bluuebunny/crossref_metadata_2025 huggingface dataset:
Missense mutations in the calcium-activated chloride channel TMEM16A promote tumor growth by activating oncogenic signaling in Human Cancer
Authors: Cruz-Rangel Silvia , De Jesus-Perez Jose Juan , Gopalkrishnan Avani , Gomez-Casal Roberto , Pacheco Jonathan , Brown Maya R , Yassin-Kassab Abdulkader , Hammond Gerald RV , Bertrand Carol A , Arreola Jorge , Kiselyov Kirill , Umamaheswar Duvvuri
Published: June 2023

The calcium-activated chloride channel TMEM16A is overexpressed in several tumors. This condition is associated with a poor survival prognosis but highlights TMEM16A’s potential as a biomarker and target for anti-cancer therapies. Numerous somatic mutations of TMEM16A have been reported; however, their potential and molecular mechanism of oncogenesis are unknown. Here, we investigate the function and oncogenicity of nine-point mutations found in human cancerous tissues (R451P, R455Q, M546I, R557W, F604L, D902N, K913E, D914H, and Q917K). These mutations are located on the extracellular side and near the third Ca2+-binding site, near a PtdIns(4,5)P2 site in the human TMEM16A channel. Our findings reveal that these mutations affected gating, Ca2+sensitivity, phosphorylation of essential signaling proteins, cell proliferation, and tumor growth. Notably, R451P and D902N exhibit low Ca2+sensitivity, yet their overexpression promotes phosphorylation of EGFR and AKT, as well asin vivotumorigenesis, without Ca2+-enhancing stimuli. Conversely, the charged-neutralizing mutation R451Q and the conservative mutation D902E restored Ca2+sensitivity and altered cell proliferation and tumor growth as wild-type did. Thus, we conclude that the oncogenic phenotype of TMEM16A missense mutations is independent of chloride flux but involves the differential activation of cell signaling components associated with cell proliferation.
Genome-wide identification of notochord enhancers comprising the regulatory landscape of theBrachyury(T) locus in mouse
Authors: Schifferl Dennis , Scholze-Wittler Manuela , Luque Alba Villaronga , Pustet Milena , Wittler Lars , Veenvliet Jesse V. , Koch Frederic , Herrmann Bernhard G.
Published: June 2023

The node and notochord are important signaling centers organizing dorso-ventral patterning of cells arising from neuro-mesodermal progenitors forming the embryonic body anlage. Due to the scarcity of notochordal progenitors and notochord cells, a comprehensive identification of regulatory elements driving notochord-specific gene expression has been lacking. Here we have used ATAC-seq analysis of FACS-purified notochordal cells from TS12-13 mouse embryos to identify 8921 putative notochord enhancers. In addition, we established a new model for generating notochordal cells in culture, and found 3728 of these enhancers occupied by the essential notochordal regulators Brachyury (T) and/or Foxa2. We describe the regulatory landscape of the T locus comprising 10 putative enhancers occupied by these factors and confirmed the regulatory activity of 3 of these elements. Moreover, we characterized one new notochord enhancer, termedTNE2, in embryos.TNE2complements the loss ofTNEin the trunk notochord, and is essential for notochordal cell proliferation and differentiation in the tail. Our data demonstrate the essential role of Foxa2 in switching T expressing cells from a NMP/mesodermal trajectory to the notochordal fate.

Summary statement

Combining multi-omics assays of purified embryonic and in vitro generated cells we identified thousands of notochord enhancers comprisingTNE2essential forTexpression and tail development of the mouse embryo.
Model-free Identification of Phenotype-Relevant Variables From Dose Response Data
Authors: Veliz-Cuba Alan , Murrugarra David , Voss Randal
Published: June 2023

Complex phenotypic changes occur during development and in response to injury and disease. Identifying key regulators of phenotypic change is a shared aim of many different fields of research, including life history, tissue regeneration, and cancer. These examples of phenotypic change involve coordinated changes in cellular behaviors and associated changes in gene expression which if disrupted, can alter and even block completion of the phenotypic transition. Experimental treatments that effectively block the completion of a phenotypic transition can be quantitatively manipulated to identify key regulatory genes through changes in transcriptional dose response. In this paper, we present a “model free” approach to identify “bifurcation-like” behaviors of key regulatory genes by tracking spikes in their transcriptional sensitivities. Genes that exhibit such behavior are predicted to comprise nodes in subnetworks or modules that regulate the phenotypic transition. We applied our method to an in-silico data set where we also studied the impact of noise in the predictions. We also applied the method to a gene expression data that were collected during tail regeneration in axolotls. Our code for gene identification, which can be extended more generally to other component variables of complex phenotypic change, is freely available via the following GitHub sitegithub.com/alanavc/id-vars-from-resp-data.
Neural Circuits for Fast Poisson Compressed Sensing in the Olfactory Bulb
Authors: Zavatone-Veth Jacob A. , Masset Paul , Tong William L. , Zak Joseph D. , Murthy Venkatesh N. , Pehlevan Cengiz
Published: June 2023

Within a single sniff, the mammalian olfactory system can decode the identity and concentration of odorants wafted on turbulent plumes of air. Yet, it must do so given access only to the noisy, dimensionally-reduced representation of the odor world provided by olfactory receptor neurons. As a result, the olfactory system must solve a compressed sensing problem, relying on the fact that only a handful of the millions of possible odorants are present in a given scene. Inspired by this principle, past works have proposed normative compressed sensing models for olfactory decoding. However, these models have not captured the unique anatomy and physiology of the olfactory bulb, nor have they shown that sensing can be achieved within the 100-millisecond timescale of a single sniff. Here, we propose a rate-based Poisson compressed sensing circuit model for the olfactory bulb. This model maps onto the neuron classes of the olfactory bulb, and recapitulates salient features of their connectivity and physiology. For circuit sizes comparable to the human olfactory bulb, we show that this model can accurately detect tens of odors within the timescale of a single sniff. We also show that this model can perform Bayesian posterior sampling for accurate uncertainty estimation. Fast inference is possible only if the geometry of the neural code is chosen to match receptor properties, yielding a distributed neural code that is not axis-aligned to individual odor identities. Our results illustrate how normative modeling can help us map function onto specific neural circuits to generate new hypotheses.
Strong epistasis constrains the evolution of strict substrate specificity in apicomplexan lactate dehydrogenases
Authors: Wirth Jacob D. , Boucher Jeffrey I. , Xu Changhan , Classen Scott , Theobald Douglas L.
Published: June 2023

The homologous enzymes lactate and malate dehydrogenase (L/MDH) are structurally similar but are specific for different substrates. LDH vs MDH specificity is canonically governed by the identity of a single “specificity residue” at position 102. However, LDH function has convergently evolved from a specific MDH at least four times, and the catalytic role of residue 102 is not conserved between different phyla. The apicomplexa are a phylum of obligate, intracellular eukaryotic parasites responsible for wide-spread disease such asPlasmodium falciparum(malaria),Cryptosporidium parvum(cryptosporidiosis),Toxoplasma gondii(toxoplasmosis), andEimeria maxima(eimeriosis). The apicomplexan LDH evolved via a five-residue insertion that produced a novel specificity residue, W107f. The commonly accepted mechanism of LDH specificity involves charge balance and steric occlusion, but our data shows that the general mechanism of apicomplexan LDHs does not use W107f as a steric block. OnlyPlasmodiumLDHs evolved substantial steric specificity, making them exceptional among Apicomplexa. Strong protein epistasis constrained this evolution, making it difficult to revert to ancestral phenotypes. Here, we use ancestral sequence reconstruction (ASR), steady-state kinetics, and x-ray crystallography to characterize apicomplexan LDHs which challenge current assumptions about the evolution of L/MDH activity. We demonstrate the unique specificity ofPlasmodiumLDHs and identify the active site residues controlling their substrate recognition. The extraordinarily high specificity ofPlasmodiumLDHs presents difficulties for small-molecule inhibitor development, and successful drugs against Plasmodium LDH may not be efficacious against other Apicomplexa LDHs and their diseases.
Loops are Geometric Catalysts for DNA Integration
Authors: Battaglia Cleis , Michieletto Davide
Published: June 2023

The insertion of HIV and other DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of these insertions are not random and occupy specific positions within the genome but the physical mechanisms underlying the integration site selection are poorly understood. Here we perform Molecular Dynamics simulations to study the insertion of DNA elements, such as HIV viral DNA or transposons, into naked DNA or chromatin substrate. More specifically, we explore the role of loops in the DNA substrate and discover that they act as “geometric catalysts” for DNA integration. Additionally, we discover that the 1D and 3D clustering of loops affects the distribution of integration sites. Finally, we show that loops may compete with nucleosomes at attracting DNA integrations. These results may be testedin vitroand they may help to understand patterns of DNA insertions with implications in genome evolution and gene therapy.
Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex
Authors: Zhou Xueyin , Yang Yuqi , Wang Guopeng , Wang Shanshan , Sun Dongjie , Ou Xiaomin , Lian Yuke , Li Long
Published: June 2023

Most mitochondrial proteins need to be imported from the cytosol. Over half of mitochondrial proteins are imported through the pre-sequence pathway that is controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. It is unclear on the molecular level how proteins cross the mitochondrial double membranes through the TOM and TIM23 complexes. Here, we report the assembly of the active TOM-TIM23 supercomplex with translocating polypeptide substrates captured in the import pathway. Electron cryo-microscopy (Cryo-EM) analyses reveal that during translocation across the outer membrane, the polypeptide substrates pass through the center of the Tom40 channel while interacting with a glutamine-rich patch in the inner wall of Tom40. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17, and Mgr2 in the inner membrane. Tim17 and Mgr2 shield the polypeptide substrates from the lipid environment. The import pathway consists of two highly conserved residue patches of Tim17, one negatively charged patch at the entrance and one hydrophobic patch in the middle of the pathway. These data reveal an unexpected pre-sequence pathway mediated by the TOM-TIM23 supercomplex for facilitating protein import across the double membranes of mitochondria.
Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment
Authors: Rowdo Florencia P. Madorsky , Xiao Gu , Khramtsova Galina F , Nguyen John , Olopade Olufunmilayo I , Martini Rachel , Stonaker Brian , Boateng Richard , Oppong Joseph K. , Adjei Ernest K. , Awuah Baffour , Kyei Ishmael , Aitpillah Frances S. , Adinku Michael O. , Ankomah Kwasi , Osei-Bonsu Ernest B. , Gyan Kofi K. , Altorki Nasser K. , Cheng Esther , Ginter Paula S. , Hoda Syed , Newman Lisa , Elemento Olivier , Davis Melissa B. , Martin M. Laura , Bargonetti Jill
Published: June 2023

Poly (ADP-ribose) polymerase inhibitors (PARPi) are used for patients withBRCA1/2mutations, but patients with other mutations may benefit from PARPi treatment. Another mutation that is present in more cancers thanBRCA1/2is mutation to theTP53gene. In 2D breast cancer cell lines, mutant p53 (mtp53) proteins tightly associate with replicating DNA and Poly (ADP-ribose) polymerase (PARP) protein. Combination drug treatment with the alkylating agent temozolomide and the PARPi talazoparib kills mtp53 expressing 2D grown breast cancer cell lines. We evaluated the sensitivity to the combination of temozolomide plus PARPi talazoparib treatment to breast and lung cancer patient-derived tumor organoids (PDTOs). The combination of the two drugs was synergistic for a cytotoxic response in PDTOs with mtp53 but not for PDTOs with wtp53. The combination of talazoparib and temozolomide induced more DNA double-strand breaks in mtp53 expressing organoids than in wild-type p53 expressing organoids as shown by increased ψ-H2AX protein expression. Moreover, breast cancer tissue microarrays (TMAs) showed a positive correlation between stable p53 and high PARP1 expression in sub-groups of breast cancers, which may indicate sub-classes of breast cancers sensitive to PARPi therapy. These results suggest that mtp53 could be a biomarker to predict response to the combination of PARPi talazoparib-temozolomide treatment.
Machine learning prediction of enzyme optimum pH
Authors: Gado Japheth E. , Knotts Matthew , Shaw Ada Y. , Marks Debora , Gauthier Nicholas P. , Sander Chris , Beckham Gregg T.
Published: June 2023

The relationship between pH and enzyme catalytic activity, especially the optimal pH (pHopt) at which enzymes function, is critical for biotechnological applications. Hence, computational methods to predict pHopt will enhance enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at specific pH levels, and by elucidating sequence-function relationships. In this study, we proposed and evaluated various machine-learning methods for predicting pHopt, conducting extensive hyperparameter optimization, and training over 11,000 model instances. Our results demonstrate that models utilizing language model embeddings markedly outperform other methods in predicting pHopt. We present EpHod, the best-performing model, to predict pHopt, making it publicly available to researchers. From sequence data, EpHod directly learns structural and biophysical features that relate to pHopt, including proximity of residues to the catalytic center and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pHopt prediction and will potentially speed up the development of enzyme technologies.
The Arabidopsis BUB1/MAD3 family protein BMF3 requires BUB3.3 to recruit CDC20 to kinetochores in spindle assembly checkpoint signaling
Authors: Deng Xingguang , Peng Felicia , Tang Xiaoya , Lee Yuh-Ru Julie , Lin Hong-Hui , Liu Bo
Published: June 2023

Mitosis is monitored by the spindle assembly checkpoint (SAC) which remains active until all chromosomes have their kinetochores attached to microtubules originated from opposite spindle poles. Plants produce both highly conserved and sequence-diverged SAC components, so it has been largely unknown how SAC activation leads to the assembly of these proteins at the unattached kinetochores to prevent anaphase onset in plants. InArabidopsis thaliana, the noncanonical BUB3.3 protein was detected at kinetochores throughout mitosis, unlike MAD1 and the plant specific BUB1/MAD3 family protein BMF3 that associated with unattached chromosomes only. However, BUB3.3 was required to arrest mitotic progression when one or more chromosomes did not congress at the metaphase plate. Nevertheless, BUB3.3 was not required for the kinetochore localization of other SAC components andvice versa. BUB3.3 specifically interacted with BMF3 in a novel region containing two internal repeats that were not required for the kinetochore localization of BMF3. This interaction was important for BMF3 to recruit the CDC20 protein to the unattached kinetochores. Our results showed that the Arabidopsis BUB3.3 protein functioned in the activation of BMF3 for CDC20 recruitment, rather than the recruitment of BMF proteins as what has been found in fungi and animals, in order to arrest mitosis at prometaphase. Therefore, activated SAC resulted in BUB3.3-independent localization of BMF3 and MAD1 to kinetochores and BUB3.3-dependent licensing of BMF3 for CDC20 recruitment inA.thaliana.

SIGNIFICANCE STATEMENT

Mitotic progression into anaphase is monitored by spindle assembly checkpoint that is poorly understood in plants. UsingArabidopsis thalianaas a reference system, we discovered a novel interaction pattern centered at the BUB1 and MAD3 protein BMF3 at kinetochores. A noncanonical isoform of the evolutionarily conserved BUB3 family protein BUB3.3 interacted with two novel internal repeats in BMF3 for recruiting the CDC20 protein to unattached kinetochores in order to inhibit its function in anaphase onset. Hence, our work sheds light on how spindle assembly checkpoint operates in flowering plants that produce the highly conserved BUB3.3 protein but highly divergent BMF proteins.
Development of a computational model to inform environmental surveillance sampling plans forSalmonella entericaserovar Typhi in wastewater
Authors: Burnor Elisabeth , Morin Cory W. , Shirai Jeffry H. , Zhou Nicolette A. , Meschke John Scott
Published: June 2023

Typhoid fever – an acute febrile disease caused by infection with the bacteriumSalmonella entericaserotype Typhi (S.Typhi) – continues to be a leading cause of global morbidity and mortality, especially in developing countries with limited access to safe drinking water and adequate sanitation. Environmental surveillance, the process of detecting and enumerating disease-causing agents in wastewater, enables estimating disease prevalence and trends within a community and is a useful tool to monitor the circulation of typhoid fever in endemic regions. This study presents a computational model, which combines dynamic and probabilistic modeling techniques, to predict – on a spatial and temporal scale – the probability of detectingS.Typhi in a wastewater system. This model may be utilized in communities to inform environmental surveillance sampling plans and may provide useful insight into selecting appropriate sampling locations and times.
Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury
Authors: DiGiovanni Gianluca T. , Han Wei , Sherrill Taylor , Taylor Chase J. , Nichols David S. , Geis Natalie M. , Singha Ujjal K. , Calvi Carla L. , Scott McCall A. , Dixon Molly M. , Lui Yang , Jang Ji-Hoon , Gutor Sergey S. , Polosukhin Vasiliy V. , Blackwell Timothy S. , Kropski Jonathan A. , Gokey Jason J.
Published: June 2023

A hallmark of idiopathic pulmonary fibrosis (IPF) and other interstitial lung diseases is dysregulated repair of the alveolar epithelium. The Hippo pathway effector transcription factors YAP and TAZ have been implicated as essential for type 1 and type 2 alveolar epithelial cell (AT1 and AT2) differentiation in the developing lung, yet aberrant activation of YAP/TAZ is a prominent feature of the dysregulated alveolar epithelium in IPF. In these studies, we sought to define the functional role of YAP/TAZ activity during alveolar regeneration. We demonstrate that Yap and Taz are normally activated in AT2 cells shortly after injury, and deletion of Yap/Taz in AT2 cells led to pathologic alveolar remodeling, failure of AT2 to AT1 cell differentiation, increased collagen deposition, exaggerated neutrophilic inflammation, and increased mortality following injury induced by a single dose of bleomycin. Loss of Yap/Taz activity prior to a LPS injury prevented AT1 cell regeneration, led to intra-alveolar collagen deposition, and resulted in persistent innate inflammation. Together these findings establish that AT2 cell Yap/Taz activity is essential for functional alveolar epithelial repair and prevention of fibrotic remodeling.
An uncanonical CDK6 activity inhibits cilia function by suppressing axoneme polyglutamylation
Authors: He Kai , Sun Xiaobo , Chen Chuan , Luc San , Hao Jielu , Zhang Yingyi , Huang Yan , Wang Haitao , Ling Kun , Hu Jinghua
Published: June 2023

Tubulin polyglutamylation is a post-translational modification that occurs primarily along the axoneme of cilia. Defective axoneme polyglutamylation impairs cilia function and has been correlated with ciliopathies, including Joubert Syndrome (JBTS). However, the precise mechanisms regulating proper axoneme polyglutamylation remain vague. Here, we show that Cyclin-Dependent Kinase 6 (CDK6), but not its paralog CDK4, localizes to cilia base and suppresses axoneme polyglutamylation by phosphorylating RAB11-interacting protein FIP5 at site S641, a critical regulator of cilia import of glutamylases. S641 phosphorylation disrupts the ciliary recruitment of FIP5 by impairing its association with RAB11, thereby reducing the ciliary import of glutamylases. Interestingly, significant upregulation of CDK6 and defective axoneme polyglutamylation were observed in Autosomal dominant polycystic kidney disease (ADPKD) cells. Encouragingly, the FDA-approved CDK4/6 inhibitor Abemaciclib can effectively restore cilia function in JBTS and ADPKD cells with defective glutamylation and suppresses renal cystogenesis in anex vivoADPKD model. In summary, our study elucidates regulatory mechanisms governing axoneme polyglutamylation and suggests developing CDK6-specific inhibitors could be a promising therapeutic strategy to enhance cilia function in ciliopathy patients.
PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida
Authors: Koh Eugene , Goh William , Julca Irene , Villanueva Erielle , Mutwil Marek
Published: June 2023

The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ∼60,000 manually annotated RNA-seq samples, and more than four million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis and investigating the biosynthetic pathway components of capsaicin inCapsicum annuum. The database is freely available athttps://expression.plant.tools/.
Pax3 and Pax7 function in combination with Mitf to generate melanophores and xanthophores in medaka and zebrafish
Authors: Miyadai Motohiro , Takada Hiroyuki , Shiraishi Akiko , Kimura Tetsuaki , Watakabe Ikuko , Kobayashi Hikaru , Nagao Yusuke , Naruse Kiyoshi , Higashijima Shin-ichi , Shimizu Takashi , Kelsh Robert N. , Hibi Masahiko , Hashimoto Hisashi
Published: June 2023

Neural crest cells generate numerous derivatives, including pigment cells, and are a model for studying how fate specification from multipotent progenitors is controlled. In mammals, the core gene regulatory network (GRN) for melanocytes (their only pigment cell-type) contains three transcription factors Sox10, Pax3 and Mitf, with the latter considered a master regulator of melanocyte development. In teleosts, which have three to four pigment cell types (melanophores, iridophores and xanthophores, plus leucophores e.g. in medaka), GRNs governing fate specification are poorly understood, although Mitf function is considered conserved. Here, we show that the regulatory relationships between Sox10, Pax3 and Mitf are conserved in zebrafish, but the role for Mitf is more complex than previously emphasised, affecting xanthophore development too. Similarly, medaka Mitf is necessary for melanophore, xanthophore and leucophore formation. Furthermore, expression patterns and mutant phenotypes ofpax3andpax7suggest that Pax3 and Pax7 act sequentially, activatingmitfexpression. Pax7 modulates Mitf function, driving co-expressing cells to differentiate as xanthophores and leucophores rather than melanophores. We propose that pigment cell fate specification is better considered as resulting from the combinatorial activity of Mitf with other transcription factors.
First large-scale peach gene coexpression network: A new tool for predicting gene function
Authors: Pérez de los Cobos Felipe , García-Gómez Beatriz E. , Orduña-Rubio Luis , Batlle Ignasi , Arús Pere , Matus José Tomás , Eduardo Iban
Published: June 2023

Transcriptomics studies generate enormous amounts of biological information. Nowadays, representing this complex data as gene coexpression networks (GCNs) is becoming commonplace. Peach is a model for Prunus genetics and genomics, but identifying and validating genes associated to peach breeding traits is a complex task. A GCN capable of capturing stable gene-gene relationships would help researchers overcome the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created the first large-scale GCN in peach, applying aggregated and non-aggregated methods to create four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations using a machine-learning algorithm based on the ‘guilty-by-association’ principle. The GCN with the best performance was COO300, encompassing 21,956 genes and an average AUROC of 0.746. To validate its performance predicting gene function, we used two well-characterized genes involved in fruit flesh softening in peach: the endopolygalacturonasesPpPG21andPpPG22. Genes coexpressing withPpPG21andPpPG22were extracted and named as melting flesh (MF) subnetwork. Finally, we performed an enrichment analysis of MF subnetwork and compared the results with the current knowledge regarding peach fruit softening process. The MF subnetwork mainly included genes involved in cell wall expansion and remodeling, with expression triggered by ripening-related phytohormones such as ethylene, auxin and methyl jasmonates. All these processes are closely related with peach fruit softening and therefore related to the function ofPpPG21andPpPG22. These results validate COO300 as a powerful tool for peach andPrunusresearch. COO300, renamed as PeachGCN v1.0, and the scripts necessary to perform a function prediction analysis using it, are available athttps://github.com/felipecobos/PeachGCN.
The mechanism for polar localization of the type IVa pilus machine
Authors: Herfurth Marco , Pérez-Burgos María , Søgaard-Andersen Lotte
Published: June 2023

Type IVa pili (T4aP) are important for bacterial motility, adhesion, biofilm formation and virulence. This versatility is based on their cycles of extension, adhesion, and retraction. The conserved T4aP machine (T4aPM) drives these cycles, however the piliation pattern varies between species. To understand how these patterns are established, we focused on the T4aPM inMyxococcus xanthusthat assembles following an outside-in pathway, starting with the polar incorporation of the PilQ secretin forming a multimeric T4aP conduit in the outer membrane. We demonstrate that PilQ recruitment to the nascent poles initiates during cytokinesis, but most is recruited to the new poles in the daughters after completion of cytokinesis. This recruitment depends on the peptidoglycan-binding AMIN domains in PilQ. Moreover, the pilotin Tgl stimulates PilQ multimerization in the outer membrane, is transiently recruited to the nascent and new poles in a PilQ-dependent manner, and dissociates after completion of secretin assembly. Altogether, our data support a model whereby PilQ polar recruitment and multimerization occur in two steps: The PilQ AMIN domains bind septal and polar peptidoglycan, thereby enabling polar Tgl localization, which then stimulates secretin multimerization in the outer membrane. Using computational analyses, we provide evidence for a conserved mechanism of T4aPM pilotins whereby the pilotin transiently interacts with the unfolded β-lip, i.e. the region that eventually inserts into the outer membrane, of the secretin monomer. Finally, we suggest that the presence/absence of AMIN domain(s) in T4aPM secretins determines the different T4aPM localization patterns across bacteria.

Importance

Type IVa pili (T4aP) are widespread bacterial cell surface structures with important functions in motility, surface adhesion, biofilm formation and virulence. Different bacteria have adapted different piliation patterns. To address how these patterns are established, we focused on the bipolar localization of the T4aP machine in the model organismM. xanthusby studying the localization of the PilQ secretin, the first component of this machine that assembles at the poles. Based on experiments using a combination of fluorescence microscopy, biochemistry and computational structural analysis, we propose that PilQ, and specifically its AMIN domains, binds septal and polar peptidoglycan, thereby enabling polar Tgl localization, which then stimulates PilQ multimerization in the outer membrane. We also propose that the presence and absence of AMIN domains in T4aP secretins determine the different piliation patterns across bacteria.
Cellular insights of beech leaf disease reveal abnormal ectopic cell division of symptomatic interveinal leaf areas
Authors: Vieira Paulo , Kantor Mihail R. , Jansen Andrew , Handoo Zafar A. , Eisenback Jonathan D.
Published: June 2023

The beech leaf disease nematode,Litylenchus crenataesubsp.mccannii,is recognized as a newly emergent nematode species that causes beech leaf disease (BLD) in beech trees (Fagusspp.) in North America. Changes of leaf morphology induced by BLD can provoke dramatic effects into the leaf architecture and consequently to tree performance and development. The initial symptoms of BLD appear as dark green interveinal banding patterns of the leaf. Despite the fast progression of this disease, the cellular mechanisms leading to the formation of such type of aberrant leaf phenotype remains totally unknown. To understand the cellular basis of BLD, we employed several microscopy approaches to provide an exhaustive characterization of nematode-infected buds and leaves. Histological sections revealed a dramatic cell change composition of these nematode-infected tissues. Diseased bud scale cells were typically hypertrophied and showed a high variability of size. Moreover, while altered cell division had no influence on leaf organogenesis, induction of cell proliferation on young leaf primordia led to a dramatic change in cell layer architecture. Hyperplasia and hypertrophy of the different leaf cell layers, coupled with an abnormal proliferation of chloroplasts specially in the spongy mesophyll cells, resulted in the typical interveinal leaf banding. These discrepancies in leaf cell structure were depicted by an abnormal rate of cellular division of the leaf interveinal areas infected by the nematode, promoting significant increase of cell size and leaf thickness. The formation of symptomatic BLD leaves is therefore orchestrated by distinct cellular processes, to enhance the value of these feeding sites and to improve their nutrition status to the nematode. These results revealed a high specialized mode of parasitism ofL. crenataesubsp.mccannii.
Exposure to the aryl hydrocarbon receptor agonist dioxin disrupts formation of the muscle, nerves, and vasculature in the developing jaw
Authors: Cintrón-Rivera Layra G. , Burns Nicole , Patel Ratna , Plavicki Jessica
Published: June 2023

Human exposures to environmental pollutants can disrupt embryonic development and impact juvenile and adult health outcomes by adversely affecting cell and organ function. Notwithstanding, environmental contamination continues to increase because of industrial development, insufficient regulations, and the mobilization of pollutants due to extreme weather events. Dioxins are a class of structurally related persistent organic pollutants that are highly toxic, carcinogenic, and teratogenic. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent dioxin compound and has been shown to induce toxic effects in developing organisms by activating the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor targeted by multiple persistent organic pollutants. Contaminant-induced AHR activation results in malformations in the craniofacial cartilages and neurocranium; however, the mechanisms mediating these phenotypes are not entirely understood. In this study, we utilized the optically transparent zebrafish model to elucidate novel transcriptional and structural targets of embryonic TCDD exposure leading to craniofacial malformations. To this end, we exposed zebrafish embryos at 4 hours post fertilization (hpf) to TCDD and employed a mixed-methods approach utilizing immunohistochemistry staining, transgenic reporter lines, fixed andin vivoconfocal imaging, and timelapse microscopy to determine the targets mediating TCDD-induced craniofacial phenotypes. Our data shows that embryonic TCDD exposure reduced jaw and pharyngeal arch Sox10+ chondrocytes and Tcf21+ pharyngeal mesoderm progenitors. Exposure to TCDD correspondingly led to a reduction in collagen type II deposition in Sox10+ domains. Embryonic TCDD exposure impaired development of tissues derived from or guided by Tcf21+ progenitors, namely: nerves, muscle, and vasculature. Specifically, TCDD exposure disrupted development of the hyoid and mandibular arch muscles, decreased neural innervation of the jaw, resulted in compression of cranial nerves V and VII, and led to jaw vasculature malformations. Collectively, these findings reveal novel transcriptional and structural targets of TCDD-induced toxicity, showcasing how contaminant exposures lead to congenital craniofacial malformations.

Highlights

Embryonic TCDD exposure diminishes Sox10+ craniofacial chondrocytes.

Following TCDD exposure Col2a1 deposition is reduced in Sox10+ domains.

Exposure to TCDD decreases Tcf21+ progenitors and impairs muscle formation.

TCDD exposure leads to defects jaw innervation and cranial nerve establishment.

Early TCDD exposure results in vasculature malformations in the jaw.

Graphical Abstract
Characterization of the Oral Bacteriome of the Healthy Lewis Rat
Authors: Schramm Sareda TJ , DeCurtis Emily , Wheelis Sutton E. , Jorgeson Ian , Rodrigues Danieli BC , Palmer Kelli
Published: June 2023

Rodents are the most frequently utilized animals forin vivoresearch, and rats are the most abundant rodent used to study peri-implantitis disease and progression. However, there are very few studies available that elucidate the healthy oral microbiome of rats. The aim of this study was to characterize the healthy oral bacteriome of the male Lewis rat at two unique niches, the gums and first molar, by sequencing the 16S rDNA v1-v3 region. We collected the microbiota of 12 male Lewis rats at the toothless alveolar crest and the first molar, on both sides of the mouth. We identified an average of 20,820 sequences per sample. There were no significant differences between the rat groups or sample sites in the diversity (α or β) of the bacteriome. A total of 359 amplicon sequence variants (ASVs) were identified in the bacteriome, correlating to the phylaFirmicutes,Actinobacteria,Proteobacteria, andBacteroidetes. Parallels exist at the genus level between human and rat oral bacteriomes, however, the overall diversity between comparable sites is lower in rats than humans. Similar findings were reached when using pooled or individual swab samples of rat mouths. This study characterizes two unique ecological niches within the healthy rat oral bacteriome and provides a baseline for comparison with future studies.

IMPORTANCE

Rats are frequently used for dental research, but little is known about their normal oral microbiota. Here, we use DNA sequence analysis to identify bacterial groups colonizing the rat mouth at the tooth surface and at the gums. This work contributes to our knowledge of bacterial diversity in the rat mouth.
snoRNA-guided tRNA 2’-O-methylation controls codon-biased gene expression and cellular states
Authors: Zhang Minjie , Li Kongpan , Bai Jianhui , Van Damme Ryan , Zhang Wei , Alba Mario , Stiles Bangyan L. , Chen Jian-Fu , Lu Zhipeng
Published: June 2023

snoRNAs are a large family of noncoding (nc)RNAs present across eukaryotes and archaea. While a subset of them guide 2’-O- methylation (Nm) and pseudouridylation (Ψ) of rRNAs and snRNAs, targets of most snoRNAs remain unknown. Here we used PARIS2 to map snoRNA targets, revealing an extensive and conserved snoRNA-tRNA interaction network. Using optimized denatured RiboMeth-seq (dRMS), we discovered snoRNA-guided Nm sites in ncRNAs, including tRNAs. Loss of snoRNAs and their associated 2’-O-methyltransferase FBL reduced tRNA modifications and increased fragmentation. CRISPR knockout of the D97/D133 family of snoRNAs reduced the activity and levels of several target tRNAs, including elongator (e)Met-CAU, leading to codon-biased transcriptome and translatome in human cells. The codon-biased gene expression tipped the balance between the dichotomous cellular states of proliferation and differentiation, and skewed germ layer potential of mouse embryonic stem cells. Together, we discovered a snoRNA-guided tRNA modification mechanism controlling codon-biased gene expression and cellular states.
Structural Basis for Autoinhibition by the Dephosphorylated Regulatory Domain of Ycf1
Authors: Khandelwal Nitesh Kumar , Tomasiak Thomas M.
Published: June 2023

Yeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding Cassette (ABC) transporters characterized by long flexible linkers, notably the regulatory domain (R-domain). R-domain phosphorylation is necessary for activity, whereas dephosphorylation induces autoinhibition through an undefined mechanism. Because of its transient and dynamic nature, no structure of the dephosphorylated Ycf1 exists, limiting understanding of this R-domain regulation. Here, we capture the dephosphorylated Ycf1 using cryo-EM and show that the unphosphorylated R-domain indeed forms an ordered structure with an unexpected helix-strand hairpin topology bound within the Ycf1 substrate cavity. This architecture and binding mode resemble that of a viral peptide inhibitor of an ABC transporter and the secreted bacterial WXG peptide toxins. We further reveal the subset of phosphorylation sites within the hairpin turn that drive the reorganization of the R-domain conformation, suggesting a mechanism for Ycf1 activation by phosphorylation-dependent release of R-domain mediated autoinhibition.
The HPV8 E6 protein targets the Hippo and Wnt signaling pathways as part of its arsenal to restrain keratinocyte differentiation
Authors: Wu Sharon C. , Grace Miranda , Munger Karl
Published: June 2023

Infections with β-genus HPVs cause hyperplastic cutaneous lesions. In individuals with the rare hereditary skin disease, epidermodysplasia verruciformis, such lesions can progress to cutaneous squamous cell carcinomas (cSCC). β-HPV infections may also underlie cSCC development in chronically immunosuppressed individuals. Despite their prevalence and disease association, these viruses are not as well studied as the cancer-associated high-risk α-genus HPVs. HPV-associated lesions are characterized by a marked expansion of dividing, basal-like, poorly differentiated viral cells that contain viral genomes. This reflects the ability of HPVs to inhibit epithelial cell differentiation which is likely driven by the need to establish and maintain long-term viral infections in basal-like epithelial cells. Remarkably, the β-HPVs accomplish this by targeting different cellular effectors than the α-genus HPVs. It was previously reported that the HPV8 E6 protein restrains epithelial cell differentiation by inhibiting Notch and TGF-β signaling. Here we report that the HPV8 E6 protein can subvert Hippo signaling by activating TEAD transcriptional programs that inhibit the expression of keratinocyte differentiation markers. Moreover, we determined that HPV8 E6 can interfere with gene expression programs triggered by Wnt signaling by binding to the β-catenin-associated transcriptional co-activator BCL9L and that this also serves to restrain the expression of epithelial differentiation markers. Hence the HPV8 E6 protein has evolved a remarkably large array of mechanisms to subvert the differentiation program of the infected epithelial cells.

IMPORTANCE

Human papillomaviruses (HPVs) infect basal epithelial cells and cause a dramatic expansion of basal-like, proliferative cells. This reflects the ability of papillomaviruses to delay keratinocyte differentiation thereby maintaining aspects of the basal cell identity of persistently infected cells. This may enable papillomaviruses to establish and maintain long-term infections in squamous epithelial tissues. Previous work has revealed that the ability of β-HPV8 E6 protein to inhibit NOTCH and TGF-β signaling importantly contributes to this activity. Here we present evidence that HPV8 E6 also subverts Hippo and Wnt signaling and that these activities also aid in restraining keratinocyte differentiation.
Protocol for a scoping review of the impact of digital assistive technologies on the quality of life for people with dementia
Authors: Schneider Charlotte , Kowatsch Tobias , Vinay Rasita
Published: June 2023

Introduction

Digital assistive technologies (e.g., applications, wearables, and robots) have emerged as promising tools for managing various aspects of daily life, such as basic assistance, encompassing social interaction, memory support, leisure activities, location tracking and health monitoring. In order to understand how these technologies can be utilized for people living with dementia, their impacts must first be reviewed. Currently, there is limited literature available on the topic, usually only focusing on a particular kind of digital assistive technology. Therefore, this paper presents a protocol for a scoping review that aims to provide a general overview of the impact digital assistive technologies can have on the quality of life for people living with dementia.

Methods and analysis

We will follow the scoping review framework proposed by Arksey and O’Malley. A comprehensive search will be performed to identify original research articles or clinical trials published between 2013 and 2023 across online databases. The review will encompass both qualitative and quantitative themes derived from the literature. Relevant studies will be identified through a comprehensive search using specific search terms related to the population (people with dementia), intervention (digital assistive technologies), and outcome (quality of life). The screening of titles, abstracts, and full texts will be performed to select eligible studies based on predetermined inclusion and exclusion criteria. Data will be extracted using a standardized form, and the findings will be synthesized and reported qualitatively and quantitatively.

Ethics and dissemination

Ethical approval is not required because this study is a scoping review based on published data. We intend to publish our findings in a peer-reviewed journal.

OSF Registration

https://osf.io/zcnx8/

Strengths and limitations of this study

This scoping review represents the first attempt to provide a comprehensive overview of digital assistive technologies and their impact on quality of life for PWD

An extensive search strategy will be implemented, covering five electronic databases, spanning a period of ten years.

However, given the rapidly expanding field of digital health technologies, it is possible that this systematic review may overlook ongoing or planned studies.
First genome-based characterization ofListeria monocytogenesin Costa Rica
Authors: Giralt-Zúñiga María , Redondo-Solano Mauricio , Moura Alexandra , Tessaud-Rita Nathalie , Bracq-Dieye Hélène , Vales Guillaume , Thouvenot Pierre , Leclercq Alexandre , Chaves-Ulate Carolina , Núñez-Montero Kattia , Guillén-Watson Rossy , Rivas-Solano Olga , Chanto-Chacón Grettel , Duarte-Martínez Francisco , Soto-Blanco Vanessa , Pizarro-Cerdá Javier , Lecuit Marc
Published: June 2023

Genomic data on the foodborne pathogenListeria monocytogenesfrom Central America are scarse. We analysed 92 isolates collected in Costa Rica over a decade from different regions, compared them to publicly available genomes and identified unnoticed outbreaks. This study calls for mandatory reporting of listeriosis to improve pathogen surveillance.
Microplastics may reduce the efficiency of the biological carbon pump by decreasing the settling velocity and carbon content of marine snow
Authors: Roberts Cordelia , Flintrop Clara M. , Khachikyan Alexander , Milucka Jana , Munn Colin B. , Iversen Morten H.
Published: June 2023

Plastics are pervasive in marine ecosystems and ubiquitous in both shallow and deep oceans. Microfibers, amongst other microscopic plastics, accumulate in deep sea sediments at concentrations up to four orders of magnitude higher than in surface waters. This is at odds with the fact that most microfibers are positively buoyant; therefore, it is hypothesized that settling aggregates are vectors for downward transport of microfibers in the ocean. However, little is known about the impact of microfibers on carbon export. We formed diatom aggregates with differing concentrations of microfibers using roller tanks and observed that microfiber addition stimulated aggregate formation, but decreased their structural cohesion and caused them to break apart more readily, resulting in smaller average sizes. Incorporation of positively buoyant microfibers into settling aggregates reduced their size-specific sinking velocities proportional to the microfiber concentration. Slower sinking may extend aggregate retention time in the upper ocean, thereby increasing the time available for organic matter remineralization in the upper water column. Here, we show that microfiber concentrations typical of those in the English Channel and Atlantic Ocean decrease potential export flux by 15-50%. Present day microfiber concentrations in surface waters may therefore be substantially reducing the efficiency of the biological carbon pump relative to the pre-plastic era.