bluuebunny/crossref_metadata_2025 huggingface dataset:
Efferent projections ofNps-expressing neurons in the parabrachial region
Authors: Zhang Richie , Huang Dake , Gasparini Silvia , Geerling Joel C.
Published: August 2023

In the brain, connectivity determines function. Neurons in the parabrachial nucleus (PB) relay diverse information to widespread brain regions, but the connections and functions of PB neurons that expressNps(neuropeptide S) remain mysterious. Here, we use Cre-dependent anterograde tracing and whole-brain analysis to map their output connections. While many other PB neurons project ascending axons through the central tegmental tract, NPS axons reach the forebrain via distinct periventricular and ventral pathways. Along the periventricular pathway, NPS axons target the tectal longitudinal column and periaqueductal gray then continue rostrally to target the paraventricular nucleus of the thalamus. Along the ventral pathway, NPS axons blanket much of the hypothalamus but avoid the ventromedial and mammillary nuclei. They also project prominently to the ventral bed nucleus of the stria terminalis, A13 cell group, and magnocellular subparafasciular nucleus. In the hindbrain, NPS axons have fewer descending projections, targeting primarily the superior salivatory nucleus, nucleus of the lateral lemniscus, and periolivary region. Combined with what is known about NPS and its receptor, the output pattern ofNps-expressing neurons in the PB region predicts a role in threat response and circadian behavior.
Uncovering the lung cancer mechanisms through the chromosome structural ensemble characteristics
Authors: Chu Wen-Ting , Wang Jin
Published: August 2023

Lung cancer is one of the most common cancers in human. However, it is still lack of understanding the mechanisms of a normal cell developing to the cancer cell. Here we develop the chromosome dynamic structural model and quantify the important characteristics of the chromosome structural ensemble of the normal lung cell and the lung cancer A549 cell. Our results demonstrate the essential relationship among the chromosome ensemble, the epigenetic marks, and the gene expressions, which suggests the linkage between chromosome structure and function. The analysis reveals that the lung cancer cell may have higher level of relative ensemble fluctuation as well as higher degree of the phase separation between the two compartments than the normal lung cells. In addition, the significant conformational“switching off”events (from compartment A to B) are more than the significant conformational“switching on”events during the lung cancerization. The kinetic lung cancerization pathway is not the same as the reversion pathway by characterizing the hot spots and interaction networks of the lung cancer transitions. These investigations have revealed the cell fate determination mechanism of the lung cancer process, which will be helpful for the further prevention and control of cancers.
Early spiral arteriole remodeling in the uterine-placental interface: a rat model
Authors: Bacon Sarah J. , Zhu Yuxi , Ghosh Priyanjali
Published: August 2023

The mammalian placenta’s interface with the parent is a richly vascularized tissue whose development relies upon communication between many different cell types within the uterine microenvironment. The uterine blood vessels of the interface are reshaped during pregnancy into wide-bore, flaccid vessels that convey parental blood to the exchange region of the placenta. Fetally-derived invasive trophoblast as well as parental uterine macrophages and Natural Killer cells are involved in the stepwise remodeling of these vessels and their respective contributions to this crucial process are still being delineated. However, the earliest steps in arteriole remodeling are understudied as they are difficult to study in humans, and other species lack the deep trophoblast invasion that is so prominent a feature of placentation in humans. Here, we establish the rat, with deep hemochorial placentation akin to humans, as a model system in which to tease apart the earliest, relatively understudied events in spiral arteriole remodeling. We show that the rat uterine placental interface increases in size and vascularity rapidly, before trophoblast invasion. The remodeling stages in the arterioles of the rat uterine-placental interface follow a sequence of anatomical changes similar to those in humans, and there are changes to the arterioles’ muscular tunica media prior to the marked influx of immune cells. The rat is a tractable model in which to better understand the cell/cell interactions occurring in vivo in an intact tissue microenvironment over time.
Water diviners multiplied: cryptic diversity in theNiphargus aquilexspecies complex in Northern Europe
Authors: Weber Dieter , Brad Traian , Weigand Alexander , Flot Jean-François
Published: August 2023

As for many other groups, patterns of biodiversity for subter-ranean crustaceans in Europe indicate larger morphospecies ranges at higher latitudes (the so-called Rapoport effect). However, this observed correlation may be artefactual if many of those high-latitude, widely distributed morphospecies are actually species complexes. To test this hypothesis, we looked for previously undetected species boundaries withinNiphargus aquilexandNiphargus schellenbergi, two closely related morphospecies of groundwater amphipods widely distributed in northern Europe, by sequencing fragments of the mitochondrial cytochromecoxidase subunit I gene (COI) and of the nuclear 28S ribosomal RNA gene of 198 individuals collected across their area of distribution. Distance-based and allele sharing-based species delimitation approaches were congruent in revealing the existence of at least eight species withinN. aquilexand at least two species withN. schellenbergi. Our data demonstrate that these two common morphospecies with large ranges are actually complexes of species with narrower distributions, suggesting that the Rapoport effect might be the result of increased morphological stasis at high latitudes rather than actual differences in sizes of distribution ranges.
SARS-CoV-2 Neutralizing Antibodies Following a Second BA.5 Bivalent Booster
Authors: Wang Qian , Bowen Anthony , Ho Jerren , Zhang Richard , Valdez Riccardo , Stoneman Emily , Gordon Aubree , Liu Lihong , Ho David D.
Published: August 2023

Bivalent COVID-19 mRNA vaccines expressing both the ancestral D614G and Omicron BA.5 spike proteins were introduced in August 2022 with the goal of broadening immunity to emerging SARS-CoV-2 Omicron subvariants. Subsequent studies on bivalent boosters found neutralizing antibody responses similar to boosters with the original monovalent vaccine, likely the result of immunological imprinting. Guidelines allow for administration of a second bivalent booster in high-risk groups, but it remains unknown whether this would broaden antibody responses. To address this question, we assessed longitudinal serum SARS-CoV-2-neutralizing titers in 18 elderly immunocompetent individuals (mean age 69) following a fourth monovalent booster and two BA.5 bivalent booster vaccines using pseudovirus neutralization assays against D614G, Omicron BA.5, and Omicron XBB.1.5. There was a small but significant increase in peak neutralizing antibody responses against Omicron BA.5 and XBB.1.5 following the first bivalent booster, but no significant increase in peak titers following the second bivalent booster. Omicron-specific neutralizing titers remained low after both doses of the BA.5 bivalent booster. Our results suggest that a second dose of the BA.5 bivalent booster is not sufficient to broaden antibody responses and to overcome immunological imprinting. A monovalent vaccine targeting only the spike of the recently dominant SARS-CoV-2 may mitigate the “back boosting” associated with the “original antigenic sin.”
The Spatial Patterns and Determinants of Cerebrospinal Fluid Circulation in the Human Brain
Authors: Nazeri Arash , Dehkharghanian Taher , Lindsay Kevin E. , LaMontagne Pamela , Shimony Joshua S. , Benzinger Tammie L.S. , Sotiras Aristeidis
Published: August 2023

The circulation of cerebrospinal fluid (CSF) is essential for maintaining brain homeostasis and clearance, and impairments in its flow can lead to various brain disorders. Recent studies have shown that CSF circulation can be interrogated using low b-value diffusion magnetic resonance imaging (low-bdMRI). Nevertheless, the spatial organization of intracranial CSF flow dynamics remains largely elusive. Here, we developed a whole-brain voxel-based analysis framework, termed CSF pseudo-diffusion spatial statistics (CΨSS), to examine CSF mean pseudo-diffusivity (MΨ), a measure of CSF flow magnitude derived fromlow-bdMRI. We showed that intracranial CSF MΨ demonstrates characteristic covariance patterns by employing seed-based correlation analysis. Importantly, we applied non-negative matrix factorization analysis to further elucidate the covariance patterns of CSF MΨ in a hypothesis-free, data-driven way. We identified distinct CSF spaces that consistently displayed unique pseudo-diffusion characteristics across multiple imaging datasets. Our study revealed that age, sex, brain atrophy, ventricular anatomy, and cerebral perfusion differentially influence MΨ across these CSF spaces. Notably, individuals with anomalous CSF flow patterns displayed incidental findings on multimodal neuroradiological examinations. Our work sets forth a new paradigm to study CSF flow, with potential applications in clinical settings.
Fitting a square beam in a square camera: novel condenser apertures for low-dose transmission electron microscopy
Authors: Brown Hamish G. , Smith Dan , Wardle Benjamin C. , Hanssen Eric
Published: August 2023

In transmission electron microscopy (TEM) cameras are square or rectangular but beams are round. With a beam size chosen to fill the camera at a given image magnification, the circular lobes of the beam will extend beyond the camera’s field of view and irradiate areas that are not acquired on the camera, damaging and precluding them from future acquisitions if the sample is beam sensitive. In this paper we present development of condenser aperture plates for TEM that have square and rectangular apertures which improve the efficiency of sample area usage by 44% or greater in low dose TEM applications. We demonstrate that the use of these apertures is compatible with high-resolution cryogenic (cryo) TEM by reconstructing sub 2 Å apo-ferritin models from a datasets recorded with both square and rectangular apertures. Moreover the design of our aperture plates should improve the flexibility of 2 condenser systems for cryo-TEM acquisitions with multiple shots per hole by tailored matching of beam sizes to camera sizes at each magnification.
Evolutionary conservation of secondary structures in the lncRNAs of plants
Authors: Corona-Gomez Jose Antonio , Stadler Peter F. , Fernandez-Valverde Selene L.
Published: August 2023

LncRNAs are essential regulators of eukaryotic gene expression. They exert their gene regulatory functions by interacting with DNA, RNA, and protein. These functions are considered at least in part associated with their capacity to fold into complex three-dimensional structures. The conservation of lncRNA structure in mammalian genomes has been assessed in several studies, however, very little is known about the conservation of lncRNA structures in plants. Here, we analyze the structural conservation of lncRNAs inBrassicaceae, using a whole genome alignment of 16Brassicaceaespecies. We found that 44.2% (1925 of 4354) of the intergenic lncRNAs (lincRNAs) and 75.1% (1549 of 2060) of the natural antisense transcripts (NATs) ofArabidopsis thalianahave conserved structural motifs in at least 2 of the 16 species. Also, 3612 lncRNAs have conserved structural motifs in multiple species; 2264 of which are tissue-specific, and 841 can be associated with a function by a co-expression network inA. thaliana. Indeed, we find evidence for the conservation of structural motifs in several lncRNAs with known functions, including,lncCOBRA1, FLORE, IPS1, ELENA1andCOOLAIR.The latter was shown previously to have a conserved structure. Overall, we have identified numerous lncRNAs with conserved structures inBrassicaceaethat warrant further experimental explorationin vivoto understand whether these lncRNAs and their conserved structures are of biological significance.
Inbreeding or outbreeding depression? How to manage an endangered and locally adapted population of red grouseLagopus scotica
Authors: Walsh Grace , McMahon Barry J. , Thörn Filip , Rödin-Mörch Patrik , Irestedt Martin , Höglund Jacob
Published: August 2023

The balance between the inbreeding and outbreeding continuum is a fundamental debate within conservation genomics. To inform this debate we use genome wide data to show that inbreeding is higher in Irish red grouse (Lagopus scotica) and that this smaller and isolated population exhibits divergence from the British. Outlier analysis identified divergence in several genomic regions linked to genes coding for ecologically important traits such as phenotypic differences in plumage colour and sequence divergence among coding regions in the melanin pathway. We also find differences among immune genes and loci involved in food intake and energy control. The two populations thus appear locally adapted. Divergence between the source and the target population when used for conservation aided restocking may have negative consequences if locally adapted alleles are swamped and/or maladapted genotypes are introduced, leading to outbreeding depression. While avoiding inbreeding by maintaining large populations is important, our study illustrates that conservationists and managers should also consider population divergence and local adaptation. We argue against translocations among Ireland and Britain as a conservation strategy. The results of our study demonstrate the value of focusing on local populations and habitat management when aiming to enhance the conservation status of specific species.
An ancestral dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes
Authors: Silale Augustinas , Zhu Yiling , Witwinowski Jerzy , Smith Robert E. , Newman Kahlan E. , Bhamidimarri Satya P. , Baslé Arnaud , Khalid Syma , Beloin Christophe , Gribaldo Simonetta , Berg Bert van den
Published: August 2023

The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan (PG) for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria group lack well-characterised OM attachment systems such as Braun’s lipoprotein, Pal and OmpA, but instead have the OmpM protein. OmpM has a periplasmic region containing an S-layer homology domain and a β-barrel region that is embedded in the OM. Here, we have determined the structure of the most abundant OmpM protein from the diderm firmicuteVeillonella parvulaby single particle cryogenic electron microscopy (cryo-EM). We reveal an OM portion similar to well-characterised trimeric general porins and a mobile periplasmic PG-binding region. Combining the cryo-EM data with crystal structures, structure predictions and molecular dynamics simulations, we show that the periplasmic region of OmpM likely adopts multiple conformations. Single-channel electrophysiology demonstrates ion conductance properties similar toE. coliOmpF. Finally, we demonstrate via functional assays that the four OmpM paralogues are likely to be the only general porins inV. parvula. Together, our results show that OM tethering and nutrient acquisition are genetically linked inV. parvula(and other diderm Firmicutes), suggesting that concurrent loss of two key OM-related functions, tethering and nutrient uptake, promoted the multiple OM loss events that have been inferred in the Terrabacteria.
Targeting adipocyte ESRRA promotes osteogenesis and vascular formation in adipocyte-rich bone marrow
Authors: Huang Tongling , Lu Zhaocheng , Wang Zihui , Cheng Lixin , Gao Lu , Gao Jun , Zhang Ning , Geng Chang-An , Zhao Xiaoli , Wang Huaiyu , Wong Chi-Wai , Yeung Kelvin W K , Pan Haobo , Lu William Weijia , Guan Min
Published: August 2023

Ectopic bone marrow adipocytes (BMAds) accumulation occurring under diverse pathophysiological conditions leads to bone deterioration. Estrogen-related receptor α (ESRRA) is a key regulator responding to metabolic stress. Here, we show that adipocyte-specific ESRRA deficiency rescues osteogenesis and vascular formation in adipocyte-rich bone marrow due to estrogen deficiency or obesity. Mechanistically, adipocyte ESRRA interferes with E2/ESR1 signaling resulting in transcriptional repression of secreted phosphoprotein 1 (Spp1); and positively modulatesLeptinexpression by binding to its promoter. ESRRA abrogation results in enhanced SPP1 and decreased LEPTIN secretion from both visceral adipocytes and BMAds, concertedly dictating bone marrow stromal stem cell fate commitment and restoring type H vessel formation, constituting a feed-forward loop for bone formation. Pharmacological inhibition of ESRRA protects obese mice against bone loss and high marrow adiposity. Thus, our findings highlight a therapeutic approach via targeting adipocyte ESRRA to preserve bone formation especially in detrimental adipocyte-rich bone milieu.

Graphic abstract
Detecting inbreeding depression in structured populations
Authors: Lavanchy Eléonore , Weir Bruce S. , Goudet Jérôme
Published: August 2023

Measuring inbreeding as well as its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the most appropriate method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. In this project, we simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structure (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients (F) to quantify the strength of inbreeding depression: allele sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model including a genetic relatedness matrix (GRM) as random effect to account for the non-independence of observations. We find linear mixed models give better results in scenarios with population or family structure. Within the mixed models, we compare three different GRM matrices and show that in homogeneous populations, there is little difference among the differentFand GRM for inbreeding depression quantification. However, as soon as strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if (i) the phenotypes are regressed on inbreeding coefficient based on a weighted version of the correlation of uniting gametes, which gives more weight to common alleles and (ii) with the GRM obtained from an allele sharing relatedness estimator.
Effects of combined exposure to ethanol and delta-9-tetrahydrocannabinol during adolescence on synaptic plasticity in the prefrontal cortex of Long Evans rats
Authors: Shi Linyuan , Kang Shuo , Choi Chan Young , Noonan Brynn L. , Carrica Lauren K. , Liang Nu-Chu , Gulley Joshua M.
Published: August 2023

Significant exposure to alcohol or cannabis during adolescence can induce lasting disruptions of neuronal signaling in brain regions that are later to mature, such as the medial prefrontal cortex (mPFC). Considerably less is known about the effects of alcohol and cannabis co-use, despite its common occurrence. Here, we used male and female Long-Evans rats to investigate the effects of early-life exposure to ethanol, delta-9-tetrahydrocannabinol (THC), or their combination on high frequency stimulation (HFS)-induced plasticity in the prelimbic region of the mPFC. Animals were injected daily from postnatal days 30 to 45 with vehicle or THC (escalating doses, 3-20 mg/kg) and allowed to drink vehicle (0.1% saccharin) or 10% ethanol immediately after each injection.In vitrobrain slice electrophysiology was then used to record population responses of layer V neurons following HFS in layer II/III after 3-4 weeks of abstinence. We found that THC exposure reduced body weight gains observed inad libitumfed rats, and reduced intake of saccharin and ethanol. Compared to controls, there was a significant reduction in HFS-induced long-term depression (LTD) in rats exposed to either drug alone, and an absence of LTD in rats exposed to the drug combination. Bath application of indiplon or AR-A014418, which enhance GABAAreceptor function or inhibit glycogen synthase kinase 3β (GSK3β), respectively, suggested the effects of ethanol, THC or their combination were due in part to lasting adaptations in GABA and GSK3β signaling. These results suggest the potential for long-lasting adaptations in mPFC output following co-exposure to alcohol and THC.
Soft rot pathogenDickeya dadantii3937 produces tailocins resembling the tails ofEnterobacteriabacteriophage P2
Authors: Borowicz Marcin , Krzyżanowska Dorota M. , Narajczyk Magdalena , Sobolewska Marta , Rajewska Magdalena , Czaplewska Paulina , Węgrzyn Katarzyna , Czajkowski Robert
Published: August 2023

Tailocins are nanomolecular machines with bactericidal activity. They are produced by bacteria to contribute to fitness in mixed communities, and hence, they play a critical role in their ecology in a variety of habitats. Here, we characterized the new tailocin produced byDickeya dadantiistrain 3937, a well-characterized member of plant pathogenic Soft RotPectobacteriaceae(SRP). Tailocins induced inD. dadantiiwere ca. 166 nm long tubes surrounded by contractive sheaths with baseplates having tail fibers at one end. A 22-kb genomic cluster involved in their synthesis and having high homology to the cluster coding for the tail of the Enterobacteriophage P2 was identified. TheD. dadantiitailocins, termed dickeyocin P2D1 (phage P2-like dickeyocin 1), were resistant to inactivation by pH (3.5 – 12), temperature (4 – 50 °C), and elevated osmolarity (NaCl concentration: 0.01 – 1 M). P2D1 could kill a variety of differentDickeyaspp. but not any strain ofPectobacteriumspp. tested and were not toxic toCaenorhabditis elegans.

Teaser

Tailocins are nanomolecular entities similar to syringes that are produced by various bacteria to fight other microorganisms present in the same environment.
An actor-model framework for visual sensory encoding
Authors: Leong Franklin , Rahmani Babak , Psaltis Demetri , Moser Christophe , Ghezzi Diego
Published: August 2023

A fundamental challenge in neuroengineering is determining a proper input to a sensory system that yields the desired functional output. In neuroprosthetics, this process is known as sensory encoding, and it holds a crucial role in prosthetic devices restoring sensory perception in individuals with disabilities. For example, in visual prostheses, one key aspect of image encoding is to down-sample the images captured by a camera to a size matching the number of inputs and resolution of the prosthesis. Here, we show that down-sampling an image using the inherent computation of the retinal network yields better performance compared to a learning-free down-sampling encoding. We validated a learning-based approach (actor-model framework) that exploits the signal transformation from photoreceptors to retinal ganglion cells measured in explanted retinas. The actor-model framework generates down-sampled images eliciting a neuronal response in-silico and ex-vivo with higher neuronal reliability to the one produced by original images compared to a learning-free approach (i.e. pixel averaging). In addition, the actor-model learned that contrast is a crucial feature for effective down-sampling. This methodological approach could serve as a template for future image encoding strategies. Ultimately, it can be exploited to improve encoding strategies in visual prostheses or other sensory prostheses such as cochlear or limb.
Gene editing in the Chagas disease vectorRhodnius prolixusby Cas9-mediated ReMOT Control
Authors: Lima Leonardo , Berni Mateus , Mota Jamile , Bressan Daniel , Julio Alison , Cavalcante Robson , Macias Vanessa , Li Zhiqian , Rasgon Jason L. , Bier Ethan , Araujo Helena
Published: August 2023

Rhodnius prolixusis currently the model vector of choice for studying Chagas disease transmission, a debilitating disease caused byTrypanosoma cruziparasites. Despite the broad use of double-stranded RNA interference for the knockdown of gene function inR. prolixus, transgenesis and gene editing protocols are still lacking. Here we tested Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) and direct parental injection of CRISPR (DIPA-CRISPR) for the maternal delivery of CRISPR/Cas9 elements to developingR. prolixusoocytes, and strategies for the identification of insertions/deletions (indels) in target loci of resulting gene-edited G0 nymphs. We demonstrate successful ReMOT Control-mediated gene editing of the eye color markersRp-scarletandRp-white, and the cuticle color markerRp-yellow,with highest effectiveness obtained using the ovary-targeting BtKV ligand. These results provide proof-of-concepts for generating somatic mutations inR. prolixusand potentially for generating germline edited lines in triatomines. Our studies also suggest that optimal strategies for recovery of mutations include performing multiple gRNA injections and the use of visible phenotypes such as those displayed in theRp-scarlet, Rp-whiteandRp-yellowloci for future Co-CRISPR experiments. These results will lay the foundation for gene editing protocols for triatomines and could lead to the development of novel control strategies for vectors of Chagas disease.

Author Summary

Rhodnius prolixusis an insect vector of the protozoanTrypanossoma cruzi, causative agent of debilitating Chagas disease. To fight the spread of the disease, it has been suggested that biological control of the insect should be attempted. Gene editing by the novel CRISPR methodology holds great promise in this sense, as it enables to target almost any gene in the genome for mutagenesis, thus allowing the control of insect physiology and reproduction. Here we have tested protocols for the delivery of CRISPR reagents as an attempt to enable genome editing of the vector. Our results show that maternal delivery of CRISPR by the ReMOT Control method is efficient for mutating eye and cuticle color genes in the resulting nymphs, generating edited animals with red eyes, white eyes or a yellow cuticle. This is the first report of gene editing in a vector of Chagas disease and should lay the basis to produce modified animals either unable to carry theT. cruziparasite or to reproduce.
Combination Treatment to Improve Mucociliary Transport ofPseudomonas aeruginosaBiofilms
Authors: Rouillard Kaitlyn R. , Esther Christopher P. , Kissner William J. , Plott Lucas M. , Bowman Dean W. , Markovetz Matthew R. , Hill David B.
Published: August 2023

People with muco-obstructive pulmonary diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) often have acute or chronic respiratory infections that are difficult to treat due in part to the accumulation of hyperconcentrated mucus within the airway. Mucus accumulation and obstruction promote chronic inflammation and infection and reduce therapeutic efficacy. Bacterial aggregates in the form of biofilms exhibit increased resistance to mechanical stressors from the immune response (e.g., phagocytosis) and chemical treatments including antibiotics. Herein, combination treatments designed to disrupt the mechanical properties of biofilms and potentiate antibiotic efficacy are investigated against mucus-grownPseudomonas aeruginosabiofilms and optimized to 1) alter biofilm viscoelastic properties, 2) increase mucociliary transport rates, and 3) reduce bacterial viability. A disulfide bond reducing agent (tris(2-carboxyethyl)phosphine, TCEP), a surfactant (NP40), a biopolymer (hyaluronic acid, HA), a DNA degradation enzyme (DNase), and an antibiotic (tobramycin) are tested in various combinations to maximize biofilm disruption. The viscoelastic properties of biofilms are quantified with particle tracking microrheology and transport rates are quantified in a mucociliary transport device comprised of fully differentiated primary human bronchial epithelial cells. The combination of the NP40 with hyaluronic acid and tobramycin was the most effective at increasing mucociliary transport rates, decreasing the viscoelastic properties of mucus, and reducing bacterial viability. Multimechanistic targeting of biofilm infections may ultimately result in improved clinical outcomes, and the results of this study may be translated into future in vivo infection models.

Author Summary

One of the major challenges associated with chronic respiratory infections in cystic fibrosis and chronic obstructive pulmonary disease is difficult to treat biofilms that form in hyperconcentrated mucus. Biofilms are mechanically robust due to an exterior polymeric matrix that protects from the immune response and antibiotics. Antibiotics like tobramycin alone have little impact on the biofilm matrix, but disruption of viscous mucus and the biofilm architecture has previously been shown to improve antibiotic efficacy. Combination treatments must be used to break up mucus and biofilms and simultaneously kill bacteria. The most promising combination in this study includes the surfactant NP40, the biopolymer hyaluronic acid, and the antibiotic tobramycin which together decreased biofilm viscosity, reduced bacterial load, and increased mucociliary transport rates. The results from this study may be translated to an infected animal study for eventual clinical trials.
Proteogenomic characterization reveals antitumor mechanisms of intrahepatic cholangiocarcinoma
Authors: Wang Weibing , Xu Shifeng
Published: August 2023

Diagnosing and managing intrahepatic cholangiocarcinoma (iCCA) poses a significant oncological hurdle as it is a deadly form of liver cancer.A significant role is played by nonapoptotic regulatory cell death (NRCD) in the tumor immune microenvironment (TME) of iCCA. Nevertheless, the precise functions of NRCD-associated genes (NRGs) in the tumor microenvironment (TME) are still not well understood. Transcriptomics, proteomic analysis, and single-cell RNA analysis were utilized to distinguish two NRG-related clusters in iCCA patients from the FU-iCCA cohort in this study. We have shown the clear disparities in immune traits and predictive categorization among two groups. To address the risk stratification and prognosis prediction, a prognostic signature model called NPS (NRG-related risks core prognostic signature model) was created using the FU-iCCA cohort. The validation of the NRG-associated risk score in prognosis and immunotherapy confirmed its predictive capabilities. In iCCA patients with high-risk, the secretion of CP and TGF-β proteins strengthened the enriched TGF-β signaling network between CD4+ T cells and erythroid cells. Patients exhibiting a low-risk score demonstrated improvement in the effector function of CD4+ T cells, resulting in a more favorable reaction to chemotherapy medications. The NPS-risk score showed a significant negative correlation with the IC50 values of four drugs (Trametinib, CI-1040, X17-ACC, and PD-0325901). From these findings, it can be inferred that a clear connection exists between the NRG and the TME in iCCA. Additionally, the risk score has the potential to act as a reliable prognostic indicator, offering advantageous outcomes for chemotherapy and immunotherapy. This could aid in making informed clinical decisions for patients with iCCA.
Effect of foot position during plantarflexion on the neural drive to thegastrocnemiiin runners with Achilles tendinopathy
Authors: Fernandes Gabriel L. , Orssatto Lucas B. R. , Shield Anthony J. , Trajano Gabriel S.
Published: August 2023

Runners with Achilles tendinopathy (AT) have reduced neural drive to thegastrocnemius lateralis(GL). This study investigated if the strategy of pointing feet-inward (feet-in) during isometric plantarflexion would increasegastrocnemius lateraliselectromyography root mean square amplitude (RMS) and motor unit discharge rates, compared to feet-in neutral position (feet-neutral), in runners with Achilles Tendinopathy (AT). High-density electromyograms were recorded fromgastrocnemius lateralisandmedialis, during 20-sfeet-inandfeet-neutralisometric heel raise, in runners with (n=18) and without (n=19) AT. Duringfeet-in, GL RMS was higher duringfeet-inin both groups and GM RMS was lower only duringfeet-inin the AT. Conversely, motor unit discharge rates were lower duringfeet-inin GL (p<0.001) and in GM in the AT group. The AT group had lowertriceps suraeendurance during single leg heel raise. In summary,feet-inincreases GL RMS in both groups, conversely reducing motor unit discharge rates in the AT group, compared tofeet-neutral. Additionally,feet-inreduces GM RMS and motor unit discharge rates only in the AT group, compared tofeet-neutral. This would shift thegastrocnemius lateralis/medialisratio excitation, favouringgastrocnemius lateralis. Nonetheless, while this strategy holds promise, it remains uncertain whether performing plantarflexion exercise with feet pointed inwards would provide additional benefits for the treatment of runners with Achilles tendinopathy. Our findings suggest that the increased GL RMS duringfeet-inis effective in increasing GL excitation but not as consequence of increased MUDR and, but it might be a result of recruitment of more motor units.
CD61 identifies a superior population of aged murine hematopoietic stem cells and is required to preserve quiescence and self-renewal
Authors: Skinder Natalia , Fernández Irene Sanz , Dethmers-Ausema Albertien , Weersing Ellen , de Haan Gerald
Published: August 2023

Aging leads to a decline in function of hematopoietic stem cells (HSCs) and increases susceptibility to hematological disease. We found CD61 to be highly expressed in aged HSCs. Here we investigate the role of CD61 in identifying distinct subpopulations of aged HSCs and assess how expression of CD61 affects stem cell function. We show that HSCs with high expression of CD61 are functionality superior and retain self-renewal capacity in serial transplantations. A population of aged HSCs with highest CD61 expression is functionally comparable to young HSCs. These CD61HighHSCs display a notably higher quiescence compared to their CD61Lowcounterparts. We also show that CD61Highand CD61LowHSCs are transcriptomically distinct populations within aged HSCs. Collectively, our research identifies CD61 as a key player in maintaining stem cell quiescence during aging, ensuring the preservation of their functional integrity and potential. Moreover, CD61 emerges as a marker to prospectively isolate a superior, highly dormant population of young and aged HSCs, making it a valuable tool both in fundamental and clinical research.

Highlights

CD61 expression marks a functionally superior population of long-term hematopoietic stem cells and plays a pivotal role in the maintenance of aged LT-HSCs by regulating their dormancy

Aged LT-HSCs with high expression of CD61 are functionally comparable to their young counterparts
Pairing interacting protein sequences using masked language modeling
Authors: Lupo Umberto , Sgarbossa Damiano , Bitbol Anne-Florence
Published: August 2023

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids within protein chains. It also captures inter-chain coevolution, despite being trained on single-chain data. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. Starting from sequences paired by DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer. It also achieves competitive performance with using orthology-based pairing.

Significance statement

Deep learning has brought major advances to the analysis of biological sequences. Self-supervised models, based on approaches from natural language processing and trained on large ensembles of protein sequences, efficiently learn statistical dependence in this data. This includes coevolution patterns between structurally or functionally coupled amino acids, which allows them to capture structural contacts. We propose a method to pair interacting protein sequences which leverages the power of a protein language model trained on multiple sequence alignments. Our method performs well for small datasets that are challenging for existing methods. It can improve structure prediction of protein complexes by supervised methods, which remains more challenging than that of single-chain proteins.
Cigarette smoking promotes the spread of antimicrobial resistance in the human lung and the environment
Authors: Fang Peiju , Konyali Diala , Fischer Emily , Mayer Robin Pascal , Huang Jin , Elena Alan Xavier , Orzechowski Gerit Hartmut , Tony-Odigie Andrew , Kneis David , Dalpke Alexander , Krebs Peter , Li Bing , Berendonk Thomas U. , Klümper Uli
Published: August 2023

While immediate health risks of cigarette smoking are well-established, indirect health impacts of cigarette-derived pollutants through proliferation of antimicrobial resistance (AMR) among bacteria remain understudied. Here, exposure to cigarette smoke condensate at relevant concentrations resulted in >2-fold elevated transfer rates of a multi-drug-resistance encoding plasmid betweenPseudomonasstrains in artificial lung sputum medium. This effect was connected to elevated reactive oxygen species production as part of the bacterial stress response when exposed to cigarette-derived toxicants. Similar results were obtained under exposure to cigarette ash leachate in environmental medium. Further, used cigarette filters enriched in toxic residues were submerged in a wastewater stream, and colonized by altered microbial communities compared to unused filters. These communities were significantly enriched in pathogens and AMR. Hence, filters could facilitate hitchhiking of high-risk bacteria to novel environments. We demonstrate that cigarette-derived compounds can promote the spread of AMR within the human lung and natural environments.
Met58 and di-acidic motif located at C-terminal region of SARS-CoV-2 ORF6 plays a crucial role in its structural conformations
Authors: Kumar Prateek , Saumya Kumar Udit , Bhardwaj Taniya , Giri Rajanish
Published: August 2023

Despite being mostly neglected in structural biology, the C-terminal Regions (CTRs) are studied to be multifunctional in humans as well as in viruses. Their role in cellular processes such as trafficking, protein-protein interactions, and protein-lipid interactions are known due to their structural properties. In our previous findings on SARS-CoV-2 Spike and NSP1 proteins, the C-terminal regions (CTRs) are observed to be disordered and experimental evidence showed a gain of structure properties in different physiological environments. In this line, we have investigated the structural dynamics of CTR (residues 38-61) of SARS-CoV-2 ORF6 protein, disrupting bidirectional transport between the nucleus and cytoplasm. Like Spike and NSP1-CTR, the ORF6-CTR is also disordered in nature but possesses gain of structure properties in minimal physiological conditions. As per studies, the residue such as Methionine at 58thposition in ORF6 is critical for interaction with Rae1-Nup98. Therefore, along with M58, we have identified a few other mutations from the literature and performed extensive structure modelling and dynamics studies using computational simulations. The exciting revelations in CTR models provide evidence of its structural flexibility and possible capabilities to perform multifunctionality inside the host.
GalNAc-siRNA Mediated Knockdown of Ketohexokinase Versus Systemic, Small Molecule Inhibition of its Kinase Activity Exert Divergent Effects on Hepatic Metabolism in Mice on a HFD
Authors: Park Se-Hyung , Fadhul Taghreed , Conroy Lindsey R. , Clarke Harrison , Sun Ramon C. , Wallenius Kristina , Boucher Jeremie , O’Mahony Gavin , Boianelli Alessandro , Persson Marie , Martinez Genesee J. , Hinds Terry D. , Divanovic Senad , Softic Samir
Published: August 2023

Consumption of diets high in sugar and fat are well-established risk factors for the development of obesity and its metabolic complications, including non-alcoholic fatty liver disease. Metabolic dysfunction associated with sugar intake is dependent on fructose metabolism via ketohexokinase (KHK). Here, we compared the effects of systemic, small molecule inhibition of KHK enzymatic activity to hepatocyte-specific, GalNAc-siRNA mediated knockdown of KHK in mice on a HFD. Both modalities led to an improvement in liver steatosis, however, via substantially different mechanisms. KHK knockdown profoundly decreased lipogenesis, while the inhibitor increased the fatty acid oxidation pathway. Moreover, hepatocyte-specific KHK knockdown completely prevented hepatic fructose metabolism and improved glucose tolerance. Conversely, KHK inhibitor only partially reduced fructose metabolism, but it also decreased downstream triokinase. This led to the accumulation of fructose-1 phosphate, resulting in glycogen accumulation, hepatomegaly, and impaired glucose tolerance. In summary, KHK profoundly impacts hepatic metabolism, likely via both kinase-dependent and independent mechanisms.

HIGHLIGHTS

KHK knockdown or inhibition of its kinase activity differently target hepatic metabolism.

KHK inhibitor increases F1P and glycogen accumulation as it also lowers triokinase.

KHK knockdown completely prevents hepatic fructose metabolism and lipogenesis.

E of wild type, but not mutant, kinase dead KHK-C increases glycogen accumulation.
Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression
Authors: Gamage Hashni Epa Vidana , Shahoei Sayyed Hamed , Albright Samuel T. , Wang Yu , Smith Amanda J. , Farmer Rachel , Fink Emma C. , Jacquin Elise , Weisser Erin , Bautista Rafael O. , Henn Madeline A. , Schane Claire P. , Nelczyk Adam T. , Ma Liqian , Gupta Anasuya Das , Bendre Shruti V. , Nguyen Tiffany , Tiwari Srishti , Krawczynska Natalia , He Sisi , Tjoanda Evelyn , Chen Hong , Sverdlov Maria , Gann Peter H. , Boidot Romain , Vegran Frederique , Fanning Sean W. , Apetoh Lionel , Hergenrother Paul J. , Nelson Erik R.
Published: August 2023

Immune checkpoint blockade (ICB) has revolutionized cancer therapy but has had limited utility in several solid tumors such as breast cancer, a major cause of cancer-related mortality in women. Therefore, there is considerable interest in alternate strategies to promote an anti-cancer immune response. We demonstrate that NR0B2, a protein involved in cholesterol homeostasis, functions within myeloid immune cells to modulate the NLRP3 inflammasome and reduce the expansion of immune-suppressive regulatory T cells (Treg). Loss of NR0B2 increased mammary tumor growth and metastasis. Small molecule agonists, including one developed here, reduced Tregexpansion, reduced metastatic growth and improved the efficacy of ICB. This work identifies NR0B2 as a target to re-educate myeloid immune cells providing proof-of-principle that this cholesterol-homeostasis axis may have utility in enhancing ICB.

Brief Summary

Immune therapy has been disappointing for breast cancer. NR0B2 within myeloid immune cells reduces the expansion of Tregs, a highly immune suppressive subtype historically challenging to target. NR0B2 within myeloid immune cells represses the inflammasome, leading to reduced Tregexpansion and subsequent tumor growth/metastasis. Activation of NR0B2 with small molecule agonists, including one developed herein, attenuates tumor growth and metastasis in murine models of mammary cancer.
Seasonal effects of long-term warming on ecosystem function and bacterial diversity
Authors: Shinfuku Melissa S. , Domeignoz-Horta Luiz A. , Choudoir Mallory J. , Frey Serita D. , Mitchell Megan F. , Ranjan Ravi , DeAngelis Kristen M.
Published: August 2023

1

Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5 °C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having higher function than summer samples. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial diversity in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community diversity.
Mucus physically restricts influenza A viral particle access to the epithelium
Authors: Kaler Logan , Engle Elizabeth M , Iverson Ethan , Boboltz Allison , Ignacio Maxinne A , Rife Maria , Scull Margaret A , Duncan Gregg
Published: August 2023

Prior work suggests influenza A virus (IAV) crosses the airway mucus barrier in a sialic acid-dependent manner through the actions of the viral envelope proteins, hemagglutinin and neuraminidase. However, host and viral factors that influence how efficiently mucus traps IAV remain poorly defined. In this work, we assessed how the physicochemical properties of mucus influence its ability to effectively capture IAV with altered sialic acid preference using fluorescence video microscopy and multiple particle tracking. We found an airway mucus gel layer must be produced with pores on the order of size of the virus to physically constrain IAV. Sialic acid binding by IAV also improves mucus trapping efficiency, but interestingly, sialic acid preferences had little impact on the fraction of IAV particles expected to penetrate the mucus barrier. Together, this work provides new insights on mucus barrier function toward IAV with important implications on innate host defense and interspecies transmission.