bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing the accuracy of an ultrasound height measurement device with a wooden measurement board among children aged 2-5 years in rural Lao People’s Democratic Republic: a methods-comparison study
Authors: Huang Shan , Homer Caroline S.E. , Conkle Joel , Kounnavong Sengchanh , Phongluxa Khampheng , Vogel Joshua P.
Published: July 2023

Background

Height is a key component of nutrition assessments in children from limited-resource settings. Traditional measurement boards are bulky and difficult to transport. We aimed to assess whether a handheld digital ultrasound device provides comparable accuracy to the measurement board for measuring children’s height.

Methods

We trained 12 health workers to measure the standing height of 222 children aged 2-5 years in rural Lao People’s Democratic Republic using the ultrasound device and measurement board. The Bland-Altman method was used to depict limits of agreement and potential bias. We reported the technical error of measurement (TEM) for precision, accuracy and assessed results against the Standardized Monitoring and Assessment for Relief and Transition (SMART) Manual 2.0 and the WHO Multicentre Growth Reference Study (MGRS).

Results

The average difference between the ultrasound and board measurements was 0.096 cm (95% limits-of-agreement: 0.041cm, 0.61cm) with a systematic bias of 0.1cm (95% confidence interval: 0.067,0.134), suggesting the ultrasound measurements measured slightly higher than those from the board. The ultrasound and board TEMs for precision were 0.157cm and 0.113 respectively. The accuracy TEM was 0.208cm. All TEMs were within SMART and WHO MGRS limits.

Conclusion

The ultrasound device is comparable to the measurement board among standing Lao children aged 2-5 years for precision and accuracy TEMs but showed a bias of 0.1cm. Further studies are required to assess whether calibration of device can minimise this bias and determine the ultrasound’s accuracy on recumbent length for infants and younger children.
National trends in suicides and male twin live births in the US, 2003 to 2019: an updated test of collective optimism and selectionin utero
Authors: Singh Parvati , Gailey Samantha , Das Abhery , Bruckner Tim A.
Published: July 2023

Prior research based on Swedish data suggests that collective optimism, as measured by monthly incidence of suicides, correlates inversely with selectionin uteroagainst male twins in a population. We test this finding in the US, which reports the highest suicide rate of all high-income countries, and examine whether monthly changes in overall suicides precede changes in the ratio of male twin to male singleton live births. Consistent with prior work, we also examine as a key independent variable, suicides among women aged 15-49 years. We retrieved monthly data on suicides and the ratio of male twin to singleton live births from CDC WONDER, 2003 to 2019, and applied Box-Jenkins iterative time-series routines to detect and remove autocorrelation from both series. Results indicate that a one percent increase in monthly change in overall suicides precedes a 0.005 unit decline in male twin live births ratio 6 months later (coefficient = -0.005,Pvalue = 0.004). Results remain robust to use of suicides among reproductive-aged women as the independent variable (coefficient = -0.0012,Pvalue = 0.014). Our study lends external validity to prior research and supports the notion that a decline in collective optimism corresponds with greater selectionin utero.
A temperature-controlled, circular maintenance system for studying growth and development of pelagic tunicates (Salps)
Authors: Müller Svenja J. , Wessels Wiebke , Driscoll Sara , Pakhomov Evgeny A. , Auerswald Lutz , Michael Katharina , Meyer Bettina
Published: July 2023

Salps are pelagic tunicates that are able to form large blooms under favorable conditions by alternating between sexual and asexual reproduction. While their role in the regional carbon cycle is receiving attention, our knowledge of their physiology is still limited. This knowledge gap is mainly due to their fragile gelatinous nature, which makes it difficult to capture intact specimens and maintain them in the laboratory. We present here a modified kreisel tank system, that was tested onboard using the Southern Ocean salpSalpa thompsoniand station-based using the Mediterranean speciesSalpa fusiformis. Successful maintenance over days to weeks allowed us to obtain comparable relative growth and developmental rates asin situ, and provided insight into their potential life cycle strategies. By providing a starting point for successful maintenance, we hope to stimulate future experimental research on this understudied taxonomic group.
Serotonergic and dopaminergic neurons in the dorsal raphe are differentially altered in a mouse model for parkinsonism
Authors: Boi Laura , Johansson Yvonne , Tonini Raffaella , Moratalla Rosario , Fisone Gilberto , Silberberg Gilad
Published: July 2023

Parkinson’s disease (PD) is characterized by motor impairments caused by degeneration of dopamine neurons in the substantia nigra pars compacta. In addition to these symptoms, PD patients often suffer from non-motor co-morbidities including sleep and psychiatric disturbances, which are thought to depend on concomitant alterations of serotonergic and noradrenergic transmission. A primary locus of serotonergic neurons is the dorsal raphe nucleus (DRN), providing brain-wide serotonergic input. Here, we identified electrophysiological and morphological parameters to classify serotonergic and dopaminergic neurons in the murine DRN under control conditions and in a PD model, following striatal injection of the catecholamine toxin, 6-hydroxydopamine (6-OHDA). Electrical and morphological properties of both neuronal populations were altered by 6-OHDA. In serotonergic neurons, most changes were reversed when 6-OHDA was injected in combination with desipramine, a noradrenaline reuptake inhibitor, protecting the noradrenergic terminals. Our results show that the depletion of both noradrenaline and dopamine in the 6-OHDA mouse model causes changes in the DRN neural circuitry.
Predicting the Beat Bin: Beta Oscillations Predict the Envelope Sharpness in a Rhythmic Sequence
Authors: Leske Sabine , Endestad Tor , Volehaugen Vegard , Foldal Maja D. , Blenkmann Alejandro O. , Solbakk Anne-Kristin , Danielsen Anne
Published: July 2023

Periodic sensory inputs entrain oscillatory brain activity, reflecting a neural mechanism that might be fundamental to temporal prediction and perception. Most environmental rhythms, such as music or speech, however, are rather quasi-periodic. Research has shown that neural tracking of speech is driven by modulations of the amplitude envelope, especially via sharp acoustic edges, which serve as prominent temporal landmarks. In the same vein, research on rhythm processing in music supports the notion that perceptual timing precision varies systematically with the sharpness of acoustic onset edges, conceptualized in the beat bin hypothesis. Increased envelope sharpness induces increased precision in localizing a sound in time. Despite this tight relationship between envelope shape and temporal processing, it is currently unknown how the brain uses predictive information about envelope features to optimize temporal perception.

With the current study, we show that the predicted sharpness of the amplitude envelope is encoded by pre-target neural activity in the beta band (15–25 Hz), and has an impact on the temporal perception of sounds. Using probabilistic sound cues in an EEG experiment, we informed participants about the sharpness of the amplitude envelope of an upcoming target sound embedded in a quasi-isochronous beat. The predictive information about the envelope shape modulated the performance in the timing judgment task and pre-target beta power. Interestingly, these conditional beta-power modulations correlated positively with behavioral performance in the timing-judgment task and with perceptual temporal precision in a click-alignment task.

This study provides new insight into the neural processes underlying prediction of the sharpness of the amplitude envelope during beat perception, which modulate the temporal perception of sounds. This finding could reflect a process that is involved in temporal prediction, exerting top-down control on neural entrainment via the prediction of acoustic edges in the auditory stream.
Exploring Liquid-Liquid Phase Separation in the organization of Golgi Matrix Proteins
Authors: Mendes Luis Felipe S. , Oliveira Carolina G. , Kava Emanuel , Costa-Filho Antonio J.
Published: July 2023

The Golgi apparatus is a critical organelle in protein sorting and lipid metabolism. Characterized by its stacked, flattened cisternal structure, the Golgi exhibits distinct polarity with itscis- andtrans-faces orchestrating various protein maturation and transport processes. At the heart of its structural integrity and organization are the Golgi Matrix Proteins (GMPs), predominantly comprising Golgins and GRASPs. These proteins contribute to this organelle’s unique stacked and polarized structure and ensure the precise localization of Golgi-resident enzymes, which is crucial for accurate protein processing. Despite over a century of research since its discovery, the Golgi architecture’s intricate mechanisms still need to be fully understood. Here, we demonstrate that GMPs present a significant tendency to form biocondensates through Liquid-Liquid Phase Separation (LLPS) across different Eukaryotic lineages. Moreover, we validated experimentally that members of the GRASP family also exhibit a strong tendency for LLPS. Our findings offer a new perspective on the possible roles of protein disorder and LLPS of GMPs in the Golgi organization.
Molecular responses of agroinfiltratedNicotiana benthamianaleaves expressing suppressor of silencing P19 and influenza virus-like particles
Authors: Hamel Louis-Philippe , Tardif Rachel , Poirier-Gravel Francis , Rasoolizadeh Asieh , Brosseau Chantal , Giroux Geneviève , Lucier Jean-François , Goulet Marie-Claire , Barrada Adam , Roussel Élise , Comeau Marc-André , Lavoie Pierre-Olivier , Moffett Peter , Michaud Dominique , D’Aoust Marc-André
Published: July 2023

The production of influenza vaccines in plants is achieved through transientAgrobacterium-mediated expression of viral hemagglutinins (HAs). These proteins are produced and matured through the secretory pathway of plant cells, before being trafficked to the plasma membrane where they induce formation of virus-like particles (VLPs). Production of VLPs unavoidably impacts plant cells, as do viral suppressors of RNA silencing (VSRs) that are often co-expressed to increase protein yields. However, little information is available on host molecular responses to these foreign proteins. The present work provides a comprehensive overview of transcriptomic, metabolic, and signaling changes occurring inNicotiana benthamianaleaf cells transiently expressing the VSR P19, or co-expressing P19 and an influenza HA. Our data identifies generic responses toAgrobacterium-mediated expression of foreign proteins, including shutdown of chloroplast gene expression, activation of oxidative stress responses, and reinforcement of the plant cell wall through lignification. Our results also indicate that P19 expression promotes salicylic acid (SA) signaling, a process apparently antagonized by co-expression of HA. As the latter induces specific signatures, with effects on lipid metabolism, lipid distribution, and oxylipin signaling, dampening of P19 responses suggests crosstalk between SA and oxylipin pathways. Consistent with the upregulation of oxidative stress-related genes and proteins, we finally show that reduction of oxidative stress damage through exogenous application of ascorbic acid improves plant biomass quality during production of VLPs.

One-sentence summary

Agrobacterium-mediated expression of influenza virus-like particles induces a unique molecular signature inNicotiana benthamianaleaf cells.
Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes
Authors: Westphall Michael S. , Lee Kenneth W. , Hemme Colin , Salome Austin Z. , Mertz Keaton , Grant Timothy , Coon Joshua J.
Published: July 2023

We describe an apparatus for the cryogenic landing of particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. We demonstrate that as compared to room temperature landings, use of this cryogenic landing device greatly improves the structural preservation of deposited protein–protein complexes. Further, landing under cryogenic conditions can increase the diversity of particle orientations, allowing for improved 3D structural interpretation. Finally, we conclude that this approach allows for the direct coupling of mass spectrometry with cryo-electron microscopy.
Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression
Authors: Zhang Junli , Xiong Hongchun , Burguener Germán F. , Vasquez-Gross Hans , Liu Qiujie , Debernardi Juan M. , Akhunova Alina , Campbell-Garland Kim , Kianian Shahryar F. , Brown-Guedira Gina , Pozniak Curtis , Faris Justin D. , Akhunov Eduard , Dubcovsky Jorge
Published: July 2023

Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. New functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more non-synonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the new promoter dataset, we selected two mutations within the promoter of theVRN-A1vernalization gene. Both mutations, located within transcription factor binding sites, significantly alteredVRN-A1expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.

Significance Statement

We sequenced 4.3 million induced mutations in the promoters and 4.7 million in the coding regions of most wheat genes. We also show how this public resource can be used to understand gene function, modulate gene expression, and generate changes in valuable wheat agronomic traits.
Salmonella injectisome penetration of macrophages triggers rapid translation of transcription factors and protection against cell death
Authors: Wood George , Johnson Rebecca , Powell Jessica , Bryant Owain J. , Lastovka Filip , Brember Matt , Tourlomousis Pani , Carr John P. , Bryant Clare E. , Chung Betty Y.W.
Published: July 2023

During bacterial infection both the host cell and its invader must divert intracellular resources to synthesise specific proteins in a timely manner. For the host, these factors may be needed for innate immune responses, including programmed cell death, and in the bacteria newly synthesized proteins may be survival factors needed to counteract host responses.Salmonellais an important food-borne bacterial pathogen that invades and multiplies within host cells. It is well established that invasion of epithelial cells is dependent upon the SPI-1 Type III injectisome, a biological needle that penetrates and secretes effectors into host cells to promote internalization. However, the importance of the SPI-1 injectisome in infection of professional phagocytes such as macrophages, which are the predominant host cell type during systemic infection, is less clear. Through time resolved parallel transcriptomic and translatomic studies of macrophage infection, we revealed that SPI-1 injectisome-dependent infection of macrophages triggers rapid translation of transcription factor mRNAs, including Early Growth Response 1 (Egr1). Despite the short half-life of EGR1 protein, its swift synthesis within the initial hour of infection is sufficient to inhibit transcription of pro-inflammatory genes and thereby restrain inflammatory responses and programmed cell death within the first hour of during early infection. This transient period of inflammatory suppression in macrophages is exploited bySalmonellato establish infection and sheds new insight on the importance of translational activation in host-pathogen dynamics duringSalmonellainfection.
Reactive oxygen species acceleratede novoacquisition of antibiotic resistance inE. coli
Authors: Qi Wenxi , Jonker Martijs J. , de Leeuw Wim , Brul Stanley , ter Kuile Benno H.
Published: July 2023

Reactive oxygen species (ROS) produced as a secondary effect of bactericidal antibiotics are hypothesized to play a role in killing bacteria. However, the role of ROS in the development ofde novoresistance as a result of sublethal levels of bactericidal antibiotics has barely been investigated. Here, we report that single-gene knockout strains with reduced ROS scavenging exhibited enhanced ROS accumulation and more rapid acquisition of resistance when exposed to sublethal levels of bactericidal antibiotics. Consistent with this observation, the ROS scavenger thiourea in the medium decelerated resistance development. Thiourea downregulated the transcriptional level of error-prone DNA polymerase and DNA glycosylase MutM, which counters the incorporation and accumulation of 8-hydroxy-2’-deoxyguanosine (8-HOdG) in the genome. The level of 8-HOdG significantly increased following incubation with bactericidal antibiotics but decreased after treatment with the ROS scavenger thiourea. These observations suggest that inE. colisublethal levels of ROS stimulatede novodevelopment of resistance, providing a mechanistic basis for hormetic responses induced by antibiotics.

Importance

Exposure to sublethal concentrations of antimicrobials is known to result inde novoresistance development against the specific compound. Particularly, the use of antibiotics as feed additives to enhance productivity may result in the development of drug resistance in environmental and veterinary microorganisms, which could subsequently transfer to human populations. Nevertheless, the mechanisms underlyingde novoresistance development have not been extensively explored. In this study, we indicate the role of ROS in promoting the formation of resistance to bactericidal antibiotics and show the potential of ROS scavengers to reduce mutation rates and slow down resistance formation under long-term selection. Thus, the supplementary use of antioxidants during prolonged antibiotic administration potentially contributes to mitigating the emergence of antimicrobial resistance.
hnRNPUL1 ensures efficient Integrator-mediated cleavage of snRNAs and is mutated in amyotrophic lateral sclerosis
Authors: Yonchev Ivaylo D. , Apostol Carmen V. , Griffith Llywelyn , Li Ang , Butler Larissa , Patrick Helen , Aguilar-Martinez Elisa , Whelan Ashleigh G. R. , Evans Caroline , Dickman Mark J. , Cooper-Knock Johnathan , Shaw Pamela J. , West Steven , Barbaric Ivana , Sudbery Ian M. , Wilson Stuart A.
Published: July 2023

Integrator cleaves nascent RNA, triggering RNA polymerase II transcription termination, but how cleavage is regulated is poorly understood. Here we show hnRNPUL1 ensures efficient Integrator-mediated cleavage of nascent RNA downstream of snRNA genes and, in the case of U2 snRNA, binds a terminal stem-loop involved in this process. In the nucleoplasm, hnRNPUL1 binds U4 snRNA and SART3 and enables efficient reformation of the U4:U6 di-snRNP for further rounds of pre-mRNA splicing. Sustained hnRNPUL1 loss leads to reduced levels of snRNAs, defects in histone mRNA 3′ end processing and loss of Cajal bodies. hnRNPUL1 binds RNA through multiple domains, including a globular central domain comprising tightly juxtaposed SPRY and dead polynucleotide kinase folds. This latter fold allows binding to 5′-monophosphorylated RNAs in a mutually exclusive manner with ATP binding and functions as an XRN2 antagonist when overexpressed. We identify a cohort of amyotrophic lateral sclerosis patients harbouring disruptive mutations in hnRNPUL1. SMN loss in spinal muscular atrophy and hnRNPUL1 loss both disrupt snRNP biogenesis, leading to motor neuron death, suggesting a common aetiology.
A functional microbiome catalog crowdsourced from North American rivers
Authors: Borton Mikayla A. , McGivern Bridget B. , Willi Kathryn R. , Woodcroft Ben J. , Mosier Annika C. , Singleton Derick M. , Bambakidis Ted , Pelly Aaron , Liu Filipe , Edirisinghe Janaka N. , Faria José P. , Leleiwi Ikaia , Daly Rebecca A. , Goldman Amy E. , Wilkins Michael J. , Hall Ed K. , Pennacchio Christa , Roux Simon , Eloe-Fadrosh Emiley A. , Good Stephen P. , Sullivan Matthew B. , Henry Christopher S. , Wood-Charlson Elisha M. , Ross Matthew R.V. , Miller Christopher S. , Crump Byron C. , Stegen James C. , Wrighton Kelly C.
Published: July 2023

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial processes governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling, sequencing, and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. Specifically, GROWdb encompasses 1,469 microbial species from 27 phyla, including novel lineages from 10 families and 128 genera, and defines the core river microbiome for the first time at genome level. GROWdb analyses coupled to extensive geospatial information revealed local and regional drivers of microbial community structuring, while also presenting a myriad of foundational hypotheses about ecosystem function. Building upon the previously conceived River Continuum Concept1, we layer on microbial functional trait expression, which suggests the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures2, 3so that it can be widely accessed across disciplines for watershed predictive modeling and microbiome-based management practices.
Assessing the impact of autologous neutralizing antibodies on viral rebound in postnatally SHIV-infected ART-treated infant rhesus macaques
Authors: Mainou Ellie , Berendam Stella J , Obregon-Perko Veronica , Uffman Emilie A , Phan Caroline T , Shaw George M , Bar Katherine J , Kumar Mithra R , Fray Emily J , Siliciano Janet M , Siliciano Robert F , Silvestri Guido , Permar Sallie R , Fouda Genevieve G , McCarthy Janice , Chahroudi Ann , Conway Jessica M , Chan Cliburn
Published: July 2023

Abstract

While the benefits of early antiretroviral therapy (ART) initiation in perinatally infected infants are well documented, early ART initiation is not always possible in postnatal pediatric HIV infections, which account for the majority of pediatric HIV cases worldwide. The timing of onset of ART initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.
Polyreactivity of antibodies from different B cell subpopulations is determined by distinct sequence patterns of variable region
Authors: Lecerf Maxime , Lacombe Robin V. , Dimitrov Jordan D.
Published: July 2023

An antibody molecule that is able to bind to multiple distinct antigens is defined as polyreactive. In the present study we performed statistical analyses to assess sequence correlates of polyreactivity of >600 antibodies cloned from different B cell types of healthy humans. The data reveled a number of sequence patterns of variable regions of heavy and light immunoglobulin chains that determine polyreactivity. The most prominent identified patterns were increased number of basic amino acid residues, reduced frequency of acidic residues, increased number of aromatic and hydrophobic residues, as well as longer length of CDR L1. Importantly, our study revealed that antibodies isolated from different B cell population used distinct sequence patterns (or combinations of them) for polyreactive antigen binding. Furthermore, we combined the data from sequence analyses with molecular modeling of selected polyreactive antibodies, and demonstrate that human antibodies can use multiple pathways for achieving antigen binding promiscuity. These data reconcile some contradictions in literature regarding the determinants of antibody polyreactivity. Moreover, our study demonstrates that mechanism of polyreactivity of antibodies evolves during immune response and might be tailored to specific functional properties of different B cell compartments. Finally, these data can be of use for efforts in development and engineering of therapeutic antibodies.
Zmiz1 is a novel regulator of lymphatic endothelial cell gene expression and function
Authors: K C Rajan , Patel Nehal R , Shenoy Anoushka , Scallan Joshua P , Chiang Mark Y , Galazo Maria J , Meadows Stryder M
Published: July 2023

Zinc Finger MIZ-Type Containing 1 (Zmiz1), also known as ZIMP10 or RAI17, is a transcription cofactor and member of the Protein Inhibitor of Activated STAT (PIAS) family of proteins. Zmiz1 is critical for a variety of biological processes including vascular development. However, its role in the lymphatic vasculature is unknown. In this study, we utilized human dermal lymphatic endothelial cells (HDLECs) and an inducible, lymphatic endothelial cell (LEC)-specificZmiz1knockout mouse model to investigate the role of Zmiz1 in LECs. Transcriptional profiling ofZmiz1-deficient HDLECs revealed downregulation of genes crucial for lymphatic vessel development. Additionally, our findings demonstrated that loss of Zmiz1 results in reduced expression of proliferation and migration genes in HDLECs and reduced proliferation and migrationin vitro. We also presented evidence that Zmiz1 regulates Prox1 expressionin vitroandin vivoby modulating chromatin accessibility at Prox1 regulatory regions. Furthermore, we observed that loss ofZmiz1in mesenteric lymphatic vessels significantly reduced valve density. Collectively, our results highlight a novel role of Zmiz1 in LECs and as a transcriptional regulator of Prox1, shedding light on a previously unknown regulatory factor in lymphatic vascular biology.
Large pilin subunits provide distinct structural and mechanical properties for theMyxococcus xanthustype IV pilus
Authors: Treuner-Lange Anke , Zheng Weili , Viljoen Albertus , Lindow Steffi , Herfurth Marco , Dufrêne Yves F. , Søgaard-Andersen Lotte , Egelman Edward H.
Published: July 2023

Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While the major pilins of structurally characterized T4P have lengths of up to 161 residues, the major pilin PilA ofMyxococcus xanthusis unusually large with 208 residues. All major pilins have a highly conserved N-terminal domain and a highly variable C-terminal domain, and the additional residues in theM. xanthusPilA are due to a larger C-terminal domain. We solved the structure of theM. xanthusT4P (T4PMx) at a resolution of 3.0 Å using cryo-electron microscopy (cryo-EM). The T4PMxfollows the structural blueprint observed in other T4P with the pilus core comprised of the extensively interacting N-terminal α1-helices while the globular domains decorate the T4P surface. The atomic model of PilA built into this map shows that the large C-terminal domain has much more extensive intersubunit contacts than major pilins in other T4P. As expected from these greater contacts, the bending and axial stiffness of the T4PMxis significantly higher than that of other T4P and supports T4P-dependent motility on surfaces of different stiffnesses. Notably, T4PMxvariants with interrupted intersubunit interfaces had decreased bending stiffness and strongly reduced motility on all surfaces. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4P that expands the environmental conditions in which the T4P system functions.
CTCF/cohesin organize the ground state of chromatin-nuclear speckle association
Authors: Yu Ruofan , Roseman Shelby , Siegenfeld Allison P. , Nguyen Son C. , Joyce Eric F. , Liau Brian B. , Krantz Ian D. , Alexander Katherine A. , Berger Shelley L.
Published: July 2023

The interchromatin space in the cell nucleus contains various membrane-less nuclear bodies. Recent findings indicate that nuclear speckles, comprising a distinct nuclear body, exhibit interactions with certain chromatin regions in a ground state. Key questions are how this ground state of chromatin-nuclear speckle association is established and what are the gene regulatory roles of this layer of nuclear organization. We report here that chromatin structural factors CTCF and cohesin are required for full ground state association between DNA and nuclear speckles. Disruption of ground state DNA-speckle contacts via either CTCF depletion or cohesin depletion had minor effects on basal level expression of speckle-associated genes, however we show strong negative effects on stimulus-dependent induction of speckle-associated genes. We identified a putative speckle targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association. In contrast to reduction of CTCF or RAD21, depletion of the cohesin releasing factor WAPL stabilized cohesin on chromatin and DNA-speckle contacts, resulting in enhanced inducibility of speckle-associated genes. In addition, we observed disruption of chromatin-nuclear speckle association in patient derived cells with Cornelia de Lange syndrome (CdLS), a congenital neurodevelopmental diagnosis involving defective cohesin pathways, thus revealing nuclear speckles as an avenue for therapeutic inquiry. In summary, our findings reveal a mechanism to establish the ground organizational state of chromatin-speckle association, to promote gene inducibility, and with relevance to human disease.
CuticleTrace: A toolkit for capturing cell outlines of leaf cuticle with implications for paleoecology and paleoclimatology
Authors: Lloyd Benjamin A. , Barclay Richard S. , Dunn Regan E. , Currano Ellen D. , Mohamaad Ayuni I. , Skersies Kymbre , Punyasena Surangi W.
Published: July 2023

Premise

Leaf epidermal cell morphology is closely tied to plants’ evolutionary histories and growth environments, and is therefore of interest to many plant biologists. However, cell measurement can be time-consuming and restrictive with current methods. CuticleTrace is a suite of FIJI and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities.

Methods and Results

We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand-tracings across a taxonomically diverse 50-image dataset of variable image qualities. We observed ∼93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods.

Conclusions

CuticleTrace is broadly applicable, modular, and customizable, and integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape datasets.
Autoencoder-transformed transcriptome improves genotype-phenotype association studies
Authors: Li Qing , Bian Jiayi , Weeraman Janith , Leung Albert , Yang Guotao , Chekouo Thierry , Yan Jun , Wu Jingjing , Long Quan
Published: July 2023

Transcriptome-wide association study (TWAS) is an emerging model leveraging gene expressions to direct genotype-phenotype association mapping. A key component in TWAS is the prediction of gene expressions; and many statistical approaches have been developed along this line. However, a problem is that many genes have low expression heritability, limiting the performance of any predictive model. In this work, hypothesizing that appropriate denoising may improve the quality of expression data (including heritability), we propose AE-TWAS, which adds a transformation step before conducting standard TWAS. The transformation is composed of two steps by first splitting the whole transcriptome into co-expression networks (modules) and then using autoencoder (AE) to reconstruct the transcriptome data within each module. This transformation removes noise (including nonlinear ones) from the transcriptome data, paving the path for downstream TWAS. We showed two inspiring properties of AE-TWAS: (1) After transformation, the transcriptome data enjoy higher expression heritability at the low-heritability spectrum and possess higher connectivity within the modules. (2) The transferred transcriptome indeed enables better performance of TWAS; and moreover, the newly formed highly connected genes (i.e., hub genes) are more functionally relevant to diseases, evidenced by their functional annotations and overlap with TWAS hits.
Improving PD-1 blockade plus chemotherapy for complete remission of lung cancer by nanoPDLIM2
Authors: Sun Fan , Yan Pengrong , Xiao Yadong , Zhang Hongqiao , Shapiro Steven D. , Xiao Gutian , Qu Zhaoxia
Published: July 2023

Background

Immune checkpoint inhibitors (ICIs) and their combination with other therapies such as chemotherapy, fail in most cancer patients. We previously identified the PDZ-LIM domain-containing protein 2 (PDLIM2) as abona fidetumor suppressor that is repressed in lung cancer to drive cancer and its chemo and immunotherapy resistance, suggesting a new target for lung cancer therapy improvement.

Methods

Human clinical samples and data were used to investigatePDLIM2genetic and epigenetic changes in lung cancer. Using an endogenous mouse lung cancer model faithfully recapitulating refractory human lung cancer and a clinically feasible nano-delivery system, we investigated the therapeutic efficacy, action mechanism, and safety of systemically administrated PDLIM2 expression plasmids encapsulated in nanoparticles (nanoPDLIM2) and its combination with PD-1 antibody and chemotherapeutic drugs.

Results

PDLIM2 repression in human lung cancer involves both genetic deletion and epigenetic alteration. NanoPDLIM2 showed low toxicity, high tumor specificity, antitumor activity, and greatly improved the efficacy of anti-PD-1 and chemotherapeutic drugs, with complete tumor remission in most mice and substantial tumor reduction in the remaining mice by their triple combination. Mechanistically, nanoPDLIM2 increased major histocompatibility complex class I (MHC-I) expression, suppressed multi-drug resistance 1 (MDR1) induction and survival genes and other tumor-related genes expression in tumor cells, and enhanced lymphocyte tumor infiltration, turning the cold tumors hot and sensitive to ICIs and rendering them vulnerable to chemotherapeutic drugs and activated tumor-infiltrating lymphocytes (TILs) including those unleashed by ICIs.

Conclusions

These studies established a clinically applicable PDLIM2-based combination therapy with great efficacy for lung cancer and possibly other cold cancers.
Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across Reference Proteomes
Authors: Cascarina Sean M. , Ross Eric D.
Published: July 2023

Low-complexity domains (LCDs) in proteins are typically enriched in one or two predominant amino acids. As a result, LCDs often exhibit unusual structural/biophysical tendencies and can occupy functional niches. However, for each organism, protein sequences must be compatible with intracellular biomolecules and physicochemical environment, both of which vary from organism to organism. This raises the possibility that LCDs may occupy sequence spaces in select organisms that are otherwise prohibited in most organisms. Here, we report a comprehensive survey of LCDs in all known reference proteomes (>21k organisms), with added focus on rare and unusual types of LCDs. LCDs were sorted into a rich hierarchical database according to both the primary amino acid and secondary amino acid in each LCD sequence, facilitating detailed comparisons of LCD class frequencies across organisms. Examination of LCD classes at different depths (i.e., domain of life, organism, protein, and per- residue levels) reveals unique facets of LCD frequencies and functions. To our surprise, all 400 LCD classes occur in nature, although some are exceptionally rare. A number of rare classes can be defined for each domain of life, with many LCD classes appearing to be eukaryote- specific. Multiple eukaryote-specific LCD classes could be linked to consistent sets of functions across organisms. Our analysis methods enable simultaneous, direct comparison of all LCD classes between individual organisms, resulting in a proteome-scale view of differences in LCD frequencies and functions. Together, these results highlight the remarkable diversity and functional specificity of LCDs across all known life forms.
Unraveling the Potential of Epicatechin Gallate fromCrataegus oxyacanthain Targeting Aberrant Cardiac Ca2+ Signalling Proteins: An in-depthIn-SilicoInvestigation for Heart Failure Therapy
Authors: Praveen J , Anusuyadevi M , Jayachandra KS
Published: July 2023

The cardiovascular sarcoplasmic reticulum (SR) calcium (Ca2+) ATPase is an imperative determinant of cardiac functionality. In addition, anomalies in Ca2+ handling protein and atypical energy metabolism are inherent in heart failure (HF). Moreover, Ca2+ overload in SR leads to mitochondrial matrix Ca2+ overload, which can trigger the generation of Reactive Oxygen Species (ROS), culminating in the triggering of the Permeability Transition Pore (PTP) and Cytochrome C release, resulting in apoptosis that leads to arrhythmias and numerous disorders. Although proteins involved in the molecular mechanism of Ca2+ dysfunction regarding mitochondrial dysfunction remains elusive, this study aims to assess the major Ca2+ handling proteins which may be involved in the Ca2+ malfunction that causes mitochondrial dysfunction and predicting the most effective drug by targeting the analyzed Ca2+ handling proteins through variousinsilicoanalyses.Thirteen proteins absorbed from interaction analysis were docked with four optimal phytochemicals fromCrataegus oxyacantha(COC) to identify the potential agonist/antagonist against those anomalies causing Ca2+ handling signaling proteins. Furthermore,The ADMET profile of tyramine, vitexin, epicatechin, and epicatechin gallate was acclimated to evaluate potential drugability utilizing QikProp by Schrodinger.Keeping this in view, critical molecular docking evaluations were performed using Glide (Maestro), autodock, and autodock vina.Based on the results of 156 dockings by Maestro, auto-dock, and auto-dock vina, PKA Cα with epicatechin gallate exhibits good interaction. Therefore, a 2000ns molecular dynamics (MD) simulation was utilized to assess the feasible phytochemical epicatechin gallate - PKA Cα complex binding stability utilizing Desmond. As a result, the molecular dynamics simulation study confirmed that epicatechin gallate from COC has high possibilities to inhibit the aberrant cardiac Ca2+ signaling proteins due to its conformational rigidity.
Combined representation of visual features in the scene-selective cortex
Authors: Kang Jisu , Park Soojin
Published: July 2023

Visual features of separable dimensions like color and shape conjoin to represent an integrated entity. We investigated how visual features bind to form a complex visual scene. Specifically, we focused on features important for visually guided navigation: direction and distance. Previously, separate works have shown that directions and distances of navigable paths are coded in the occipital place area (OPA). Using functional magnetic resonance imaging (fMRI), we tested how separate features are concurrently represented in the OPA. Participants saw eight different types of scenes, in which four of them had one path and the other four had two paths. In single-path scenes, path direction was either to the left or to the right. In double-path scenes, both directions were present. Each path contained a glass wall located either near or far, changing the navigational distance. To test how the OPA represents paths in terms of direction and distance features, we took three approaches. First, the independent-features approach examined whether the OPA codes directions and distances independently in single-path scenes. Second, the integrated-features approach explored how directions and distances are integrated into path units, as compared to pooled features, using double-path scenes. Finally, the integrated-paths approach asked how separate paths are combined into a scene. Using multi-voxel pattern similarity analysis, we found that the OPA’s representations of single-path scenes were similar to other single-path scenes of either the same direction or the same distance. Representations of double-path scenes were similar to the combination of two constituent single-paths, as a combined unit of direction and distance rather than pooled representation of all features. These results show that the OPA combines the two features to form path units, which are then used to build multiple-path scenes. Altogether, these results suggest that visually guided navigation may be supported by the OPA that automatically and efficiently combines multiple features relevant for navigation and represent anavigation file.
Patterns of speciation in a parapatric pair ofSaturniamoths as revealed by Target Capture
Authors: Khan Maria , Joshi Mukta , Espeland Marianne , Huemer Peter , Vaamonde Carlos Lopez , Mutanen Marko
Published: July 2023

The focus of this study is to understand the evolutionary relationships and taxonomy of widely distributed parapatric species pair of wild silk moths,Saturnia pavoniaandSaturnia pavoniella(Lepidoptera: Saturniidae) in Europe. To address species delimitation challenges associated with many parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, species delimitation, admixture and introgression analyses. The dataset included individuals from both species, two hybrids generated in the lab, as well as individuals from outside the contact zone. Nuclear markers strongly supported bothS. pavoniaandS. pavoniellaas two distinct species, with the hybrids grouping together as intermediate and separate from both species. However, the maximum likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency may be attributed to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization or incomplete lineage sorting) or alternatively operational factors (e.g., incorrect species delimitation). We further provide the evidence of past introgression to have taken place, but no evidence of current admixture between the two species. Finally, we discuss our results from evolutionary point of view taking into consideration the past climatic oscillations that has likely shaped the present dynamics between the species. Overall, this study demonstrated the effectiveness of the target enrichment approach in resolving the phylogenetic relationships between closely related parapatric species and providing insights into their taxonomic delimitation.
A heterozygousCEBPAmutation disrupting the bZIP domain causes MDS disease progression
Authors: Almaghrabi Ruba , Alyayhawi Yara , Keane Peter , Ward Carl , Bayley Rachel , Sargas Claudia , Menendez Pablo , Murphy George J. , Sobahy Turki , Baghdadi Mohammed A. , Flemban Arwa F , Kabrah Saeed , Akerman Ildem , Raghavan Manoj , Barragan Eva , Bonifer Constanze , Garcia Paloma
Published: July 2023

Myelodysplastic syndrome disease (MDS) has a variable risk for progression to AML. Mutations inCEBPAare associated with a high risk of disease progression, but whether this mutation is causative for AML development is unclear. To answer this question, we generated patient-derived, MDS-specific iPSCs recapitulating the patient disease phenotype upon differentiation to blood, with hematopoietic progenitor cells showing erythroid and myeloid-dysplasia. Introduction of a frameshift mutation affecting the C/EBPα bZIP domain led to disease progression, with a reduction in clonogenic potential, block in granulocyte development and increased self-renewal capacity of erythroid progenitors. ATAC-seq revealed that the acquisition of this mutation reshaped the chromatin landscape at distal cis-regulatory regions, promoting changes in clonal composition as observed by single cell RNAseq. Our work identifies mutantCEBPAas causative for MDS disease progression, providing a new isogenic MDS experimental model for drug screening to improve diagnostic and therapeutic strategies.

Highlights

Development of isogenic iPSC model of clonal evolution of MDS

Monoallelic disruption of CEBPA bZIP domain is causative for MDS disease progression

Monoallelic disruption of CEBPA bZIP reshapes chromatin landscape

Patient derived iPSCs recapitulate drug responsiveness