bluuebunny/crossref_metadata_2025 huggingface dataset:
Virucidal and antiviral activity of astodrimer sodium against SARS-CoV-2 in vitro
Authors: Paull Jeremy R.A. , Heery Graham P. , Bobardt Michael D. , Castellarnau Alex , Luscombe Carolyn A. , Fairley Jacinth K. , Gallay Philippe A.
Published: August 2020

An effective response to the ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will involve a range of complementary preventive modalities. The current studies were conducted to evaluate the in vitro SARS-CoV-2 antiviral and virucidal activity of astodrimer sodium, a dendrimer with broad spectrum antimicrobial activity, including against enveloped viruses in in vitro and in vivo models, that is marketed for antiviral and antibacterial applications. We report that astodrimer sodium inhibits replication of SARS-CoV-2 in Vero E6 and Calu-3 cells, with 50% effective concentrations (EC50) for i) reducing virus-induced cytopathic effect of 0.002 to 0.012 mg/mL in Vero E6 cells, and ii) infectious virus release by plaque assay of 0.019 to 0.031 mg/mL in Vero E6 cells and 0.031 to 0.045 mg/mL in Calu-3 cells. The selectivity index (SI) in these assays was as high as 2197. Astodrimer sodium was also virucidal, reducing SARS-CoV-2 infectivity by >99.9% (>3 log10) within 1 minute of exposure, and up to >99.999% (>5 log10) shown at astodrimer sodium concentrations of 10 to 30 mg/mL in Vero E6 and Calu-3 cell lines. Astodrimer sodium also inhibited infection in a primary human airway epithelial cell line. The data were similar for all investigations and were consistent with the potent antiviral and virucidal activity of astodrimer sodium being due to inhibition of virus-host cell interactions, as previously demonstrated for other viruses. Further studies will confirm if astodrimer sodium binds to SARS-CoV-2 spike protein and physically blocks initial attachment of the virus to the host cell. Given the in vitro effectiveness and significantly high SI, astodrimer sodium warrants further investigation for potential as a nasally administered or inhaled antiviral agent for SARS-CoV-2 prevention and treatment applications.
A simple, high-throughput method of protein and label removal from extracellular vesicle samples
Authors: Welsh Joshua A. , Killingsworth Bryce , Kepley Julia , Traynor Tim , McKinnon Kathy , Savage Jason , Appel Deven , Aldape Kenneth , Camphausen Kevin , Berzofsky Jay A. , Ivanov Alexander R. , Ghiran Ionita H. , Jones Jennifer C.
Published: August 2020

Evidence continues to increase of the clinical utility extracellular vesicles (EVs) can provide as translational biomarkers. While a wide variety of EV isolation and purification methods have been implemented, few techniques are high-throughput and scalable for removing excess fluorescent reagents (e.g. dyes, antibodies). EVs are too small to be recovered from routine cell-processing procedures, such as filtration or centrifugation. The lack of suitable methods for removing unbound labels, especially in optical assays, is a major roadblock to accurate EV phenotyping and utilization of EV assays in a translational or clinical setting. Therefore, we developed a method for using a multi-modal resin, referred to as EV-Clean, to remove unbound labels from EV samples, and we demonstrate improvement in flow cytometric EV analysis with the use of this EV-Clean method.
Qualitative and quantitative bioanalytical methods validation of aristolochic acid DNA adducts and application in human formalin-fixed paraffin-embedded hepatocellular carcinoma tissues
Authors: xin Wang , jinping Song , yapping Dong , linghua Hu , xiaoying Chen , fangfang Yang , haiyang Qi , xinming Qi , wen Wen , shuzhen Chen , guozhen Xing , jin Ren
Published: August 2020

Mutation signature of aristolochic acid (AA) found in urothelial or hepatocellular carcinoma causes public concern about the cancer risk of AA. In contrast, direct evidence based on the reliable bioanalytical method for the exposure of AA is still lacking and not universal. Here, we strictly complied with the qualitative and quantitative guidance for forensic toxicological analysis: In the sample preprocessing, DNA from formalin-fixed and paraffin-embedded (FFPE) tissues was digested to single nucleotide by a series of enzymes with 70% enzymatic digestion efficiency. After protein precipitation, the samples were submitted to an ABI6500+ mass spectrometer for LC-MS/MS analysis. Ion pairs 543.2/427.2 and 543.2/395.2 of dA-AAI were selected from 5 ion pairs due to their higher LC-MS/MS response. Both these ion pairs have excellent selectivity and specificity in rat liver DNA matrix, and a linear regression range from 5 pg/mL to 200 pg/mL with the best fit and determination coefficient (r) greater than 0.99. The intra and inter batch accuracy and precision of these two ion pairs are also acceptable with less than 15% variation. The total recovery for ion pair 543.2/427.2 and 543.2/395.2 of dA-AAI was 90.06% and 90.76%, respectively. Our method has a minor matrix effect and good stability under different temperature and time conditions. With signal to noise ratio ≥ 3, 2 ion pairs (< 50 % relative abundance variation), the lower limit of quantification (LLOQ) of our method is set to 5 pg/mL(∼3.6 AAI-DNA adducts per 108DNA bases). By using this validated bioanalytical method of dA-AAI, 165 human HCC FFPE tissues were analyzed, the total ratio of samples with peak543.2/427.2is 17.0% (28/165), with peak543.2/395.2is 9.09% (15/165) which yields the total ratio of samples combined peak543.2/427.2and peak543.2/395.2is 7.27% (12/165). Two samples are higher than 5 pg/mL under the qualitative requirements. In conclusion, we first reported a fully validated methods to analyze the DNA adducts level of aristolochic acid, which could be qualitatively and quantitatively applied to the investigation of AA exposure in the human and other species.
Feasibility and promise of circulating tumor DNA analysis in dogs with naturally-occurring sarcoma
Authors: Favaro Patricia Filippsen , Stewart Samuel D. , McDonald Bradon R. , Cawley Jacob , Contente-Cuomo Tania , Wong Shukmei , Hendricks William P.D. , Trent Jeffrey M. , Khanna Chand , Murtaza Muhammed
Published: August 2020

Comparative studies of naturally-occurring canine cancers have provided new insight into many areas of cancer research. The inclusion of pet dogs in the development and validation of circulating tumor DNA (ctDNA) diagnostics may be uniquely informative for human translation for many reasons, including: high incidence of certain spontaneous cancers, repeated access to blood and tumor from the same individuals during the course of disease progression, and molecular heterogeneity of naturally-occurring cancers in dogs. Here, we present a feasibility study of ctDNA analysis performed in 9 healthy dogs and 39 dogs with either benign or malignant splenic tumors (hemangiosarcoma) using shallow whole genome sequencing (sWGS) of cell-free DNA. To enable detection and quantification of ctDNA using sWGS, we adapted two informatic approaches and compared their performance for the canine genome. At presentation, mean ctDNA tumor fraction in dogs with malignant splenic tumors was 11.2%, significantly higher than dogs with benign lesions (3.2%; p 0.001), achieving an AUC of 0.84. ctDNA tumor fraction was 14.3% and 9.0% in dogs with metastatic and localized disease, respectively although this difference was not statistically significant (p 0.227). In paired analysis, ctDNA fraction decreased from 11.0% to 7.9% after resection of malignant tumors (p 0.047). Our results demonstrate that ctDNA analysis is feasible in dogs with hemangiosarcoma using a cost-effective approach such as sWGS. Future studies are underway to validate these findings, and further evaluate the role of ctDNA to assess burden of disease and treatment response during drug development.
Foliar water uptake as a source of hydrogen and oxygen in plant biomass
Authors: Kagawa Akira
Published: August 2020

Introductory biology lessons around the world typically teach that plants absorb water through their roots, but, unfortunately, absorption of water through leaves and subsequent transport and use of this water for biomass formation remains a field limited mostly to specialists. Recent studies have identified foliar water uptake as a significant but still unquantified net water source for terrestrial plants. The growing interest in the development of a new model that includes foliar uptake of liquid water to explain hydrogen and oxygen isotope ratios in leaf water and tree rings requires a method for distinguishing between these two water sources. I therefore devised a method utilizing two different heavy waters (HDO and H218O) to simultaneously label both foliar-uptake water and root-uptake water and quantify their relative contributions to plant biomass. Using this new method, I here present evidence that, in the case of well-wateredCryptomeria japonica, hydrogen and oxygen incorporated into new leaf cellulose in the rainy season derives mostly from foliar-uptake water, while that of new root cellulose derives mostly from root-uptake water, and new branch xylem is somewhere in between. Abandoning the assumption that these elements are supplied from soil water alone may have vast implications in fields ranging from isotope dendroclimatology, silviculture, to biogeochemistry.
Centriole-less pericentriolar material serves as a microtubule organizing center at the base ofC. eleganssensory cilia
Authors: Magescas Jérémy , Eskinazi Sani , Tran Michael V. , Feldman Jessica L.
Published: August 2020

During mitosis in animal cells, the centrosome acts as a microtubule organizing center (MTOC) to assemble the mitotic spindle. MTOC function at the centrosome is driven by proteins within the pericentriolar material (PCM), however the molecular complexity of the PCM makes it difficult to differentiate the proteins required for MTOC activity from other centrosomal functions. We used the natural spatial separation of PCM proteins during mitotic exit to identify a minimal module of proteins required for centrosomal MTOC function inC. elegans. Using tissue specific degradation, we show that SPD-5, the functional homolog of CDK5RAP2, is essential for embryonic mitosis while SPD-2/CEP192 and PCMD-1, which are essential in the zygote, are dispensable. Surprisingly, although the centriole is known to be degraded in the ciliated sensory neurons inC. elegans[1-3], we find evidence for “centriole-less PCM” at the base of cilia and use this structure as a minimal testbed to dissect centrosomal MTOC function. Super-resolution imaging revealed that this PCM inserts inside the lumen of the ciliary axoneme and directly nucleates the assembly of dendritic microtubules towards the cell body. Tissue-specific degradation in ciliated sensory neurons revealed a role for SPD-5 and the conserved microtubule nucleator γ-TuRC, but not SPD-2 or PCMD-1, in MTOC function at centriole-less PCM. This MTOC function was in the absence of regulation by mitotic kinases, highlighting the intrinsic ability of these proteins to drive microtubule growth and organization and further supporting a model that SPD-5 is the primary driver of MTOC function at the PCM.
PeptideMind – applying machine learning algorithms to assess replicate quality in shotgun proteomic data
Authors: Handler D.C.L. , Haynes P.A.
Published: August 2020

Assessment of replicate quality is an important process for any shotgun proteomics experiment. One fundamental question in proteomics data analysis is whether any specific replicates in a set of analyses are biasing the downstream comparative quantitation. In this paper, we present an experimental method to address such a concern. PeptideMind uses a series of clustering Machine Learning algorithms to assess outliers when comparing proteomics data from two states with six replicates each. The program is a JVM native application written in the Kotlin language with Python sub-process calls to scikit-learn. By permuting the six data replicates provided into four hundred triplet non redundant pairwise comparisons, PeptideMind determines if any one replicate is biasing the downstream quantitation of the states. In addition, PeptideMind generates useful visual representations of the spread of the significance measures, allowing researchers a rapid, effective way to monitor the quality of those identified proteins found to be differentially expressed between sample states.
Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers
Authors: Sinnott-Armstrong Nasa , Seoane Jose A. , Sallari Richard , Pritchard Jonathan K. , Curtis Christina , Snyder Michael P.
Published: August 2020

Although much effort has been devoted to identifying coding mutations across cancer types, regulatory mutations remain poorly characterized. Here, we describe a framework to identify non-coding drivers by aggregating mutations in cell-type specific regulatory regions for each gene. Application of this approach to 2,634 patients across 11 human cancer types identified 60 pan-cancer, 22 pan-breast and 192 cancer specific candidate driver genes that were enriched for expression changes. Analysis of high-throughput CRISPR knockout screens revealed large, cancer specific growth effects for these genes, on par with coding mutations and exceeding that for promoter mutations. Amongst the five candidate drivers selected for further analysis, four (IPO9, MED8, PLEKHA6, andOXNAD1)were associated with survival across multiple cancer types. These studies demonstrate the power of our cell-type aware, convergent regulatory framework to define novel tissue specific cancer driver genes, considerably expanding evidence of functional non-coding mutations in cancer.
Time mating guinea pigs by monitoring changes to the vaginal membrane throughout the estrus cycle and with ultrasound confirmation
Authors: Wilson Rebecca L , Lampe Kristin , Matushewski Brad J , Regnault Timothy RH , Jones Helen N
Published: August 2020

Guinea pig developmentin uterois more similar to humans than any other rodent species. As such, their importance to reproductive studies is evident, particularly those studies focused on therapeutic interventions to improve human pregnancy outcome. Tracking the guinea pig estrus cycle is imperative to ensuring appropriately timed mating and can be performed by monitoring the guinea pig vaginal membrane. Here, we describe, and provide picture representation, of changes to the guinea pig vaginal membrane throughout the estrus cycle. Utilization of this monitoring enabled a 100% pregnancy success rate on the first mating attempt in a cohort of five guinea pigs. This approach, along with early pregnancy ultrasounds as a secondary method to confirm pregnancy, offers a cost effective and reliable approach to timed-mating in the guinea pig.
DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A
Authors: Leon Kelly E. , Buj Raquel , Lesko Elizabeth , Dahl Erika S. , Chen Chi-Wei , Imamura Yuka , Kossenkov Andrew V. , Hobbs Ryan P. , Aird Katherine M.
Published: August 2020

Cellular senescence is characterized as a stable cell cycle arrest that can occur as a stress response associated with oncogenic activation, termed oncogene-induced senescence (OIS). Cells undergoing OIS acquire a unique microenvironment termed the senescence-associated secretory phenotype (SASP), which can be both beneficial and detrimental in a context-dependent manner. Additionally, senescent cells are characterized by robust changes in their epigenome. Here, we globally assessed the histone landscape of cells induced to senesce by oncogenic RAS and discovered a novel epigenetic regulatory mechanism of the key SASP regulator IL1A. OIS cells displayed increased di- and tri-methylation of histone H3 lysine 79 (H3K79me2/3), two active histone marks. Depletion of the H3K79 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) during OIS resulted in decreased H3K79me2/3 occupancy at theIL1Agene locus, which corresponded to decreased IL1A mRNA and cell surface expression. Decreased expression and secretion of downstream cytokines without a change in senescence markers were also observed upon DOT1L depletion. Overexpression of DOT1L increased H3K79me2/3 occupancy at theIL1Alocus and upregulated the SASP, indicating that DOT1L is both necessary and sufficient for SASP gene expression. Mechanistically, we found that STING, an essential mediator of SASP transcription, is upstream of DOT1L in the epigenetic regulation of the SASP. Together, our studies establish DOT1L as an epigenetic regulator of the SASP whose expression is uncoupled from the senescence-associated cell cycle arrest, providing a potential strategy to inhibit the negative side effects of senescence while maintaining the beneficial inhibition of proliferation.
Theta and alpha power across fast and slow timescales in cognitive control
Authors: Huycke Pieter , Verbeke Pieter , Boehler C. Nico , Verguts Tom
Published: August 2020

Theta and alpha frequency neural oscillations are important for learning and cognitive control, but their exact role has remained obscure. In particular, it is unknown whether they operate at similar timescales, and whether they support different cognitive processes. We recorded EEG in 30 healthy human participants while they performed a learning task containing both novel (block-unique) and repeating stimuli. We investigated behavior and electrophysiology at both fast (i.e., within blocks) and slow (i.e., between blocks) time scales. Behaviorally, both response time and accuracy improved (resp. decrease and increase) over both fast and slow timescales. However, on the spectral level, theta power significantly decreased along the slow timescale, whereas alpha power instead significantly increased along the fast timescale. We thus demonstrate that theta and alpha both play a role during learning, but operate at different timescales. This result poses important empirical constraints for theories on learning, cognitive control, and neural oscillations.
Lanthipeptide Synthetases Participate the Biosynthesis of 2-Aminovinyl-Cysteine Motifs in Thioamitides
Authors: Lu Jingxia , Wu Yuan , Li Jiao , Li Yuqing , Zhang Yingying , Bai Zengbing , Zheng Jie , Zhu Jiapeng , Wang Huan
Published: August 2020

Thioamitides are a group of ribosomally synthesized and post-translational modified peptides with potent antiproliferative and pro-apoptotic activities. Their biosynthesis remains largely unknown, especially for the characteristic C-terminal 2-aminovinyl-Cysteine (AviCys) motifs. Herein, we report the discovery that homologs of class III lanthipeptide synthetases (LanKCts)encodedoutsideputative thioamitide biosynthetic gene clusters (BGCs) fully dehydrate the precursor peptides. Remarkably, LanKCtenzymes bind tightly to cysteine decarboxylases encodedinsidethioamitide BGCs, and the resulting complex complete the macrocyclization of AviCys rings. Furthermore, LanKCtenzymes are present in the genomes of many thioamitide-producing strains and are functional when in complex with cysteine decarboxylases to produce AviCys macrocycles. Thus, our study reveals the participation of lanthipeptide synthetases as a general strategy for dehydration and AviCys formation during thioamitides biosynthesis and thus paves the way for the bioengineering of this class of bioactive natural products.
A dietary sterol trade off determines lifespan responses to dietary restriction inDrosophila melanogaster
Authors: Zanco Brooke , Mirth Christen K. , Sgrò Carla M. , Piper Matthew D.W.
Published: August 2020

Diet plays a significant role in maintaining lifelong health. In particular, lowering the dietary protein : carbohydrate ratio can improve lifespan. This has been interpreted as a direct effect of these macronutrients on physiology. UsingDrosophila melanogaster, we show that the role of protein and carbohydrate on lifespan is indirect, acting by altering the partitioning of limiting amounts of dietary sterols between reproduction and lifespan. Shorter lifespans in flies fed on high protein : carbohydrate diets can be rescued by supplementing their food with cholesterol. Not only does this fundamentally alter the way we interpret the mechanisms of lifespan extension by dietary restriction, these data highlight the important principle that life histories can be affected by nutrient-dependent trade-offs that are indirect and independent of the nutrients (often macronutrients) that are the focus of study. This brings us closer to understanding the mechanistic basis of dietary restriction.
An Acentriolar Centrosome At TheC. elegansCiliary Base
Authors: Garbrecht Joachim , Laos Triin , Holzer Elisabeth , Dillinger Margarita , Dammermann Alexander
Published: August 2020

In animal cells the functions of the cytoskeleton are coordinated by centriole-based centrosomes via microtubule-nucleating γ-tubulin complexes embedded in the pericentriolar material or PCM [1]. PCM assembly has been best studied in the context of mitosis, where centriolar SPD-2 recruits PLK-1, which in turn phosphorylates key scaffolding components such as SPD-5 and CNN to promote expansion of the PCM polymer [2–4]. To what extent these mechanisms apply to centrosomes in interphase or in differentiated cells remains unclear [5]. Here, we examine a novel type of centrosome found at the ciliary base ofC. eleganssensory neurons, which we show plays important roles in neuronal morphogenesis, cellular trafficking and ciliogenesis. These centrosomes display similar dynamic behavior to canonical, mitotic centrosomes, with a stable PCM scaffold and dynamically localized client proteins. Unusually, however, they are not organized by centrioles, which degenerate early in terminal differentiation [6]. Yet, PCM not only persists but continues to grow with key scaffolding proteins including SPD-5 expressed under control of the RFX transcription factor DAF-19. This assembly occurs in the absence of the mitotic regulators SPD-2, AIR-1 and PLK-1, but requires tethering by PCMD-1, a protein which also plays a role in the initial, interphase recruitment of PCM in early embryos [7]. These results argue for distinct mechanisms for mitotic and non-mitotic PCM assembly, with only the former requiring PLK-1 phosphorylation to drive rapid expansion of the scaffold polymer.

ETOC BLURB

Centrioles play a critical role in mitotic centrosome assembly. Here, Garbrechtet al.show that pericentriolar material (PCM) persists at the ciliary base ofC. eleganssensory neurons after centriole degeneration, where it contributes to neuronal morphogenesis and cellular trafficking. Remarkably, this PCM displays dynamic properties similar to canonical centrosomes, yet its continued assembly and maintenance is independent of known mitotic regulators, suggesting differential mechanisms for mitotic and non-mitotic centrosome assembly.

HIGHLIGHTS

PCM persists at the acentriolar ciliary base inC. elegans

PCM assembles in a SPD-2, AIR-1 and PLK-1-independent manner

PCMD-1 tethers PCM at the ciliary base in the absence of centrioles

PCM is required for neuronal morphogenesis and cilium assembly
Inoculum effect of antimicrobial peptides
Authors: Loffredo M. R. , Savini F. , Bobone S. , Casciaro B. , Franzyk H. , Mangoni M. L. , Stella L.
Published: August 2020

The activity of many antibiotics depends on the initial density of cells used in bacteria growth inhibition assays. This phenomenon, termed the inoculum effect, can have important consequences for the therapeutic efficacy of the drugs, since bacterial loads vary by several orders of magnitude in clinically relevant infections. Antimicrobial peptides are a promising class of molecules to fight drug-resistant bacteria, since they act mainly by perturbing the cell membranes rather than by inhibiting intracellular targets. Here we report the first systematic characterization of the inoculum effect for this class of antibacterial compounds. Thirteen peptides (including all-D enantiomers) and peptidomimetics were analyzed by measuring minimum inhibitory concentration values, covering more than 7 orders of magnitude in inoculated cell density. In all cases, we observed a significant inoculum effect for cell densities above 5 × 104cells/mL, while the active concentrations remained constant (within the micromolar range) for lower densities. In the case of membrane-active peptides, these data can be rationalized by considering a simple model, taking into account peptide-cell association and hypothesizing that a threshold number of cell-bound peptide molecules is required in order to cause a killing effect. The observed effects question the clinical utility of activity and selectivity determinations performed at a fixed, standardized cell density. A routine evaluation of the inoculum dependence of the activity of antimicrobial peptides and peptidomimetics should be considered.

Significance statement

Bacterial drug resistance is a crucial threat to global health and antimicrobials with novel mechanisms of action are severely needed. Antimicrobial peptides are natural molecules that kill bacteria mostly by perturbing their membranes and represent promising compounds to fight resistant microbes. Their activity is normally tested under standardized conditions of bacterial density. However, the bacterial load in clinically relevant infections varies by many orders of magnitude. Here we showed that the minimum peptide concentration needed for bacterial killing can vary by more than 100 times with an increase in the density of cells in the initial inoculum of the assay (inoculum effect) These findings question utility of the presently used activity screening assays and our current understanding of antimicrobial peptides.
Increased and synchronous recruitment of release sites underlies hippocampal mossy fiber presynaptic potentiation
Authors: Orlando Marta , Dvorzhak Anton , Bruentgens Felicitas , Maglione Marta , Rost Benjamin R. , Sigrist Stephan J. , Breustedt Jörg , Schmitz Dietmar
Published: August 2020

Synaptic plasticity is a cellular model for learning and memory. However, the expression mechanisms underlying presynaptic forms of plasticity are not well understood. Here, we investigate functional and structural correlates of long-term potentiation at large hippocampal mossy fiberboutonsinduced by the adenylyl cyclase activator forskolin. We performed two-photon imaging of the genetically encoded glutamate sensor iGluuthat revealed an increase in the surface area used for glutamate release at potentiated terminals. Moreover, time-gated stimulated emission depletion microscopy revealed no change in the coupling distance between immunofluorescence signals from calcium channels and release sites. Finally, by high-pressure freezing and transmission electron microscopy analysis, we found a fast remodeling of synaptic ultrastructure at potentiatedboutons: synaptic vesicles dispersed in the terminal and accumulated at the active zones, while active zone density and synaptic complexity increased. We suggest that these rapid and early structural rearrangements likely enable long-term increase in synaptic strength.
Effect of cleanup of spiked sludge on corn growth biosorption and leaching of metals
Authors: Barraoui Driss , Blais Jean-François , Labrecque Michel
Published: August 2020

Abstract

A chemical leaching process has been used for the cleanup of two municipal biosolids (MOS and BES) spiked with Cd, Cu, Zn or their mixture prior to agricultural use. Non-cleaned, cleaned and washed biosolids were compared as soil amendments for corn cultivation inside glasshouse. Corn growth, biosorption of metals and leaching of these metals in leachate were measured. Results showed that biosolid amendments tend to produce more aerial biomass. Cleanup and washing of BES biosolid significantly augmented total biomass of roots and stalks, respectively. Regarding biosorption of metals, Cd could not be found neither in corn seeds, nor in stalks, while slight amounts of Cu were detected. Whereas Cd and Cu diminished in the order roots > leaves > stalks, Zn diminished from leaves > roots > stalks. Cleanup and washing of MOS and BES biosolids significantly lowered biosorption of Cd, Cu, Zn, and other metals. Leaching into the outlet water varied with time, but average concentrations were moderately low. There were significant amounts of metal leached from MOS biosolid. The effects of cleanup and washing of both biosolids on biosorption and leaching depended on the initial metallic charge and the biosolid type.
Effects of scent enrichment on behavioural and physiological indicators of stress in zoo primates
Authors: Vaglio Stefano , Kaburu Stefano S. K. , Pearce Richard , Bryant Luke , McAuley Ailie , Lott Alexandria , Sheppard Demi J. , Smith Sarah , Tompkins Beth , Elwell Emily , Fontani Sara , Young Christopher , Marliani Giovanna , Accorsi Pier Attilio
Published: August 2020

Captive breeding is vital for primate conservation, with modern zoos serving a crucial role in breeding populations of threatened species and educating the general public. However, captive populations can experience welfare issues that may also undermine their reproductive success. In order to enhance the well-being of endangered zoo primates, we conducted a study to assess the effects of a new scent enrichment programme on captive red-ruffed lemurs (Varecia rubra), black howler monkeys (Alouatta caraya), siamangs (Symphalangus syndactylus), Lar gibbons (Hylobates lar) and orangutans (Pongo pygmaeus pygmaeus). We combined behavioural observations and faecal endocrinology analyses to evaluate the effects of a series of essential oils (benzoin, lavender, lemongrass) on five captive troops (N = 19) housed at Dudley Zoo & Castle and Twycross Zoo (UK). We recorded observations of natural species-specific and abnormal stress-related behaviours for 480 hr using instantaneous scan sampling. We collected 189 faecal samples and measured the faecal cortisol concentrations using radioimmunoassay. We found a significant effect of the scent enrichment on behaviours, with red-ruffed lemurs and black howler monkeys reducing their social interactions, as well as red-ruffed lemurs and Lar gibbons decreasing their stress-related behaviours, after they were exposed to the series of essential oils. We also found that red-ruffed lemurs displayed a significant increase in faecal glucocorticoids following the exposure to essential oils. Our contradictory findings suggest that the effects of this series of essential oils may change depending on the species-specific social lives and olfactory repertoires of primates. In conclusion, we cannot recommend using these essential oils widely with zoo primates without additional evaluation.
A haplotype-phased genome of wheat stripe rust pathogenPuccinia striiformisf. sp.tritici, race PST-130 from the Western USA
Authors: Vasquez-Gross Hans , Kaur Sukhwinder , Epstein Lynn , Dubcovsky Jorge
Published: August 2020

More virulent and aggressive races ofPuccinia striiformisf. sp.tritici(Pst), the pathogen causing wheat stripe rust, have been spreading around the world since 2000 causing large grain yield losses. A better understanding of the genome and genetic diversity of these newPstraces will be useful to develop new strategies to ameliorate production losses. In this study, we generated an improved genome assembly of a very virulent race from the Western USA designated as PST-130. We implemented a haplotype phasing strategy using the diploid-aware assembler, Falcon-Unzip and new long-read technology from PacBio to phase the two genomes of this dikaryotic organism. The combination of these new technologies resulted in an improved PST-130 assembly with only 151 contigs (85.4 Mb, N50 of 1.44 Mb), and a complementary assembly (haplotigs) with 458 contigs (65.9 Mb, N50 of 0.235 Mb, PRJNA650506). This new assembly improved gene predictions resulting in 228 more predicted complete genes than in the initial Illumina assembly (29,178 contigs, N50 of 5 kb). The alignment of the non-repetitive primary and haplotig contigs revealed and average of 5.22 SNP/kb, with 39.1% showing <2 SNP/kb and 15.9% >10 SNP/kb. This large divergent regions may represent introgressions of chromosome segments from more divergentPstraces in regions wherePstcan complete its sexual cycle and where recombination is possible. We hypothesize that some of the divergent regions in PST-130 may be related to the European “Warrior” race PST-DK0911 because this latter genome is more similar to PST-130 (3.18 SNP/kb) than to the older European race PST-104E (3.75 SNP/kb). Phasing of additionalPstgenomes or sequencing individual nuclei will facilitate the tracing of nuclei introduced by the newPstraces into local populations.
Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs
Authors: Pontes Camila , Ruiz-Serra Victoria , Lepore Rosalba , Valencia Alfonso
Published: August 2020

The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the β-CoV spike protein family, using sequence information alone, can provide rich information on the molecular basis of the specificity of β-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptors adaptation of circulating and future novel β-CoVs.

Significance

Unraveling the molecular basis for host cell receptor usage among β-CoVs is crucial to our understanding of cross-species transmission, adaptation and for molecular-guided epidemiological monitoring of potential outbreaks. In the present study, we survey the sequence conservation patterns of the β-CoV spike protein family to identify the evolutionary constraints shaping the functional specificity of the protein across the β-CoV lineage. We show that the unsupervised analysis of statistical patterns in a MSA of the spike protein family can help tracing the amino acid space encoding the specificity of β-CoVs to their cognate host cell receptors. We argue that the results obtained in this work can provide a framework for monitoring the evolution of SARS-CoV-2 specificity to the hACE2 receptor, as the virus continues spreading in the human population and differential virulence starts to arise.
Intronic enhancers regulate the expression of genes involved in tissue-specific functions and homeostasis
Authors: Borsari Beatrice , Villegas-Mirón Pablo , Laayouni Hafid , Segarra-Casas Alba , Bertranpetit Jaume , Guigó Roderic , Acosta Sandra
Published: August 2020

Tissue function and homeostasis reflect the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are central to control this tissue-specific gene expression pattern. Here, we explore the correlation between the genomic location of enhancers and their role in tissue-specific gene expression. We found that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, while housekeeping genes are more often controlled by intergenic enhancers. Notably, an intergenic-to-intronic active enhancers continuum is observed in the transition from developmental to adult stages: the most differentiated tissues present higher rates of intronic enhancers, while the lowest rates are observed in embryonic stem cells. Altogether, our results suggest that the genomic location of active enhancers is key for the tissue-specific control of gene expression.
Connectomic Alterations Linked to Transdiagnostic Risk for Psychopathology at the Transition to Adolescence
Authors: Sripada Chandra , Angstadt Mike , Rutherford Saige , Taxali Aman , Greathouse Tristan , Clark D. Angus , Hyde Luke , Weigard Alex , Brislin Sarah , Hicks Brian , Heitzeg Mary
Published: August 2020

BACKGROUND

Convergent research identifies a general factor (“P factor”) that confers transdiagnostic risk for psychopathology. However, brain functional connectivity patterns that underpin the P factor remain poorly understood, especially at the transition to adolescence when many serious mental disorders have their onset.

OBJECTIVE

Identify a distributed connectome-wide neurosignature of the P factor and assess the generalizability of this neurosignature in held out samples.

DESIGN, SETTING, AND PARTICIPANTS

This study used data from the full baseline wave of the Adolescent Brain and Cognitive Development (ABCD) national consortium study, a prospective, population-based study of 11,875 9- and 10-year olds. Data for this study were collected from September 1, 2016 to November 15, 2018 at 21 research sites across the United States.

MAIN OUTCOMES AND MEASURES

We produced whole brain functional connectomes for 5,880 youth with high quality resting state scans. We then constructed a low rank basis set of 250 components that captures interindividual connectomic differences. Multi-level regression modeling was used to link these components to the P factor, and leave-one-site-out cross-validation was used to assess generalizability of P factor neurosignatures to held out subjects across 19 ABCD sites.

RESULTS

The set of 250 connectomic components was highly statistically significantly related to the P factor, over and above nuisance covariates alone (ANOVA nested model comparison, incremental R-squared 6.05%, χ2(250) =412.1,p<4.6×10−10). In addition, two individual connectomic components were statistically significantly related to the P factor after Bonferroni correction for multiple comparisons (t(5511)= 4.8,p<1.4×10−06; t(5121)= 3.9, p<9.7×10−05). Functional connections linking control networks and default mode network were prominent in the P factor neurosignature. In leave-one-site-out cross-validation, the P factor neurosignature generalized to held out subjects (average correlation between actual and predicted P factor scores across 19 held out sites=0.13;pPERMUTATION<0.0001). Additionally, results remained significant after a number of robustness checks.

CONCLUSIONS AND RELEVANCE

The general factor of psychopathology is associated with connectomic alterations involving control networks and default mode network. Brain imaging combined with network neuroscience can identify distributed and generalizable signatures of transdiagnostic risk for psychopathology during emerging adolescence.
Value shapes the structure of schematic representations in the medial prefrontal cortex
Authors: Paulus Philipp C. , Charest Ian , Benoit Roland G.
Published: August 2020

Adaptive cognition is fostered by knowledge about the structure and value of our environment. Here, we hypothesize that these two kinds of information are inherently intertwined as value-weighted schemas in the medial prefrontal cortex (mPFC). Schemas (e.g., of a social network) emerge by extracting commonalities across experiences and can be understood as graphs comprising nodes (e.g., people) and edges (e.g., their relationships). We sampled information about unique real-life environments (i.e., about personally familiar people and places) and probed the neural representations of their schemas with fMRI. Using representational similarity analysis, we show that the mPFC encodes indeed both, the nodes and edges of the schemas. Critically, as hypothesized, the strength of the edges is not only determined by experience and centrality of a node but also by value. We thus account for the involvement of the mPFC in disparate functions and suggest that valuation emerges naturally from encoded memory representations.
Oviduct epithelial cells constitute two developmentally distinct lineages that are spatially separated along the distal-proximal axis
Authors: Ford Matthew J , Harwalkar Keerthana , Pacis Alain S , Maunsell Helen , Wang Yu Chang , Badescu Dunarel , Teng Katie , Yamanaka Nobuko , Bouchard Maxime , Ragoussis Jiannis , Yamanaka Yojiro
Published: August 2020

Owing to technical advances in single cell biology, the appreciation of cellular heterogeneity has increased, which has aided our understanding of organ function, homeostasis and disease progression. The oviduct (also known as the fallopian tube in humans) is the distal-most portion of the female reproductive tract. It is essential for reproduction and the proposed origin of high grade serous ovarian carcinoma (HGSOC). In mammals, the oviduct is morphologically segmented along the ovary-uterus axis into four evolutionally conserved regions. It is unknown however if there is a diversification of epithelial cell characteristics between these regions. In this study, we identified transcriptionally distinct populations of secretory and multiciliated cells restricted to the distal and proximal regions of the oviduct. We demonstrated that these distal and proximal populations are distinct lineages specified early in Müllerian duct development and are maintained separately. These results aid our understanding of epithelial development, homeostasis and initiation of disease from the oviduct.
Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungusPodospora anserina
Authors: Carlier F , Debuchy R , Maroc L , Souaid C , Noordermeer D , Grognet P , Malagnac F
Published: August 2020

Selective gene silencing is key to development. The H3K27me3 enriched heterochromatin maintains transcription repression established during early development and regulates cell fate. Conversely, H3K9me3 enriched heterochromatin prevents differentiation but constitutes a permanent protection against transposable element. We exploited the fungusPodospora anserina, a valuable alternative to higher eukaryote models to question the biological relevance and interplay of these two distinct heterochromatin conformations. We found that H3K27me3 and H3K9me3 modifications are mutually exclusive within gene-rich regions but not within repeats. Lack of PaKmt6 EZH2-like enzyme resulted in loss of H3K27me3 and in significant H3K9me3 reduction, whereas lack of PaKmt1 SU(VAR)3-9-like enzyme caused loss of H3K9me3 only. We established thatP. anserinadevelopmental programs require H3K27me3 mediated silencing unlike most fungi studied to date. Our findings provide new insight into roles of these histone marks and into the relationship between chromatin modifications and development.
SOX11 is a lineage-dependency factor and master epigenetic regulator in neuroblastoma
Authors: Decaesteker Bieke , Louwagie Amber , Loontiens Siebe , De Vloed Fanny , Roels Juliette , Vanhauwaert Suzanne , De Brouwer Sara , Sanders Ellen , Denecker Geertrui , D’haene Eva , Van Haver Stéphane , Van Loocke Wouter , Van Dorpe Jo , Creytens David , Van Roy Nadine , Pieters Tim , Van Neste Christophe , Fischer Matthias , Van Vlierberghe Pieter , Roberts Stephen S , Schulte Johannes , Ek Sara , Versteeg Rogier , Koster Jan , van Nes Johan , De Preter Katleen , Speleman Frank
Published: August 2020

The pediatric extra-cranial tumor neuroblastoma (NB) is characterised by a low mutation burden while copy number alterations are present in most high-risk cases. We identified SOX11 as a strong lineage dependency transcription factor in adrenergic NB based on recurrent chromosome 2p focal gains and amplifications, its specific expression in the normal sympatho-adrenal lineage and adrenergic NBs and its regulation by multiple adrenergic specific cis-interacting (super-)enhancers. Adrenergic NBs are strongly dependent on highSOX11expression levels for growth and proliferation. Through genome-wide DNA-binding and transcriptome analysis, we identified and validated functional SOX11 target genes, several of which implicated in chromatin remodeling and epigenetic modification. SOX11 controls chromatin accessibility predominantly affecting distal adrenergic lineage-specific enhancers marked by binding sites of the adrenergic core regulatory circuitry. During normal sympathoblast differentiation we find expression of SOX11 prior to members of the adrenergic core regulatory circuitry. Given the broad control of SOX11 of multiple epigenetic regulatory complexes and its presumed pioneer factor function, we propose that adrenergic NB cells have co-opted the normal role of SOX11 as a crucial regulator of chromatin accessibility and cell identity.
CASP microdomain formation requires cross cell wall stabilization of domains and non-cell autonomous action of LOTR1
Authors: Kolbeck Andreas , Marhavý Peter , De Bellis Damien , Li Baohai , Kamiya Takehiro , Fujiwara Toru , Kalmbach Lothar , Geldner Niko
Published: August 2020

Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction inlotr1leads to fully functional CSDs at ectopic positions, forming “half strips” LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establishLOTR1as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.
Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses
Authors: Pratibha  , Shaju C. , Kamal
Published: August 2020

Each amino acid in a polypeptide chain has a distinctive R-group associated with it. We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. In an otherwise pseudo-random sequence, we search for forbidden combinations ofkth order. We applied this method to analyze the available protein sequences of various viruses including SARS-CoV-2. We found that these ubiquitous forbidden orders (UFO) are unique to each of the viruses we analyzed. This unique structure of the viruses may provide an insight into viruses’ chemical behavior and the folding patterns of the proteins. This finding may have a broad significance for the analysis of coding sequences of species in general.