bluuebunny/crossref_metadata_2025 huggingface dataset:
Additive and Synergistic Cardiovascular Disease Risk Factors and HIV Disease Markers' Effects on White Matter Microstructure in Virally Suppressed HIV
Authors: Calon Maëliss , Menon Kritika , Carr Andrew , Henry Roland G. , Rae Caroline D. , Brew Bruce J. , Cysique Lucette A.
Published: December 2020

Background:

It is unclear whether intermediate to high cardiovascular disease (CVD) risk and HIV disease status may have additive (ie, independent statistical effects concomitantly tested) or synergistic effects on white matter microstructure and cognition in virally suppressed HIV-infected (HIV+) men relative to sex and age-matched controls.

Setting:

Tertiary health care observational cohort.

Methods:

Eighty-two HIV+ men (mean age 55 ± 6 years, 10%–30% on various CVD drugs; 20% with previous CVD) and 40 HIV-uninfected (HIV−) men (none with previous CVD; 10%–20% on various CVD drugs) underwent diffusion tensor imaging and neuropsychological testing. A standard classification of intermediate to high CVD risk (CVD+ group) was based on the Framingham score ≥15% cutoff and/or a history of CVD. Fractional anisotropy (FA) and mean diffusivity (MD) were quantified in 11 white matter tracts.

Results:

Within the HIV− group, the CVD+ group had lower FA (P = 0.03) and higher MD (P = 0.003) in the corona radiata and higher MD in the corpus callosum (P = 0.02) and superior fasciculi (P = 0.03) than the CVD− group. Within the HIV+ group, the CVD+ group had lower FA in the superior fasciculi (P = 0.04) and higher MD in the uncinate fasciculus (P = 0.04), and lower FA (P = 0.01) and higher MD (P = 0.03) in the fornix than the CVD− group. The fornix alterations were also abnormal compared with the HIV− groups. The HIV+ CVD+ was more likely to have HIV-associated dementia. Older age, antihypertensive use, longer HIV duration, and higher C-reactive protein associated with lower FA and higher MD. Higher blood CD4+ lymphocyte count and CD4/CD8 ratio associated with higher FA and lower MD.

Conclusions:

In virally suppressed HIV, CVD risk factors have a mostly additive contribution to white matter microstructural alterations, leading to a different distribution of injury in HIV− and HIV+ persons with CVD. There was also evidence of a synergistic effect of CVD and HIV factors on the fornix white matter injury.
Mate competition during pseudocopulation in shipworms
Authors: Shipway J. Reuben , Treneman Nancy C. , Distel Daniel L.
Published: December 2020

Shipworms are predominantly wood-eating bivalves that play fundamental roles in biodegradation, niche creation and nutrient cycling across a range of marine ecosystems. Shipworms remain confined to the wood they colonize as larvae; however, continual feeding and rapid growth to large sizes degrade both food source and habitat. This unique lifestyle has led to the evolution of a stunning diversity of reproductive strategies, from broadcast spawning to spermcasting, larval brooding and extreme sexual size dimorphism with male dwarfism. Some species also engage in pseudocopulation, a form of direct fertilization where groups of neighbouring individuals simultaneously inseminate one another via their siphons—the only part of the animal extending beyond the burrow. Among the Bivalvia, this exceptionally rare behaviour is unique to shipworms and remains infrequently observed and poorly understood. Herein, we document pseudocopulation with video footage in the giant feathery shipworm (
Bankia setacea
) and novel competitive behaviours, including siphon wrestling, mate guarding and the removal of a rival's spermatozoa from the siphons of a recipient. As successful sperm transfer is likely greater for larger individuals with longer siphons, we suggest that these competitive behaviours are a factor selecting for rapid growth and large size in species that engage in pseudocopulation.
Mechanical stimuli and matrix properties modulate cancer spheroid growth in three-dimensional gelatin culture
Authors: Curtis Kimberly J. , Schiavi Jessica , Mc Garrigle Myles J. , Kumar Vatsal , McNamara Laoise M. , Niebur Glen L.
Published: December 2020

Most patients who succumb to cancer have metastases to bone that contribute to their death. Cancer cells that metastasize to bone are regularly subjected to mechanical stimuli that may affect their proliferation, growth and protein expression. Understanding why some cancer cells thrive in this environment could provide insight into new approaches to prevent or treat metastasis to bone. We used 4T1 cells as a model of breast cancer cells, and implanted them in gelatin hydrogels with moduli of 1 or 2.7 kPa to mimic the properties of bone marrow. The constructs were subjected to either perfusion of media through the hydrogel or combined perfusion and cyclic mechanical compression for 1 h d
−1
for 4 d. Controls were cultured in free-swelling conditions. The cells formed spheroids during the 4 d of culture, with larger spheroids in the statically cultured constructs than in perfusion or compressed constructs. In stiffer gelatin, smaller spheroids formed in compressed constructs than perfusion alone, while compression had no effect compared to perfusion in the softer gelatin. Immunostaining indicated that the spheroids expressed osteopontin, parathyroid hormone-related protein and fibronectin, which are all hallmarks of bone metastasis. The proliferative marker Ki67 was present in all spheroids on day 4. In the 1 kPa gelatin, Ki67 staining intensity was greater in the statically cultured, free-swelling constructs than in bioreactor culture, regardless of dynamic compression. By contrast, proliferation was higher in the compressed gelatins compared to perfusion alone in the 2.7 kPa constructs, although the spheroids were smaller, on average. This suggests the stiffer gelatin may restrict spheroid growth at the same time that it enhances mechanobiological signalling during compression. Taken together, 4T1 breast cancer cells are mechanically sensitive, and mechanical stimuli can alter their proliferation and protein expression within soft materials with mechanical properties similar to bone marrow. As such, both
in vivo
and
in vitro
models of cancer metastasis should consider the role of the mechanical environment in the bone.
In-water observations highlight the effects of provisioning on whale shark behaviour at the world's largest whale shark tourism destination
Authors: Legaspi Christine , Miranda Joni , Labaja Jessica , Snow Sally , Ponzo Alessandro , Araujo Gonzalo
Published: December 2020

The whale shark is the world's largest fish that forms predictable aggregations across its range, many of which support tourism industries. The largest non-captive provisioned whale shark destination globally is at Oslob, Philippines, where more than 500 000 tourists visit yearly. There, the sharks are provisioned daily, year-round, allowing the human–shark interaction in nearshore waters. We used in-water behavioural observations of whale sharks between 2015 and 2017 to understand the relationship between external stimuli and shark behaviour, whether frequency of visits at the site can act as a predictor of behaviour, and the tourist compliance to the code of conduct. Mixed effects models revealed that the number of previous visits at the site was a strong predictor of whale shark behaviour, and that provisioned sharks were less likely to exhibit avoidance. Compliance was poor, with 93% of surveys having people less than 2 m from the animal, highlighting overcrowding of whale sharks at Oslob. Given the behavioural implications to whale sharks highlighted here and the local community's reliance on the tourism industry, it is imperative to improve management strategies to increase tourist compliance and strive for sustainable tourism practices.
Portable smartphone-integrated paper sensors for fluorescence detection of As(III) in groundwater
Authors: Liu Sha , Li Yong , Yang Chao , Lu Liqiang , Nie Yulun , Tian Xike
Published: December 2020

Arsenic contamination in groundwater is a supreme environmental problem, and levels of this toxic metalloid must be strictly monitored by a portable, sensitive and selective analytical device. Herein, a new system of smartphone-integrated paper sensors with Cu nanoclusters was established for the effective detection of As(III) in groundwater. For the integration system, the fluorescence emissive peak of Cu nanoclusters at 600 nm decreased gradually with increasing As(III) addition. Meanwhile, the fluorescence colour also changed from orange to colourless, and the detection limit was determined as 2.93 nM (0.22 ppb) in a wide detection range. The interfering ions also cannot influence the detection selectivity of As(III). Furthermore, the portable paper sensors based on Cu nanoclusters were fabricated for visual detection of As(III) in groundwater. The quantitative determination of As(III) in natural groundwater has also been accomplished with the aid of a common smartphone. Our work has provided a portable and on-site detection technique toward As(III) in groundwater with high sensitivity and selectivity.
A duality between scattering poles and transmission eigenvalues in scattering theory
Authors: Cakoni Fioralba , Colton David , Haddar Houssem
Published: December 2020

In this paper, we develop a conceptually unified approach for characterizing and determining scattering poles and interior eigenvalues for a given scattering problem. Our approach explores a duality stemming from interchanging the roles of incident and scattered fields in our analysis. Both sets are related to the kernel of the relative scattering operator mapping incident fields to scattered fields, corresponding to the exterior scattering problem for the interior eigenvalues and the interior scattering problem for scattering poles. Our discussion includes the scattering problem for a Dirichlet obstacle where duality is between scattering poles and Dirichlet eigenvalues, and the inhomogeneous scattering problem where the duality is between scattering poles and transmission eigenvalues. Our new characterization of the scattering poles suggests a numerical method for their computation in terms of scattering data for the corresponding interior scattering problem.
Nonlinear generalized functions on manifolds
Authors: Nigsch E. A. , Vickers J. A.
Published: December 2020

In this work, we adopt a new approach to the construction of a global theory of algebras of generalized functions on manifolds based on the concept of smoothing operators. This produces a generalization of previous theories in a form which is suitable for applications to differential geometry. The generalized Lie derivative is introduced and shown to extend the Lie derivative of Schwartz distributions. A new feature of this theory is the ability to define a covariant derivative of generalized scalar fields which extends the covariant derivative of distributions at the level of association. We end by sketching some applications of the theory. This work also lays the foundations for a nonlinear theory of distributional geometry that is developed in a subsequent paper that is based on Colombeau algebras of tensor distributions on manifolds.
A nonlinear theory of distributional geometry
Authors: Nigsch E. A. , Vickers J. A.
Published: December 2020

This paper builds on the theory of nonlinear generalized functions begun in Nigsch & Vickers (Nigsch, Vickers 2021
Proc. R. Soc. A
20200640 (
doi:10.1098/rspa.2020.0640
)) and extends this to a diffeomorphism-invariant nonlinear theory of generalized tensor fields with the sheaf property. The generalized Lie derivative is introduced and shown to commute with the embedding of distributional tensor fields and the generalized covariant derivative commutes with the embedding at the level of association. The concept of a generalized metric is introduced and used to develop a non-smooth theory of differential geometry. It is shown that the embedding of a continuous metric results in a generalized metric with well-defined connection and curvature and that for
C
2
metrics the embedding preserves the curvature at the level of association. Finally, we consider an example of a conical metric outside the Geroch–Traschen class and show that the curvature is associated to a delta function.
Gated feedforward inhibition in the frontal cortex releases goal-directed action
Authors: Kim Jae-Hyun , Ma Dong-Hyun , Jung Eunji , Choi Ilsong , Lee Seung-Hee
Published: December 2020

Cortical circuits process sensory information and generate motor signals in animals performing perceptual tasks. However, it is still unclear how sensory inputs generate motor signals in the cortex to initiate goal-directed action. Here, we identified a visual-to-motor inhibitory circuit in the anterior cingulate cortex (ACC) that induced action initiation in mice performing visual Go/No-go tasks. Interestingly, higher activity in sensory neurons and faster suppression in motor neurons of the ACC predicted faster reaction times. Notably, optogenetic activation of visual inputs in the ACC evoked strong suppression of neighboring motor neurons by activating fast-spiking sensory neurons and drove task-relevant actions in mice via activating striatal neurons. Finally, the ACC network activity maintained low during spontaneous and perceptual actions and increased during action cancellation in response to the stop signals. Collectively, our data demonstrate that visual salience in the frontal cortex exerts gated feedforward inhibition to release goal-directed actions.
Using publicly available data to conduct rapid assessments of extinction risk
Authors: Levin Michael O. , Meek Jared B. , Boom Brian , Kross Sara M. , Eskew Evan A.
Published: December 2020

The IUCN Red List plays a key role in setting global conservation priorities. Species are added to the Red List through a rigorous assessment process that, while robust, can be quite time-intensive. Here, we test the rapid preliminary assessment of plant species extinction risk using a single Red List metric: Extent of Occurrence (EOO). To do so, we developed REBA (Rapid EOO-Based Assessment), a workflow that harvests and cleans data from the Global Biodiversity Information Facility (GBIF), calculates each species’ EOO, and assigns Red List categories based on that metric. We validated REBA results against 1,546 North American plant species already on the Red List and found ~90% overlap between REBA’s rapid classifications and those of full IUCN assessments. Our preliminary workflow can be used to quickly evaluate data deficient Red List species or those in need of reassessment, and can prioritize unevaluated species for a full assessment.
Cholecystokinin-like Peptide Mediates Satiety by Inhibiting Sugar Attraction
Authors: Guo Di , Zhang Yi-Jie , Zhang Su , Li Jian , Guo Chao , Pan Yu-Feng , Liu Chen-Xi , Jia Ya-Long , Li Chen-Yu , Ma Jun-Yu , Nässel Dick R. , Gao Cong-Fen , Wu Shun-Fan
Published: December 2020

Feeding is essential for animal survival and reproduction and is regulated by both internal states and external stimuli. However, little is known about how internal states influence the perception of external sensory cues that regulate feeding behavior. Here, we investigated the neuronal and molecular mechanisms behind nutritional state-mediated regulation of gustatory perception in control of feeding behavior in the brown planthopper andDrosophila. We found that feeding increases the expression of the cholecystokinin-like peptide, sulfakinin (SK), and the activity of a set of SK-expressing neurons. Starvation elevates the transcription of the sugar receptor Gr64f and SK negatively regulates the expression of Gr64f in both insects. This Gr64f regulation is by direct action of SK neurons on Gr64f-expressing neurons of the proboscis and proleg tarsi that co-express the SK receptor CCKLR-17D3. Our findings thus demonstrate how nutritional state induces peptide signaling to modulate sweet perception and thereby feeding behavior.
Fish metabolome from sub-urban lakes of the Paris area (France) and potential influence of noxious metabolites produced by cyanobacteria
Authors: Marie Benjamin , Gallet Alison
Published: December 2020

The recent democratization of high-throughput molecular phenotyping allows the rapid expansion of promising untargeted multi-dimensional approaches (e.g.epigenomics, transcriptomics, proteomics, metabolomics, …). Indeed, these emerging omics tools, processed for ecologically relevant species, may present innovative perspectives for environmental assessments, that could provide early warning of eco(toxico)logical impairs. In a previous pilot study (Sotton et al., Chemosphere 2019), we explore by1H NMR the bio-indicative potential of metabolomics analyses on the liver of 2 sentinel fish species (Perca fluviatilisandLepomis gibbosus) collected in 8 water bodies of the peri-urban Paris’ area (France). In the present study, we further investigate on the same samples the great potential of high-throughput UHPLC-HRMS/MS analyses. We show that the LC-MS metabolome remarkably allows clear separation of individuals according to the species, but also according to their respective sampling lakes. Interestingly, similar variations ofPercaandLepomismetabolomes occur locally indicating that site-specific environmental constraints drive the metabolome variations beyond the obvious genetic differences between the two species, and seem to be influenced by the production of noxious metabolites by cyanobacterial blooms in certain lakes. Thus, the development of such reliable environmental metabolomics approaches is constituting an innovative bio-indicative tool for ecological stress assessment, such as toxigenic cyanobacterial blooms, and aim at being further follow up.
Mycobacterial infection-induced miR-206 inhibits protective neutrophil recruitment via the CXCL12/CXCR4 signalling axis
Authors: Wright Kathryn , de Silva Kumudika , Plain Karren M. , Purdie Auriol C. , Blair Tamika A , Duggin Iain G , Britton Warwick J. , Oehlers Stefan H.
Published: December 2020

Pathogenic mycobacteria actively dysregulate protective host immune signalling pathways during infection to drive the formation of permissive granuloma microenvironments. Dynamic regulation of host microRNA (miRNA) expression is a conserved feature of mycobacterial infections across host-pathogen pairings. Here we examine the role of miR-206 in the zebrafish model ofMycobacterium marinuminfection, which allows investigation of the early stages of granuloma formation. We find miR-206 is upregulated following infection by pathogenicM. marinumand that antagomir-mediated knockdown of miR-206 is protective against infection. We observed striking upregulation ofcxcl12aandcxcr4bin infected miR-206 knockdown zebrafish embryos and live imaging revealed enhanced recruitment of neutrophils to sites of infection. We used Crispr/Cas9-mediated knockdown ofcxcl12aandcxcr4bexpression and AMD3100 inhibition of Cxcr4 to show that the enhanced neutrophil response and reduced bacterial burden caused by miR-206 knockdown was dependent on the Cxcl12/Cxcr4 signalling axis. Together, our data illustrate a pathway through which pathogenic mycobacteria induce host miR-206 expression to suppress Cxcl12/Cxcr4 signalling and prevent protective neutrophil recruitment to granulomas.

Author summary

Mycobacterial infections cause significant disease burden to humans and animals, the most widely known example being tuberculosis which has killed more humans than any other infectious disease throughout history. Infectious mycobacteria are highly evolved to hijack host processes, including the very immune cells tasked with destroying them. microRNAs are host molecules that control wide-ranging programs of host gene expression and are important in the immune response to infections. Here we use the zebrafish model of mycobacterial infection to determine the role of the infection-induced microRNA miR-206 in the host response to infection. We found pathogenic mycobacteria trigger the host to produce more miR-206 in order to suppress the otherwise protective recruitment of neutrophils to sites of infection via the host Cxcl12/Cxcr4 signalling pathway. Our study provides new insight into the role of mycobacterial infection-induced miR-206 function in the context of a whole host.
Plastic ingestion in Asian elephants in the forested landscapes of Uttarakhand, India
Authors: Katlam Gitanjali , Prasad Soumya , Pande Anant , Ramchiary Nirala
Published: December 2020

Impacts of plastic pollution, recognized as a driver of change in the global environment, have been under reported in terrestrial fauna. In this study, we looked at presence of plastic in the diet of Asian elephant and other megaherbivores in the forest habitats of Haridwar and Lansdowne, Uttarakhand state, India. We collected dung and pellet samples from forest edges and forest interiors and quantified plastic particles and other anthropogenic waste present. Each anthropogenic waste item was measured, weighed and sub-categorized into the type of plastic or other categories. Thirty-two percent of the elephant dung samples showed presence of plastic and other waste. Plastic particles comprised of 85% of the waste recovered from the dung with 100% occurrence in elephant dung samples (mean 47.08±12.85 particles per sample). We found twice as many plastic particles (85.27±33.7 per 100g of dung samples) in forest samples as compared to forest edge samples (35.34±11.14 plastic particles/100g of dung samples). Other non-biodegradable anthropogenic waste recovered from elephant dung (glass, metal, rubber bands, clay pottery and tile pieces) was found to be much higher for forest samples (34.79±28.41 items/100g sample) as compared to forest edge samples (9.44±1.91items/100g). This study is the first systematic documentation of occurrence of non-biodegradable waste in the diet of Asian elephants. Dominance of plastic compared to other non-biodegradable material in elephant dung samples highlights its widespread use and poor waste segregation practices. We recommend developing a comprehensive solid waste management strategy to mitigate the threat of plastic pollution around these critical elephant habitats.
Circumventing drug treatment? Polyethylenimine functionalized nanoparticles inherently and selectively kill patient-derived glioblastoma stem cells
Authors: Prabhakar Neeraj , Merisaari Joni , Joncour Vadim Le , Peurla Markus , Karaman Didem Şen , Casals Eudald , Laakkonen Pirjo , Westermarck Jukka , Rosenholm Jessica M.
Published: December 2020

Glioblastoma (GB) is the most frequent malignant tumor originating from the central nervous system. Despite breakthroughs in treatment modalities for other cancer types, GB remains largely irremediable due to its high degree of intratumoral heterogeneity, infiltrative growth, and intrinsic resistance towards multiple treatments. These resistant and aggressive sub-populations of GBs including the glioblastoma stem cells (GSCs) can circumvent treatment. GSCs act as a reservoir of cancer-initiating cells; they are a major challenge for successful therapy. We have discovered, as opposed to well-reported anti-cancer drug based therapeutical approach for GB therapy, the role of polyethylenimine (PEI) in inducing selective death of patient-derived GSCs via lysosomal membrane rupturing. Even at very low doses (1 μg/ml), PEI surface-functionalized mesoporous silica nanoparticles (PEI-MSNs), without any additional anti-cancer drug, very potently and selectively killed multiple GSC lines. Very importantly, PEI-MSNs did not affect the survival of well-established GB cells, or other type of cancer cells even at 25x higher doses. Remarkably, any sign of predominant cell death pathways such as apoptosis and autophagy was absent. Instead, as a potential explanation for their GSC selective killing function, we demonstrate that the internalized PEI-MSNs accumulated inside the lysosomes, subsequently causing a rupture of the vulnerable lysosomal membranes, exclusively in GSCs. As a further evaluation, we observed blood-brain-barrier (BBB) permeability of these PEI-MSNsin vitroandin vivo. Taking together the recent indications for the vulnerability of GSCs for lysosomal targeting, and GSC selectivity of the PEI-MSNs described here, the results suggest that PEI-functionalized nanoparticles could have a potential role in the eradication of GSCs.
Susceptibility status of larvalAedes aegyptimosquitoes in Saudi Arabia
Authors: Al Nazawi Ashwaq M , Ashall Simon , Weetman David
Published: December 2020

Vector control programs worldwide are facing the challenge of mosquitoes becoming resistant to available insecticides. Larviciding is a crucial preventative measure for dengue control but data on insecticide resistance of larvalAe. aegyptiin the Middle Eastern Region are limited. This study assesses the susceptibility status ofAe. aegypticollected from the two most important dengue foci in Saudi Arabia, Jeddah and Makkah, to important chemical and biological larvicides; the organophosphate temephos andBacillus thuringiensis israelensis,Bti). Whilst worldwide, and particularly in Latin America, high-level resistance to temephos is common, Jeddah and Makkah populations exhibited full susceptibility to both temephos andBti.These data suggest each can be considered by vector control programs for preventative dengue control in the region, as part of temporal rotations or spatial mosaics to manage insecticide resistance.
Exp2Ipynb: A general machine-learning workflow for the analysis of promoter libraries
Authors: Liebal Ulf W. , Köbbing Sebastian , Blank Lars M.
Published: December 2020

Strain engineering in biotechnology modifies metabolic pathways in microorganisms to overproduce target metabolites. To modify metabolic pathway activity in bacteria, gene expression is an effective and easy manipulated process, specifically the promoter sequence recognized by sigma factors. Promoter libraries are generated to scan the expression activity of different promoter sequences and to identify sequence positions that predict activity. To maximize information retrieval, a well-designed experimental setup is required. We present a computational workflow to analyse promoter libraries; by applying this workflow to seven libraries, we aim to identify critical design principles. The workflow is based on a Python Jupyter Notebook and covers the following steps: (i) statistical sequence analysis, (ii) sequence-input to expression-output predictions, (iii) estimator performance evaluation, and (iv) new sequence prediction with defined activity. The workflow can process multiple promoter libraries, across species or reporter proteins, and classify or regress expression activity. The strongest predictions in the sample libraries were achieved when the promoters in the library were recognized by a single sigma factor and a unique reporter system. A tradeoff between sample size and sequence diversity reduces prediction quality, and we present a relationship to estimate the minimum sample size. The workflow guides the user through analysis and machine-learning training, is open source and easily adaptable to include alternative machine-learning strategies and to process sequence libraries from other expression-related problems. The workflow is a contribution to increase insight to the growing application of high-throughput experiments and provides support for efficient strain engineering.

Availability

Freely available on GitHub:https://qithub.com/iAMB-RWTH-Aachen/Exp2Ipynband licensed under the terms of GPLv3.

Contact

ulf.liebal@rwth-aachen.de

Supplementary information

Supplementary data available in the Git folder.
Widespread introgression across a phylogeny of 155Drosophilagenomes
Authors: Suvorov Anton , Kim Bernard Y. , Wang Jeremy , Armstrong Ellie E. , Peede David , D’Agostino Emmanuel R. R. , Price Donald K. , Wadell Peter , Lang Michael , Courtier-Orgogozo Virginie , David Jean R. , Petrov Dmitri , Matute Daniel R. , Schrider Daniel R. , Comeault Aaron A.
Published: December 2020

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across nine monophyletic radiations within the genusDrosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history ofDrosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the nine clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history ofDrosophilaand highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.
OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life
Authors: McTavish Emily Jane , Sanchez Reyes Luna Luisa , Holder Mark T.
Published: December 2020

The Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the python packageopentree, which provides a user friendly python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.
Multispectral Fingerprinting Resolves Dynamics of Nanomaterial Trafficking in Primary Endothelial Cells
Authors: Gravely Mitchell , Roxbury Daniel
Published: December 2020

Intracellular vesicle trafficking involves a complex series of biological pathways used to sort, recycle, and degrade extracellular components, including engineered nanomaterials which gain cellular entryviaactive endocytic processes. A recent emphasis on routes of nanomaterial uptake has established key physicochemical properties which direct certain mechanisms, yet relatively few studies have identified their effect on intracellular trafficking processes past entry and initial subcellular localization. Here, we developed and applied an approach where single-walled carbon nanotubes (SWCNTs) play a dual role - that of an engineered nanomaterial (ENM) undergoing intracellular processing, in addition to functioning as the signal transduction element reporting these events in individual cells with single organelle resolution. We used the unique optical properties exhibited by non-covalent hybrids of single-stranded DNA and SWCNTs (DNA-SWCNTs) to report the progression of intracellular processing eventsviatwo orthogonal hyperspectral imaging approaches of near-infrared (NIR) fluorescence and resonance Raman scattering. A positive correlation between fluorescence and G-band intensities was uncovered within single cells, while exciton energy transfer and eventual aggregation of DNA-SWCNTs were observed to scale with increasing time after internalization. These were confirmed to be consequences of intracellular processes using pharmacological inhibitors of endosomal maturation, which suppressed spectral changes through two distinct mechanisms. An analysis pipeline was developed to colocalize and deconvolute the fluorescence and Raman spectra of subcellular regions of interest (ROIs), allowing for single-chirality component spectra to be obtained with sub-micron spatial resolution. This approach uncovered a complex relationship between DNA-SWCNT concentration, fluorescence intensity, environmental transformations, and irreversible aggregation resulting from the temporal evolution of trafficking events. Finally, a spectral clustering analysis was applied to delineate the dynamic sequence of processes into four distinct populations, allowing stages of the intracellular trafficking process to be identified by the multispectral fingerprint of encapsulated DNA-SWCNTs.

TOC Graphic
Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus
Authors: Korn Abby M. , Hillhouse Andrew E. , Sun Lichang , Gill Jason J.
Published: December 2020

The majority of previously describedStaphylococcus aureusbacteriophages belong to three major groups: P68-likePodoviridae, Twort-like or K-likeMyoviridae,and a more diverse group of temperateSiphoviridae. Here we present three novelS. aureus“jumbo” phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade ofS. aureus Myoviridaethat is largely unrelated to other knownS. aureusphages. The average genome size for these phages is ~269 kb with each genome encoding ~263 predicted protein-coding genes. Phage genome organization and content is most similar to known jumbo phages ofBacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete viral and non-viral RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect humanS. aureusisolates.

Importance of work

This study describes the comparative genomics of three novelS. aureusjumbo phages: MarsHill, Madawaska, and Machias. These threeS. aureus Myoviridaerepresent a new class ofS. aureusphage that have not been described previously. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, not only are these phages an exciting new type ofS. aureusphage, they also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. The data and methods presented in this study could be useful for an audience far beyond those working inS. aureusphage biology. This work is original and has not been submitted for publication in any other journal.
Aging and MPTP-sensitivity depend on molecular and ultrastructural signatures of astroglia and microglia in mice substantia nigra
Authors: Abhilash PL , Bharti Upasna , Rashmi Santhosh Kumar , Philip Mariamma , Raju T. R. , Kutty Bindu M. , Chandrasekhar Sagar B.K. , Alladi Phalguni Anand
Published: December 2020

Both astroglia and microglia show region-specific distribution in CNS and often maladapt to age-associated alterations within their niche. Studies on autopsied substantia nigra (SN) of Parkinson’s disease (PD) patients and experimental models propose gliosis as a trigger for neuronal loss. Epidemiological studies propose an ethnic bias in PD prevalence, since Caucasians are more susceptible than non-whites. Similarly, different mice strains are variably sensitive to MPTP. We had earlier likened divergent MPTP-sensitivity of C57BL/6J and CD-1 mice with differential susceptibility to PD, based on the numbers of SN neurons.

Here, we examined whether the variability was incumbent to inter-strain differences in glial features of male C57BL/6J and CD-1 mice. Stereological counts showed relatively more microglia and fewer astrocytes in the SN of normal C57BL/6J mice, suggesting persistence of an immune-vigilant state. MPTP-induced microgliosis and astrogliosis in both strains, suggests their involvement in pathogenesis. ELISA of pro-inflammatory cytokines in the ventral-midbrain revealed augmentation of TNF-α and IL-6 at middle-age in both strains that reduced at old-age, suggesting middle-age as a critical, inflamm-aging associated time-point. TNF-α levels were high in C57BL/6J, through aging and post-MPTP; while IL-6 and IL-1β were upregulated at old-age. CD-1 had higher levels of anti-inflammatory cytokine TGF-β. MPTP-challenge caused upregulation of enzymes MAO-A, MAO-B and iNOS in both strains. Post-MPTP enhancement in fractalkine and hemeoxygenase-1; may be neuron-associated compensatory signals. Ultrastructural observations of elongated astroglial/microglial mitochondria vis-à-vis the shrunken ones in neurons, suggest a scale-up of their functions with neurotoxic consequences. Thus, astroglia and microglia modulate aging and PD-susceptibility.

Highlights

Substantia nigra of C57BL/6J and CD-1 show no baseline differences in glial numbers

Both mice show age and MPTP-induced gliosis in the substantia nigra pars compacta

CD-1 nigra has lower levels of pro- and higher levels of anti-inflammatory cytokines

Tilt of balance between pro- and anti-inflammatory cytokines begins at middle age

Astrocytes and microglia show elongated mitochondria and intact ER upon MPTP-injection
Human Erbb2-induced Erk Activity Robustly Stimulates Cycling and Functional Remodeling of Rat and Human Cardiomyocytes
Authors: Strash Nicholas , DeLuca Sophia , Janer Carattini Geovanni L. , Heo Soon Chul , Gorsuch Ryne , Bursac Nenad
Published: December 2020

Multiple mitogenic pathways capable of promoting mammalian cardiomyocyte (CM) proliferation have been identified as potential candidates for functional heart repair following myocardial infarction. However, it is unclear whether the effects of these mitogens are species-specific and how they directly compare in the same cardiac setting. Here, we examined how CM-specific lentiviral expression of various candidate mitogens affects human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and neonatal rat ventricular myocytes (NRVMs)in vitro. In 2D-cultured CMs from both species, and in highly mature 3D-engineered cardiac tissues generated from NRVMs, a constitutively-active mutant form of the human gene Erbb2 (cahErbb2) was the most potent tested mitogen. Persistent expression of cahErbb2 induced CM proliferation, sarcomere loss, and remodeling of tissue structure and function, which were attenuated by small molecule inhibitors of Erk signaling. These results suggest transient activation of Erbb2/Erk axis in cardiomyocytes as a potential strategy for regenerative heart repair.
Widespread premature transcription termination ofArabidopsis thalianaNLR genes by the spen protein FPA
Authors: Parker Matthew T. , Knop Katarzyna , Zacharaki Vasiliki , Sherwood Anna V. , Tome Daniel , Yu Xuhong , Martin Pascal , Beynon Jim , Michaels Scott , Barton Geoffrey J. , Simpson Gordon G.
Published: December 2020

Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers ofnucleotide-binding,leucine-rich repeatreceptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
Nigratine as first-in-class dual inhibitor of necroptosis and ferroptosis regulated cell death
Authors: Delehouzé Claire , Comte Arnaud , Hauteville Marcelle , Goekjian Peter , Dimanche-Boitrel Marie-Thérèse , Rousselot Morgane , Bach Stéphane
Published: December 2020

Nigratine (also known as 6E11), a natural flavanone derivative, was characterized as highly specific non-ATP competitive inhibitor of RIPK1 kinase, one of the key component of necroptotic cell death signaling. We show here that nigratine inhibited both necroptosis (induced by Tumor Necrosis Factor-α) and ferroptosis (induced by glutamate, erastin or RSL3 small chemical compounds) with EC50in the µM range. Altogether, the data obtained showed that nigratine is the first-in-class dual inhibitor of necroptosis and ferroptosis cell death routes and opened new therapeutic avenues for treating complex necrosis-related diseases.
Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants
Authors: Procko Carl , Murthy Swetha E , Keenan William T , Reza Mousavi Seyed Ali , Dabi Tsegaye , Coombs Adam , Procko Erik , Baird Lisa , Patapoutian Ardem , Chory Joanne
Published: December 2020

In response to touch, some carnivorous plants such as the Venus flytrap have evolved spectacular movements to capture animals for nutrient acquisition. However, the molecules that confer this sensitivity remain unknown. We used comparative transcriptomics to show that expression of three genes encoding homologs of the MscS-Like (MSL) and OSCA/TMEM63 family of mechanosensitive ion channels are localized to touch-sensitive trigger hairs of Venus flytrap. We focus here on the candidate with the most enriched expression in trigger hairs, the MSL homolog FLYCATCHER1 (FLYC1). We show thatFLYC1transcripts are localized to mechanosensory cells within the trigger hair, transfecting FLYC1 induces chloride-permeable stretch-activated currents in naïve cells, and transcripts coding for FLYC1 homologs are expressed in touch-sensing cells of Cape sundew, a related carnivorous plant of the Droseraceae family. Our data suggest that the mechanism of prey recognition in carnivorous Droseraceae evolved by co-opting ancestral mechanosensitive ion channels to sense touch.
Palmitoylation of KChIP3 controls baseline mucin secretion
Authors: Cantero-Recasens G , Burballa C , Duran M , Brouwers N , Malhotra V
Published: December 2020

Baseline mucin secretion (BMS) is independent of external agonists and controlled by a small calcium binding protein named KChIP3. KChIP3-hosting mucin granules are not released until intracellular cytosolic calcium oscillations reach a threshold, KChIP3 binds calcium and detaches from granules, allowing their fusion to plasma membrane. Loss of KChIP3 or blocking its membrane attachment causes mucin hypersecretion. How is KChIP3 recruited to mucin granules? We show here that zDHHC (aspartate-histidine-histidine-cysteine motif in a cysteine-rich, zinc finger–like domain) S-acyl-transferase dependent palmitoylation modulates binding of KChIP3 to mucin granules thereby affecting mucin secretion. We have found that inhibiting zDHHC-mediated palmitoylation in differentiated HT29-18N2, which express the Golgi-localized zDHHC3 and zDHHC4, releases KChIP3 from mucin granules and increases baseline mucin secretion. Mutation of the palmitoylation sites in KChIP3 (Cysteines 122 and 123 to Alanine) quantitatively reduces its attachment to mucin granules. Expression of KChIP3-WT in HT29-18N2 cell lines stably depleted of KChIP3 inhibits mucin secretion, whereas expression of non-palmitoylated KChIP3 (KChIP3-AA) only partially rescues the effect of KChIP3 depletion and the cells maintain higher levels of baseline secretion compared to KChIP3-WT cells. Altogether, our data suggest that zDHHC3 or zDHHC4-dependent palmitoylation is involved in KChIP3 recruitment to mucin granules to control the baseline mucin secretion.
Optimizing laboratory X-ray diffraction contrast tomography for grain structure characterization of pure iron
Authors: Lindkvist Adam , Fang Haixing , Juul Jensen Dorte , Zhang Yubin
Published: December 2020

Laboratory diffraction contrast tomography (LabDCT) is a recently developed technique for 3D nondestructive grain mapping using a conical polychromatic beam from a laboratory-based X-ray source. The effects of experimental parameters, including accelerating voltage, exposure time and number of projections used for reconstruction, on the characterization of the 3D grain structure in an iron sample are quantified. The experiments were conducted using a commercial X-ray tomography system, ZEISS Xradia 520 Versa, equipped with a LabDCT module; and the data analysis was performed using the software package GrainMapper3D, which produces a 3D reconstruction from binarized 2D diffraction patterns. It is found that the exposure time directly affects the background noise level and thus the ability to distinguish weak spots of small grains from the background. With the assistance of forward simulations, it is found that spots from the first three strongest {hkl} families of a large grain can be seen with as few as 30–40 projections, which is sufficient for indexing the crystallographic orientation and resolving the grain shape with a reasonably high accuracy. It is also shown that the electron current is a more important factor than the accelerating voltage to be considered for optimizing the photon numbers with energies in the range of 20–60 keV. This energy range is the most important one for diffraction of common metals, e.g. iron and aluminium. Several suggestions for optimizing LabDCT experiments and 3D volume reconstruction are finally provided.
High-pressure small-angle X-ray scattering cell for biological solutions and soft materials
Authors: Rai Durgesh K. , Gillilan Richard E. , Huang Qingqiu , Miller Robert , Ting Edmund , Lazarev Alexander , Tate Mark W. , Gruner Sol M.
Published: December 2020

Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion transduction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing aqrange of 0.01 <q< 0.7 Å−1, pressures of 0–400 MPa and an achievable temperature range of 0–80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.