bluuebunny/crossref_metadata_2025 huggingface dataset:
Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity
Authors: Valsecchi Elena , Arcangeli Antonella , Lombardi Roberto , Boyse Elizabeth , Carr Ian M. , Galli Paolo , Goodman Simon J.
Published: May 2021

Marine environmental DNA (eDNA) is an important tool for biodiversity research and monitoring but challenges remain in scaling surveys over large spatial areas, and increasing the frequency of sampling in remote locations at reasonable cost. Here we demonstrate the feasibility of sampling from commercial vessels (Mediterranean ferries) while underway, as a strategy to facilitate replicable, systematic marine eDNA surveys in locations that would normally be challenging and expensive for researchers to access. Sixteen eDNA samples were collected from 4 fixed sampling stations, and in response to 4 cetacean sightings, across three cruises undertaken along the 300 km ferry route between Livorno (Tuscany) and Golfo Aranci (Sardinia) in the Ligurian/Tyrrhenian Seas, June-July 2018. Using 12SrDNA and 16SrDNA metabarcoding markers, we recovered diverse marine vertebrate Molecular Operational Taxonomic Units (MOTUs) from teleost fish, elasmobranchs, and cetaceans. We detected sample heterogeneity consistent with previously known variation in species occurrences, including putative species spawning peaks associated with specific sea surface temperature ranges, and increased night time abundance of bathypelagic species known to undertake diel migrations through the water column. We suggest commercial vessel based marine eDNA sampling using the global shipping network has potential to facilitate broad-scale biodiversity monitoring in the world’s oceans.
SWAN Identification of Common Aneuploidy-Based Oncogenic Drivers
Authors: Bowers Robert R. , Jones Christian M. , Paz Edwin A. , Barrows John K. , Armeson Kent E. , Long David T. , Delaney Joe R.
Published: May 2021

Haploinsufficiency drives Darwinian evolution. Siblings, while alike in many aspects, differ due to monoallelic differences inherited from each parent. In cancer, solid tumors exhibit aneuploid genetics resulting in hundreds to thousands of monoallelic gene-level copy-number alterations (CNAs) in each tumor. Aneuploidy patterns are heterogeneous, posing a challenge to identify drivers in this high-noise genetic environment. Here, we developed Shifted Weighted Annotation Network (SWAN) analysis to assess biology impacted by cumulative monoallelic changes. SWAN enables an integrated pathway-network analysis of CNAs, RNA expression, and mutations via a simple web platform. SWAN is optimized to best prioritize known and novel tumor suppressors and oncogenes, thereby identifying drivers and potential druggable vulnerabilities within cancer CNAs. Protein homeostasis, phospholipid dephosphorylation, and ion transport pathways are commonly suppressed. An atlas of CNA pathways altered in each cancer type is released. These CNA network shifts highlight new, attractive targets to exploit in solid tumors.

Highlights

Copy-number alteration pathways define solid tumor biology

SWAN is released as an integrative point-and-click pathway analysis tool

Moderate impact drivers highlighted by SWAN validatedin vitro

Copy-number altered pathways associate with mutations and survival
The self-regulated response of the Wnt pathway to an oncogenic mutation in β-catenin
Authors: Moshkovsky Ana R , Ma Wenzhe , Kirschner Marc W
Published: May 2021

Oncogenic mutations in β-catenin can inhibit degradation of β-catenin by preventing phosphorylation of its degron. Degron phosphorylation is mediated by the Axin scaffold, Casein Kinase 1α (CK1α) and Glycogen Synthase Kinase 3 (GSK3). We studied an oncogenic form of β-catenin with a deletion of serine 45 (S45), a site that is phosphorylated by the kinase CK1α. When the S45 site is phosphorylated, it promotes the GSK3-mediated phosphorylations of the β-catenin degron. Deletion of S45 would be expected to prevent GSK3-mediated phosphorylation of the mutant protein and thus block degradation. We found that the S45 mutant was still phosphorylatable by GSK3, and its expression increased the concentration of Axin, restoring the rate of GSK3-mediated phosphorylation to levels comparable to those observed for the wild-type β-catenin. We conclude that there is one core mechanism for creating the phosphodegron for both primed and unprimed β-catenin, which involves the generation of an Axin-GSK3 complex.

SIGNIFICANCE

Understanding how the Wnt pathway responds to mutations in β-catenin phosphodegron can reveal important properties of the pathway in normal and cancer cells and is valuable for the design of more effective therapeutic strategies.
One Scaffold – Different Organelles Sensors: pH-Activable Fluorescent Probes for Targeting Live Primary Microglial Cell Organelles
Authors: Jethava Krupal P. , Prakash Priya , Manchanda Palak , Arora Harshit , Chopra Gaurav
Published: May 2021

Targeting live cell organelles is important for imaging and to understand and control specific biochemical processes. Typically, fluorescent probes with distinct structural scaffolds have been used for targeting specific cell organelle. Herein, we aimed to design modular one-step synthetic strategies using a common reaction intermediate to develop new lysosomal, mitochondrial and nucleus targeting pH-activable fluorescent probes that are all based on a single boron dipyrromethane analogs. The divergent cell organelle targeting was achieved by synthesizing pH-activable fluorescent probes with specific functional groups changes to the main scaffold resulting in differential fluorescence and pKa. Specifically, we show that the functional group transformation of the same scaffold influences cellular localization and specificity of pH-activable fluorescent probes in live primary microglial cells with pKa’s ranging from ~4.5-6.0. We introduce a structure-organelle-relationship (SOR) framework targeting the nucleus (NucShine), lysosomes (LysoShine) and mitochondria (MitoShine) in primary mouse microglial cells. This work will result in future applications of SOR beyond imaging to target and control organelle-specific biochemical processes in disease-specific models.
The petrosal and basicranial morphology ofProtoceras celer
Authors: Robson Selina Viktor , Seale Brendon , Theodor Jessica M.
Published: May 2021

Protoceratids are an extinct family of endemic North American artiodactyls. The phylogenetic position of protoceratids in relation to camelids and ruminants has been contentious for over a century. The petrosal morphology of basal (Leptotragulus) and derived (Syndyoceras) protoceratids has suggested that protoceratids are closely related to ruminants, whereas a prior description of a disarticulated intermediate protoceratid petrosal (Protoceras celer) indicated that protoceratids were closely related to camelids. This contradictory evidence implied that there were several character reversals within the protoceratid lineage and brought into question the utility of basicranial characters in artiodactyl phylogenetics. Here, we provide descriptions of an additionalP. celerpetrosal. The descriptions are based on data produced by computed tomography scans, which allowed us to image the petrosalin situin the skull. Our results indicate that the petrosal morphology ofP. celeris similar to that of other protoceratids, implying that, contrary to previous evidence, petrosal morphology is conserved within the Protoceratidae.
Visualization of lake succession as indicated by macrophyte species composition and trophic levels in lakes subdivided by volcanic eruption at Akan Caldera, Hokkaido, Japan
Authors: Wakana Isamu , Kadono Yasuro , Urabe Jotaro , Tamura Yuki , Suzuki Yoshifusa , Yamada Hiroyuki , Oyama Yoichi , Wada Keiji , Hasegawa Takeshi , Ohara Masashi
Published: May 2021

It is not feasible to continuously observe ecological succession in lakes because of the long time-scales generally involved. Thus, the process has been inductively deduced by comparing many lakes with different succession states, or indirectly simulated by tracking studies of smaller water bodies, experiments using microcosms or mesocosms, and reconstruction of lake history by sediment analysis. However, the reality of succession processes in large lakes with slow succession is not well understood, and new approaches are needed. Theoretically, in a group of large and small lakes of similar ages and with similar initial and watershed environments, the rate of nutrient accumulation in each lake depends on the ratio of watershed area to lake size, and the lakes are predicted to evolve to different trophic levels over time. Here, we tested this hypothesis on the 10 lakes of varying sizes in Akan Caldera, Japan, which were formed thousands of years ago by fragmentation due to volcanic eruptions within the caldera. Topographic and water quality studies showed that the ratio of accumulated watershed area to lake size (area and volume), expressed logarithmically, had a positive linear regression with the total phosphorus concentration, an indicator of trophic level. The trophic levels of the lakes were diverse, including oligotrophic, mesotrophic, and eutrophic types in the traditional “lake type” classification based on total phosphorus and chlorophyll-a concentrations. Furthermore, 21 species of aquatic macrophytes were observed by a diving survey, and the plant species composition was classified into five groups corresponding to the trophic status of the lakes, indicating a conventional “hydrarch succession”. The diversity of water quality and aquatic vegetation in a group of lakes with similar origins paves the way for new comparative studies of lakes, including large lakes.
Network Pharmacology Integrated Molecular Docking Based Prediction of Active Compounds and Potential Targets inTinospora crispaLinn. as Insulin Sensitizer
Authors: Zuhri Ummu Mastna , Purwaningsih Erni Hernawati , Fadilah  , Yuliana Nancy Dewi
Published: May 2021

Insulin resistance is a metabolic disorder characterized by the decreased response to insulin in muscle, liver, and adipose cells. The normal insulin levels are unable to control glucose, lipids, and energy homeostasis. This condition remains a complex phenomenon that involves several genetic defects and environmental stresses, such as obesity. A full understanding is required to understand the entire itinerary and functional consequences of the occurrence of insulin resistance to develop a potent drug in diabetes management. In the present study, we investigated the mechanism of known phytochemical constituents ofTinospora crispaand its interaction with insulin resistant target proteins by using network pharmacology and molecular docking. The insulin sensitizer activities ofTinospora crispamay be associated with the inhibition of the activation of the inflammatory pathway and the activation of insulin signaling. Tinoscorside A, Makisterone C, Borapetoside A and B, and β sitosterol consider the main phytoconstituents ofTinospora crispaby its binding with active sites of main protein targets of insulin resistance potential therapy. In conclusion,Tinospora crispawas one of the promising therapeutic agent in type 2 diabetes mellitus management. Regulation in glucose homeostasis, adipolysis, cell proliferation, and antiapoptosis may be the critical mechanism ofTinospora crispaas an insulin sensitizer.
XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
Authors: Maguire Jack B. , Grattarola Daniele , Klyshko Eugene , Mulligan Vikram Khipple , Melo Hans
Published: May 2021

Graph representations are traditionally used to represent protein structures in sequence design protocols where the folding pattern is known. This infrequently extends to machine learning projects: existing graph convolution algorithms have shortcomings when representing protein environments. One reason for this is the lack of emphasis on edge attributes during massage-passing operations. Another reason is the traditionally shallow nature of graph neural network architectures. Here we introduce an improved message-passing operation that is better equipped to model local kinematics problems such as protein design. Our approach, XENet, pays special attention to both incoming and outgoing edge attributes.

We compare XENet against existing graph convolutions in an attempt to decrease rotamer sample counts in Rosetta’s rotamer substitution protocol. This use case is motivating because it allows larger protein design problems to fit onto near-term quantum computers. XENet outperformed competing models while also displaying a greater tolerance for deeper architectures. We found that XENet was able to decrease rotamer counts by 40% without loss in quality. This decreased the problem size of our use case by more than a factor of 3. Additionally, XENet displayed an ability to handle deeper architectures than competing convolutions.

Author summary

Graphs data structures are ubiquitous in the field of protein design and are at the core of the recent advances in artificial intelligence brought forth by graph neural networks (GNNs). GNNs have led to some impressive results in modeling protein interactions, but are not as common as other tensor representations.

Most GNN architectures tend to put little to no emphasis on the information stored on edges; however, protein modeling tools often use edges to represent vital geometric relationships about residue pair interactions. In this paper, we show that a more advanced processing of edge attributes can lead to considerable benefits when modeling chemical data.

We introduce XENet, a new member of the GNN family that is shown to have improved ability to model protein residue environments based on chemical and geometric data. We use XENet to intelligently simplify the optimization problem that is solved when designing proteins. This task is important to us and others because it allows larger proteins to be designed on near-term quantum computers. We show that XENet is able to train on our protein modeling data better than existing methods, successfully resulting in a dramatic decrease in protein design sample space with no loss in quality.
A statistical test for clonal exclusivity in tumour evolution
Authors: Kuipers Jack , Moore Ariane L. , Jahn Katharina , Schraml Peter , Wang Feng , Morita Kiyomi , Andrew Futreal P. , Takahashi Koichi , Beisel Christian , Moch Holger , Beerenwinkel Niko
Published: May 2021

Tumour progression is an evolutionary process in which different clones evolve over time, leading to intra-tumour heterogeneity. Interactions between clones can affect tumour evolution and hence disease progression and treatment outcome. Pairs of mutations that are overrepresented in a clonally exclusive fashion over a cohort of patient samples may be suggestive of a synergistic effect between the different clones carrying these mutations. We therefore developed a novel statistical test, called GeneAccord, to identify such gene pairs that are altered in distinct subclones of the same tumour. We analysed our test for calibration and power. By comparing its performance to baseline methods, we demonstrate that to control type I errors, it is essential to account for the evolutionary dependencies among clones. In applying GeneAccord to the single-cell sequencing of a cohort of 123 acute myeloid leukaemia patients, we find 6 clonally exclusive and 2 clonally co-occurring gene pairs. The clonally exclusive pairs mostly involve genes of the key signalling pathways.
Subtly altered topological asymmetry of brain structural covariance networks in autism spectrum disorder across 43 datasets from the ENIGMA consortium
Authors: Sha Zhiqiang , van Rooij Daan , Anagnostou Evdokia , Arango Celso , Auzias Guillaume , Behrmann Marlene , Bernhardt Boris , Bolte Sven , Busatto Geraldo F. , Calderoni Sara , Calvo Rosa , Daly Eileen , Deruelle Christine , Duan Meiyu , Souza Duran Fabio Luis , Durston Sarah , Ecker Christine , Ehrlich Stefan , Fair Damien , Fedor Jennifer , Fitzgerald Jacqueline , Floris Dorothea L. , Franke Barbara , Freitag Christine M. , Gallagher Louise , Glahn David C , Haar Shlomi , Hoekstra Liesbeth , Jahanshad Neda , Jalbrzikowski Maria , Janssen Joost , King Joseph A. , Lazaro Luisa , Luna Beatriz , McGrath Jane , Medland Sarah E. , Molloy Ciara , Muratori Filippo , Murphy Declan G.M. , Neufeld Janina , O’Hearn Kirsten , Oranje Bob , Parellada Mara , Pariente Jose C. , Postema Merel C. , Remnelius Karl Lundin , Retico Alessandra , Penteado Rosa Pedro Gomes , Rubia Katya , Shook Devon , Tammimies Kristiina , Taylor Margot J. , Tosetti Michela , Wallace Gregory L. , Zhou Fengfeng , Thompson Paul M. , Fisher Simon E. , Buitelaar Jan K. , Francks Clyde
Published: May 2021

Small average differences in the left-right asymmetry of cerebral cortical thickness have been reported in individuals with autism spectrum disorder (ASD) compared to typically developing controls. Although these alterations affect multiple and widespread cortical regional asymmetries, the extent to which specific structural networks might be affected remains unknown. Inter-regional morphological covariance analysis can capture network connectivity relations between different cortical areas at the macroscale level. Here, we used cortical thickness data from 1,455 individuals with ASD and 1,560 controls, across 43 independent datasets of the ENIGMA consortium’s ASD Working Group, to assess hemispheric asymmetries of intra-individual structural covariance networks, using graph theory-based topological metrics. Compared with typical features of small-world architecture in controls, the ASD sample showed significantly altered asymmetry of hemispheric networks involving the fusiform, rostral middle frontal, and medial orbitofrontal cortex, driven by shifts toward higher randomization of the corresponding right-hemispheric networks in ASD. A network involving the superior frontal cortex showed decreased right-hemisphere randomization. Based on comparisons with meta-analyzed functional neuroimaging data, the altered connectivity asymmetry particularly affected networks that subserve working memory, executive functions, language, reading, and sensorimotor processes. Taken together, these findings provide new insights into how altered brain left-right asymmetry in ASD affects specific structural and functional brain networks. Altered asymmetrical brain development in ASD may be partly propagated among spatially distant regions through structural connectivity.
Drug distribution along the cochlea is strongly enhanced by low-frequency round window micro vibrations
Authors: Flaherty Samuel M. , Russell Ian J. , Lukashkin Andrei N.
Published: May 2021

The cochlea’s inaccessibility and complex nature provide significant challenges to delivering drugs and other agents uniformly, safely and efficiently, along the entire cochlear spiral. Large drug concentration gradients are formed along the cochlea when drugs are administered to the middle ear. This undermines the major goal of attaining therapeutic drug concentration windows along the whole cochlea. Here, utilizing a well-known physiological effect of salicylate, we demonstrate a proof of concept in which drug distribution along the entire cochlea is enhanced applying round window membrane low-frequency micro vibrations with a probe that only partially covers the round window. We provide evidence of enhanced drug influx into the cochlea and cochlear apical drug distribution without breaching cochlear boundaries. It is further suggested that ossicular functionality is not required for the effective drug distribution we report. The novel method of local drug delivery to the cochlea presented here could be implemented when ossicular functionality is absent or impeded and can be incorporated in clinically approved auditory protheses for patients who suffer with conductive, sensorineural or mixed hearing loss.
Blood-based liquid biopsy for comprehensive cancer genomic profiling using next-generation sequencing: an emerging paradigm for noninvasive cancer detection and management in dogs
Authors: Kruglyak Kristina M , Chibuk Jason , McLennan Lisa , Nakashe Prachi , Hernandez Gilberto E , Motalli-Pepio Rita , Fath Donna M , Tynan John A , Holtvoigt Lauren E , Chorny Ilya , Grosu Daniel S , Tsui Dana WY , Flory Andi
Published: May 2021

This proof-of-concept study demonstrates that blood-based liquid biopsy using next generation sequencing of cell-free DNA can noninvasively detect multiple classes of genomic alterations in dogs with cancer, including alterations that originate from spatially separated tumor sites.

Eleven dogs with a variety of confirmed cancer diagnoses (including localized and disseminated disease) who were scheduled for surgical resection, and 5 presumably cancer-free dogs, were enrolled. Blood was collected from each subject, and multiple spatially separated tumor tissue samples were collected during surgery from 9 of the cancer subjects.

All samples were analyzed using an advanced prototype of a novel liquid biopsy test designed to noninvasively interrogate multiple classes of genomic alterations for the detection, characterization, and management of cancer in dogs.

In 5 of the 9 cancer patients with matched tumor and plasma samples, pre-surgical liquid biopsy testing identified genomic alterations, including single nucleotide variants and copy number variants, that matched alterations independently detected in corresponding tumor tissue samples. Importantly, the pre-surgical liquid biopsy test detected alterations observed in spatially separated tissue samples from the same subject, demonstrating the potential of blood-based testing for comprehensive genomic profiling of heterogeneous tumors. Among the 3 patients with post-surgical blood samples, genomic alterations remained detectable in one patient with incomplete tumor resection, suggesting utility for noninvasive detection of minimal residual disease following curative-intent treatment.

Liquid biopsy allows for noninvasive profiling of cancer-associated genomic alterations with a simple blood draw and has potential to overcome the limitations of tissue-based testing posed by tissue-level genomic heterogeneity.
Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of anN-arylbenzdiimidazole ligand’s rescue of Parkinson’s-associated cell toxicity
Authors: Hatstat A. Katherine , Quan Baiyi , Bailey Morgan , Fitzgerald Michael C. , Reinhart Michaela C. , McCafferty Dewey G.
Published: May 2021

The development of phenotypic models of Parkinson’s disease (PD) has enabled screening and identification of phenotypically active small molecules that restore complex biological pathways affected by PD toxicity. While these phenotypic screening platforms are powerful, they do not inherently enable direct identification of the cellular targets of promising lead compounds. To overcome this, chemoproteomic platforms like Thermal Proteome Profiling (TPP) and Stability of Proteins from Rates of Oxidation (SPROX) can be implemented to reveal protein targets of biologically active small molecules. Here we utilize both of these chemoproteomic strategies to identify targets of anN-arylbenzdiimidazole compound, NAB2, which was previously identified for its ability to restore viability in cellular models of PD-associated α-synuclein toxicity. The combined results from our TPP and SPROX analyses of NAB2 and the proteins in a neuroblastoma-derived SHSY5Y cell lysate reveal a previously unrecognized protein target of NAB2. This newly recognized target, Rab1a, is a small GTPase that acts as a molecular switch to regulate ER-to-Golgi trafficking, a process that is disrupted by α-synuclein toxicity and restored by NAB2 treatment. Further validation reveals that NAB2 binds to Rab1a with selectivity for its GDP-bound form and that NAB2 treatment phenocopies Rab1a overexpression in alleviation of α-synuclein toxicity. Finally, we conduct a preliminary investigation into the relationship between Rab1a and the E3 ubiquitin ligase, Nedd4, a previously identified NAB2 target. Together, these efforts expand our understanding of the mechanism of NAB2 in the alleviation of α-synuclein toxicity and reinforce the utility of chemoproteomic identification of the targets of phenotypically active small molecules that regulate complex biological pathways.
Prior aerosol infection with lineage A SARS-CoV-2 variant protects hamsters from disease, but not reinfection with B.1.351 SARS-CoV-2 variant
Authors: Yinda Claude Kwe , Port Julia R. , Bushmaker Trenton , Fischer Robert J. , Schulz Jonathan E. , Holbrook Myndi G. , Shaia Carl , de Wit Emmie , van Doremalen Neeltje , Munster Vincent J.
Published: May 2021

The circulation of SARS-CoV-2 has resulted in the emergence of variants of concern (VOCs). It is currently unclear whether previous infection with SARS-CoV-2 provides protection against reinfection with VOCs. Here, we show that low dose aerosol exposure to hCoV-19/human/USA/WA-CDC-WA1/2020 (WA1, lineage A), resulted in a productive mild infection. In contrast, low dose of SARS-CoV-2 via fomites did not result in productive infection in the majority of exposed hamsters and these animals remained non-seroconverted. After recovery, hamsters were re-exposed to hCoV-19/South African/KRISP-K005325/2020 (VOC B.1.351) via an intranasal challenge. Seroconverted rechallenged animals did not lose weight and shed virus for 3 days. They had little infectious virus and no pathology in the lungs. In contrast, shedding, weight loss and extensive pulmonary pathology caused by B.1.351 replication was observed in the non-seroconverted animals. The rechallenged seroconverted animals did not transmit virus to naïve sentinels via direct contact transmission, in contrast to the non-seroconverted animals. Reinfection with B.1.351 triggered an anamnestic response that boosted not only neutralizing titers against lineage A, but also titers against B.1.351. Our results confirm that aerosol exposure is a more efficient infection route than fomite exposure. Furthermore, initial infection with SARS-CoV-2 lineage A does not prevent heterologous reinfection with B.1.351 but prevents disease and onward transmission. These data suggest that previous SARS-CoV-2 exposure induces partial protective immunity. The reinfection generated a broadly neutralizing humoral response capable of effectively neutralizing B.1.351 while maintaining its ability to neutralize the virus to which the initial response was directed against.
Current challenges in microbiome metadata collection
Authors: Rosenfeld Gabriel , Angelova Angelina , Shin Chris , Quinones Mariam , Hurt Darrell
Published: May 2021

While the biomedical community has embraced data sharing (e.g. results, raw data) and supported establishment of large research consortia (e.g. the Human Microbiome Project) aimed to standardize the quality of important sets of microbiome sequencing data, the reusability of most microbiome data is still limited by the quality of its associated metadata. To ensure that microbiome data is indeed FAIR (Findable, Accessible, Interoperable, and Reusable), it is necessary to consider tools and approaches that make it easier to provide high-quality metadata that is fit for purpose moving forward. Such tools and approaches could be informed by current efforts to harmonize and improve the quality of extant microbiome metadata.
Seasonal song variation in male Carolina Wrens (Thryothorus ludovicianus)
Authors: Keating Holly R. , Reichard Dustin G.
Published: May 2021

Birdsong’s primary function is attracting and stimulating mates and repelling rivals during the breeding season. However, many species also sing during the nonbreeding season, which raises questions about the function of nonbreeding song and the proximate mechanisms underlying its production. In this study, we compared spectral and temporal measurements from a large sample of breeding (N= 267) and nonbreeding songs (N= 283) of Carolina Wrens (Thryothorus ludovicianus), a nonmigratory, temperate species that sings year-round. We found that breeding songs were longer than nonbreeding songs and had more syllables within each song. Trill rate, the number of notes per syllable, minimum and maximum frequency and frequency bandwidth did not differ detectably between the two seasons. This study is the first to examine seasonal song differences in Carolina Wrens and provides a basis for future investigations into the drivers behind this seasonal variation.
Metamorphosis imposes variable constraints on genome expansion through effects on development
Authors: Mueller Rachel L , Cressler Clayton E , Schwarz Rachel S , Chong Rebecca A , Butler Marguerite A
Published: May 2021

Genome size varies ~ 100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, have the largest vertebrate genomes — 3 to 40 times that of humans — as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.
Differential Regulation of Rice Transcriptome toRhizoctonia solaniinfection
Authors: Das Akash , Mazahar Moin , Sahu Ankur , Kshattry Mrinmoy , Kirti P.B. , Barah Pankaj
Published: May 2021

Sheath Blight (SB) disease in rice crop caused by the infection of the fungal pathogenRhizoctonia solani(R. solani) is one of the severe rice diseases that can cause up to 50% yield losses. Naturally occurring rice varieties resistant to SB have not been reported yet. We have performed a Time-Series RNA-Seq analysis on a widely cultivated rice variety BPT-5204 for identifying its transcriptomic response signatures toR. solaniinfection at 1st, 2ndand 5thday post inoculation (dpi). In total, 428, 3225 and 1225 genes were differentially expressed in the treated rice plants post 1, 2 and 5 dpi, respectively. GO and KEGG enrichment analysis identified significant processes and pathways differentially altered in the rice plant after the fungal infection. Machine learning and network based integrative approach was used to construct Transcriptional Regulatory Networks (TRNs) of the rice plant at the three Time Points. Regulatory network analysis identified SUB1B, MYB30 and CCA1 as important regulatory hub Transcription Factors in rice duringR. solaniinfection. Jasmonic acid signaling pathway was activated and in contrast, photosynthesis and carbon fixation processes were significantly compromised. Involvement of MAPK, CYPs, Peroxidases and PAL genes was observed in response to the fungal infection. Circadian clock was also strongly influenced byR. solaniinfection. Our integrative analysis identified 7 putative SB resistant genes altered in rice afterR. solaniinfection and provided a better understanding of rice plant response toR. solaniinfection.

One sentence summary

Time series expression analysis of rice variety BPT-5204 identifies key molecular signatures involved in rice plant response toR. solaniinfection.
A Phylogenomic Framework for Charting the Diversity and Evolution of Giant Viruses
Authors: Aylward Frank O. , Moniruzzaman Mohammad , Ha Anh D. , Koonin Eugene V.
Published: May 2021

Large DNA viruses of the phylumNucleocytoviricotahave recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a strong need for a robust phylogenomic and taxonomic framework for these viruses. Here we report a comprehensive phylogenomic analysis of theNucleocytoviricota, present a set of giant virus orthologous groups (GVOGs) together with a benchmarked reference phylogeny, and delineate a hierarchical taxonomy within this phylum. We show that the majority ofNucleocytoviricotadiversity can be partitioned into 6 orders, 32 families, and 344 genera, substantially expanding the number of currently recognized taxonomic ranks for these viruses. We integrate our results within a megataxonomy that has been adopted for all viruses to establish a unifying framework for the study ofNucleocytoviricotadiversity, evolution, and environmental distribution.
The CTPase activity of ParB acts as a timing mechanism to control the dynamics and function of prokaryotic DNA partition complexes
Authors: Osorio-Valeriano Manuel , Altegoer Florian , Das Chandan K. , Steinchen Wieland , Panis Gaël , Connolley Lara , Giacomelli Giacomo , Feddersen Helge , Corrales-Guerrero Laura , Giammarinaro Pietro , Hanßmann Juri , Bramkamp Marc , Viollier Patrick H. , Murray Seán , Schäfer Lars V. , Bange Gert , Thanbichler Martin
Published: May 2021

DNA partitioning CTPases of the ParB family mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded atparSmotifs in the centromeric region of target DNA molecules and then spread laterally to form large nucleoprotein complexes that serve as docking points for the DNA segregation machinery. Here, we identify conformational changes that underlie the CTP- andparS-dependent closure of ParB clamps. Moreover, we solve crystal structures of ParB in the pre- and post-hydrolysis state and provide insights into the catalytic mechanism underlying nucleotide hydrolysis. The characterization of CTPase-deficient ParB variants reveals that CTP hydrolysis serves as a timing mechanism to control the sliding time of ParB. Hyperstable clamps are trapped on the DNA, leading to excessing spreading and severe chromosome segregation defectsin vivo. These findings clarify the role of the ParB CTPase cycle in partition complex dynamics and function and thus complete our understanding of this prototypic CTP-dependent molecular switch.
Identification of Splice Regulators of Fibronectin-EIIIA and EIIIB by Direct Measurement of Exon Usage in a Flow-Cytometry Based CRISPR Screen
Authors: Hensel Jessica , Heineman Brent , Kimble Amy , Jellison Evan , Reese Bo , Murphy Patrick
Published: May 2021

The extracellular matrix protein fibronectin (FN) is alternatively spliced in a variety of inflammatory conditions, resulting in increased inclusion of alternative exons EIIIA and EIIIB. Inclusion of these exons affects fibril formation, fibrosis, and inflammation. To define upstream regulators of alternative splicing in FN, we have developed anin vitroflow-cytometry based assay, using RNA-binding probes to determine alternative exon inclusion level in aortic endothelial cells. This approach allows us to detect exon inclusion in the primary transcripts themselves, rather than in surrogate splicing reporters. We validated this assay in cells with and without FN-EIIIA and –EIIIB expression. In a small-scale CRISPR KO screen of candidate regulatory splice factors, we successfully detected known regulators of EIIIA and EIIIB splicing, and detected several novel regulators. Finally, we show the potential in this approach to broadly interrogate upstream signaling pathways in aortic endothelial cells with a genome-wide CRISPR-KO screen, implicating the TNFalpha and RIG-I-like signaling pathways and genes involved in the regulation of fibrotic responses. Thus, we provide a novel means to screen the regulation of splicing of endogenous transcripts, and predict novel pathways in the regulation of FN-EIIIA inclusion.
Amino acid sensor conserved from bacteria to humans
Authors: Gumerov Vadim M. , Andrianova Ekaterina P. , Matilla Miguel A. , Dolphin Annette C. , Krell Tino , Zhulin Igor B.
Published: May 2021

Amino acids are recognized as signals by various receptors in bacteria, archaea, and eukaryotes. However, no common mechanism for amino acid recognition is currently known. Here we show that a subclass of a ubiquitous extracellular domain dCache_1 contains a simple amino acid recognition motif, and it is found throughout the Tree of Life. In bacteria, this motif exclusively binds amino acids, including GABA, and it is present in all major receptor types. In humans, this motif is found in α2δ subunits of voltage-gated calcium channels that are implicated in neuropathic pain and neurodevelopmental disorders. Our findings suggest that GABA-derived drugs bind to the same motif in human α2δ subunits that binds natural GABA ligands in bacterial chemoreceptors.
Simultaneous Brain, Brainstem and Spinal Cord pharmacological-fMRI reveals endogenous opioid network interactions mediating attentional analgesia
Authors: Oliva Valeria , Hartley-Davies Ron , Moran Rosalyn , Pickering Anthony E. , Brooks Jonathan C.W.
Published: May 2021

Pain perception is decreased by shifting attentional focus away from a threatening event. This attentional analgesia engages parallel descending control pathways from anterior cingulate (ACC) to locus coeruleus, and ACC to periaqueductal grey (PAG) – rostral ventromedial medulla (RVM), indicating possible roles for noradrenergic or opioidergic neuromodulators. To determine which pathway modulates nociceptive activity in humans we used simultaneous whole brain-spinal cord pharmacological-fMRI (N=39) across three sessions. Noxious thermal forearm stimulation generated somatotopic-activation of dorsal horn (DH, C6 segment) whose activity mirrored attentional pain modulation. Activity in an adjacent cluster reported the interaction between task and noxious stimulus. Effective connectivity analysis revealed that ACC recruits PAG and RVM to modulate spinal cord activity. Blocking endogenous opioids with Naltrexone impairs attentional analgesia and disrupts RVM-DH and ACC-PAG connectivity. Noradrenergic augmentation with Reboxetine did not alter attentional analgesia. Cognitive pain modulation is mediated by opioidergic ACC-PAG-RVM descending control which supresses spinal nociceptive activity.
Inherited Human Sex Reversal due to Loss of a Water-Mediated Hydrogen Bond at a Conserved Protein-DNA Interface
Authors: Chen Yen-Shan , Racca Joseph , Amir Dan , Haas Elisha , Weiss Michael A.
Published: May 2021

Male sex determination in mammals is initiated by SRY, a Y-encoded architectural transcription factor. The protein contains a high-mobility-group (HMG) box that mediates sequence-specific DNA bending. Mutations in SRY causing XY gonadal dysgenesis (Swyer syndrome) cluster in the box. Although such mutations usually arisede novoin spermatogenesis, some are inherited: male development occurs in one genetic background (the father) but not another (the sterile XY daughter). Here, we comparede novoand inherited mutations at an invariant Tyr adjoining the motif’s basic tail (consensus position 72; Y127C and Y127F in intact SRY). Crystal structures of homologous SOX-DNA complexes suggest that the wild-type side chain’spara-OH group anchors a water-mediated hydrogen bond to the DNA backbone. In an embryonic gonadal cell line, Y127C (de novo) led to accelerated proteasomal proteolysis and blocked transcriptional activity; activity remained low on rescue of expression by chemical proteasome inhibition. Y127F (inherited) preserved substantial transcriptional activity: 91(±11)% on SRY overexpression and 65(±17)% at physiological expression. Control studies indicated no change in protein lifetime or nuclear localization. Only subtle biophysical perturbations were observedin vitro. Although though inherited variant’s specific DNA affinity was only twofold lower than wild type, stopped-flow kinetic analysis revealed a sevenfold decrease in lifetime of the complex. Time-resolved fluorescence energy transfer (using a 15-base pair DNA site) demonstrated native mean DNA bending but with a slightly widened distribution of end-to-end DNA distances. Our findings highlight the contribution of a single water-mediated hydrogen bond to robustness of a genetic switch in human development.
YAP/TAZ Maintain the Proliferative Capacity and Structural Organization of Radial Glial Cells During Brain Development
Authors: Lavado Alfonso , Gangwar Ruchika , Paré Joshua , Wan Shibiao , Fan Yiping , Cao Xinwei
Published: May 2021

The Hippo pathway regulates the development and homeostasis of many tissues and in many species. It controls the activity of two paralogous transcriptional coactivators, YAP and TAZ (YAP/TAZ). Although previous studies have established that aberrant YAP/TAZ activation is detrimental to mammalian brain development, whether and how endogenous levels of YAP/TAZ activity regulate brain development remain unclear. Here, we show that during mammalian cortical development, YAP/TAZ are specifically expressed in apical neural progenitor cells known as radial glial cells (RGCs). The subcellular localization of YAP/TAZ undergoes dynamic changes as corticogenesis proceeds. YAP/TAZ are required for maintaining the proliferative potential and structural organization of RGCs, and their ablation during cortical development reduces the numbers of cortical projection neurons and causes the loss of ependymal cells, resulting in hydrocephaly. Transcriptomic analysis using sorted RGCs reveals gene expression changes in YAP/TAZ-depleted cells that correlate with mutant phenotypes. Thus, our study has uncovered essential functions of YAP/TAZ during mammalian brain development and revealed the transcriptional mechanism of their action.
Reinforcement learning modeling reveals a reward-history-dependent strategy underlying reversal learning in squirrel monkeys
Authors: Bari Bilal A. , Moerke Megan J. , Jedema Hank P. , Effinger Devin P. , Cohen Jeremiah Y. , Bradberry Charles W.
Published: May 2021

Insight into psychiatric disease and development of therapeutics relies on behavioral tasks that study similar cognitive constructs in multiple species. The reversal learning task is one popular paradigm that probes flexible behavior, aberrations of which are thought to be important in a number of disease states. Despite widespread use, there is a need for a high-throughput primate model that can bridge the genetic, anatomic, and behavioral gap between rodents and humans. Here, we trained squirrel monkeys, a promising preclinical model, on an image-guided deterministic reversal learning task. We found that squirrel monkeys exhibited two key hallmarks of behavior found in other species: integration of reward history over many trials and a side-specific bias. We adapted a reinforcement learning model and demonstrated that it could simulate monkey-like behavior, capture training-related trajectories, and provide insight into the strategies animals employed. These results validate squirrel monkeys as a model in which to study behavioral flexibility.
Predicting T Cell Quality During Manufacturing Through an Artificial Intelligence-based Integrative Multi-Omics Analytical Platform
Authors: Odeh-Couvertier Valerie Y. , Dwarshuis Nathan J. , Colonna Maxwell B. , Levine Bruce L. , Edison Arthur S. , Kotanchek Theresa , Roy Krishnendu , Torres-Garcia Wandaliz
Published: May 2021

Large-scale, reproducible manufacturing of therapeutic cells with consistently high quality is vital for translation to clinically effective and widely accessible cell therapies. However, the biological and logistical complexity of manufacturing a living product, including challenges associated with their inherent variability and uncertainties of process parameters, currently make it difficult to achieve predictable cell-product quality. Using a degradable microscaffold-based T cell process as an example, we developed an Artificial Intelligence (AI)-driven experimental-computational platform to identify a set of critical process parameters (CPP) and critical quality attributes (CQA) from heterogeneous, high dimensional, time-dependent multi-omics data, measurable during early stages of manufacturing and predictive of end-of-manufacturing product quality. Sequential, Design-of-Experiment (DOE)-based studies, coupled with an agnostic machine-learning framework, were used to extract feature combinations from media assessment that were highly predictive of total live CD4+and CD8+naïve and central memory (CD63L+CCR7+) T cells and their ratio in the end-product. This computational workflow could be broadly applied to any cell therapy and provide a roadmap for discovering CQAs and CPPs in cell manufacturing.
Meta-analytic maps of brain activity evoked by cognitive function diverge from resting state networks
Authors: Palmucci Matías , Tagliazucchi Enzo
Published: May 2021

Spontaneous human brain activity is organized into resting state networks (RSN), complex patterns of synchronized activity that account for the majority of brain metabolism. The correspondence between these patterns and those elicited by task performance suggests that spontaneous brain activity originates from the stream of ongoing cognitive processing. Here we investigate a large number of meta-analytic activation maps obtained from Neurosynth (www.neurosynth.org) to establish that task-rest similarity can be inflated by two potential sources of bias. Applying a hierarchical module detection algorithm to a network representation of activation map similarity, we showed that the correspondence between RSN and task-evoked activity tends to hold only for the largest spatial scales. Second, we established that this correspondence is biased by the inclusion of maps related to neuroanatomical terms (e.g. “parietal”, “occipital”, “cingulate”, etc.). Our results challenge the cognitive origin of spontaneous brain activity, suggesting that anatomically-constrained homeostatic processes could also play an important role in the inception and shaping of human resting state activity fluctuations.
Quantitative assessment of multiple fish species around artificial reefs using environmental DNA metabarcoding
Authors: Sato Masaaki , Inoue Nariaki , Nambu Ryogen , Furuich Naoki , Imaizumi Tomohito , Ushio Masayuki
Published: May 2021

Since the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs (i.e., quantitative MiSeq sequencing) makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using quantitative MiSeq sequencing and echo sounder survey. Using the quantitative metabarcoding method, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with eco sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicates a highly localized signal of eDNA at each sampling station. These results suggest that quantitative MiSeq sequencing is a promising technique to complement conventional methods to monitor distributions of multiple fish species.