bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial working memory representations in human cortex are robust to a task-irrelevant interrupting stimulus
Authors: Vu-Cheung Kelvin , Ester Edward F , Sprague Thomas C
Published: September 2021

Visual working memory (WM) enables the maintenance and manipulation of information no longer accessible in the visual world. Previous research has identified spatial WM representations in activation patterns in visual, parietal, and frontal cortex. In natural vision, the period between the encoding of information into WM and the time when it is used to guide behavior (the delay period) is rarely “empty”, as is the case in most of the above laboratory experiments. In naturalistic conditions, eye movements, movement of the individual, and events in the environment result in visual signals which may overwrite or impair the fidelity of WM representations, especially in early sensory cortices. Here, we evaluated the extent to which a brief, irrelevant interrupting visual stimulus presented during a spatial WM delay period impaired behavioral performance and WM representation fidelity assayed using an image reconstruction technique (inverted encoding model). On each trial, participants (both sexes) viewed two target dots and were immediately post-cued to remember the precise spatial position of one dot. On 50% of trials, a brief interrupter stimulus appeared. While we observed strong transient univariate visual responses to the distracter stimulus, we saw no change in reconstructed neural WM representations under distraction, nor a change in behavioral performance on a continuous recall task. This suggests that spatial WM representations may be particularly robust to interference from incoming task-irrelevant visual information, perhaps related to their role in guiding movements.
Genetically engineered microglia-like cells have therapeutic potential for neurodegenerative disease
Authors: Plasschaert Robert N. , DeAndrade Mark P. , Hull Fritz , Nguyen Quoc , Peterson Tara , Yan Aimin , Loperfido Mariana , Baricordi Cristina , Barbarossa Luigi , Yoon John K. , Dogan Yildirim , Unnisa Zeenath , Schindler Jeffrey W. , van Til Niek P. , Biasco Luca , Mason Chris
Published: September 2021

Hematopoietic stem/progenitor cell gene therapy (HSPC-GT) results in the engraftment of genetically modified microglia-like cells (MLCs) in the brain. While HSPC-GT has shown a clear neurological benefit in the clinic for specific rare diseases, the nature of MLC engraftment in the brain and the functional characteristics of MLCs remain contentious. Here we comprehensively characterized how different routes of administration affect the engraftment and biodistribution of genetically engineered HSPC-derivatives in mice. Using high-throughput single-cell profiling, we show that MLCs bear a transcriptional signature similar to resident microglia rather than invading macrophages. However, MLCs could clearly be distinguished from resident microglia by expression of a specific set of genes. Finally, in murine models of Parkinson’s disease and frontotemporal dementia, we demonstrate that MLCs can provide therapeutically relevant levels of protein to the brain, thereby potentially opening avenues of HSPC-GT to address the underlying disease etiology of these and other similar disorders.
New Data and Collaborations at theSaccharomycesGenome Database: Updated reference genome, alleles, and the Alliance of Genome Resources
Authors: Engel Stacia R. , Wong Edith D. , Nash Robert S. , Aleksander Suzi , Alexander Micheal , Douglass Eric , Karra Kalpana , Miyasato Stuart R. , Simison Matt , Skrzypek Marek S. , Weng Shuai , Cherry J. Michael
Published: September 2021

Saccharomyces cerevisiaeis used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes.SaccharomycesGenome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.
Deconstructing Gastrulation at the Single Cell Level
Authors: Stern Tomer , Streichan Sebastian J. , Shvartsman Stanislav Y. , Wieschaus Eric F.
Published: September 2021

Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups 1,2,11–13,3–10. Here we take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.
Programmed cell death recruits macrophages into the developing mouse cochlea
Authors: Borse Vikrant , Kaur Tejbeer , Hinton Ashley , Ohlemiller Kevin , Warchol Mark E.
Published: September 2021

Programmed cell death (PCD) plays a critical role in the development and maturation of the cochlea. Significant remodeling occurs among cells of the greater epithelial ridge (GER) of Kölliker’s organ, leading to tissue regression and formation of the inner sulcus. In mice, this event normally occurs between postnatal days 5-15 (P5-15) and is regulated by thyroid hormone (T3). During this developmental time period, the cochlea also contains a large population of macrophages. Macrophages are frequently involved in the phagocytic clearance of dead cells, both during development and after injury, but the role of macrophages in the developing cochlea is unknown. This study examined the link between developmental cell death in the GER and the recruitment of macrophages into this region. Cell death in the basal GER begins at P5 and enhanced numbers of macrophages were observed at P7. This pattern of macrophage recruitment was unchanged in mice that were genetically deficient for CX3CR1, the receptor for fractalkine (a known macrophage chemoattractant). We found that injection of T3 at P0 and P1 caused GER cell death to begin at P3, and this premature PCD was accompanied by earlier recruitment of macrophages. We further found that depletion of macrophages from the developing cochlea (using CX3CR1DTR/+ mice and treatment with the CSF1R antagonist BLZ945) had no effects on the pattern of GER regression. Together, these findings suggest that macrophages are recruited into the GER region after initiation of developmental PCD, but that they are not essential for GER regression during cochlear remodeling.
Lactobacillus rhamnosusreduces the cytotoxic effects of Group B Streptococcus on HeLa cells
Authors: Cajulao Jan Mikhale , Chen Lily
Published: September 2021

Group B Streptococcus (GBS) is an opportunistic pathogen found in the vaginal tract and is a leading cause of preterm birth and neonatal illness. Aside from GBS, the vaginal tract is predominantly colonized by commensalLactobacillusspecies that are thought to protect the vaginal tract from pathogens, including GBS. Studies that examined if, and howLactobacillimodulate GBS pathogenicity remain limited. This study sought to investigate the potential protective role ofLactobacillus rhamnosusagainst GBS, using anin vitromodel system. Immunofluorescence microscopy and Scanning Electron Microscopy (SEM) captured images of infected HeLa cells and were analyzed using the image analysis program ImageJ. Results indicate that GBS causes HeLa cell detachment unlessL. rhamnosusis present. SEM images show that GBS reduces length and number of microvilli on HeLa cell surface, as well as size of secreted vesicles.L. rhamnosuspartially inhibits GBS-dependent microvilli and vesicle disruption. GBS also disrupts HeLa cell F-actin fibers unlessL. rhamnosusis present. These results reveal effects of GBS infection on the host cell cytoskeleton and implies a protective role ofL. rhamnosusagainst GBS colonization.
Copper(II) Gluconate Boosts the Anti-SARS-CoV-2 Effect of Disulfiram In Vitro
Authors: Xu Luyan , Xu Wei , Zhao Simeng , Zhao Suwen , Lu Lu , Lin Bo-Lin
Published: September 2021

Disulfiram is a 70-year-old anti-alcoholism drug, while copper(II) gluconate (Cu(Glu)2) is a commonly used food additive or copper supplement. Here we disclose that the combination of disulfiram and copper(II) gluconate drastically enhances the anti-SARS-CoV-2 activity at the cellular level as compared to disulfiram or copper(II) gluconate alone. A 1:1 mixture of disulfiram and copper(II) gluconate shows an EC50 value of 154 nM against SARS-CoV-2 at the cellular level, much lower than the 17.45 μM reported for disulfiram alone. Notably, previous clinical trials have shown that a combination of 250 mg disulfiram (0.843 mmol) and 8 mg copper(II) gluconate (0.0176 mmol) oral capsules per day is well tolerated (NCT03034135, NCT00742911). A preliminary mechanism is proposed to rationalize the observed promotional effect.
Data Representation in the DARPA SD2 Program
Authors: Roehner Nicholas , Beal Jacob , Bartley Bryan , Markeloff Richard , Mitchell Tom , Nguyen Tramy , Sumorok Daniel , Walczak Nicholas , Myers Chris , Zundel Zach , Scholz James , Hatch Benjamin , Weston Mark , Colonna-Romano John
Published: September 2021

1

Modern scientific enterprises are often highly complex and multidisciplinary, particularly in areas like synthetic biology where the subject at hand is itself inherently complex and multidisciplinary. Collaboration across many organizations is necessary to efficiently tackle such problems [6, 15], but remains difficult. The challenge is further amplified by automation that increases the pace at which new information can be produced, and particularly so for matters of fundamental research, where concepts and definitions are inherently fluid and may rapidly change as an investigation evolves [7].

The DARPA program Synergistic Discovery and Design (SD2) aimed to address these challenges by organizing the development of data-driven methods to accelerate discovery and improve design robustness, with one of the key domains under study being synthetic biology. The program was specifically organized such that teams provided complementary types of expertise and resources, and without any team being in a dominant organizational position, such that subject-matter investigations would necessarily require peer-level collaboration across multiple team boundaries. With more than 100 researchers across more than 20 organizations, several of which ran experimental facilities with high-throughput automation, participants were forced to confront challenges around effective data sharing.

The default architecture for scientific collaboration is essentially one of anarchy, with ad-hoc bilateral relations between pairs of collaborators or experimental phases (Figure 1(a)). This was by necessity the case during early phases of the SD2 program as well, in which incorporating new tools into pipelines was ad-hoc and time-consuming, and data was generally disconnected from genetic designs and experimental plans. The other typical approach for collaboration is one of “command and control”, in which a dominant organization determines the data sharing content and format for all participants (Figure 1(b)). This can be efficient, but tends to be limited in flexibility and extensibility, rendering it unsuitable for research collaboration, as indeed was found when we attempted this approach during the first year of the SD2 program. We addressed these problems with the application of distributed standards to create a “flexible rendezvous” model of collaboration (Figure 1(c)), enabling information flow to track evolving collaborative relationships, improving the sharing and utility of information across the community and supporting accelerated rates of experimentation.
Sister chromatid exchanges induced by perturbed replication are formed independently of homologous recombination factors
Authors: Heijink Anne Margriet , Stok Colin , Porubsky David , Manolika Eleni M. , Kok Yannick P. , Everts Marieke , de Boer H. Rudolf , Audrey Anastasia , Wierenga Elles , Guryev Victor , Spierings Diana C.J. , Knipscheer Puck , Chaudhuri Arnab Ray , Lansdorp Peter M. , van Vugt Marcel A.T.M.
Published: September 2021

Sister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, upon generation of irradiation-induced DNA breaks, SCE induction was compromised in cells deficient for canonical HR factors BRCA1, BRCA2 and RAD51. Contrarily, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs were enriched at common fragile sites (CFSs), and were accompanied by post-replicative single-stranded DNA (ssDNA) gaps. Moreover, PARP inhibitor-induced replication lesions were transmitted into mitosis, suggesting that SCEs originate from mitotic processing of under-replicated DNA. We found that DNA polymerase theta (POLQ) was recruited to mitotic DNA lesions, and loss of POLQ resulted in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Combined, our data show that PARP inhibition generates under-replicated DNA, which is transferred into mitosis and processed into SCEs, independently of canonical HR factors.
Inter-species comparison of the orientation algorithm directing larval chemotaxis in the genus Drosophila
Authors: Fink Elie , Louis Matthieu
Published: September 2021

Animals differ in their appearances and behaviors. While many genetic studies have addressed the origins of phenotypic differences between fly species, we are still lacking a quantitative assessment of the variability in the way different fly species behave. We tackled this question in one of the most robust behaviors displayed by Drosophila: chemotaxis. At the larval stage, Drosophila melanogaster navigate odor gradients by combining four sensorimotor routines in a multilayered algorithm: a modulation of the overall locomotor speed and turn rate; a bias in turning during down-gradient motion; a bias in turning toward the gradient; the local curl of trajectories toward the gradient (“weathervaning”). Using high-resolution tracking and behavioral quantification, we characterized the olfactory behavior of eight closely related species of the Drosophila group in response to 19 ecologically-relevant odors. Significant changes are observed in the receptive field of each species, which is consistent with the rapid evolution of the peripheral olfactory system. Our results reveal substantial inter-species variability in the algorithms directing larval chemotaxis. While the basic sensorimotor routines are shared, their parametric arrangements can vary dramatically across species. The present analysis sets the stage for deciphering the evolutionary relationships between the structure and function of neural circuits directing orientation behaviors in Drosophila.
MinION nanopore sequencing provides similar methylation estimates to Sanger bisulfite sequencing in the TRPA1 promoter region
Authors: Gombert Sara , Jahn Kirsten , Pathak Hansi , Burkert Alexandra , Schmidt Gunnar , Wiehlmann Lutz , Davenport Colin , Brändl Björn , Müller Franz-Josef , Leffler Andreas , Deest Maximilian , Frieling Helge
Published: September 2021

Bisulfite sequencing has long been considered the gold standard for measurement of DNA methylation at single CpG resolution. In the meantime, several new approaches have been developed, which are regarded as less error-prone. Since these errors were shown to be sequence-specific, we aimed to verify the methylation data of a particular region of the TRPA1 promoter obtained from our previous studies. For this purpose, we compared methylation rates obtained via direct bisulfite sequencing and nanopore sequencing. Thus, we were able to confirm our previous findings to a large extent.
Accumulation of the GSK3 target protein β-catenin is lethal for B cell precursors and malignant B cells
Authors: Jumaa Huda , Kistner Klaus M. , Setz Corinna , Taketo M. Mark , Jumaa Hassan , Jellusova Julia
Published: September 2021

Glycogen synthase kinase 3 (GSK3) is a ubiquitously expressed kinase involved in a myriad of biological processes. Although GSK3 mediated phosphorylation has been shown to induce the degradation of many pro-survival and pro-proliferation factors, cancer cells of different origin show reduced proliferation or survival after GSK3 inhibition. Our current understanding of the role GSK3 plays in normal mature B cells, B cell precursors and transformed B cells is incomplete and does not allow to assess whether GSK3 inhibitors can be used to treat B cell derived malignancies. Here we identify β-catenin as the major factor driving GSK3-inhibition induced changes in B cells. We show that β-catenin accumulation has opposing effects on cell metabolism and survival in mature B cells and B cell precursors. Moreover, we demonstrate that β-catenin destabilizes the commitment to the B cell lineage. In summary, our study identifies β-catenin induced signaling as a factor that can be exploited to limit the survival of malignant B cells.
Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants
Authors: Sandholm Niina , Rubio García Arcadio , Pekalski Marcin L , Inshaw Jamie RJ , Cutler Antony J , Todd John A
Published: September 2021

We recently mapped a genetic susceptibility locus on chromosome 6q22.33 for type 1 diabetes diagnosed below age of 7 years near the gene Protein tyrosine phosphatase receptor type K (PTPRK) and the thymocyte selection associated gene (THEMIS). As the thymus plays a central role in shaping the T cell repertoire, we aimed to identify the most likely causal genetic factors behind the association using thymocyte genomic data. In four thymocyte populations we identified 253 DNA sequence motifs underlying histone modifications. The G insertion allele of rs138300818, associated with protection from diabetes, created thymocyte motifs for multiple histone modifications and thymocyte types. The insertion also disrupted a predicted RFX5/7 transcription factor binding site. RFX7 is abundantly expressed in thymus. Chromatin state and RNA sequencing data suggested strong transcription overlapping rs138300818 in fetal thymus, while eQTL and chromatin conformation data indicated that the rs138300818 insertion is associated with lower THEMIS expression. Taken together, our results support a role for thymic THEMIS gene expression and the rs138300818 variant in promoting the development and diagnosis of type 1 diabetes at an earlier age.
CUX2 deficiency causes facilitation of excitatory synaptic transmission onto hippocampus and increased seizure susceptibility to kainate
Authors: Suzuki Toshimitsu , Tatsukawa Tetsuya , Sudo Genki , Delandre Caroline , Pai Yun Jin , Miyamoto Hiroyuki , Raveau Matthieu , Shimohata Atsushi , Ohmori Iori , Hamano Shin-ichiro , Haginoya Kazuhiro , Uematsu Mitsugu , Takahashi Yukitoshi , Morimoto Masafumi , Fujimoto Shinji , Osaka Hitoshi , Oguni Hirokazu , Osawa Makiko , Ishii Atsushi , Hirose Shinichi , Kaneko Sunao , Inoue Yushi , Moore Adrian Walton , Yamakawa Kazuhiro
Published: September 2021

CUX2 gene encodes a transcription factor that controls neuronal proliferation, dendrite branching and synapse formation, locating at the epilepsy-associated chromosomal region 12q24 that we previously identified by a genome-wide association study (GWAS) in Japanese population. A CUX2 recurrent de novo variant p.E590K has been described in patients with rare epileptic encephalopathies and the gene is a candidate for the locus, however the mutation may not be enough to generate the genome-wide significance in the GWAS and whether CUX2 variants appear in other types of epilepsies and physiopathological mechanisms are remained to be investigated. Here in this study, we conducted targeted sequencings of CUX2, a paralog CUX1 and its short isoform CASP harboring a unique C-terminus on 271 Japanese patients with a variety of epilepsies, and found that multiple CUX2 missense variants, other than the p.E590K, and some CASP variants including a deletion, predominantly appeared in patients with temporal lobe epilepsy (TLE). The CUX2 variants showed abnormal localization in human cell culture analysis. While wild-type CUX2 enhances dendritic arborization in fly neurons, the effect was compromised by some of the variants. Cux2- and Casp-specific knockout mice both showed high susceptibility to kainate, increased excitatory cell number in the entorhinal cortex, and significant enhancement in glutamatergic synaptic transmission to the hippocampus. CASP and CUX2 proteins physiologically bound to each other and co-expressed in excitatory neurons in brain regions including the entorhinal cortex. These results suggest that CUX2 and CASP variants contribute to the TLE pathology through a facilitation of excitatory synaptic transmission from entorhinal cortex to hippocampus.
Nanoscale organization of the endogenous ASC speck
Authors: Glueck Ivo M. , Mathias Grusha Primal , Strauss Sebastian , Ebert Thomas S. , Stafford Che , Agam Ganesh , Manley Suliana , Hornung Veit , Jungmann Ralf , Sieben Christian , Lamb Don C.
Published: September 2021

The NLRP3 inflammasome is a central component of the innate immune system. Its activation leads to the formation of a supramolecular assembly of the inflammasome adaptor ASC, denoted as 'ASC speck'. Different models of the overall structure of the ASC speck, as well as the entire NLRP3 inflammasome, have been reported in the literature. While many experiments involve overexpression or in vitro reconstitution of recombinant ASC, the cytoplasmic endogenous ASC speck remains difficult to study due to its relatively small size and structural variability. Here, we use a combination of fluorescence imaging techniques including dual-color 3D super-resolution imaging (dSTORM and DNA-PAINT) to visualize the endogenous ASC speck following NLRP3 inflammasome activation. We observe that the complex varies in diameter between ~800 and 1000 nm and is composed of a dense core from which filaments reach out into the periphery. We used a combination of anti-ASC antibodies as well as a much smaller nanobody for labeling and show that the larger complexes do not reliably label the dense core whereas the nanobody, which has a lower binding affinity, is less efficient in labeling the lower-density periphery. Imaging whole cells using dSTORM, furthermore, allowed us to sort the imaged structures into a quasi-temporal sequence suggesting that the endogenous ASC speck becomes mainly denser but not much larger during its formation.
Reversing chemorefraction in colorectal cancer cells by controlling mucin secretion
Authors: Cantero-Recasens G , Alonso-Marañón J , Lobo-Jarne T , Garrido M , Iglesias M , Espinosa L , Malhotra V
Published: September 2021

15% of colorectal cancers (CRC) cells exhibit a mucin hypersecretory phenotype, which is suggested to provide resistance to immune surveillance and chemotherapy. We now formally show that colorectal cancer cells build a barrier to chemotherapeutics by increasing mucins’ secretion. We show that low levels of KChIP3, a negative regulator of mucin secretion (Cantero-Recasens et al., 2018), is a risk factor for CRC patients’ relapse in subset of untreated tumours. Our results also reveal that cells depleted of KChIP3 are four times more resistant (measured as cell viability and DNA damage) to chemotherapeutics 5-Fluorouracil plus Irinotecan (5-FU+iri.) compared to control cells, whereas KChIP3 overexpressing cells are 10 times more sensitive to killing by chemotherapeutics. Similar increase in tumour cell death is observed upon chemical inhibition of mucin secretion by the sodium/calcium exchanger (NCX) blockers (Mitrovic et al., 2013). Finally, sensitivity of CRC patient-derived organoids to 5-FU+iri increases 40-fold upon mucin secretion inhibition. Reducing mucin secretion thus provides a means to control chemoresistance of mucinous colorectal cancer cells and other mucinous tumours.
The effect of pre-analytical and physiological variables on cell-free DNA fragmentation
Authors: van der Pol Ymke , Moldovan Norbert , Verkuijlen Sandra , Ramaker Jip , Boers Dries , Onstenk Wendy , de Rooij Johan , Bahce Idris , Pegtel D. Michiel , Mouliere Florent
Published: September 2021

Assays that account for the biological properties and fragmentation of cell-free DNA (cfDNA) can improve the performance of liquid biopsy. However, pre-analytic and physiological differences between individuals on fragmentomic analysis are poorly defined.

We analyzed the impact of collection tube, plasma processing time and physiology on the size distribution of cfDNA, their genome-wide representation and sequence diversity at the cfDNA fragment-ends using shallow Whole Genome Sequencing.

We observed that using different stabilizing collection tubes, or processing times does not affect the cfDNA fragment sizes, but can impact the genome-wide fragmentation patterns and fragment-end sequences of cfDNA. In addition, beyond differences depending on the gender, the physiological conditions tested between 63 individuals (age, body mass index, use of medication and chronic conditions) minimally influenced the outcome of fragmentomic methods.

Our results highlight that fragmentomic approaches have potential for implementation in the clinic, pending clear traceability of analytical and physiological factors.
Transcriptional and translational regulation of pathogenesis in Alzheimer’s disease model mice
Authors: Eastman Guillermo , Sharlow Elizabeth R. , Lazo John S. , Bloom George S. , Sotelo-Silveira José R.
Published: September 2021

Background

Defining the cellular mechanisms that drive Alzheimer’s disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and the ensuing periods of steadily declining cognition. Previous studies have emphasized changes in transcriptional regulation, but not translational regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD.

Objective

To identify genes whose expression might be regulated at the transcriptional, and especially at the translational levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2-/-) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling).

Methods

Identical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptional and translational levels separately, and also at the translational efficiency level. Regulated genes were functionally evaluated by gene ontology tools.

Results

Compared to WT mice, AD model mice had similar levels of transcriptional regulation, but displayed differences in translational regulation. A specific microglial signature associated with early stages of Aβ accumulation was up-regulated at both transcriptome and translatome levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to APP metabolism associated with neurotoxicity and neuroprotection.

Conclusion

This work represents the first genome-wide study of brain translational regulation in animal models of AD, and provides evidence of a tight and early translational regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.
In Silico Electrophysiology of Inner-Ear Mechanotransduction Channel TMC1 Models
Authors: Walujkar Sanket , Lotthammer Jeffrey M. , Nisler Collin R. , Sudar Joseph C. , Ballesteros Angela , Sotomayor Marcos
Published: September 2021

Inner-ear sensory hair cells convert mechanical stimuli from sound and head movements into electrical signals during mechanotransduction. Identification of all molecular components of the inner-ear mechanotransduction apparatus is ongoing; however, there is strong evidence that TMC1 and TMC2 are pore-forming subunits of the complex. We present molecular dynamics simulations that probe ion conduction of TMC1 models built based on two different structures of related TMEM16 proteins. Unlike most channels, the TMC1 models do not show a central pore. Instead, simulations of these models in a membrane environment at various voltages reveal a peripheral permeation pathway that is exposed to lipids and that shows cation permeation at rates comparable to those measured in hair cells. Furthermore, our analyses suggest that TMC1 gating mechanisms involve protein conformational changes and tension-induced lipid-mediated pore widening. These results provide insights into ion conduction and activation mechanisms of hair-cell mechanotransduction channels essential for hearing and balance.
Structural analysis and construction of thermostable antifungal chitinase
Authors: Kozome Dan , Uechi Keiko , Taira Toki , Fukada Harumi , Kubota Tomomi , Ishikawa Kazuhiko
Published: September 2021

Chitin is a biopolymer of N-acetyl-D-glucosamine with β-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the β-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzyme’s thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual applicable conditions. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. Based on the crystal structure and sequence alignment among other chitinases, we rationally introduced proline residues, a disulfide bond, and salt bridge in the chitinase using protein engineering methods. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family.

IMPORTANCE

We solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9 °C higher than wild type (WT) and a half-life at 60°C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including five proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.
Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment
Authors: Schwabkey Zaker , Wiesnoski Diana H. , Chang Chia-Chi , Tsai Wen-Bin , Pham Dung , Ahmed Saira S. , Hayase Tomo , Ortega Turrubiates Miriam R. , El-Himri Rawan K. , Sanchez Christopher A. , Hayase Eiko , Frenk Oquendo Annette C. , Miyama Takahiko , Halsey Taylor M. , Heckel Brooke E. , Brown Alexandria N. , Jin Yimei , Lorenzi Philip L. , Warmoes Marc O. , Tan Lin , Swennes Alton G. , Jensen Vanessa B. , Peterson Christine B. , Do Kim-Anh , Zhang Liangliang , Shi Yushu , Wang Yinghong , Galloway-Pena Jessica R. , Okhuysen Pablo C. , Daniel-MacDougall Carrie R. , Shono Yusuke , da Silva Marina Burgos , Peled Jonathan U. , van den Brink Marcel R.M. , Ajami Nadim , Wargo Jennifer A. , Rondon Gabriela , Srour Samer A. , Mehta Rohtesh S. , Alousi Amin M. , Shpall Elizabeth J. , Champlin Richard E. , Shelburne Samuel A. , Molldrem Jeffrey J. , Jamal Mohamed A. , Karmouch Jennifer L. , Jenq Robert R.
Published: September 2021

Not all cancer patients with severe neutropenia develop fever, and the fecal microbiome may play a role. In neutropenic hematopoietic cell transplant patients (n=119), 63 (53%) developed a subsequent fever and had increased fecal Akkermansia muciniphila, a mucus-degrading bacteria (p=0.006, corrected for multiple comparisons).

In mouse models, two therapies, irradiation and melphalan, similarly expanded A. muciniphila. Dietary restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Azithromycin treatment depleted A. muciniphila and preserved colonic mucus.

Dietary restriction raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila with lower pH and increased propionate prevented utilization of mucin. Treating irradiated mice with azithromycin or propionate preserved the mucus layer, lessened hypothermia, and reduced inflammatory cytokines in the colon. These results suggest that diet, metabolites and colonic mucus link the microbiome to neutropenic fever, and could guide future microbiome-based preventive strategies.
Symmetry breaking of hPSCs in micropattern generates a polarized spinal cord-like organoid (pSCO) with dorsoventral organization
Authors: Seo Kyubin , Cho Subin , Lee Ju-Hyun , Kim June Hoan , Lee Boram , Jang Hwanseok , Kim Youngju , Cho Hyo Min , Lee Sanghyuk , Park Yongdoo , Kim Hee Youn , Lee Taeseob , Park Woong-Yang , Kim Yong Jun , Yang Esther , Geum Dongho , Kim Hyun , Ryu Jae Ryun , Sun Woong
Published: September 2021

Brain organoid research is advancing, but generation of organoids with proper axis formation, which could lead to spatially ordered structures for complex brain structure and function, still remains a challenge. Axis formation and related spatial cell organization in the CNS are initiated by the symmetry breaking during the early embryo development. It has been demonstrated that the geometrically confined culture of human pluripotent stem cells (hPSCs) can be used to induce symmetry breaking and regionalized cell differentiation. In this study, we generated a polarized spinal cord organoid with a self-organized dorsoventral (DV) organization, using 2D cell patterning by geometric confinement. Initially, the application of caudalization signals to hPSCs promoted the regionalized cell differentiation along the radial axis and sprouting-like protrusion morphogenesis in cell colonies confined to ECM protein micropatterns. Detachment of colonies turned them into extended spinal cord-like organoids which maintained center- and edge-derived two poles. Further analyses including single cell RNA sequencing and spatial transcriptome analysis unveiled that these organoids contained rich repertoire of developing spinal cord cells and exhibited the spatially ordered DV domain formation along the long axis without external organizing signals. Modulation of BMP and Shh signaling can control the extent of DV coverage in organoids following the principles of embryo patterning. Our study provides a simple, and precisely controllable method to generate spatially-ordered organoids for understanding of biological principles of cell patterning and axis formation during neural development.
Lysosome-related organelles contain an expansion compartment that mediates delivery of zinc transporters to promote homeostasis
Authors: Mendoza Adelita D. , Dietrich Nicholas , Tan Chieh-Hsiang , Herrera Daniel , Kasiah Jennysue , Payne Zachary , Schneider Daniel L. , Kornfeld Kerry
Published: September 2021

Lysosome-related organelles play evolutionarily conserved roles in zinc storage, but mechanisms that control zinc flow in and out are not well understood. In C. elegans intestinal cells, the CDF-2 transporter stores zinc in these organelles during excess. Here we identify ZIPT-2.3 as the transporter that releases zinc during deficiency. The expression levels of CDF-2 and ZIPT-2.3 are reciprocally regulated in zinc excess and deficiency, establishing a fundamental mechanism of homeostasis. Super-resolution microscopy demonstrated these organelles are composed of a spherical acidified compartment and a hemispherical expansion compartment. The expansion compartment inflates during zinc excess and deficiency by vesicle fusion delivering zinc transporters. These results identify an unexpected structural feature of lysosome-related organelles that facilitates rapid transitions in the composition of zinc transporters to mediate homeostasis.
SPtsAnalysis: a high-throughput super-resolution single particle trajectory analysis to reconstruct organelle dynamics and membrane re-organization
Authors: Parutto P. , Heck J. , Lu M. , Kaminski C. , Heine M. , Avezov E. , Holcman D.
Published: September 2021

Super-resolution imaging can generate thousands of single-particle trajectories. These data can potentially reconstruct subcellular organization and dynamics, as well as measure disease-linked changes. However, computational methods that can derive quantitative information from such massive datasets are currently lacking. Here we present data analysis and algorithms that are broadly applicable to reveal local binding and trafficking interactions and organization of dynamic sub-cellular sites. We applied this analysis to the endoplasmic reticulum and neuronal membrane. The method is based on spatio-temporal time window segmentation that explores data at multiple levels and detects the architecture and boundaries of high density regions in areas that are hundreds of nanometers. By statistical analysis of a large number of datapoints, the present method allows measurements of nano-region stability. By connecting highly dense regions, we reconstructed the network topology of the ER, as well as molecular flow redistribution, and the local space explored by trajectories. Segmenting trajectories at appropriate scales extracts confined trajectories, allowing quantification of dynamic interactions between lysosomes and the ER. A final step of the method reveals the motion of trajectories relative to the ensemble, allowing reconstruction of dynamics in normal ER and the atlastin-null mutant. Our approach allows users to track previously inaccessible large scale dynamics at high resolution from massive datasets. The SPtsAnalysis algorithm is available as an ImageJ plugin that can be applied by users to large datasets of overlapping trajectories and offer a standard of SPTs metrics.
Sex differences in cardio-pulmonary pathology of SARS-CoV2 infected and Trypanosoma cruzi co-infected mice
Authors: Dhanyalayam Dhanya , Lizardo Kezia , Oswal Neelam , Thangavel Hariprasad , Dolgov Enriko , Perlin David S. , Nagajyothi Jyothi F.
Published: September 2021

Background

Coronavirus disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; CoV2) is a deadly contagious infectious disease. For those who survived COVID-19, post-COVID cardiac damage poses a major threat for the progression of cardiomyopathy and heart failure. Currently, the number of COVID-related cases and deaths are increasing in Latin America, where a major COVID comorbidity is Chagas’ heart disease (caused by the parasite Trypanosoma cruzi). Here, we investigated the effect of T. cruzi infection on the pathogenesis and severity of CoV2 infection and, conversely, the effect of CoV2 infection on heart pathology during coinfection.

Methodology/findings

We used transgenic human angiotensin-converting enzyme 2 (huACE2) mice infected with CoV2, T. cruzi, or coinfected with both in this study. Our study shows for the first time that white adipose tissue (WAT) serves as a reservoir for CoV2 and the persistence of CoV2 in WAT alters adipose tissue morphology and adipocyte physiology. Our data demonstrate a correlation between the loss of fat cells and the pulmonary adipogenic signaling (via adiponectin isomers) and pathology in CoV2 infection. The viral load in the lungs is inversely proportional to the viral load in WAT, which differs between male and female mice. Our findings also suggest that adiponectin-PPAR signaling may differently regulate Chagas cardiomyopathy in coinfected males and females.

Conclusion

We conclude that adipogenic signaling may play important roles in cardio-pulmonary pathogenesis during CoV2 infection and T. cruzi coinfection. The levels of adiponectin isomers differ between male and female mice during CoV2 infection and coinfection with T. cruzi, which may differently regulate inflammation, viral load, and pathology in the lungs of both the sexes. Our findings are in line with other clinical observations that reported that males are more susceptible to COVID-19 than females and suffer greater pulmonary damage.
Robust effects of working memory demand during naturalistic language comprehension in language-selective cortex
Authors: Shain Cory , Blank Idan A. , Fedorenko Evelina , Gibson Edward , Schuler William
Published: September 2021

A standard view of human language processing is that comprehenders build richly structured mental representations of natural language utterances, word by word, using computationally costly memory operations supported by domain-general working memory resources. However, three core claims of this view have been questioned, with some prior work arguing that (1) rich word-by-word structure building is not a core function of the language comprehension system, (2) apparent working memory costs are underlyingly driven by word predictability (surprisal), and/or (3) language comprehension relies primarily on domain-general rather than domain-specific working memory resources. In this work, we simultaneously evaluate all three of these claims using naturalistic comprehension in fMRI. In each participant, we functionally localize (a) a language-selective network and (b) a ‘multiple-demand’ network that supports working memory across domains, and we analyze the responses in these two networks of interest during naturalistic story listening with respect to a range of theory-driven predictors of working memory demand under rigorous surprisal controls. Results show robust surprisal-independent effects of word-by-word memory demand in the language network and no effect of working memory demand in the multiple demand network. Our findings thus support the view that language comprehension (1) entails word-by-word structure building using (2) computationally intensive memory operations that are not explained by surprisal. However, these results challenge (3) the domain-generality of the resources that support these operations, instead indicating that working memory operations for language comprehension are carried out by the same neural resources that store linguistic knowledge.

Significance Statement

This study uses fMRI to investigate signatures of working memory (WM) demand during naturalistic story listening, using a broad range of theoretically motivated estimates of WM demand. Results support a strong effect of WM demand in language-selective brain regions but no effect of WM demand in “multiple demand” regions that have previously been associated with WM in non-linguistic domains. We further show evidence that WM effects in language regions are distinct from effects of word predictability. Our findings support a core role for WM in incremental language processing, using WM resources that are specialized for language.
WDR60-mediated dynein-2 loading into cilia powers retrograde IFT and transition zone crossing
Authors: De-Castro Ana R. G. , Rodrigues Diogo R. M. , De-Castro Maria J. G. , Vieira Neide , Vieira Cármen , Carvalho Ana X. , Gassmann Reto , Abreu Carla M. , Dantas Tiago J.
Published: September 2021

The dynein-2 motor complex drives retrograde intraflagellar transport (IFT), playing a pivotal role in the assembly and functions of cilia. However, the mechanisms that regulate dynein-2 motility remain poorly understood. Here, we identify the Caenorhabditis elegans WDR60 homolog (WDR-60) and dissect the roles of this intermediate chain using genome editing and live imaging of endogenous dynein-2/IFT components. We find that loss of WDR-60 impairs dynein-2 recruitment to cilia and its incorporation onto anterograde IFT trains, reducing the availability of the retrograde motor at the ciliary tip. Consistently, we show that less dynein-2 motors power WDR-60-deficient retrograde IFT trains, which move at reduced velocities and fail to exit cilia, accumulating on the distal side of the transition zone. Remarkably, disrupting the transition zone’s NPHP module almost fully restores ciliary exit of underpowered retrograde trains in wdr-60 mutants. This work establishes WDR-60 as a major contributor to IFT and the NPHP module as a roadblock to dynein-2 passage through the transition zone.
Cochlear organoids reveal epigenetic and transcriptional programs of postnatal hair cell differentiation from supporting cells
Authors: Kalra Gurmannat , Lenz Danielle , Abdul-Aziz Dunia , Hanna Craig , Herb Brian R. , Colantuoni Carlo , Milon Beatrice , Saxena Madhurima , Shetty Amol C. , Hertzano Ronna P. , Shivdasani Ramesh A. , Ament Seth A. , Edge Albert S. B.
Published: September 2021

We explored the transcriptional and epigenetic programs underlying the differentiation of hair cells from postnatal progenitor cells in cochlear organoids. Heterogeneity in the cells including cells with the transcriptional signatures of mature hair cells allowed a full picture of possible cell fates. Construction of trajectories identified Lgr5+ cells as progenitors for hair cells and the genomic data revealed gene regulatory networks leading to hair cells. We validated these networks, demonstrating dynamic changes both in expression and predicted binding sites of these transcription factors during organoid differentiation. We identified known regulators of hair cell development, Atoh1, Pou4f3, and Gfi1, and predicted novel regulatory factors, Tcf4, an E-protein and heterodimerization partner of Atoh1, and Ddit3, a CCAAT/enhancer-binding protein (C/EBP) that represses Hes1 and activates transcription of Wnt signaling-related genes. Deciphering the signals for hair cell regeneration from mammalian cochlear supporting cells reveals candidates for HC regeneration which is limited in the adult.