bluuebunny/crossref_metadata_2025 huggingface dataset:
DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer
Authors: Nayak Tapsya , Wang Li-Ju , Ning Michael , Rubannelsonkumar Gabriela , Jin Eric , Zheng Siyuan , Houghton Peter J. , Huang Yufei , Chiu Yu-Chiao , Chen Yidong
Published: September 2022

Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to systematically link such maps. Here we present DepLink, an R Shiny server to identify genetic and pharmacologic perturbations that induce similar effects on cell viability or molecular changes. DepLink integrates heterogeneous datasets of genome-wide CRISPR loss-of-function screens, high-throughput pharmacologic screens, and perturbation expression signatures. The datasets are systematically connected by four complementary modules tailored for different query scenarios. In summary, DepLink enables easy navigation, visualization, and linkage of rapidly evolving cancer dependency maps.
Concurrent measurement of perfusion parameters related to small blood and lymphatic vessels in the human brain using dynamic dual-spin-echo perfusion (DDSEP) MRI
Authors: Cao Di , Sun Yuanqi , Su Pan , Pillai Jay J. , Qiao Ye , Lu Hanzhang , Van Zijl Peter C.M. , Knutsson Linda , Hua Jun
Published: September 2022

PURPOSE

Accumulating evidence from recent studies has indicated the importance of studying the interaction between the microvascular and lymphatic systems in the brain. To date, most imaging methods can only measure blood or lymphatic vessels separately, such as dynamic-susceptibility-contrast (DSC) MRI for blood vessels and DSC MRI in the CSF (cDSC MRI) for lymphatic vessels. An approach that can measure both blood and lymphatic vessels in a single scan will offer the advantages such as halved scan time and contrast dosage. Based on previous works on DSC and cDSC MRI, this study proposes an MRI approach for concurrent measurement of perfusion parameters related to small blood and lymphatic vessels in the brain within one single scan.

METHODS

Bloch simulations were performed to optimize a dual-echo sequence for the measurement of gadolinium(Gd)-induced blood and CSF signal changes using a short and a long echo time, respectively. MRI experiments were performed in healthy subjects to evaluate the dual-echo approach by comparing it with existing separate methods.

RESULTS

The proposed method showed consistent results in human brains as previous studies using separate methods. Signal changes from small blood vessels occurred faster than lymphatic vessels after intravenous Gd-injection.

CONCLUSION

Gd-induced signal changes in blood and CSF can be detected simultaneously in healthy subjects with the proposed sequence. To the best of our knowledge, this may be the first study in which the temporal difference in Gd-induced signal changes from small blood and lymphatic vessels after intravenous Gd-injection was measured in the same human subjects.
Historical Demography and Climate Driven Range Shifts in the Blue-spotted Salamander Under the Climate Change Scenarios
Authors: Perktaş Utku , Elverici Can , Yaylali Özge
Published: September 2022

Abstract

This study integrates phylogeography with distributional analysis to understand the demographic history and range dynamics of a limited dispersal capacity amphibian species, Blue-spotted Salamander (Ambystoma laterale), under several climate change scenarios. For this we used an ecological niche modeling approach, together with Bayesian based demographic analysis, to develop inferences regarding this species’ demographic history and range dynamics. The current model output was mostly congruent with the present distribution of the Blue-spotted Salamander. However, under both the Last Interglacial and the Last Glacial Maximum bioclimatic conditions, the model predicted a substantially narrower distribution than the present. These predictions showed almost no suitable area in the current distribution range of the species during almost the last 22.000 y before present (ybp). The predictions indicated that the distribution of this species shifted from eastern coast of northern North America to the southern part of the current distribution range of the species. The Bayesian Skyline Plot analysis, which provided good resolution of the effective population size changes over the Blue-spotted Salamander history, was mostly congruent with ecological niche modeling predictions for this species. This study provides the first investigation of the Blue-spotted Salamander’s late-Quaternary history based on ecological niche modeling and Bayesian-based demographic analysis. In terms of the main result of this study, we found that the species’ present genetic structure has been substantially affected by past climate changes, and this species has reached current distribution range almost from nothing since the Last Glacial Maximum.
A computational understanding of zoomorphic perception in the human brain
Authors: Duyck Stefanie , Bracci Stefania , de Beeck Hans Op
Published: September 2022

It is common to find objects that resemble animals on purpose (e.g., toys). While the perception of such objects as animal-like seems obvious to humans, such “Animal bias” for zoomorphic objects turned out to be a striking discrepancy between the human brain and artificial visual systems known as deep neural networks (DNNs). We provide a computational understanding of the human Animal bias. We successfully induced this bias in DNNs trained explicitly with zoomorphic objects. Alternative training schedules, focusing on previously identified differences between the brain and DNNs, failed to cause an Animal bias. Specifically, we considered the superordinate distinction between animate and inanimate classes, the sensitivity for faces and bodies, the bias for shape over texture, and the role of ecologically valid categories. These findings provide computational support that the Animal bias for zoomorphic objects is a unique property of human perception yet can be explained by human learning history.
Molecular genetics of GLUT1DS Italian pediatric cohort: 10 novel related-disease variants and structural analysis
Authors: Mauri Alessia , Duse Alessandra , Palm Giacomo , Previtali Roberto , Bova Stefania Maria , Olivotto Sara , Benedetti Sara , Coscia Francesca , Veggiotti Pierangelo , Cereda Cristina
Published: September 2022

GLUT1 deficiency syndrome (GLUT1DS1; OMIM #606777) is a rare genetic metabolic disease, characterized by infantile-onset epileptic encephalopathy, global developmental delay, progressive microcephaly and movement disorders (e.g. spasticity and dystonia). It is caused by heterozygous mutations in the SLC2A1 gene, which encodes the GLUT1 protein, a glucose transporter across the blood-brain barrier (BBB). Most commonly these variants arise de novo resulting in sporadic cases, although several familial cases with AD inheritance pattern have been described.

Twenty-seven Italian pediatric patients clinically suspect of GLUT1DS from both sporadic and familial cases have been enrolled.

We detected by trios sequencing analysis 25 different variants causing GLUT1DS. Of these, 40% of the identified variants (10 out of 25) had never been reported before, including missense, frameshift and splice site variants. Their X-ray structure analyses strongly suggested the potential pathogenic effects of these novel disease-related mutations, broadening the genotypic spectrum heterogeneity found in the SLC2A1 gene. Moreover, 24% is located in a vulnerable region of the GLUT1 protein that involves transmembrane 4 and 5 helices encoded by exon 4, confirming a mutational hotspot in the SLC2A1 gene. Lastly, we investigated possible correlations between mutation type and clinical and biochemical data observed in our GLUT1DS cohort, revealing that splice site and frameshift variants are related to a more severe phenotype and low CSF parameters.

Author summary

We investigated the molecular data of 27 pediatric patients clinically suspect of GLUT1 deficiency syndrome. By performing trios sequencing analysis, we highlighted ten novel disease-related variants, and their X-ray structure analyses, suggesting the pathogenic effects of these identified mutations. Moreover, the wide clinical and genetic heterogeneity observed in our cohort allowed possible correlations between mutation type and clinical and biochemical data. This analysis enabled to delineate that splice site and frameshift variants are related to a more severe phenotype and low CSF/glucose values. Further clinical and genetic/epigenetics studies could clearly the high phenotypic variability observed in these patients.
Tumour growth: Bayesian parameter calibration of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment
Authors: Hervas-Raluy Silvia , Wirthl Barbara , Guerrero Pedro E. , Rei Gil Robalo , Nitzler Jonas , Coronado Esther , De Mora Sainz Jaime Font , Schrefler Bernhard A. , Gomez-Benito Maria Jose , García-Aznar Jose Manuel , Wall Wolfgang A.
Published: September 2022

To unravel processes that lead to the growth of solid tumours, it is necessary to link knowledge of cancer biology with the physical properties of the tumour and its interaction with the surrounding microenvironment. Our understanding of the underlying mechanisms is however still imprecise. We therefore developed computational physics-based models, which incorporate the interaction of the tumour with its surroundings based on the theory of porous media. However, the experimental validation of such models represents a challenge to its clinical use as a prognostic tool. This study combines a physics-based model with in vitro experiments based on microfluidic devices used to mimic a 3D tumour microenvironment. By conducting a global sensitivity analysis, we identify the most influential input parameters and infer their posterior distribution based on Bayesian calibration. The resulting probability density is in agreement with the scattering of the experimental data and thus validates the modelling approach. Using the proposed workflow, we demonstrate that we can indirectly characterise the mechanical properties of neuroblastoma spheroids that cannot feasibly be measured experimentally.
Biochemical and metabolic maladaption defines pathological niches in progressive multiple sclerosis
Authors: Grant-Peters Melissa , Rich-Griffin Charlotte , Yeung Hing-Yuen , Thomas Tom , Davis Simon , Azizian Mohammad , Fisher Joseph , Fischer Roman , Cinque Gianfelice , Dendrou Calliope A.
Published: September 2022

Progressive multiple sclerosis (MS) is driven by demyelination, neuroaxonal loss, and mitochondrial damage occurring behind a closed blood-brain barrier (BBB).1,2 Patients with progressive MS typically fail to respond to available immunomodulatory drugs that reduce relapses in early disease.2 This indicates a dire need to identify non-canonical therapeutic avenues to limit neurodegeneration and promote protection and repair.3 Here, we have employed high-resolution multiomic profiling to characterise the biochemical and metabolic adaptations underpinning MS pathology, as these have been incompletely described but critically, may be amenable to BBB-permeable drug targeting. Using synchrotron radiation (SR)- and focal plane array (FPA)-based Fourier transform infrared microspectroscopy (μFTIR), we spatially mapped the biochemical features present in human progressive MS and control post-mortem brain and rare spinal cord tissue. By employing single-nuclear RNA sequencing (snRNA-seq), 10x Genomics Visium spatial transcriptomics and spatial proteomics to resolve their cellular context, we found that these biochemical features provide a uniquely and highly disease-specific barcode for distinct pathological niches within the tissue. Characterisation of the metabolic processes underpinning these niches revealed an associated re-organisation of the astrocytic landscape in the grey and white matter, with implications for the treatment of progressive MS.
Ultrastructure of synaptic connectivity within sub-regions of the SCN revealed by genetically encoded EM tag and SBEM
Authors: Calligaro Hugo , Shoghi Azarin , Chen Xinyue , Kim Keun-Young , Liu Yu Hsin , Khov Brian , Finander Benjamin , Le Hiep , Ellisman Mark H. , Panda Satchidananda
Published: September 2022

The suprachiasmatic nucleus (SCN) in the hypothalamus of the vertebrate brain is the central pacemaker regulating circadian rhythmicity throughout the body. The SCN receives photic information through melanopsin-expressing retinal ganglion cells (mRGC) to synchronize the body with environmental light cycles. Determining how these inputs fit into the network of synaptic connections on and between SCN neurons is key to impelling our understanding of the regulation of the circadian clock by light and unraveling the relevant local circuits within the SCN. To map these connections, we used a newly-developed Cre-dependant electron microscopy reporter, APEX2, to label mitochondria of mRGC axons, and serial blockface scanning electron microscopy to resolve the fine structure of mRGC in 3D volumes of the SCN. The maps thus created provide a first draft of the patterns of connectomic organization of SCN in the core and the shell, composed of different neuronal subtypes, and here shown to differ with regard to the patterning of their mRGC input as the shell receives denser mRGCs synaptic inputs compared to the core. This challenges the presently held view that photic information coming directly from the retina is mainly integrated by the core region of the SCN.
Novel phosphorylation of Rab29 that regulates its localization and lysosomal stress response in concert with LRRK2
Authors: Komori Tadayuki , Kuwahara Tomoki , Fujimoto Tetta , Sakurai Maria , Iwatsubo Takeshi
Published: September 2022

Rab proteins are small GTPases that regulate a myriad of intracellular membrane trafficking events. Rab29 is one of the Rab proteins phosphorylated by leucine-rich repeat kinase 2 (LRRK2), a Parkinson’s disease-associated kinase. Recent studies suggest that Rab29 regulates LRRK2, whereas the mechanism by which Rab29 is regulated remained unclear. Here we report a novel phosphorylation in Rab29 that is not mediated by LRRK2 and occurs under lysosomal overload stress. Mass spectrometry analysis identified the phosphorylation site of Rab29 as Ser185, and cellular expression studies of phosphomimetic mutants of Rab29 at Ser185 unveiled the involvement of this phosphorylation in counteracting lysosomal enlargement. PKCα was deemed to be responsible for this phosphorylation and control the lysosomal localization of Rab29 in concert with LRRK2. These results implicate PKCα in the lysosomal stress response pathway comprised of Rab29 and LRRK2, and further underscore the importance of this pathway in the mechanisms underlying lysosomal homeostasis.
Extracting extended vocal units from two neighborhoods in the embedding plane
Authors: Lorenz Corinna , Hao Xinyu , Tomka Tomas , Rüttimann Linus , Hahnloser Richard H.R.
Published: September 2022

Annotating and proofreading data sets of complex natural behaviors are tedious tasks because instances of a given behavior need to be correctly segmented from background noise and must be classified with minimal false positive error rate. Low-dimensional embeddings have proven very useful for this task because they provide a visually appealing overview of a data set in which relevant clusters appear spontaneously. However, low-dimensional embeddings introduce errors because they fail to preserve high dimensional distances; and embeddings represent only objects of fixed dimensionality, which conflicts with natural objects such as vocalizations that have variable dimensions stemming from their variable durations. To mitigate these issues, we introduce a semi-supervised method for simultaneous segmentation and clustering of vocalizations. We define vocal units of a given type in terms of two density-based regions in low-dimensional embedding space, one associated with onsets and the other with offsets. We demonstrate our approach on the task of clustering adult zebra finch vocalizations embedded into the 2d plane with UMAP. We show that two-neighborhood (2N) extraction allows the identification of short and long vocal renditions from continuous data streams without initially committing to a particular segmentation of the data. Also, 2N vocal extraction achieves much lower false positive error rate than approaches based on a single defining region.
Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouse
Authors: Depeux Charlotte , Branger Angèle , Moulignier Théo , Moreau Jérôme , Lemaître Jean-François , Dechaume-Moncharmont François-Xavier , Laverre Tiffany , Pauhlac Hélène , Gaillard Jean-Michel , Beltran-Bech Sophie
Published: September 2022

We tested independently the influences of increasing temperature and decreasing moisture on life history and physiological traits in the arthropodArmadillidium vulgare. Both increasing temperature and decreasing moisture led reproductive success to decrease. While the density of immune cells decreased and the β-galactosidase activity increased with increasing temperature and decreasing moisture, which suggests a negative impact of these stressors on individual performance, increased temperature and decreased moisture affected differently the other biomarkers conjuring different underlying mechanisms depending on the stress applied. Our findings demonstrate overall a negative impact of high temperature and low moisture on woodlouse welfare. Changing temperature or moisture had slightly different effects, illustrating the need to test further the respective role of each of these key components of climate change on organisms to predict more reliably the future of our ecosystems.
Targeting neuroinflammation by pharmacologic down-regulation of inflammatory pathways is neuroprotective in protein misfolding disorders
Authors: Risen Sydney J. , Boland Sean W. , Sharma Sadhana , Weisman Grace M. , Shirley Payton M. , Latham Amanda S. , Hay Arielle J.D. , Gilberto Vincenzo S. , Hines Amelia D. , Brindley Stephen , Brown Jared M. , McGrath Stephanie , Chatterjee Anushree , Nagpal Prashant , Moreno Julie A.
Published: September 2022

Neuroinflammation plays a crucial role in the development of neurodegenerative protein misfolding disorders. This category of progressive diseases includes, but is not limited to, Alzheimer’s disease, Parkinson’s disease, and prion diseases. Shared pathogenesis involves the accumulation of misfolded proteins, chronic neuroinflammation, and synaptic dysfunction, ultimately leading to irreversible neuronal loss, measurable cognitive deficits, and death. Presently, there are little to no effective treatments to halt the advancement of neurodegenerative diseases. We hypothesized directly targeting neuroinflammation by downregulating the transcription factor, NF-κB and the inflammasome protein, NLRP3, with the brain-penetrant, non-toxic, SB_NI_112, would be neuroprotective. To achieve this, we used a cocktail of RNA targeting therapeutics (SB_NI_112) shown to be brain-penetrant, non-toxic, and targeting both NF-|B and NLRP3. We utilized a mouse-adapted prion strain as a model for neurodegenerative diseases to assess aggregation of misfolded proteins, glial inflammation, neuronal loss, cognitive deficits, and lifespan. Prion-diseased mice were treated either intraperitoneally or intranasally with SB_NI_112. Behavioral and cognitive deficits were significantly protected by this combination of NF-κB and NLRP3 down-regulators. Treatment reduced glial inflammation, protected against neuronal loss, prevented spongiotic change, rescued cognitive deficits, and significantly lengthened lifespan of prion-diseased mice. We have identified a non-toxic, systemic pharmacologic that down-regulates NF-|B and NLRP3, prevents neuronal death and slows the progression of neurodegenerative disease. Though mouse models do not always predict human patient success, and the study was limited due to sample size and number of dosing methods utilized, these findings serve as a proof of principle for continued translation of the therapeutic SB_NI_112 for prion disease and other neurodegenerative diseases. Based on success in a murine prion model, we will be continual testing SB_NI_112 in a variety of neurodegenerative disease models, including Alzheimer’s Disease and Parkinson’s Disease.
Biological age and brain age in midlife: relationship to multimorbidity and mental health
Authors: Zhang Fengqing , Chang Hansoo , Schaefer Stacey M. , Gou Jiangtao
Published: September 2022

Multimorbidity, co-occurrence of two or more chronic conditions, is one of the top priorities in global health research and has emerged as the gold standard approach to study disease accumulation. As aging underlies the development of many chronic conditions, surrogate aging biomarkers are not disease-specific and capture health at the whole person level, having the potential to improve our understanding of multimorbidity. Biological age has been examined in recent years as a surrogate biomarker to capture the process of aging. However, relatively few studies have investigated the relationship between biological age and multimorbidity. More research is needed to quantify biological age using a broad range of biological markers and multimorbidity based on a comprehensive set of chronic conditions. Brain age estimated by neuroimaging data and machine learning models is another surrogate aging biomarker predictive of a wide range of health outcomes. Little is known about the relationship between brain age and multimorbidity. To answer these questions, our study investigates whether elevated biological age and accelerated brain age are associated with an increased risk of multimorbidity using a large dataset from the Midlife in the United States (MIDUS) Refresher study. Ensemble learning is utilized to combine multiple machine learning models to estimate biological age using a comprehensive set of biological markers. Brain age is obtained using convolutional neural networks and neuroimaging data. Our study is the first to examine the relationship between accelerated brain age and multimorbidity and presents the first effort to test whether sex moderates the relationship between these surrogate aging biomarkers and multimorbidity. Furthermore, it is the first attempt to explore how biological age and brain age are related to multimorbidity in mental health. Our findings hold the potential to advance the understanding of the accumulation of physical and mental health conditions, which may contribute to new strategies to improve the treatment of multimorbidity and detection of at-risk individuals.
The enrichment of self-domestication and neural crest function loci in the heritability of neurodevelopmental disorders is not independent of genomic regulatory functions
Authors: Koller Dora , Benítez-Burraco Antonio , Polimanti Renato
Published: September 2022

Self-domestication could play an important role in contributing to shape the biology of human brain and the predisposition to neurodevelopmental disorders. Leveraging genome-wide data from the Psychiatric Genomics Consortium, we tested the enrichment of self-domestication and neural crest function loci with respect to the heritability of autism spectrum disorder, schizophrenia (SCZ in East Asian and European ancestries, EAS and EUR, respectively), attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, and Tourette’s syndrome (TS). Considering only self-domestication and neural-crest-function annotations in the linkage disequilibrium score regression (LDSC) model, our partitioned heritability analysis revealed statistically significant enrichments across all disorders investigated. The estimates of the heritability enrichments for self-domestication loci were similar across neurodevelopmental disorders, ranging from 0.902 (EAS SCZ, p=4.55×10−20) to 1.577 (TS, p=5.85×10−5). Conversely, a wider spectrum of heritability enrichment estimates was present for neural crest function with the highest enrichment observed for TS (enrichment=3.453, p=2.88×10−3) and the lowest for EAS SCZ (enrichment=1.971, p=3.8l×10−3). Although these estimates appear to be strong, the enrichments for self-domestication and neural crest function were null once we included additional annotations related to different genomic features. This indicates that the effect of self-domestication on the polygenic architecture of neurodevelopmental disorders is not independent of other functions of human genome.
Clonally related, Notch-differentiated spinal neurons integrate into distinct circuits
Authors: Bello-Rojas Saul , Bagnall Martha W.
Published: September 2022

Shared lineage has diverse effects on patterns of neuronal connectivity. In mammalian cortex, excitatory sister neurons assemble into shared microcircuits, whereas throughout the Drosophila nervous system, Notch-differentiated sister neurons diverge into distinct circuits. Notch-differentiated sister neurons have been observed in vertebrate spinal cord and cerebellum, but whether they integrate into shared or distinct circuits remains unknown. Here we evaluate the connectivity between sister V2a/b neurons in the zebrafish spinal cord. Using an in vivo labeling approach, we identified pairs of sister V2a/b neurons born from individual Vsx1+ progenitors and observed that they have similar axonal trajectories and proximal somata. However, paired whole-cell electrophysiology and optogenetics revealed that sister V2a/b neurons receive input from distinct presynaptic sources, do not communicate with each other, and connect to largely distinct targets. These results resemble the divergent connectivity in Drosophila and represent the first evidence of Notch-differentiated circuit integration in a vertebrate system.
Covariance-based decoding reveals content-specific feature integration and top-down processing during visual imagery
Authors: Mantegna Francesco , Olivetti Emanuele , Schwedhelm Philipp , Baldauf Daniel
Published: September 2022

When we internally generate mental images, we need to combine multiple features into a whole. Direct evidence for such feature integration during visual imagery is still lacking. Moreover, cognitive control mechanisms, including memory and attention, exert top-down influences on the perceptual system during mental images generation. However, it is unclear whether such top-down processing is content-specific or not. Feature integration and top-down processing involve short-range connectivity within visual areas, and long-range connectivity between control and visual areas, respectively. Here, we used a minimally constrained experimental paradigm wherein imagery categories were prompted using visual word cues only, and we decoded face versus place imagery based on their underlying connectivity patterns. Our results show that face and place imagery can be decoded from both short-range and long-range connections. These findings suggest that feature integration does not require an external stimulus but occurs also for purely internally generated images. Furthermore, control and visual areas exchange information specifically tailored to imagery content.

Teaser

Decoding visual imagery from brain connectivity reveals a content-specific interconnected neural code for internal image generation.
Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis
Authors: Basnet Santosh , Ghimire Madhav Prasad , Lamichhane Tika Ram , Adhikari Rajendra , Adhikari Achyut
Published: September 2022

Human pancreatic α-amylase (HPA), which works as a catalyst for carbohydrate hydrolysis, is one of the viable targets to control type 2 diabetes. The inhibition of α-amylase lowers blood glucose levels and helps to alleviate hyperglycemia complications. Herein, we systematically screened the potential HPA inhibitors from an in-house library of natural products by molecular modeling. The modeling encompasses molecular docking, MM/GBSA binding energy calculations, MD simulations, and ADMET analysis. This research identified newboulaside B, newboulaside A, quercetin-3-O-β-glucoside, and sasastilboside A as the top four potential HPA inhibitors from the library of natural products, whose Glide docking scores and MM/GBSA binding energies range from −9.191 to −11.366 kcal/mol and −19.38 to −50.29 kcal/mol, respectively. Based on the simulation, among them, newboulaside B was found as the best HPA inhibitor. Throughout the simulation, with the deviation of 3Å (acarbose = 3Å), it interacted with ASP356, ASP300, ASP197, THR163, ARG161, ASP147, ALA106, and GLN63 via hydrogen bonding. Additionally, the comprehensive ADMET analysis revealed that it has good pharmacokinetic properties having not acutely toxic, moderately bioavailable, and non-inhibitor nature toward cytochrome P450. All the results suggest that newboulaside B might be a promising candidate for drug discovery against type 2 diabetes.

Graphical Abstract
Conserved YKL-40 changes in mice and humans after postoperative delirium
Authors: David-Bercholz Jennifer , Acker Leah , Caceres Ana I , Wu Pau Yen , Goenka Saanvi , Franklin Nathan O , Rodriguiz Ramona M , Wetsel William C , Devinney Michael , Wright Mary Cooter , Zetterberg Henrik , Yang Ting , Berger Miles , Terrando Niccolò
Published: September 2022

Delirium is a common postoperative neurologic complication among older adults. Despite its prevalence of 14-50% and likely association with inflammation, the exact mechanisms underlying postoperative delirium are unclear. This project aimed at characterizing systemic and central nervous system (CNS) inflammatory changes following surgery in both mice and humans. Matched plasma and cerebrospinal fluid (CSF) samples from the “Investigating Neuroinflammation Underlying Postoperative Brain Connectivity Changes, Postoperative Cognitive Dysfunction, Delirium in Older Adults” (INTUIT;NCT03273335) were used to parallel murine endpoints. Delirium-like behavior was evaluated in aged mice using the 5-Choice Serial Reaction Time Test (5-CSRTT). Using a well-established orthopedic surgical model in the FosTRAP reporter mouse, we detected neuronal changes in the prefrontal cortex, an area implicated in attention, but notably not in the hippocampus. In aged mice, plasma interleukin-6 (IL-6), chitinase-3-like protein 1 (YKL-40), and neurofilament light chain (NfL) levels increased after orthopedic surgery, but hippocampal YKL-40 expression was decreased. Given the growing role of YKL-40 in delirium and other neurodegenerative conditions, we assayed human plasma and CSF samples. Plasma YKL-40 levels were also similarly increased after surgery, with a trend toward greater post-operative plasma YKL-40 increase in patients with delirium. In contrast to plasma, YKL-40 levels in CSF decreased following surgery, which paralleled the findings in the mouse brain. Finally, we confirmed changes in blood-brain barrier (BBB) after surgery as early as 9 hours in mice, which warrants for more detailed and acute evaluations of BBB integrity following surgery in humans. All together, these results provide a nuanced understanding of the neuroimmune interactions underlying post-operative delirium in mice and humans, and highlight translational biomarkers to test potential cellular targets and mechanisms.
Efficient CRISPR/Cas9 mediated large insertions using long single-stranded oligonucleotide donors in C. elegans
Authors: Eroglu Matthew , Yu Bin , Derry Brent
Published: September 2022

Highly efficient generation of deletions, substitutions, and small insertions (up to ∼150 bp) into the C. elegans genome by CRISPR/Cas9 has been facilitated by use of single-stranded oligonucleotide donors as repair templates. However, efficient insertion of larger sequences such as fluorescent markers and other functional proteins remains inefficient due to lack of standardized methods for generating repair templates and labor intensive or cost prohibitive synthesis. We have optimized the simple and efficient generation of long single-stranded DNA for use as donors in CRISPR/Cas9 using a standard PCR followed by an enzymatic digest by lambda exonuclease. Comparison of long single-stranded DNA donors to previously described methods using double-stranded DNA yields orders of magnitude increased efficiency for single-stranded DNA donors. This efficiency can be leveraged to simultaneously generate multiple large insertions as well as successful edits without use of selection or co-conversion (coCRISPR) markers when necessary. Our approach complements the CRISPR/Cas9 toolkit for C. elegans to enable highly efficient insertion of longer sequences with a simple, standardized and labor-minimal protocol.
The promiscuous development of an unconventional Qa1b-restricted T cell population
Authors: Valerio Michael Manoharan , Arana Kathya , Guan Jian , Chan Shiao Wei , Yang Xiaokun , Kurd Nadia , Lee Angus , Shastri Nilabh , Coscoy Laurent , Robey Ellen A.
Published: September 2022

MHC-E restricted CD8 T cells show promise in vaccine settings, but their development and specificity remain poorly understood. Here we focus on a CD8 T cell population reactive to a self-peptide (FL9) bound to mouse MHC-E (Qa-1b) that is presented in response to loss of the MHC I processing enzyme ERAAP, termed QFL T cells. We find that mature QFL thymocytes are predominantly CD8αβ+CD4-, show signs of agonist selection, and give rise to both CD8αα and CD8αβ intraepithelial lymphocytes (IEL), as well as memory phenotype CD8αβ T cells. QFL T cells require the MHC I subunit β-2 microglobulin (β2m), but do not require Qa1bor classical MHC I for positive selection. However, QFL thymocytes do require Qa1bfor agonist selection and full functionality. Our data highlight the relaxed requirements for positive selection of an MHC-E restricted T cell population and suggest a CD8αβ+CD4-pathway for development of CD8αα IELs.
Studies on theEscherichia coliExbD Transmembrane Domain, Residue L132, and an Inhibitory Cyclic Peptide
Authors: Jana Bimal , Kopp Dale , Xie Mingchao , Vakharia-Rao Hema , Postle Kathleen
Published: September 2022

The TonB system ofEscherichia coliuses the cytoplasmic membrane protonmotive force (PMF) to energize active transport of nutrients across the otherwise unenergized outer membrane. Because it overcomes limitations for nutrient diffusion through outer membrane size-limiting porins, it provides a growth advantage and is widespread among Gram-negative bacteria. It consists of three known cytoplasmic membrane proteins, TonB, ExbB and ExbD that energize a variety of customized TonB-dependent transporters in the outer membrane. The sole ExbD transmembrane domain is proposed to consist of residues 23-43 (Kampfenkel and Braun, 1992, J. Bacteriol. 174:5485-7). Here we showed that the charge and location of residue Asp25 were essential for activity of the TonB system, thus identifying it as the only PMF-responsive element in the TonB system. The proposed boundaries of the transmembrane domain α-helix were revised to consist of residues 23-39, with residues 40-43 initiating the subsequent disordered region required for signal transduction (Kopp and Postle, 2020, J. Bacteriol. 202, e00687-19). Trapping of disulfide-linked ExbD homodimers through T42C or V43C prevented TonB system activity that was restored by addition of the reducing agent dithiothreitol, indicating a requirement for motion. Invivophoto-cross-linking experiments suggested that motion was rotation of ExbD transmembrane domains. Inactivity of ExbD L132Q, the first ExbD mutant identified, was likely due to steric hindrance. A conserved and defined site ofin vivoExbD interaction with TonB was identified. Exogenous addition of a cyclic peptide based on that site inhibited ExbD-TonB interaction while concomitantly decreasing iron transport efficiency. This suggested that a novel antimicrobial strategy against ESKAPE and other Gram-negative pathogens could be developed by targeting ExbD protein-protein interactions.
Widespread sympatry in a species-rich clade of marine fishes (Carangoidei)
Authors: Glass Jessica R. , Harrington Richard C. , Cowman Peter F. , Faircloth Brant C. , Near Thomas J.
Published: September 2022

The patterns of speciation in marine fishes are largely unknown, in part due to the deficiency of species-level phylogenies and information on species’ distributions, and partly due to conflicting relationships between species’ dispersal, range size, and patterns of co- occurrence. Most research on global patterns of marine fish speciation has focused on coral reef or pelagic species. Carangoidei is a clade of marine fishes including the trevallies, remoras, and dolphinfishes that utilize both coral reef and pelagic environments, spanning the ecologies of coral reef obligate and open-ocean species. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographic distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting a sympatric geographic distribution, regardless of node age, and most species pairs co-existing across large portions of their ranges. We also observe greater disparity in body size and water column depth utilization between sympatric than allopatric sister species. These and other ecological or behavioral attributes likely facilitate sympatry among the most closely related carangoid species, which exhibit sympatry at a larger taxonomic scale than has previously been described in marine fishes.
Traditional phylogenetic models fail to account for variations in the effective population size
Authors: Borges Rui , Kotari Ioanna , Bergman Juraj , Chase Madeline A. , Mugal Carina F. , Kosiol Carolin
Published: September 2022

A substitution represents the emergence and fixation of an allele in a population or species and is the fundamental event from which phylogenetic models of sequence evolution are devised. Because of the increasing availability of genomic sequences, we are now able to take advantage of intraspecific variability when reconstructing the tree of life. As a result, substitutions can be more realistically modeled as the product of mutation, selection, and genetic drift. However, it is still unclear whether this increased complexity affects our measures of evolutionary times and rates. This study seeks to answer this question by contrasting the traditional substitution model with a population genetic equivalent using data from 4385 individuals distributed across 179 populations and representing 17 species of animals, plants, and fungi. We found that when the population genetics dynamic is modeled via the substitution rates, the evolutionary times and rates of the two models are well correlated, suggesting that the phylogenetic model is able to capture the time and pace of its population counterpart. However, a closer inspection of this result showed that the traditional models largely ignore the effect of the effective population size, even when it is explicitly accounted for in the substitution rates. Our findings suggest that superimposing population-genetics results on the substitution rates is an effective strategy to study mutation and selection biases, while other data sources (e.g., life history traits or polymorphisms) may need to be additionally integrated to make the traditional substitution models sensitive to the impact of genetic drift. When combined with the known effect of ancestral population size on generating phylogenomic incongruence due to incomplete lineage sorting, our findings provide further evidence that unaccounted-for variations in the effective population size may be one of the primary causes of errors in phylogenetic analyses at shorter time scales.
A small molecule that inhibits the evolution of antibiotic resistance
Authors: Johnson Anna E. , Bracey Harrison , Hernandez Viera Angel Joel , Carvajal-Garcia Juan , Simsek Esra N. , Kim Kwangho , Merrikh Houra
Published: September 2022

Antimicrobial resistance (AMR) rapidly develops against almost all available therapeutics. New antibiotics target essential processes in bacteria but fail to address the root of the problem: mutagenesis and evolution. We recently proposed that inhibiting the molecular mechanisms underlying bacterial evolution is the ultimate solution to preventing AMR development. Here, we describe the first compound that inhibits the occurrence and progression of AMR by directly targeting a highly conserved bacterial evolvability factor, Mfd. We previously found that this RNA polymerase-associated translocase is required for rapid AMR development across highly divergent pathogens. Through an in vivo screen, we identified 43 potential Mfd-inhibiting compounds. Here we present on target validation, biochemical characterization, and in vivo efficacy studies of a lead compound, referred to as ARM-1. ARM-1 binds Mfd and modulates its RNA polymerase interaction. Inhibition of Mfd activity by ARM-1 delays the development of mutations and resistance acquisition, both in pure culture and during infection. Importantly, our data show that this compound prevents the evolution of AMR across highly divergent pathogens, including Pseudomonas aeruginosa, Staphylococcus aureus, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium. The novel compound we present here has the potential to develop into a clinically useful “anti-evolution” drug. This work demonstrates that the molecular mechanisms of evolution are pharmaceutically targetable, and that this strategy could help prevent AMR development.
SCFFBXW7 regulates G2-M progression through control of CCNL1 ubiquitination
Authors: O’Brien Siobhan , Kelso Susan , Steinhart Zachary , Orlicky Stephen , Mis Monika , Kim Yunhye , Lin Sichun , Sicheri Frank , Angers Stephane
Published: September 2022

FBXW7, which encodes a substrate specific receptor of an SCF E3 ligase complex, is a frequently mutated human tumor suppressor gene known to regulate the post-translational stability of various proteins involved in cellular proliferation. Here, using genome-wide CRISPR screens we report a novel synthetic lethal genetic interaction between FBXW7 and CCNL1 and describe CCNL1 as a new substrate of the SCF-FBXW7 E3 ligase. Further analysis showed that the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle since defective CCNL1 accumulation, resulting from FBXW7 mutation, leads to shorter mitotic time. Cells harboring FBXW7 loss-of-function mutations are hypersensitive to treatment with a CDK11 inhibitor, highlighting a genetic vulnerability that could be leveraged for cancer treatment.
Amyloid and Tau Pathology are Associated with Cerebral Blood Flow in a Mixed Sample of Nondemented Older Adults with and without Vascular Risk Factors for Alzheimer’s Disease
Authors: Swinford Cecily G. , Risacher Shannon L. , Vosmeier Aaron , Deardorff Rachael , Chumin Evgeny J. , Dzemidzic Mario , Wu Yu-Chien , Gao Sujuan , McDonald Brenna C. , Yoder Karmen K. , Unverzagt Frederick W. , Wang Sophia , Farlow Martin R. , Brosch Jared R. , Clark David G. , Apostolova Liana G. , Sims Justin , Wang Danny J. , Saykin Andrew J.
Published: September 2022

Alzheimer’s disease (AD) is the leading cause of dementia in individuals over 65 in the U.S. Prevalence is projected to double by 2050, but current treatments cannot stop the progression of AD. Treatments administered before severe cognitive decline may be effective; identification of biomarkers for preclinical and prodromal stages of AD is therefore imperative. Cerebral blood flow (CBF) is a potential early biomarker for AD; generally, older adults with AD have decreased CBF compared to normally aging peers. Characterization should include the relationships between CBF and AD risk factors and pathologies. We assessed the relationships between CBF quantified by arterial spin labeled MRI, hypertension,APOEε4, and tau and amyloid PET in 77 older adults: cognitively normal, subjective cognitive decline, and mild cognitive impairment. Tau and amyloid aggregation were related to altered CBF, and some of these relationships were dependent on hypertension orAPOEε4 status. Our findings suggest a complex relationship between risk factors, AD pathologies, and CBF that warrants future studies of CBF as a potential early biomarker for AD.
Ab initio calculation of mechanical, electronic and optical characteristics of chalcogenide perovskite BaZrS3 at high pressures
Authors: Rong Zhong , Zhi Chen , Jun Cao
Published: September 2022

A theoretical examination of the structural, elastic, electronic and optical properties of the chalcogenide perovskite BaZrS3 under pressures of 0 and 20 GPa was performed using density functional theory ab initio calculations. The lattice constants of the BaZrS3 structure are well reproduced from our first-principles calculations and are in excellent agreement with experimental measurements. Moreover, the values of mechanical parameters, such as the elastic constant, increased under applied pressure. The electronic parameters indicate that the chalcogenide perovskite BaZrS3 has a direct band gap of 1.75 eV. To understand the optical response, the real and imaginary parts of the dielectric function of BaZrS3 have been studied, as well as the absorption coefficient, reflectivity and extinction coefficient. The induced pressure is found to enhance the optical parameters in the different energy regions. Our calculations predict that the studied chalcogenide perovskite BaZrS3 could be a candidate in photovoltaic, optoelectronic and mechanical applications.
Structural features of chloroplast trigger factor determined at 2.6 Å resolution
Authors: Carius Yvonne , Ries Fabian , Gries Karin , Trentmann Oliver , Lancaster C. Roy D. , Willmund Felix
Published: September 2022

The folding of newly synthesized polypeptides requires the coordinated action of molecular chaperones. Prokaryotic cells and the chloroplasts of plant cells possess the ribosome-associated chaperone trigger factor, which binds nascent polypeptides at their exit stage from the ribosomal tunnel. The structure of bacterial trigger factor has been well characterized and it has a dragon-shaped conformation, with flexible domains responsible for ribosome binding, peptidyl-prolyl cis–trans isomerization (PPIase) activity and substrate protein binding. Chloroplast trigger-factor sequences have diversified from those of their bacterial orthologs and their molecular mechanism in plant organelles has been little investigated to date. Here, the crystal structure of the plastidic trigger factor from the green alga Chlamydomonas reinhardtii is presented at 2.6 Å resolution. Due to the high intramolecular flexibility of the protein, diffraction to this resolution was only achieved using a protein that lacked the N-terminal ribosome-binding domain. The eukaryotic trigger factor from C. reinhardtii exhibits a comparable dragon-shaped conformation to its bacterial counterpart. However, the C-terminal chaperone domain displays distinct charge distributions, with altered positioning of the helical arms and a specifically altered charge distribution along the surface responsible for substrate binding. While the PPIase domain shows a highly conserved structure compared with other PPIases, its rather weak activity and an unusual orientation towards the C-terminal domain points to specific adaptations of eukaryotic trigger factor for function in chloroplasts.
10-[(4-Nitrophenyl)ethynyl]-10H-phenothiazine
Authors: Okuno Tsunehisa , Doi Ikue
Published: September 2022

The title compound, C20H12N2OS, is a 10-ethynyl-10H-phenothiazine derivative. The phenothiazine unit has a butterfly shape, where the folding angle between the two benzene rings is 153.87 (7)°, which is almost as in other reported phenothiazine derivatives. The dihedral angle between the mean plane including the C atoms bonded to the phenothiazine N atom and the benzene ring of the nitrobenzene group is 10.34 (5)°. The near planar geometry of the molecule is reasonably explained by intramolecular charge-transfer interactions.