersal, suggesting a role for fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically, further supporting the hypothesis of local adaptation. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.
Sensitive protein detection using site-specifically oligonucleotide-conjugated nanobodies
Authors: Al-Amin Rasel A. , Muthelo Phathutshedzo M. , Abdurakhmanov Eldar , Vincke Cécile , Amin Shahnaz P. , Muyldermans Serge , Danielson U. Helena , Landegren Ulf
Published: January 2022

High-quality affinity probes are critical for sensitive and specific protein detection, in particular for detection of protein biomarkers at early phases of disease development. Proximity extension assays (PEA) have been used for high-throughput multiplexed protein detection of up to a few thousand different proteins in one or a few microliters of plasma. Clonal affinity reagents can offer advantages over the commonly used polyclonal antibodies (pAbs) in terms of reproducibility and standardization of such assays. Here we explore nanobodies (Nb) as an alternative to pAbs as affinity reagents for PEA. We describe an efficient site-specific approach for preparing high-quality oligo-conjugated Nb probes via enzyme coupling using Sortase A (SrtA). The procedure allows convenient removal of unconjugated affinity reagents after conjugation. The purified high-grade Nb probes were used in PEA and the reactions provided an efficient means to select optimal pairs of binding reagents from a group of affinity reagents. We demonstrate that Nb-based PEA (nano-PEA) for interleukin-6 (IL6) detection can augment assay performance, compared to the use of pAb probes. We identify and validate Nb combinations capable of binding in pairs without competition for IL6 antigen detection by PEA.
Altered retinal structure and function in Spinocerebellar ataxia type 3
Authors: Toulis Vasileios , Casaroli-Marano Ricardo , Camós-Carreras Anna , Figueras-Roca Marc , Sánchez-Dalmau Bernardo , Muñoz Esteban , Ashraf Naila S. , Ferreira Ana F. , Khan Naheed , Marfany Gemma , do Carmo Costa Maria
Published: January 2022

Spinocerebellar ataxia type 3 is an autosomal dominant neurodegenerative disorder caused by expansion of a polyglutamine (polyQ)-encoding CAG repeat in the ATXN3 gene. Because the ATXN3 protein regulates photoreceptor ciliogenesis and phagocytosis, we aimed to explore whether expanded polyQ ATXN3 impacts retinal function and integrity in SCA3 patients and transgenic mice.

We evaluated the retinal structure and function in five patients with Spinocerebellar ataxia type 3 and in a transgenic mouse model of this disease (YACMJD84.2, Q84) using, respectively, optical coherence tomography (OCT) and electroretinogram (ERG). We further determined in the transgenic mice: a) the retinal expression pattern of ATXN3 and assessed the distribution of cones and rods by immunofluorescence (IF); and b) the retinal ultrastructure by transmission electron microscopy (TEM).

Some patients with Spinocerebellar ataxia type 3 in our cohort revealed: i) reduced central macular thickness indirectly correlated with disease duration; ii) decreased thickness of the macula and the ganglion cell layer, and reduced macula volume inversely correlated with disease severity (SARA score); and iii) electrophysiological dysfunction of cones, rods, and inner retinal cells. Transgenic mice replicated the human OCT and ERG findings with aged homozygous Q84/Q84 mice showing a stronger phenotype accompanied by further thinning of the outer nuclear layer and photoreceptor layer and highly reduced cone and rod activities, thus supporting severe retinal dysfunction in these mice. In addition, Q84 mice showed progressive accumulation of ATXN3-positive aggregates throughout several retinal layers and depletion of cones alongside the disease course. TEM analysis of aged Q84/Q84 mouse retinas supported the IF ATXN3 aggregation findings by revealing the presence of high number of negative electron dense puncta in ganglion cells, inner plexiform and inner nuclear layers, and further showed thinning of the outer plexiform layer, thickening of the retinal pigment epithelium and elongation of apical microvilli.

Our results indicate that retinal alterations detected by non-invasive eye examination using OCT and ERG could represent a biological marker of disease progression and severity in patients with Spinocerebellar ataxia type 3.
Intracellular flow cytometry staining of antibody-secreting cells using phycoerythrin-conjugated antibodies: pitfalls and solutions
Authors: Renner Patrick , Crone Michael , Kornas Matthew , Pioli KimAnh T. , Pioli Peter D.
Published: January 2022

Antibody-secreting cells are terminally differentiated B cells that play a critical role in humoral immunity through immunoglobulin secretion along with possessing the potential to be long-lived. It is now appreciated that antibody-secreting cells regulate multiple aspects of biology through the secretion of various cytokines. In this regard, intracellular flow cytometry is a key tool used to assess the presence of intracellular proteins such as cytokines and transcription factors. Here, we showed that the use of phycoerythrin-containing antibody conjugates led to a false interpretation of antibody-secreting cell intracellular protein expression compared to other cell types. This was mainly due to the inappropriate retention of these antibodies specifically within antibody-secreting cells. Furthermore, we demonstrated how to reduce this retention which allowed for a more accurate comparison of intracellular protein expression between antibody-secreting cells and other cell types such as B lymphocytes. Using this methodology, our data revealed that spleen antibody-secreting cells expressed Toll-like receptor 7 as well as the pro-form of the inflammatory cytokine interleukin-1β.
Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes
Authors: Vallebueno-Estrada Miguel , Steindl Sonja , Akulova Vasilina , Riefler Julia , Slusarz Lucyna , Arizpe Alexis , Swarts Kelly
Published: January 2022

Reduced representation library approaches are still a valuable tool for breeding and population and ecological genomics, even with impressive increases in sequencing capacity in recent years. Unfortunately, current approaches only allow for multiplexing up to 384 samples. To take advantage of increased sequencing capacity, we present Multi-GBS, a massively multiplexable extension to Genotyping-by-Sequencing that is also optimized for large conifer genomes. In Norway Spruce, a highly repetitive 20Gbp diploid genome with high population genetic variation, we call over a million variants in 32 genotypes from three populations, two natural forest in the Alps and Bohemian Alps, and a managed population from southeastern Austria using the existing TASSEL GBSv2 pipeline. Metric MDS analysis of replicated genotypes shows that technical bias in resulting genotype calling is minimal and that populations cluster in biologically meaningful ways.
Vascular topology is acutely impacted by experimental febrile status epilepticus
Authors: Salehi Arjang , Salari Sirus , Daglian Jennifer , Chen Kevin , Baram Tallie Z. , Obenaus Andre
Published: January 2022

Febrile status epilepticus (FSE) is an important risk factor for temporal lobe epilepsy and early identification is vital. In a rat model of FSE, we identified an acute novel MRI signal in the basolateral amygdala (BLA) at 2 hours post FSE that predicted epilepsy in adulthood. This signal remains incompletely understood and hypothesized that it might derive from changes to vascular topology. Experimental FSE was induced in rat pups and compared to normothermic littermate controls. We examined cerebral vascular topology at 2 hours, using a novel vessel painting and analysis protocol. Blood vessel density of the cortical vasculature was significantly reduced in FSE rats, and this effect was lateralized, as reported for the MRI signal. The middle cerebral artery (MCA) exhibited abnormal topology in FSE pups but not in controls. In the BLA, significant vessel junction reductions and decreased vessel diameter were observed, together with a strong trend for reduced vessel length. In summary, FSE results in acute vascular topological changes in the cortex and BLA that may underlie the acute MRI signal that predicts progression to future epilepsy. The altered vasculature may be amenable to intervention treatments to potentially reduce the probability of progression to epilepsy following FSE.
How many bits of information can be transferred between residues in a protein and how fast?
Authors: Hacisuleyman Aysima , Erman Burak
Published: January 2022

Time resolved Raman and infrared spectroscopy experiments show the basic features of information transfer between residues in proteins. Here, we present the theoretical basis of information transfer using a simple elastic net model and recently developed entropy transfer concept in proteins. Mutual information between two residues is a measure of communication in proteins which shows the maximum amount of information that may be transferred between two residues. However, it does not explain the actual amount of transfer nor the transfer rate of information between residues. For this, dynamic equations of the system are needed. We used the Schreiber theory of information transfer and the Gaussian network Model of proteins, together with the solution of the Langevin equation, to quantify allosteric information transfer. Results of the model are in perfect agreement with ultraviolet resonance Raman measurements. Analysis of the allosteric protein Human NAD-dependent isocitrate dehydrogenase shows that a multitude of paths contribute collectively to information transfer. While the peak values of information transferred are small relative to information content of residues, considering the estimated transfer rates, which are in the order of megabits per second, sustained transfer during the activity time-span of proteins may be significant.
Membrane-active Polymers: NCMNP13-x, NCMNP21-x and NCMNP21b-x for Membrane Protein Structural Biology
Authors: Trinh Thi Kim Hoang , Catalano Claudio , Guo Youzhong
Published: January 2022

Membrane proteins are a ubiquitous group of bio-macromolecules responsible for many crucial biological processes and serve as drug targets for a wide range of modern drugs. Detergent-free technologies such as styrene-maleic acid lipid particles (SMALP), diisobutylene-maleic acid lipid particles (DIBMALP), and native cell membrane nanoparticles (NCMN) systems have recently emerged as revolutionary alternatives to the traditional detergent-based approaches for membrane protein research. NCMN systems aim to create a membrane-active polymer library suitable for high-resolution structure determination. Herein, we report our design, synthesis, characterization and comparative application analyses of three novel classes of NCMN polymers, NCMNP13-x, NCMNP21-x and NCMNP21b-x. Although each NCMN polymer can solubilize various model membrane proteins and conserve native lipids into NCMN particles, only the NCMNP21b-x series reveals lipid-protein particles with good buffer compatibility and high homogeneity suitable for single-particle cryo-EM analysis. Consequently, the NCMNP21b-x polymers that bring out high-quality NCMN particles are particularly attractive for membrane protein structural biology.

Graphical abstract

Highlights

Demonstrate straightforward strategies for tailoring styrene-maleic co-polymer (SMA) that revealed novel buffer compatible polymers, NCMNP13-50, NCMNP21-20 and NCMNP21b-x.

Elucidate how modification factors alter the membrane-active properties of these polymers, i.e., membrane protein extraction efficiency, morphology, etc.

Provide valuable insights into the rational design of membrane-active polymers for membrane protein structural biology.

NCMNP21b-x polymers are highly compatible with high-resolution structure determination using an emerging technique, cryo-EM.
Evidence for quinol oxidase activity of ImoA, a novel NapC/NirT family protein from the neutrophilic Fe(II) oxidizing bacterium Sideroxydans lithotrophicus ES-1
Authors: Jain Abhiney , Coelho Anaísa , Madjarov Joana , Todorovic Smilja , Louro Ricardo O. , Gralnick Jeffrey A. , Paquete Catarina M.
Published: January 2022

The freshwater chemolithoautotrophic Gram-negative bacterium Sideroxydans lithotrophicus ES-1 oxidizes Fe(II) at the cell surface. In this organism, it is proposed that the monoheme cytochrome MtoD from the Mto pathway transfer electrons across the periplasm to an inner membrane NapC/NirT family tetraheme cytochrome encoded by Slit_2495, for which we propose the name ImoA (inner membrane oxidoreductase). ImoA has been proposed to function as the quinone reductase, receiving electrons from iron oxidizing extracellular electron uptake pathway to reduce the quinone pool. In this study, ImoA was cloned on a pBAD plasmid vector and overexpressed in Escherichia coli. Biochemical and spectroscopic characterization of the purified ImoA reveals that this 26.5 kDa cytochrome contains one high-spin and three low-spin hemes. Our data show that ImoA can function as a quinol oxidase and is able to functionally replace CymA, a related NapC/NirT family tetraheme cytochrome required for anaerobic respiration of a wide range of substrates by Shewanella oneidensis. We demonstrate that ImoA can transfer electrons to different periplasmic proteins from S. oneidensis including STC and FccA, but in a manner that is distinct from that of CymA. Phylogenetic analysis shows that ImoA is clustered closer to NirT sequences than to CymA. This study suggests that ImoA functions as a quinol oxidase in S. oneidensis and raises questions about the directionality and/or reversibility of electron flow through the Mto pathway in S. lithotrophicus ES-1.

Importance

Fe(II)-oxidizing bacteria play an important role in the biogeochemical cycling of iron, representing a promising class of organisms for the development of novel biotechnological processes, including bioelectrosynthesis. These organisms perform extracellular electron transfer, taking up electrons from Fe(II) outside of the cell, possibly through a porin-cytochrome complex in the outer membrane. The electrons are then transferred to the quinone pool in the inner membrane via periplasmic and inner membrane electron transfer proteins. In this paper, we produced and characterized the NapC/NirT family tetraheme cytochrome ImoA, encoded by Slit_2495, an inner membrane protein from the Gram-negative Fe(II)-oxidizing bacterium Sideroxydans lithotrophicus ES-1, proposed to be involved in extracellular electron transfer to the quinone pool. We show that ImoA may function instead as a quinol oxidase. The obtained insights represent the first step in understanding mechanisms of electron flow in S. lithotrophicus ES-1 and may lead towards practical biotechnological applications of Fe(II)-oxidizing bacteria.
Heterogeneity in testing for infectious diseases
Authors: Berrig Christian , Andreasen Viggo , Nielsen Bjarke Frost
Published: January 2022

Testing strategies have varied widely between nation states during the COVID-19 pandemic, in intensity as well as methodology. Some countries have mainly performed diagnostic testing while others have opted for mass-screening for the presence of SARS-CoV-2 as well. COVID passport solutions have been introduced, in which access to several aspects of public life requires either testing, proof of vaccination or a combination thereof. This creates a coupling between personal activity levels and testing behaviour which, as we show, leverages the heterogeneous behaviours in the population and turns this heterogeneity from a disadvantage to an advantage for epidemic control.
Responses to song playback differ in sleeping versus anesthetized songbirds
Authors: Bottjer Sarah W. , Le Moing Chloé , Li Ellysia , Yuan Rachel
Published: January 2022

Vocal learning in songbirds is mediated by a highly localized system of interconnected forebrain regions, including recurrent loops that traverse the cortex, basal ganglia, and thalamus. This brain-behavior system provides a powerful model for elucidating mechanisms of vocal learning, with implications for learning speech in human infants, as well as for advancing our understanding of skill learning in general. A long history of experiments in this area has tested neural responses to playback of different song stimuli in anesthetized birds at different stages of vocal development. These studies have demonstrated selectivity for different song types that provide neural signatures of learning. In contrast to the ease of obtaining responses to song playback in anesthetized birds, song-evoked responses in awake birds are greatly reduced or absent, indicating that behavioral state is an important determinant of neural responsivity. Song-evoked responses can be elicited in sleeping as well as anesthetized zebra finches, and the selectivity of responses to song playback in adult birds tends to be highly similar between anesthetized and sleeping states, encouraging the idea that anesthesia and sleep are highly similar. In contrast to that idea, we report evidence that cortical responses to song playback in juvenile zebra finches (Taeniopygia guttata) differ greatly between sleep and urethane anesthesia. This finding indicates that behavioral states differ in sleep versus anesthesia and raises questions about relationships between developmental changes in sleep activity, selectivity for different song types, and the neural substrate for vocal learning.

Significance

Patterns of spiking activity based on electrophysiological recordings in many different taxa are known to be heavily dependent on behavioral state. Neural activity patterns are frequently similar between sleep and anesthesia, which has encouraged the idea that similar states characterize sleep and anesthesia. Based on comparisons across studies, we report that activity patterns are highly dissimilar between sleep and urethane anesthesia in a cortical region of juvenile songbirds. These data argue against the idea that similar behavioral states are achieved in sleep versus anesthesia.
Effects of larval diet on the life-history traits and phenotypic expression of pyrethroid resistance in the major malaria vectorAnopheles gambiae s.s.
Authors: Sovegnon Pierre Marie , Fanou Marie Joelle , Akoton Romaric , Djihinto Oswald Yédjinnavênan , Lagnika Hamirath Odée , Agonhossou Romuald , Djogbénou Luc Salako
Published: January 2022

The success achieved in reducing malaria transmission by vector control is threatened by insecticide resistance. To strengthen the current vector control programmes, the non-genetic factors underlying the emergence of insecticide resistance inAnophelesvectors and its widespread need to be explored. This study aimed to assess the effects of larval diet on some life-history traits and pyrethroid-insecticide susceptibility ofAnopheles gambiae s.s.

Three (3)An. gambiaestrains, namely Kisumu (insecticide susceptible), AcerKis (homozygousace-1RG119S resistant) and KisKdr (homozygouskdrRL1014F resistant) were fed with three different diets (low, medium, and high) of TetraMin®Baby fish food. Pre-imaginal developmental time, larval mortality, adult emergence rate and female wing length were measured. Mosquito females were exposed to insecticide-treated net (ITN) PermaNet 2.0 and PermaNet 3.0.

In the threeAn. gambiaestrains, significant differences in adult emergence rates (F= 1054.2;df= 2;p<0.01), mosquito wing length (F= 970.5;df= 2;p<0.01) and adult survival post insecticide exposure (χ2= 173;df= 2;p<0.01), were noticed among the three larval diets. Larvae fed with the low food diets took more time to develop, were smaller at emergence and displayed a short lifespan, while the specimens fed with a high regime developed faster and into big adults. Although being fed with a high diet, none ofAn. gambiaestrain harbouring thekdrRandace-1Rallele survived 24 hours after exposure against PermaNet 3.0.

This study showed that variation in the larval diet significantly impactsAn. gambiaelife-history traits such as larval mortality and developmental time, adult wing length, and female susceptibility to pyrethroid insecticides. Further investigations through field-based studies would allow an in-depth understanding of the implications of these non-genetic parameters on the physiological traits of malaria vectors and consequently improve resistance management.
Parasitized or non-parasitized, why? A study of factors influencing tick burden in roe deer neonates
Authors: Bariod Léa , Saïd Sonia , Calenge Clément , Chabot Stéphane , Badeau Vincent , Bourgoin Gilles
Published: January 2022

Ixodes ricinus, the most common species of tick in Europe, is known to transmit major pathogens to animals and humans such asBabesiaspp. orBorreliaspp.. Its abundance and distribution have been steadily increasing in Europe during recent decades, due to global environmental changes. Indeed, as ticks spend most of their life in the environment, their activity and life cycle are highly dependent on environmental conditions, and therefore on climate or habitat changes. Simultaneously, wild ungulates have expanded their range and increased dramatically in abundance worldwide, in particular roe deer (Capreolus capreolus), have allowed tick populations to grow and spread. Currently, tick infestation on newborn wild ungulates is poorly documented. However, newborn ungulates are considered more sensitive to tick bites and pathogen transmission because of their immature immune system. Thus, improving knowledge about the factors influencing tick infestation on newborns is essential to better understand their health risks. This study was conducted at Trois-Fontaines forest, Champagne-Ardenne, France (1992-2018). Based on a long-term monitoring of roe deer fawns, we used a novel Bayesian model of the infestation of fawns to identify which biotic or abiotic factors are likely to modify the level of infestation by ticks of 965 fawns over time. We show that tick burden increased faster during the first days of life of the fawns and became constant when fawns were 5 days old and more, which could be explained by the depletion of questing ticks or the turnover of ticks feeding on fawns. Moreover, the humidity, which favors tick activity, was weakly positively related to the tick burden. Our results demonstrate that tick infestation was highly variable among years, particularly between 2000 and 2009. We hypothesize that this results from a modification of habitat caused by hurricane Lothar.
Viscoelastic properties of suspended cells measured with shear flow deformation cytometry
Authors: Gerum Richard , Mirzahossein Elham , Eroles Mar , Elsterer Jennifer , Mainka Astrid , Bauer Andreas , Sonntag Selina , Winterl Alexander , Bartl Johannes , Fischer Lena , Abuhattum Shada , Goswami Ruchi , Girardo Salvatore , Guck Jochen , Schrüfer Stefan , Ströhlein Nadine , Nosratlo Mojtaba , Herrmann Harald , Schultheis Dorothea , Rico Felix , Müller Sebastian , Gekle Stephan , Fabry Ben
Published: January 2022

Numerous cell functions are accompanied by phenotypic changes in viscoelastic properties, and measuring them can help elucidate higher-level cellular functions in health and disease. We present a high-throughput, simple and low-cost microfluidic method for quantitatively measuring the elastic (storage) and viscous (loss) modulus of individual cells. Cells are suspended in a high-viscosity fluid and are pumped with high pressure through a 5.8 cm long and 200 µm wide microfluidic channel. The fluid shear stress induces large, near ellipsoidal cell deformations. In addition, the flow profile in the channel causes the cells to rotate in a tank-treading manner. From the cell deformation and tank treading frequency, we extract the frequency-dependent viscoelastic cell properties based on a theoretical framework developed by R. Roscoe1 that describes the deformation of a viscoelastic sphere in a viscous fluid under steady laminar flow. We confirm the accuracy of the method using atomic force microscopy-calibrated polyacrylamide beads and cells. Our measurements demonstrate that suspended cells exhibit power-law, soft glassy rheological behavior that is cell cycle-dependent and mediated by the physical interplay between the actin filament and intermediate filament networks.
Augmentation of extracellular ATP synergizes with chemotherapy in triple negative breast cancer
Authors: Manouchehri Jasmine M , Datta Jharna , Willingham Natalie , Wesolowski Robert , Stover Daniel , Ganju Ramesh K , Carson William , Ramaswamy Bhuvaneswari , Cherian Mathew A
Published: January 2022

Introduction

Breast cancer affects two million women worldwide every year and is the most common cause of cancer-related death among women. The triple-negative breast cancer (TNBC) sub-type is associated with an especially poor prognosis because currently available therapies, fail to induce long-lasting responses. Therefore, there is an urgent need to develop novel therapies that result in durable responses. One universal characteristic of the tumor microenvironment is a markedly elevated concentration of extracellular adenosine triphosphate (eATP). Chemotherapy exposure results in further increases in eATP through its release into the extracellular space of cancer cells via P2RX channels. eATP levels are reduced by eATPases. Given that high concentrations of eATP are cytotoxic, we hypothesized that augmenting the release of eATP through P2RX channels and inhibiting extracellular ATPases would sensitize TNBC cells to chemotherapy.

Methods

TNBC cell lines MDA-MB 231, Hs 578t and MDA-MB 468 and non-tumorigenic immortalized mammary epithelial MCF-10A cells were treated with increasing concentrations the chemotherapeutic agent paclitaxel in the presence of eATPase inhibitors, specific agonists or antagonists of P2RXs with cell viability and eATP content being measured. Additionally, the mRNA, protein and cell surface expressions of the purinergic receptors P2RX4 and P2RX7 were evaluated in all examined cell lines via qRT-PCR, western blot, and flow cytometry analyses, respectively.

Results

In the present study, we observed dose-dependent declines in cell viability and increases in eATP in paclitaxel-treated TNBC cell lines in the presence of inhibitors of eATPases. These effects were reversed by specific antagonists of P2RXs. Similar results were observed with P2RX activators. All examined cell lines expressed both P2RX4 and P2RX7 at the mRNA, protein and cell surface levels.

Conclusion

These results reveal that eATP modulates the chemotherapeutic response in TNBC cell lines which could be exploited to enhance the efficacy of chemotherapy regimens for TNBC.
Hydrogen production in the presence of oxygen by Escherichia coli K-12
Authors: Metcalfe George D. , Sargent Frank , Hippler Michael
Published: January 2022

Escherichia coli is a facultative anaerobe that can grow in a variety of environmental conditions. In the complete absence of O2, E. coli can perform a mixed-acid fermentation that contains within it an elaborate metabolism of formic acid. In this study, we use cavity-enhanced Raman spectroscopy (CERS), FTIR, liquid Raman spectroscopy, isotopic labelling, and molecular genetics to make advances in the understanding of bacterial formate and H2 metabolism. It is shown that, under anaerobic (anoxic) conditions, formic acid is generated endogenously, excreted briefly from the cell, and then taken up again to be disproportionated to H2 and CO2 by formate hydrogenlyase (FHL-1). However, exogenously added D-labelled formate behaves quite differently from the endogenous formate and is taken up immediately, independently, and possibly by a different mechanism, by the cell and converted to H2 and CO2. Our data support an anion-proton symport model for formic acid transport. In addition, when E. coli was grown in a micro-aerobic (micro-oxic) environment it was possible to analyse aspects of formate and O2 respiration occurring alongside anaerobic metabolism. While cells growing under micro-aerobic conditions generated endogenous formic acid, no H2 was produced. However, addition of exogenous formate at the outset of cell growth did induce FHL-1 biosynthesis and resulted in formate-dependent H2 production in the presence of O2.
Structural insights as to how iron-loaded siderophores are imported into Mycobacterium tuberculosis by IrtAB
Authors: Sun Shan , Gao Yan , Yang Xiaolin , Yang Xiuna , Hu Tianyu , Liang Jingxi , Xiong Zhiqi , Ren Pengxuan , Bai Fang , Guddat Luke W. , Yang Haitao , Rao Zihe , Zhang Bing
Published: January 2022

The ATP-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import iron-loaded siderophores. Unusually, it adopts the typical fold of canonical ABC exporters. Here, we report the structure of unliganded Mtb IrtAB and its structure in complex with ATP, ADP, and an ATP analogue (AMP-PNP) at resolutions from 2.9 to 3.5 Å. In the ATP-bound state, the two nucleotide-binding domains (NBDs) form a “head-to-tail” dimer, but IrtAB has an unexpectedly occluded conformation, with the inner core forming a large hydrophilic cavity of about 4600 Å3. Comparison of the structure of the transporter in inward-facing and occluded conformations reveals that the NBD and the intracellular helical region of transmembrane domain (TMD) have an asymmetric allosteric mechanism when ATP binding/hydrolysis such that the one exhibits rigid-body rotation and the other moves in a concerted response as a rigid body. This study provides a molecular basis for the ATP-driven conformational changes that occur in IrtAB and an explanation as to how iron-loaded siderophores are imported into Mtb by IrtAB.
Quantitative Isothermal Amplification on Paper Membranes using Amplification Nucleation Site Analysis
Authors: Sullivan Benjamin P. , Chou Yu-Shan , Bender Andrew T. , Martin Coleman D. , Kaputa Zoe G. , March Hugh , Song Minyung , Posner Jonathan D.
Published: January 2022

Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3,000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
Long-term Improvement of Air Quality Associated with Lung Function Benefits in Chinese Young Adults: A Quasi-experiment Cohort Study
Authors: Feng Shurong , Miao Jiaming , Wang Minghao , Jiang Ning , Dou Siqi , Yang Liu , Ma Yang , Yu Pei , Ye Tingting , Wu Yao , Wen Bo , Lu Peng , Li Shanshan , Guo Yuming
Published: January 2022

Background: Long-term exposure to air pollution is associated with lung function impairment. However, whether long-term improvements in air quality could improve lung function is unclear.
Methods: We conducted a prospective quasi-experiment cohort study with 1731 college students in Shandong, China from September 2019 to September 2020, covering COVID-19 lockdown period. Data on PM2.5, PM10, NO2 and SO2 concentrations were obtained from China Environmental Monitoring Station. The concentration of O3 was obtained from Tracking Air Pollution in China. Lung function indicators included forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1) and forced expiratory flow at 50% of FVC (FEF50%). Linear mixed-effects model was used to examine the associations between the change of air pollutants’ concentrations and the change of lung functions. We also conducted stratified analysis by sex.
Results: Compared with 2019, the mean FVC, FEV1 and FEF50% were elevated by 414.4ml, 321.5ml, and 28.4ml respectively in 2020. Every 5μg/m3 decrease in annual average PM2.5 concentrations was associated with 36.0ml [95% confidence interval (CI):6.0, 66.0ml], 46.1ml (95% CI:16.7, 75.5ml), and 124.2ml/s (95% CI:69.5, 178.9ml/s) increment in the FVC, FEV1, and FEF50%, respectively. Similar associations were found for PM10. There was no significant effect difference between male and female.
Conclusions: Long-term improvement of air quality can improve lung function among young adults. Stricter policies on improving air quality are needed to protect human health.
Funding: Taishan Scholar Program
Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa
Authors: Davies Mary-Ann , Kassanjee Reshma , Rousseau Petro , Morden Erna , Johnson Leigh , Solomon Wesley , Hsiao Nei-Yuan , Hussey Hannah , Meintjes Graeme , Paleker Masudah , Jacobs Theuns , Raubenheimer Peter , Heekes Alexa , Dane Pierre , Bam Jamy-Lee , Smith Mariette , Preiser Wolfgang , Pienaar David , Mendelson Marc , Naude Jonathan , Schreuder Neshaad , Mnguni Ayanda , Le Roux Susan , Murie Katie , Prozesky Hans , Mahomed Hassan , Rossouw Liezel , Wasserman Sean , Maughan Deborah , Boloko Linda , Smith Barry , Taljaard Jantjie , Symons Greg , Ntusi Ntobeko , Parker Arifa , Wolter Nicole , Jassat Waasila , Cohen Cheryl , Lessells Richard , Wilkinson Robert , Arendse Juanita , Kariem Saadiq , Moodley Melvin , Vallabhjee Krish , Wolmarans Milani , Boulle Andrew
Published: January 2022

Objectives: We aimed to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection, and whether protection against severe disease conferred by prior infection and/or vaccination was maintained.
Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.
Results: We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).
Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25% reduced risk of severe hospitalization or death compared to Delta.
SLC38A2 provides proline to fulfil unique synthetic demands arising during osteoblast differentiation and bone formation
Authors: Shen Leyao , Yu Yilin , Zhou Yunji , Pruett-Miller Shondra M. , Zhang Guo-Fang , Karner Courtney M.
Published: January 2022

Cellular differentiation is associated with the acquisition of a unique protein signature which is essential to attain the ultimate cellular function and activity of the differentiated cell. This is predicted to result in unique biosynthetic demands that arise during differentiation. Using a bioinformatic approach, we discovered osteoblast differentiation is associated with increased demand for the amino acid proline. When compared to other differentiated cells, osteoblast-associated proteins including RUNX2, OSX, OCN and COL1A1 are significantly enriched in proline. Using a genetic and metabolomic approach, we demonstrate that the neutral amino acid transporter SLC38A2 acts cell autonomously to provide proline to facilitate the efficient synthesis of proline-rich osteoblast proteins. Genetic ablation of SLC38A2 in osteoblasts limits both osteoblast differentiation and bone formation in mice. Mechanistically, proline is primarily incorporated into nascent protein with little metabolism observed. Collectively, these data highlight a requirement for proline in fulfilling the unique biosynthetic requirements that arise during osteoblast differentiation and bone formation.
Ontogenetic Color Switching in Lizards as a by-Product of Guanine Cell Development
Authors: Zhang Gan , Yallapragada Venkata Jayasurya , Shemesh Michal , Wagner Avital , Upcher Alexander , Pinkas Iddo , McClelland Harry L.O. , Hawlena Dror , Palmer Benjamin A.
Published: January 2022

Many animals undergo dramatic changes in colour during development1,2. Changes in predation risk during ontogeny are associated with spectacular switches in defensive colours, typically involving the replacement of skin or the production of new pigment cells3. Ontogenetic colour systems are ideal models for understanding the evolution and formation mechanisms of animal colour which remain largely enigmatic2. We show that defensive colour switching in lizards arises by reorganization of a single photonic system, as an incidental by-product of chromatophore maturation. The defensive blue tail colour of hatchling A. beershebensis lizards is produced by light scattering from premature guanine crystals in underdeveloped iridophore cells. Camouflaged adult tail colours emerge upon reorganization of the guanine crystals into a photonic reflector during chromatophore maturation. The substituent guanine crystals form by the attachment of individual nanoscopic plates, which coalesce during growth to form single crystals. Our results show that the blue colour of hatchlings is a fortuitous, but necessary, precursor to the development of adult colour. Striking functional colours in animals can thus arise not as distinct evolutionary innovations but via exploitation of the timing of naturally occurring changes in chromatophore cell development.
Pericentrin is a Kinesin-1 Activator that Drives Centriole Motility
Authors: Hannaford Matthew R. , Liu Rong , Billington Neil , Swider Zachary T. , Galletta Brian J. , Fagerstrom Carey J. , Combs Christian , Sellers James R. , Rusan Nasser M.
Published: January 2022

Centrosome positioning is essential for their function. Typically, centrosomes are transported to various cellular locations through the interaction of centrosome nucleated microtubules with motor proteins. However, it remains unknown how centrioles migrate in cellular contexts in which centrioles do not nucleate microtubules. Here, we demonstrate that during interphase inactive centrioles move directly along the non-centrosomal microtubule network as cargo for the motor protein Kinesin-1. We identify Pericentrin-Like-Protein (PLP) as a novel Kinesin-1 interacting molecule essential for centriole motility. PLP directly interacts with the cargo binding domain of Kinesin-1 and they comigrate on microtubules in vitro. Finally, we demonstrate that PLP-Kinesin-1 dependent transport is essential for centrosome asymmetry age-dependent centrosome inheritance in asymmetric stem cell division.
Guide RNA acrobatics: the one-for-two shuffle
Authors: Meier U. Thomas
Published: January 2022

RNA modifications are crucial for the proper function of the RNAs. The sites of pseudouridines are often specified by dual hairpin guide RNAs, with one or both hairpins identifying a target uridine. In this issue ofGenes & Development, Jády and colleagues (pp. 70–83) identify a novel mechanism by which a single guide RNA hairpin can specify two uridines adjacent to each other or separated by 1 nt; i.e., one for two or guide RNA acrobatics.
Coupling crossover and synaptonemal complex in meiosis
Authors: Grey Corinne , de Massy Bernard
Published: January 2022

During meiosis, a molecular program induces DNA double-strand breaks (DSBs) and their repair by homologous recombination. DSBs can be repaired with or without crossovers. ZMM proteins promote the repair toward crossover. The sites of DSB repair are also sites where the axes of homologous chromosomes are juxtaposed and stabilized, and where a structure called the synaptonemal complex initiates, providing further regulation of both DSB formation and repair. How crossover formation and synapsis initiation are linked has remained unknown. The study by Pyatnitskaya and colleagues (pp. 53–69) in this issue ofGenes & Developmenthighlights the central role of theSaccharomyces cerevisiaeZMM protein Zip4 in this process.