bluuebunny/crossref_metadata_2025 huggingface dataset:
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing
Authors: Bhattacharya Arjun , Hamilton Alina M. , Troester Melissa A. , Love Michael I.
Published: August 2020

Targeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we presentDeCompress, a semi-reference-free deconvolution method for targeted panels.DeCompressleverages a reference RNA-seq or microarray dataset from similar tissue to expand the feature space of targeted panels using compressed sensing. Ensemble reference-free deconvolution is performed on this artificially expanded dataset to estimate cell-type proportions and gene signatures. In simulated mixtures, four public cell line mixtures, and a targeted panel (1199 samples; 406 genes) from the Carolina Breast Cancer Study,DeCompressrecapitulates cell-type proportions with less error than reference-free methods and finds biologically relevant compartments. We integrate compartment estimates intocis-eQTL mapping in breast cancer, identifying a tumor-specificcis-eQTL forCCR3(C-C Motif Chemokine Receptor 3) at a risk locus.DeCompressimproves upon reference-free methods without requiring expression profiles from pure cell populations, with applications in genomic analyses and clinical settings.
SARS-CoV-2 Infection And Longitudinal Fecal Screening In Malayan Tigers (Panthera tigris jacksoni), Amur Tigers (Panthera tigris altaica), And African Lions (Panthera leo krugeri) At The Bronx Zoo, New York, USA
Authors: Bartlett Susan L. , Diel Diego G. , Wang Leyi , Zec Stephanie , Laverack Melissa , Martins Mathias , Caserta Leonardo Cardia , Killian Mary Lea , Terio Karen , Olmstead Colleen , Delaney Martha A. , Stokol Tracy , Ivančić Marina , Jenkins-Moore Melinda , Ingerman Karen , Teegan Taryn , McCann Colleen , Thomas Patrick , McAloose Denise , Sykes John M. , Calle Paul P.
Published: August 2020

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged as the cause of a global pandemic in 2019-2020. In March 2020 New York City became the USA epicenter for the pandemic. On March 27, 2020 a Malayan tiger (Panthera tigris jacksoni) at the Bronx Zoo in New York City developed a cough and wheezing with subsequent inappetence. Over the next week, an additional Malayan tiger and two Amur tigers (P. t. altaica) in the same building and three lions (Panthera leo krugeri) in a separate building also became ill. The index case was immobilized, and physical examination and bloodwork results were unremarkable. Thoracic radiography and ultrasonography revealed peribronchial cuffing with bronchiectasis, and mild lung consolidation with alveolar-interstitial syndrome, respectively. SARS-CoV-2 RNA was identified by real-time, reverse transcriptase PCR (rRT-PCR) on oropharyngeal and nasal swabs and tracheal wash fluid. Cytologic examination of tracheal wash fluid revealed necrosis, and viral RNA was detected in necrotic cells by in situ hybridization, confirming virus-associated tissue damage. SARS-CoV-2 was isolated from the tracheal wash fluid of the index case, as well as the feces from one Amur tiger and one lion. Fecal viral RNA shedding was confirmed in all seven clinical cases and an asymptomatic Amur tiger. Respiratory signs abated within 1-5 days for most animals, though persisted intermittently for 16 days in the index case. Fecal RNA shedding persisted for as long as 35 days beyond cessation of respiratory signs. This case series describes the clinical presentation, diagnostic evaluation, and management of tigers and lions infected with SARS-CoV-2, and describes the duration of viral RNA fecal shedding in these cases. This report documents the first known natural transmission of SARS-CoV-2 from humans to animals in the USA, and is the first report of SARS-CoV-2 in non-domestic felids.
Phosphorylation of Serine114 of the transcription factor ABSCISIC ACID INSENSITIVE 4 is essential for activity
Authors: Eisner Nadav , Maymon Tzofia , Sanchez Ester Cancho , Bar-Zvi Dana , Brodsky Sagie , Finkelstein Ruth , Bar-Zvi Dudy
Published: August 2020

The transcription factor ABA-INSENSITIVE(ABI)4 has diverse roles in regulating plant growth, including inhibiting germination and reserve mobilization in response to ABA and high salinity, inhibiting seedling growth in response to high sugars, inhibiting lateral root growth, and repressing light-induced gene expression. ABI4 activity is regulated at multiple levels, including gene expression, protein stability, and activation by phosphorylation. Although ABI4 can be phosphorylated at multiple residues by MAPKs, we found that S114 is the preferred site of MPK3. To examine the possible biological role of S114 phosphorylation, we transformedabi4-1mutant plants withABI4pro::ABI4constructs encoding wild type (114S), phosphorylation-null (S114A) or phosphomimetic (S114E) forms of ABI4. Phosphorylation of S114 is necessary for the response to ABA, glucose, salt stress, and lateral root development, where theabi4phenotype could be complemented by expressing ABI4(114S) or ABI4(S114E) but not ABI4(S114A). Comparison of root transcriptomes in ABA-treated roots ofabi4-1mutant plants transformed with constructs encoding the different phosphorylation-forms of S114 of ABI4 revealed that 85% of the ABI4-regulated genes whose expression pattern could be restored by expressing ABI4(114S) are down-regulated by ABI4. Over half of the ABI4-modulated genes were independent of the phosphorylation state of ABI4; these are enriched for stress responses. Phosphorylation of S114 was required for regulation of 35% of repressed genes, but only 17% of induced genes. The genes whose repression requires the phosphorylation of S114 are mainly involved in embryo and seedling development, growth and differentiation, and regulation of gene expression.

Highlights

Transcription factor ABI4 is a substrate of MAP kinases.

MPK3 preferentially phosphorylates Serine 114 of ABI4.

Phosphorylated Serine 114 of ABI4 is required for the complementation of abi4 mutants.

Phosphorylated ABI4 acts primarily as a repressor.
A novel compound that disrupts mitotic spindle poles in human cells
Authors: Jaunky Dilan , Husser Mathieu , Larocque Kevin , Liu Peter , Thampipillai Sajinth , Forgione Pat , Piekny Alisa
Published: August 2020

We characterize the mechanism of action of a new microtubule-targeting compound in cells. Microtubule-targeting drugs are used as successful anti-cancer therapies. We synthesized a family of compounds that share a common scaffold and have several functional groups amenable to modifications. We found that one of the active derivatives, C75, reduces cell viability and prevents microtubule polymerizationin vitro. In this study, we explore the phenotypes caused by C75 in cells. It causes mitotic arrest and spindle phenotypes in several cancer cell lines in the nanomolar range. C75 can bind to the Colchicine-pocket on tubulinin vitro, but causes different effects on microtubules in cells. While Colchicine causes a decrease in microtubules and spindle pole collapse without re-growth, similar concentrations of C75 cause a rapid loss of microtubules and spindle pole fragmentation followed by microtubule re-growth to form multipolar spindles. In addition, C75 and Colchicine synergize for reduced viability and spindle phenotypes. Importantly, the phenotypes caused by C75 are similar to those caused by the depletion of ch-TOG, a microtubule polymerase, and tubulin and ch-TOG are displaced and oscillate in C75-treated cells. This suggests that C75 causes microtubule depolymerization in cells either directly or indirectly via inhibiting ch-TOG. This unique effect of C75 on microtubules warrants further exploration of its anti-cancer potential.
3D Bioprinting of Graphene Oxide-Incorporated Cell-laden Bone Mimicking Scaffolds for Promoting Scaffold Fidelity, Osteogenic Differentiation and Mineralization
Authors: Zhang Jianhua , Eyisoylu Hande , Qin Xiao-Hua , Rubert Marina , Müller Ralph
Published: August 2020

Bioprinting is a promising technique for facilitating the fabrication of engineered bone tissues for patient-specific defect repair and for developingin vitrotissue/organ models forex vivotests. However, polymer-based ink materials often result in insufficient mechanical strength, low scaffold fidelity and loss of osteogenesis induction because of the intrinsic swelling/shrinking and bioinert properties of most polymeric hydrogels. In this work, we developed a novel human mesenchymal stem cell (hMSC)-laden graphene oxide (GO)/alginate/gelatin composite bioink to form 3D bone mimicking scaffolds. Our results showed that the GO composite bioinks with higher GO concentrations improved the bioprintability, scaffold fidelity, compressive modulus and cell viability. The higher GO concentration increased the cell body size and DNA content. The 1GO group had the highest osteogenic differentiation of hMSC with the upregulation of osteogenic-related gene expression at day 42. To mimic critical-sized calvarial bone defects in mice, 3D cell-laden GO defect scaffolds with complex geometries were successfully bioprinted. 1GO maintained the best scaffold fidelity and had the highest mineral volume after culturing in the bioreactor for 42 days. Finally, the 1GO bioink has been demonstrated great potential for 3D bioprinting in applications of bone model and bone tissue engineering.
Post-tetanic potentiation lowers the energy barrier for synaptic vesicle fusion independently of Synaptotagmin-1
Authors: Huson Vincent , Meijer Marieke , Dekker Rien , ter Veer Mirelle , Ruiter Marvin , van Weering Jan , Verhage Matthijs , Cornelisse L. Niels
Published: August 2020

Previously, we showed that modulation of the energy barrier for synaptic vesicle fusion boosts release rates supralinearly (Schotten, 2015). Here we show that mouse hippocampal synapses employ this principle to trigger Ca2+-dependent vesicle release and post-tetanic potentiation (PTP). We assess energy barrier changes by fitting release kinetics in response to hypertonic sucrose. Mimicking activation of the C2A domain of the Ca2+-sensor Synaptotagmin-1 (Syt1), by adding a positive charge (Syt1D232N) or increasing its hydrophobicity (Syt14W), lowers the energy barrier. Removing Syt1 or impairing its release inhibitory function (Syt19Pro) increases spontaneous release without affecting the fusion barrier. Both phorbol esters and tetanic stimulation potentiate synaptic strength, and lower the energy barrier equally well in the presence and absence of Syt1. We propose a model where tetanic stimulation activates Syt1 dependent and independent mechanisms that lower the energy barrier independently in an additive manner to produce PTP by multiplication of release rates.
Molecular crowding in single eukaryotic cells: using cell environment biosensing and single-molecule optical microscopy to probe dependence on extracellular ionic strength, local glucose conditions, and sensor copy number
Authors: Shepherd Jack W , Lecinski Sarah , Wragg Jasmine , Shashkova Sviatlana , MacDonald Chris , Leake Mark C
Published: August 2020

The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to readout localized molecular crowding in single live yeast cells. Confocal microscopy allows us to build subcellular crowding heatmaps using ratiometric FRET, while whole-cell analysis demonstrates crowding is reduced when yeast is grown in elevated glucose concentrations. Simulations indicate that the cell membrane is largely inaccessible to these sensors and that cytosolic crowding is broadly uniform across each cell over a timescale of seconds. Millisecond single-molecule optical microscopy was used to track molecules and obtain brightness estimates that enabled calculation of crowding sensor copy numbers. The quantification of diffusing molecule trajectories paves the way for correlating subcellular processes and the physicochemical environment of cells under stress.
ELAV proteins bind and stabilize C/EBP mRNA in the induction of long-term memory in Aplysia
Authors: Mirisis Anastasios A. , Kopec Ashley M. , Carew Thomas J.
Published: August 2020

Long-term memory (LTM) formation is a critical survival process by which an animal retains information about prior experiences in order to guide future behavior. In the experimentally advantageous marine mollusk Aplysia, LTM for sensitization can be induced by the presentation of two aversive shocks to the animal’s tail. Each of these training trials recruits distinct growth factor signaling systems that promote LTM formation. Specifically, whereas intact TrkB signaling during Trial 1 promotes an initial and transient increase of the immediate early gene apc/ebp mRNA, a prolonged increase in apc/ebp gene expression required for LTM formation requires the addition of TGFβ signaling during Trial 2. Here we explored the molecular mechanisms by which Trial 2 achieves the essential prolonged gene expression of apc/ebp. We find that this prolonged gene expression is not dependent on de novo transcription, but that apc/ebp mRNA synthesized by Trial 1 is post-transcriptionally stabilized by interacting with the RNA-binding protein ApELAV. This interaction is promoted by p38 MAPK activation initiated by TGFβ. We further demonstrate that blocking the interaction of ApELAV with its target mRNA during Trial 2 blocks both the prolonged increase in apc/ebp gene expression and the behavioral induction of LTM. Collectively, our findings elucidate both when and how ELAV proteins are recruited for the stabilization of mRNA in LTM formation.

Significance Statement

In the present paper we significantly extend the general field of molecular processing in LTM by describing a novel form of pre-translational processing required for LTM which relies on the stabilization of a newly synthesized mRNA by a unique class of RNA binding proteins (ELAVs). In the broad field of molecular mechanisms of transcription-dependent LTM, there are now compelling data showing that important processing can occur after transcription of a gene, but before translation of the message into protein. Although the potential importance of ELAV proteins in LTM formation has previously been reported, to date there has been no mechanistic insight into the specific actions of ELAV proteins in stabilization of mRNAs known to be critical for LTM. Our new findings thus complement and extend this literature by demonstrating when and how this post-transcriptional gene regulation is mediated in the induction of LTM.
Multisensory processes can compensate for attention deficits in schizophrenia
Authors: Moran James K. , Keil Julian , Masurovsky Alexander , Gutwinski Stefan , Montag Christiane , Senkowski Daniel
Published: August 2020

Studies on schizophrenia (SCZ) and aberrant multisensory integration (MSI) show conflicting results. These divergent results are potentially confounded by attention deficits in SCZ. To test this, we examined the interplay between MSI and intersensory attention (IA) in healthy controls (N=27) and in SCZ (N=27). Evoked brain potentials to unisensory-visual (V), unisensory-tactile (T) or bisensory VT stimuli were measured with high density electroencephalography, whilst participants attended block-wise to either visual or tactile inputs. Behaviourally, IA effects in SCZ are uncompromised for bisensory stimuli, but diminished for unisensory stimuli. At the neural level, we observed reduced IA effects for bisensory stimuli over mediofrontal scalp regions (230-320ms) in SCZ. The analysis of MSI revealed multiple phases of integration over occipital and frontal scalp regions (240-364ms), with comparable performance between HC and SCZ. The magnitudes of IA and MSI effects were both positively related to the behavioural performance in SCZ, indicating that IA and MSI mutually facilitate bisensory stimulus processing. Our study suggests that widely intact MSI, which facilitates stimulus processing, can compensate for top-down attention deficits in SCZ. Further, the interplay of IA and MSI implies that differences in attentional demands may account for previous conflicting findings on MSI in schizophrenia.
The risks of using the chi-square periodogram to estimate the period of biological rhythms
Authors: Tackenberg Michael C. , Hughey Jacob J.
Published: August 2020

The chi-square periodogram (CSP), developed over 40 years ago, continues to be one of the most popular methods to estimate the period of circadian (circa 24-h) rhythms. Previous work has indicated the CSP is sometimes less accurate than other methods, but understanding of why and under what conditions remains incomplete. Using simulated rhythmic time-courses, we found that the CSP is prone to underestimating the period in a manner that depends on the true period and the length of the time-course. This underestimation bias is most severe in short time-courses (e.g., 3 days), but is also visible in longer simulated time-courses (e.g., 12 days) and in experimental time-courses of mouse wheel-running and ex vivo bioluminescence. We traced the source of the bias to discontinuities in the periodogram that are related to the number of time-points the CSP uses to calculate the observed variance for a given test period. By revising the calculation to avoid discontinuities, we developed a new version, the greedy CSP, that shows reduced bias and improved accuracy. Nonetheless, even the greedy CSP tended to be less accurate on our simulated time-courses than an alternative method, namely the Lomb-Scargle periodogram. Thus, although our study describes a major improvement to a classic method, it also suggests that users should generally avoid the CSP when estimating the period of biological rhythms.
The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution
Authors: Eriksson Peter R. , Clark David J.
Published: August 2020

Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form closed-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.
Embodied Cognition and Decision-Making in the Primate Superior Colliculus
Authors: Jun E.J. , Bautista A. , Nunez M.D. , Tak T. , Alvarez E. , Basso M.A.
Published: August 2020

A popular model of decision-making suggests that in primates, including humans, decisions evolve within forebrain structures responsible for preparing voluntary actions; a concert referred to as embodied cognition. Embodied cognition posits that in decision tasks, neuronal activity generally associated with preparing an action, actually reflects the accumulation of evidence for a particular decision. Testing the embodied cognition model causally is challenging because dissociating the evolution of a decision from preparing a motor act is difficult, if the same neuronal activity instantiates both processes. Ideally, one would show that manipulation of neuronal activity thought to be involved in movement preparation actually alters decisions, and not movement preparation. Here, trained monkeys performed a two-choice perceptual decision-making task in which they judged the orientation of a dynamic Glass pattern before and after unilateral, reversible inactivation of a brainstem area involved in preparing eye movements, the superior colliculus (SC). Surprisingly, we found that unilateral SC inactivation produced significant decision biases and changes in reaction times consistent with a role for the SC in evidence accumulation. Fitting signal detection theory and sequential sampling models (drift-diffusion and urgency-gating) to the data revealed that SC inactivation produced a decrease in the relative evidence for contralateral decisions. Control experiments showed that SC inactivation did not result in eye movement biases ruling out interpretations based on motor preparation or spatial attentional impairment. The results provide causal evidence for an embodied cognition model of perceptual decision-making and provide compelling evidence that the SC of primates plays a causal role in how evidence is accumulated for perceptual decisions, a process that is usually attributed to the cerebral cortex.
WgLink: reconstructing whole-genome viral haplotypes usingL0+L1-regularization
Authors: Cao Chen , Greenberg Matthew , Long Quan
Published: August 2020

Many tools can reconstruct viral sequences based on next generation sequencing reads. Although existing tools effectively recover local regions, their accuracy suffers when reconstructing the whole viral genomes (strains). Moreover, they consume significant memory when the sequencing coverage is high or when the genome size is large. We present WgLink to meet this challenge. WgLink takes local reconstructions produced by other tools as input and patches the resulting segments together into coherent whole-genome strains. We accomplish this using anL0+L1-regularized regression synthesizing variant allele frequency data with physical linkage between multiple variants spanning multiple regions simultaneously. WgLink achieves higher accuracy than existing tools both on simulated and real data sets while using significantly less memory (RAM) and fewer CPU hours. Source code and binaries are freely available athttps://github.com/theLongLab/wglink.
Parallel processing of quickly and slowly mobilized reserve vesicles in hippocampal synapses
Authors: Rodríguez Gotor Juan José , Mahfooz Kashif , Pérez-Otaño Isabel , Wesseling John F.
Published: August 2020

Vesicles within presynaptic terminals are thought to be segregated into a variety of readily releasable and reserve pools. The nature of the pools and trafficking between them is not well understood, but pools that are slow to mobilize when synapses are active are often assumed to feed pools that are mobilized more quickly, in a series. However, electrophysiological studies of synaptic transmission have suggested instead a parallel organization where vesicles within slowly and quickly mobilized reserve pools would separately feed independent reluctant- and fast-releasing subdivisions of the readily releasable pool. Here we use FM-dyes to confirm the existence of multiple reserve pools at hippocampal synapses and a parallel organization that prevents intermixing between the pools, even when stimulation is intense enough to drive exocytosis at the maximum rate. The experiments additionally demonstrate extensive heterogeneity among synapses in the relative sizes of the slowly and quickly mobilized reserve pools, which suggests equivalent heterogeneity in the numbers of reluctant and fast-releasing readily releasable vesicles that may be relevant for understanding information processing and storage.
BamA and BamD are essential for the secretion of trimeric autotransporter adhesins
Authors: Rooke Jessica L. , Icke Chris , Wells Timothy J. , Rossiter Amanda E. , Browning Douglas F. , Morris Faye C. , Leo Jack C. , Schütz Monika S. , Autenrieth Ingo B , Cunningham Adam F. , Linke Dirke , Henderson Ian R.
Published: August 2020

The BAM complex inEscherichia coliis composed of five proteins, BamA-E. BamA and BamD are essential for cell viability and are required for the assembly of β-barrel outer membrane proteins. Consequently, BamA and BamD are indispensable for secretion via the classical autotransporter pathway (Type 5a secretion). In contrast, BamB, BamC and BamE are not required for the biogenesis of classical autotransporters. Recently, we demonstrated that TamA, a homologue of BamA, and its partner protein TamB, were required for efficient secretion of proteins via the classical autotransporter pathway. The trimeric autotransporters are a subset of the Type 5-secreted proteins. Unlike the classical autotransporters, they are composed of three identical polypeptide chains which must be assembled together to allow secretion of their cognate passenger domains. In contrast to the classical autotransporters, the role of the Bam and Tam complex components in the biogenesis of the trimeric autotransporters has not been investigated fully. Here, using theSalmonella entericatrimeric autotransporter SadA and the structurally similar YadA protein ofYersiniaspp., we identify the importance of BamA and BamD in the biogenesis of the trimeric autotransporters and reveal that BamB, BamC, BamE, TamA and TamB are not required for secretion of functional passenger domain on the cell surface.

Importance

The secretion of trimeric autotransporters (TAA’s) has yet to be fully understood. Here we show that efficient secretion of TAAs requires the BamA and D proteins, but does not require BamB, C or E. In contrast to classical autotransporter secretion, neither trimeric autotransporter tested required TamA or B proteins to be functionally secreted.
ConvertingEscherichia coliMG1655 into a chemical overproducer through inactivating defense system against exogenous DNA
Authors: Wang Jingge , Huang Chaoyong , Guo Kai , Ma Lianjie , Meng Xiangyu , Wang Ning , Huo Yi-Xin
Published: August 2020

Escherichia colistrain K-12 MG1655 has been proposed as an appropriate host strain for industrial production. However, the direct application of this strain suffers from the transformation inefficiency and plasmid instability. Herein, we conducted genetic modifications at a serial of loci of MG1655 genome, generating a robust and universal host strain JW128 with higher transformation efficiency and plasmid stability that can be used to efficiently produce desired chemicals after introducing the corresponding synthetic pathways. Using JW128 as the host, the titer of isobutanol reached 5.76 g/L in shake-flask fermentation, and the titer of lycopene reached 1.91 g/L in test-tube fermentation, 40-fold and 5-fold higher than that of original MG1655, respectively. These results demonstrated JW128 is a promising chassis for high-level production of value-added chemicals.
Vortex chip incorporating an orthogonal turn for size-based isolation of circulating cells
Authors: Rastogi Navya , Seth Pranjal , Bhat Ramray , Sen Prosenjit
Published: August 2020

Label-free separation of rare cells (e.g. circulating tumor cells (CTCs)) based on their size is attractive due to its wider applicability, simpler sample preparation, faster turnaround, better efficiency and higher purity. Amongst cognate protocols for the same, vortex-trapping based techniques offer high throughput but operate at high flow velocities where the resulting hydrodynamic shear stress is likely to damage cells and compromise their viability for subsequent assays. We present here an orthogonal vortex chip which can carry out size-differentiated trapping at significantly lower (38% of previously reported) flow velocities. Fluid flowing through the chip is constrained to exit the trapping chamber at right angles to that of its entry. Such a flow configuration leads to the formation of vortex in the chamber. Above a critical flow velocity, larger particles are trapped in the vortex whereas smaller particles get ejected with the flow: we call this phenomenon the turn-effect. We have characterized the critical velocities for trapping of cells and particles of different sizes on chips with distinct entry-exit configurations. Optimal architectures for stable vortex trapping at low flow velocities are identified. We explain how shear-gradient lift, centrifugal and Dean flow drag forces contribute to the turn-effect by acting on cells which pushes them into specific vortices in a size- and velocity-dependent fashion. Finally, we demonstrate selective trapping of human breast cancer cells mixed with whole blood at low-concentration. Our findings suggest that the device shows promise for the gentle isolation of rare cells from blood.
Dendritic spikes in apical oblique dendrites of cortical layer 5 pyramidal neurons
Authors: Castañares Michael Lawrence G. , Stuart Greg J. , Daria Vincent R.
Published: August 2020

Dendritic spikes in layer 5 pyramidal neurons (L5PNs) play a major role in cortical computation. While dendritic spikes have been studied extensively in apical and basal dendrites of L5PNs, whether oblique dendrites, which ramify in the input layers of the cortex, also generate dendritic spikes is unknown. Here we report the existence of dendritic spikes in apical oblique dendrites of L5PNs.In silicoinvestigations indicate that oblique branch spikes are triggered by brief, low-frequency action potential (AP) trains (~40 Hz) and are characterized by a fast sodium spike followed by activation of voltage-gated calcium channels.In vitroexperiments confirmed the existence of oblique branch spikes in L5PNs during brief AP trains at frequencies of around 60 Hz. Oblique branch spikes offer new insights into branch-specific computation in L5PNs and may be critical for sensory processing in the input layers of the cortex.
Protocol for clustering of non-unified protein sequences through memory-map guided deep learning
Authors: Prakash Om
Published: August 2020

Protocol established and validated for clustering of non-unified protein sequences through memorymap guided deep learning. Data evaluated belongs to the disease causing proteins/genes from human hormonal system. Possibilities for future experiments validation was found for genes as: ACTHR, AGMX1, ATK, BPK, DPDE3, ERBA2, FSHB, GH1, GHSR, GNAS1, GSP, HANF, LCGR, LGR2, LGR3, LHRHR, NR1A2, PKR1, PRKAR1, RNF216, SBP2, SECISBP2, THR1, THRB, TPIT, TRIAD3, TSE1, UBCE7IP1, XAP2, and ZIN. Protocol is recommended for implementation with small to large dataset (protein/ DNA/ RNA sequences of unified or non-unified length) with unclassified data flags.
Nitric oxide prevents aortic valve calcification by S-nitrosylation of USP9X to activate NOTCH signaling
Authors: Majumdar Uddalak , Manivannan Sathiyanarayanan , Basu Madhumita , Ueyama Yukie , Blaser Mark C. , Cameron Emily , McDermott Michael R. , Lincoln Joy , Cole Susan E. , Wood Stephen , Aikawa Elena , Lilly Brenda , Garg Vidu
Published: August 2020

Calcific aortic valve disease (CAVD) is an increasingly prevalent condition and endothelial dysfunction is implicated in its etiology. We previously identified nitric oxide (NO) as a calcification inhibitor by its activation ofNOTCH1, which is genetically linked to human CAVD. Here, we show that NO rescues calcification by a S-nitrosylation-mediated mechanism in porcine aortic valve interstitial cells (pAVICs) and single cell RNA-seq demonstrated regulation of NOTCH pathway by NO. A unbiased proteomic approach to identify S-nitrosylated proteins in valve cells found enrichment of the ubiquitin proteasome pathway and implicated S-nitrosylation of USP9X in NOTCH regulation during calcification. Furthermore, S-nitrosylated USP9X was shown to deubiquitinate and stabilize MIB1 for NOTCH1 activation. Consistent with this, genetic deletion ofUsp9xin mice demonstrated aortic valve disease and human calcified aortic valves displayed reduced S-nitrosylation of USP9X. These results demonstrate a novel mechanism by which S-nitrosylation dependent regulation of ubiquitin-associated pathway prevents CAVD.
Human ORC/MCM density is low in active genes and correlates with replication time but does not solely define replication initiation zones
Authors: Kirstein Nina , Buschle Alexander , Wu Xia , Krebs Stefan , Blum Helmut , Hammerschmidt Wolfgang , Lacroix Laurent , Hyrien Olivier , Audit Benjamin , Schepers Aloys
Published: August 2020

Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication timing and fork directionality profiles obtained by RNA-seq, Repli-seq and OK-seq. ORC and MCM are strongly and homogeneously depleted from transcribed genes, enriched at gene promoters, and more abundant in early-than in late-replicating domains. Surprisingly, after controlling these variables, no difference in ORC/MCM density is detected between initiation zones, termination zones, unidirectionally replicating and randomly replicating regions. Therefore, ORC/MCM density correlates with replication timing but does not solely regulate the probability of replication initiation. Interestingly, H4K20me3, a histone modification proposed to facilitate late origin licensing, was enriched in late replicating initiation zones and gene deserts of stochastic replication fork direction. We discuss potential mechanisms that specify when and where replication initiates in human cells.
A maternal effect regulates global DNA methylation patterns
Authors: Loos Remco , Carola Valeria , Audero Enrica , Brini Elena , Iacono Luisa Lo , Moles Anna , Bertone Paul , Gross Cornelius
Published: August 2020

Variation in DNA methylation between individuals has been shown to be influenced by both genetic and environmental factors. However, the relative impact of genetic and non-genetic factors on DNA methylation patterns across the mammalian genome has not been systematically studied. We performed whole-genome methylation analysis in two inbred mouse strains, revealing striking differences in the global distribution of DNA methylation. Although global methylation patterns were indistinguishable for most genomic features, a significant increase in the number of unmethylated CpG-island promoters and first exons was observed between strains. Experiments using F1 reciprocal hybrid strains demonstrated that the genotype of the mother dictated global DNA methylation patterns. Cross-fostering experiments ruled out a postnatal maternal effect on these differences and suggested that they were driven by a prenatal maternal effect, possibly via differential deposition of maternal gene products into the oocyte or uterine environment. These data demonstrate that maternal effects have a major impact on global DNA methylation patterns.
Asymmetric histone inheritance regulates stem cell fate inDrosophilamidgut
Authors: Zion Emily , Chen Xin
Published: August 2020

A fundamental question in developmental biology is how distinct cell fates are established and maintained through epigenetic mechanisms in multicellular organisms. Here, we report that preexisting (old) and newly synthesized (new) histones H3 and H4 are asymmetrically inherited by the distinct daughter cells during asymmetric division ofDrosophilaintestinal stem cells (ISCs). By contrast, in symmetrically dividing ISCs that produce two self-renewed stem cells, old and new H3 and H4 show symmetric inheritance patterns. These results indicate that asymmetric histone inheritance is tightly associated with the distinct daughter cell fates. To further understand the biological significance of this asymmetry, we express a mutant histone that compromises asymmetric histone inheritance pattern. We find increased symmetric ISC division and ISC tumors during aging under this condition. Together, our results demonstrate that asymmetric histone inheritance is important for establishing distinct cell identities in a somatic stem cell lineage, consistent with previous findings in asymmetrically dividing male germline stem cells inDrosophila. Therefore, this work sheds light on the principles of histone inheritance in regulating stem cell fatein vivo.
Airborne point counts: a method for estimating songbird abundance with drones
Authors: Somers McKenzie D. , Glass Darren B. , Immordino Marisa A. , Ozoh Precious S. , Sherman Lauren B. , Wilson Andrew M.
Published: August 2020

Using drones to conduct airborne bioacoustic surveys is a potentially useful new way to estimate the abundance of vocal bird species. Here we show that by using two recording devices suspended from a quadcopter drone it is possible to estimate distances to birds with precision. In an experimental test, the mean error of our estimated distances to a broadcast song across 11 points between 0 and 100 m away was just 3.47 m. In field tests we compared 1-minute airborne counts with 5-minute terrestrial counts at 34 count locations. We found that the airborne counts yielded similar data to the terrestrial point counts for most of the 10 the songbirds included in our analysis, and that the effective detection radii were also similar. However, airborne counts significantly under-detected the Northern Cardinal (χ29= 22.8, post-hoc testP= 0.007), which we attribute to a behavioral response to the drone. Airborne counts work best for species that vocalize close to the ground and have high frequency-range songs. Under those circumstances, airborne bioacoustics could have several advantages over ground-based surveys, including increased precision, increased repeatability, and easier access in difficult terrain. Further, we show that it is possible to do rapid surveys using airborne techniques, which could lead to the development of much more efficient survey protocols than are possible using traditional survey techniques.

Lay Summary

We show that it is possible to estimate the distance of singing birds from a drone, which then allows bird counts to be converted to true abundance or population densities.

Using drones to count birds allows researchers to survey areas that may be difficult or dangerous to access on foot.

Airborne counts are potentially a highly efficient and highly repeatable way to estimate populations of vocal bird species.
Hearing loss in Alzheimer Disease is associated with altered serum lipidomic biomarker profiles
Authors: Llano Daniel A. , Issa Lina K. , Devanarayan Priya , Devanarayan Viswanath ,   Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: August 2020

Recent data have found that aging-related hearing loss (ARHL) is associated with the development of Alzheimer Disease (AD). However, the nature of the relationship between these two disorders is not clear. There are multiple potential factors that link ARHL and AD, and previous investigators have speculated that shared metabolic dysregulation may underlie the propensity to develop both disorders. Here, we investigate the distribution of serum lipidomic biomarkers in AD subjects with or without hearing loss in a publicly available dataset. Serum levels of 349 known lipids from 16 lipid classes were measured in 185 AD patients. Using previously defined co-regulated sets of lipids, both age- and sex-adjusted, we found that lipid sets enriched in phosphatidylcholine and phosphatidylethanolamine showed a strong inverse association with hearing loss. Examination of biochemical classes confirmed these relationships and revealed that serum phosphatidylcholine levels were significantly lower in AD subjects with hearing loss. A similar relationship was not found in normal subjects. These data suggest that a synergistic relationship may exist between AD, hearing loss and metabolic biomarkers, such that in the context of a pathological state such as AD, alterations in serum metabolic profiles are associated with hearing loss. These data also point to a potential role for phosphatidylcholine, a molecule with antioxidant properties, in the underlying pathophysiology of ARHL in the context of AD, which has implications for our understanding and potential treatment of both disorders.
Rapid cost-effective viral genome sequencing by V-seq
Authors: Guo Longhua , Boocock James , Tome Jacob M. , Chandrasekaran Sukantha , Hilt Evann E. , Zhang Yi , Sathe Laila , Li Xinmin , Luo Chongyuan , Kosuri Sriram , Shendure Jay A. , Arboleda Valerie A. , Flint Jonathan , Eskin Eleazar , Garner Omai B. , Yang Shangxin , Bloom Joshua S. , Kruglyak Leonid , Yin Yi
Published: August 2020

Conventional methods for viral genome sequencing largely use metatranscriptomic approaches or, alternatively, enrich for viral genomes by amplicon sequencing with virus-specific PCR or hybridization-based capture. These existing methods are costly, require extensive sample handling time, and have limited throughput. Here, we describe V-seq, an inexpensive, fast, and scalable method that performs targeted viral genome sequencing by multiplexing virus-specific primers at the cDNA synthesis step. We designed densely tiled reverse transcription (RT) primers across the SARS-CoV-2 genome, with a subset of hexamers at the 3’ end to minimize mis-priming from the abundant human rRNA repeats and human RNA PolII transcriptome. We found that overlapping RT primers do not interfere, but rather act in concert to improve viral genome coverage in samples with low viral load. We provide a path to optimize V-seq with SARS-CoV-2 as an example. We anticipate that V-seq can be applied to investigate genome evolution and track outbreaks of RNA viruses in a cost-effective manner. More broadly, the multiplexed RT approach by V-seq can be generalized to other applications of targeted RNA sequencing.
BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion ofArthrobacterphage cluster FE
Authors: Demo Stephanie , Kapinos Andrew , Bernardino Aaron , Guardino Kristina , Hobbs Blake , Hoh Kimberly , Lee Edward , Vuong Iphen , Reddi Krisanavane , Freise Amanda C. , Parker Jordan Moberg
Published: August 2020

Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of relatedMycobacteriaandArthrobacterphage genomes relied on nucleotide identity thresholds but, more recently, clustering ofGordoniaandMicrobacteriumphages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novelArthrobacterphage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity withArthrobacterphages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clusteringGordoniaandMicrobacteriumphages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.
Exploring how independent directors view CSR inequality using a quasi-natural experiment
Authors: Ongsakul Viput , Jiraporn Napatsorn , Jiraporn Pornsit
Published: August 2020

Purpose

The purpose of this paper is to explore corporate social responsibility (CSR) inequality, which is the inequality across different CSR categories. Higher inequality suggests a less balanced CSR policy. To determine if CSR inequality is beneficial or harmful, this paper investigates how independent directors view CSR inequality, using an exogenous regulatory shock introduced by the passage of the Sarbanes–Oxley Act.

Design/methodology/approach

To draw causality, this study relies on a quasi-natural experiment based on an exogenous regulatory shock that forced certain firms to raise board independence. This approach is significantly less vulnerable to endogeneity and is much more likely to show a causal effect. The results using propensity score matching, principal component analysis and instrumental-variable analysis are confirmed.

Findings

The difference-in-difference estimates show that independent directors view CSR inequality unfavorably. Specifically, board independence diminishes CSR inequality by approximately 34%-43%. Because the empirical strategy is based on a quasi-natural experiment, the results are more likely to show causality. The results also imply that CSR inequality is a crucially important aspect of CSR.

Originality/value

Although a substantial volume of research has examined CSR, one vital aspect of CSR has been largely unexplored. Filling this void in the literature, the CSR inequality is investigated. The study is the first to explore how independent directors view CSR inequality using a quasi-natural experiment.
A systematic review of circular economy research in the construction industry
Authors: Osobajo Oluyomi A. , Oke Adekunle , Omotayo Temitope , Obi Lovelin Ifeoma
Published: August 2020

Purpose

While circular economy (CE) is fast becoming a political and economic agenda for global urban development, there are still substantial knowledge gaps in possible strategies to speed up such transition, especially in the construction industry. This study analyses literature surrounding CE to unpack current trends possible future research directions to foster CE implementation in the construction industry.

Design/methodology/approach

The study undertakes a systematic review of CE literature published between 1990 and 2019. It adopts a five-stage procedure as a methodological approach for the review: formulation of the research question(s), locating and identifying relevant studies, selection and evaluation of studies, analysis or synthesis and results reporting.

Findings

The findings on CE research in the construction industry show extensive focus on resource use and waste management. There are limited investigations in other areas of construction such as supply chain integration, building designs, policy, energy efficiency, land use, offsite manufacturing, whole life costing, and risk, cost reduction, cost management, health and safety management. The study findings provide evidence that current CE practice fails to incorporate other areas that would facilitate the network of true circular construction industry.

Originality/value

This research provides a comprehensive overview of research efforts on CE in the construction context, identifying areas of extensive and limited coverage over three decades. Besides, it identifies possible pathways for future research directions on CE implementation, towards the accelerated transition to a true circular construction industry for the benefit of funding bodies and researchers.