bluuebunny/crossref_metadata_2025 huggingface dataset:
Mobile phone-based surveillance for animal disease in rural communities: implications for detection of zoonoses spillover
Authors: Thumbi Samuel M. , Njenga M. Kariuki , Otiang Elkanah , Otieno Linus , Munyua Peninah , Eichler Sarah , Widdowson Marc-Alain , McElwain Terry F. , Palmer Guy H.
Published: August 2019

Improving the speed of outbreak detection and reporting at the community level are critical in managing the threat of emerging infectious diseases, many of which are zoonotic. The widespread use of mobile phones, including in rural areas, constitutes a potentially effective tool for real-time surveillance of infectious diseases. Using longitudinal data from a disease surveillance system implemented in 1500 households in rural Kenya, we test the effectiveness of mobile phone animal syndromic surveillance by comparing it with routine household animal health surveys, determine the individual and household correlates of its use and examine the broader implications for surveillance of zoonotic diseases. A total of 20 340 animal and death events were reported from the community through the two surveillance systems, half of which were confirmed as valid disease events. The probability of an event being valid was 2.1 times greater for the phone-based system, compared with the household visits. Illness events were 15 times (95% CI 12.8, 17.1) more likely to be reported through the phone system compared to routine household visits, but not death events (OR 0.1 (95% CI 0.09, 0.11)). Disease syndromes with severe presentations were more likely to be reported through the phone system. While controlling for herd and flock sizes owned, phone ownership was not a determinant of using the phone-based surveillance system, but the lack of a formal education, and having additional sources of income besides farming were associated with decreased likelihood of reporting through the phone system. Our study suggests that a phone-based surveillance system will be effective at detecting outbreaks of diseases such as Rift Valley fever that present with severe clinical signs in animal populations, but in the absence of additional reporting incentives, it may miss early outbreaks of diseases such as avian influenza that present primarily with mortality.

This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
Mechanistic dose–response modelling of animal challenge data shows that intact skin is a crucial barrier to leptospiral infection
Authors: Gostic Katelyn M. , Wunder Elsio A. , Bisht Vimla , Hamond Camila , Julian Timothy R. , Ko Albert I. , Lloyd-Smith James O.
Published: August 2019

Leptospirosis is a widespread and potentially life-threatening zoonotic disease caused by spirochaetes of the genus
Leptospira
. Humans become infected primarily via contact with environmental reservoirs contaminated by the urine of shedding mammalian hosts. Populations in high transmission settings, such as urban slums and subsistence farming communities, are exposed to low doses of
Leptospira
on a daily basis. Under these conditions, numerous factors determine whether infection occurs, including the route of exposure and inoculum dose. Skin wounds and abrasions are risk factors for leptospirosis, but it is not known whether broken skin is necessary for spillover, or if low-dose exposures to intact skin and mucous membranes can also cause infection. To establish a quantitative relationship between dose, route and probability of infection, we performed challenge experiments in hamsters and rats, developed mechanistic dose–response models representing the spatial dynamics of within-host infection and persistence, and fitted models to experimental data. Results show intact skin is a strong barrier against infection, and that broken skin is the predominant route by which low-dose environmental exposures cause infection. These results identify skin integrity as a bottleneck to spillover of
Leptospira
and underscore the importance of barrier interventions in the prevention of leptospirosis.

This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
Aging-associated changes in transcriptional elongation influence metazoan longevity
Authors: Debès Cédric , Papadakis Antonios , Grönke Sebastian , Karalay Özlem , Tain Luke , Mizi Athanasia , Nakamura Shuhei , Hahn Oliver , Weigelt Carina , Josipovic Natasa , Zirkel Anne , Brusius Isabell , Sofiadis Konstantinos , Lamprousi Mantha , Lu Yu-Xuan , Huang Wenming , Esmaillie Reza , Kubacki Torsten , Späth Martin R. , Schermer Bernhard , Benzing Thomas , Müller Roman-Ulrich , Antebi Adam , Partridge Linda , Papantonis Argyris , Beyer Andreas
Published: August 2019

Physiological homeostasis becomes compromised during aging, as a result of impairment of cellular processes, including transcription and RNA splicing. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here, we profiled and analyzed genome-wide, aging-related changes in transcriptional processes across different organisms: nematode worms, fruit flies, mice, rats and humans. The average transcriptional elongation speed (Pol-II speed) increased with age in all five species. Along with these changes in elongation speed we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs. Two lifespan-extending interventions, dietary restriction and lowered insulin/Igf signaling, both reversed most of these aging-related changes. Genetic variants in Pol-II that reduced its speed in worms and flies increased their lifespan. Similarly, reducing Pol-II speed by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal aging and lifespan-extending interventions, and point to possible preventative measures.
SIDT2 RNA transporter promotes lung and gastrointestinal tumor development
Authors: Nguyen Tan A , Bieging-Rolett Kathryn T , Putoczki Tracy L , Wicks Ian P , Attardi Laura D , Pang Ken C
Published: August 2019

RNautophagy is a newly-described type of selective autophagy whereby cellular RNAs are transported into lysosomes for degradation. This process involves the transmembrane protein SIDT2, which transports double-stranded RNA (dsRNA) across the endolysosomal membrane. We previously demonstrated that SIDT2 is a transcriptional target ofp53, but its role in tumorigenesis – if any - is unclear. Unexpectedly, we show here thatSidt2−/−mice with concurrent oncogenicKrasG12Dactivation develop significantly fewer tumors than littermate controls in a mouse model of lung adenocarcinoma (LUAD). Consistent with this observation, loss of SIDT2 also leads to enhanced survival and delayed tumor development in anApcmin/+mouse model of intestinal cancer. Within the intestine,Apcmin/+;Sidt2−/−mice display accumulation of dsRNA in association with increased phosphorylation of eIF2α and JNK as well as elevated rates of apoptosis. Taken together, our data demonstrate a role for SIDT2 - and by extension RNautophagy - in promoting tumor development.
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix
Authors: Moriarty Nigel W. , Janowski Pawel A. , Swails Jason M. , Nguyen Hai , Richardson Jane S. , Case David A. , Adams Paul D.
Published: August 2019

The refinement of biomolecular crystallographic models relies on geometric restraints to help address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here we present an integration of the full all-atom Amber molecular dynamics force field into Phenix crystallographic refinement, which enables a more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of non-bonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over twenty-two thousand protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better; clash scores and MolProbity scores are significantly improved; and the modelling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined with traditional geometry restraints. We find in general that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum mechanical representation of active sites and improved geometric restraints for simulated annealing.

IMPORTANT

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Synopsis

The full Amber force field has been integrated into Phenix as an alternative refinement target. With a slight loss in speed, it achieves improved stereochemistry, fewer steric clashes and better hydrogen bonds.
Interactions between the N- and C- termini of mechanosensitive ion channel AtMSL10 are consistent with a three-step mechanism for activation
Authors: Basu Debarati , Shoots Jennette M. , Haswell Elizabeth S.
Published: August 2019

Although a growing number of mechanosensitive ion channels are being identified in plant systems, the molecular mechanisms by which they function are still under investigation. Overexpression of the mechanosensitive ion channel MSL (MscS-Like)10 fused to GFP triggers a number of developmental and cellular phenotypes including the induction of cell death, and this function is influenced by seven phosphorylation sites in its soluble N-terminus. Here, we show that these and other phenotypes required neither overexpression nor a tag and could be also induced by a previously identified point mutation in the soluble C-terminus (S640L). The promotion of cell death and hyperaccumulation of H2O2 in 35S:MSL10S640L-GFP overexpression lines was suppressed by N-terminal phosphomimetic substitutions, and the soluble N- and C-terminal domains of MSL10 physically interacted. We propose a three-step model by which tension-induced conformational changes in the C-terminus are transmitted to the N-terminus, leading to its dephosphorylation and the induction of adaptive responses. Taken together, this work expands our understanding of the molecular mechanisms of mechanotransduction in plants.

HIGHLIGHT

Cell death is triggered by mutations in either the cytoplasmic N- or C-terminus of AìMSLlü. Our proposed model explains how membrane tension may activate signaling through the interaction of these two domains.
sumrep: a summary statistic framework for immune receptor repertoire comparison and model validation
Authors: Olson Branden J , Moghimi Pejvak , Schramm Chaim , Obraztsova Anna , Ralph Duncan , Vander Heiden Jason A , Shugay Mikhail , Shepherd Adrian , Lees William , Matsen Frederick A
Published: August 2019

The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these receptors arise by a complex recombination process followed by a series of productivity-based filters, as well as affinity maturation for B cells, giving considerable diversity to the circulating pool of receptor sequences. Although these datasets hold considerable promise for medical and public health applications, the complex structure of the resulting adaptive immune receptor repertoire sequencing (AIRR-seq) datasets makes analysis difficult. In this paper we introducesumrep, an R package that efficiently performs a wide variety of repertoire summaries and comparisons, and show howsumrepcan be used to perform model validation. We find that summaries vary in their ability to differentiate between datasets, although many are able to distinguish between covariates such as donor, timepoint, and cell type for BCR and TCR repertoires. We show that deletion and insertion lengths resulting from V(D)J recombination tend to be more discriminative characterizations of a repertoire than summaries that describe the amino acid composition of the CDR3 region. We also find that state-of-the-art generative models excel at recapitulating gene usage and recombination statistics in a given experimental repertoire, but struggle to capture many physiochemical properties of real repertoires.
Isolation and characterisation of novel phages infectingLactobacillus plantarumand proposal of a new genus, “Silenusvirus”
Authors: Kyrkou Ifigeneia , Carstens Alexander Byth , Ellegaard-Jensen Lea , Kot Witold , Zervas Athanasios , Djurhuus Amaru Miranda , Neve Horst , Franz Charles M.A.P. , Hansen Martin , Hansen Lars Hestbjerg
Published: August 2019

Bacteria ofLactobacillussp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge onLactobacillusphage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-relatedLactobacillus plantarumstrains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the familySiphoviridaeand the proposal of the new phage genus “Silenusvirus”.
Characterization of evolutionarily conserved key players affecting eukaryotic flagellar motility and fertility using a moss model
Authors: Meyberg Rabea , Perroud Pierre-François , Haas Fabian B. , Schneider Lucas , Heimerl Thomas , Renzaglia Karen , Rensing Stefan A.
Published: August 2019

Defects in flagella/cilia are often associated with infertility and disease. Motile male gametes (sperm cells) with flagella are an ancestral eukaryotic trait that has been lost in several lineages, for example in flowering plants. Here, we made use of a phenotypic male fertility difference between two moss (Physcomitrella patens) strains to explore spermatozoid function. We compare genetic and epigenetic variation as well as expression profiles between the Gransden and Reute strain to identify a set of genes associated with moss male infertility. Defects in mammal and algal homologs of these genes coincide with a loss of fertility, demonstrating the evolutionary conservation of flagellar function related to male fertility across kingdoms. As a proof of principle, we generated a loss-of-function mutant of a coiled-coil domain containing 39 (ccdc39) gene that is part of the flagellar hydin network. Indeed, the Ppccdc39 mutant resembles the male infertile Gransden strain phenotype. Potentially, several somatic (epi-)mutations occurred during prolonged vegetative propagation of P. patens Gransden, causing regulatory differences of e.g. the homeodomain transcription factor BELL1. Probably these somatic changes are causative for the observed male fertility. We propose that P. patens spermatozoids might be employed as an easily accessible system to study male infertility of human and animals.
Commensal bacteria differentially shape the nutritional requirements ofDrosophiladuring juvenile growth
Authors: Consuegra Jessika , Grenier Théodore , Baa-Puyoulet Patrice , Rahioui Isabelle , Akherraz Houssam , Gervais Hugo , Parisot Nicolas , da Silva Pedro , Charles Hubert , Calevro Federica , Leulier François
Published: August 2019

The interplay between nutrition and the microbial communities colonizing the gastro-intestinal tract (i.e. gut microbiota) determines juvenile growth trajectory. Nutritional deficiencies trigger developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how commensal bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobioticDrosophila melanogasterlarvae independently associated with two model commensal bacterial strains,Acetobacter pomorumWJL(ApWJL) andLactobacillus plantarumNC8(LpNC8), we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with genome-based metabolic network reconstruction to define the biosynthetic capacities ofDrosophilagerm-free (GF) larvae and its two commensal bacteria. We first established that ApWJLand LpNC8differentially fulfills the nutritional requirements of the ex-GF larvae and parsed such difference down to individual amino acids, vitamins, other micronutrients and trace metals. We found thatDrosophilacommensal bacteria not only fortify the host’s diet with essential nutrients but, in specific instances, functionally compensate for host auxotrophies, by either providing a metabolic intermediate or nutrient derivative to the host or by uptaking, concentrating and sparing contaminant traces of micronutrients. Our systematic work reveals that, beyond the molecular dialogue engaged between the host and its commensal partners,Drosophilaand its facultative bacterial partners establish an integrated nutritional network relying on nutrients sparing and utilization.
A role for astroglial calcium in mammalian sleep
Authors: Ingiosi Ashley M. , Hayworth Christopher R. , Harvey Daniel O. , Singletary Kristan G. , Rempe Michael J. , Wisor Jonathan P. , Frank Marcos G.
Published: August 2019

Mammalian sleep is characterized by dramatic changes in neuronal activity, and waking neuronal activity is thought to increase sleep need. Changes in other brain cells (glia) across the natural sleep-wake cycle and their role in sleep regulation are comparatively unexplored. We show that sleep is also accompanied by large changes in astroglial activity as measured by intracellular calcium concentrations in unanesthetized mice. These changes in calcium vary across different vigilance states and are most pronounced in distal astroglial processes. We find that reducing intracellular calcium in astrocytes impaired the homeostatic response to sleep deprivation. Thus, astroglial calcium changes dynamically across vigilance states and is a component of the sleep homeostat.

One Sentence Summary

Astroglial calcium concentrations vary with sleep and wake, change after sleep deprivation, and mediate sleep need.
Timing and original features of flagellum assembly in trypanosomes during development in the tsetse fly
Authors: Lemos Moara , Mallet Adeline , Bertiaux Eloïse , Imbert Albane , Rotureau Brice , Bastin Philippe
Published: August 2019

Trypanosoma bruceiexhibits a complex life cycle alternating between tsetse flies and mammalian hosts. When parasites infect the fly, cells differentiate to adapt to life in various tissues, which is accompanied by drastic morphological and biochemical modifications especially in the proventriculus. This key step represents a bottleneck for salivary gland infection. Here we monitored flagellum assembly in trypanosomes during differentiation from the trypomastigote to the epimastigote stage, i.e. when the nucleus migrates to the posterior end of the cell. Three-dimensional electron microscopy (Focused Ion Bean Scanning Electron Microscopy, FIB-SEM) and immunofluorescence assays provided structural and molecular evidence that the new flagellum is assembled while the nucleus migrates towards the posterior region of the body. Two major differences with well known procyclic cells are reported. First, growth of the new flagellum begins when the associated basal body is found in a posterior position relative to the mature one. Second, the new flagellum acquires its own flagellar pocket before rotating on the left side of the anterior-posterior axis. FIB-SEM revealed the presence of a structure connecting the new and mature flagellum and serial sectioning confirmed morphological similarities with the flagella connector of procyclic cells. We discuss potential function of the flagella connector in trypanosomes from the proventriculus. These findings show thatT. bruceifinely modulates its cytoskeletal components to generate highly variable morphologies.

Author Summary

Trypanosoma bruceiis a flagellated parasitic protist that causes human African trypanosomiasis, or sleeping sickness and that is transmitted by the bite of tsetse flies. The complex life cycle ofT. bruceiinside the tsetse digestive tract requires adaptation to specific organs and follow a strictly defined order. It is marked by morphological modifications in cell shape and size, as well organelle positioning. In the proventriculus of tsetse flies,T. bruceiundergoes a unique asymmetric division leading to two very different daughter cells: one with a short and one with a long flagellum. This organelle is crucial for the trypanosome life cycle as it is involved in motility, adhesion and morphogenesis. Here we investigated flagellum assembly using molecular and 3D Electron Microscopy approaches revealing that flagellum construction in proventricular trypanosomes is concomitant with parasite differentiation. During flagellum growth, the new flagellum is connected to the mature one and rotates around the mature one after its emergence at the cell surface. The sequence of events is different from what is observed in the well-studied procyclic stage in culture revealing different processes governing morphological development. These results highlight the importance to study pathogen development in their natural environment.
Modelling Osteocyte Network Formation: Healthy and Cancerous Environments
Authors: Taylor-King Jake P. , Buenzli Pascal R. , Chapman S. Jon , Lynch Conor C. , Basanta David
Published: August 2019

Advanced cancers, such as prostate and breast cancers, commonly metastasize to bone. In the bone matrix, dendritic osteocytes form a spatial network allowing communication between osteocytes and the osteoblasts located on the bone surface. This communication network facilitates coordinated bone remodelling. In the presence of a cancerous microenvironment, the morphology of this network changes. Commonly osteocytes appear to be either overdifferentiated (i.e., there are more dendrites than healthy bone) or underdeveloped (i.e., dendrites do not fully form). In addition to structural changes, histological sections from metastatic breast cancer xenografted mice show that number of osteocytes per unit area is different between healthy bone and cancerous bone. We present a stochastic agent-based model for bone formation incorporating osteoblasts and osteocytes that allows us to probe both network structure and density of osteocytes in bone. Our model both allows for the simulation of our spatial network model and analysis of mean-field equations in the form of integro-partial differential equations. We considered variations of our model to study specific physiological hypotheses related to osteoblast differentiation; for example predicting how changing biological parameters, such as rates of bone secretion, rates of cancer formation and rates of osteoblast differentiation can allow for qualitatively different network morphologies. We then used our model to explore how commonly applied therapies such as bisphosphonates (e.g. zoledronic acid) impact osteocyte network formation.
Development of an N-Cadherin Biofunctionalized Hydrogel to Support the Formation of Synaptically Connected Neural Networks
Authors: O’Grady Brian J. , Balotin Kylie M. , Bosworth Allison M. , McClatchey P. Mason , Weinstein Robert M. , Gupta Mukesh , Poole Kara S. , Bellan Leon M. , Lippmann Ethan S.
Published: August 2019

In vitro models of the human central nervous system (CNS), particularly those derived from induced pluripotent stem cells (iPSCs), are becoming increasingly recognized as useful complements to animal models for studying neurological diseases and developing therapeutic strategies. However, current 3D CNS models suffer from deficits that limit their research utility. Notably, it remains difficult to drive iPSC-derived neurons to a mature and synaptically connected state. Moreover, the most common extracellular matrices (ECMs) used to fabricate 3D CNS models are either difficult to pattern into complex structures due to their mechanical properties or lack appropriate bioinstructive cues. Here, we describe the functionalization of gelatin methacrylate (GelMA) with an N-cadherin extracellular peptide epitope to create a biomaterial termed GelMA-Cad. After photopolymerization, GelMA-Cad forms soft hydrogels that can maintain patterned architectures. The N-cadherin functionality promotes survival and maturation of iPSC-derived glutamatergic neurons into synaptically connected networks as determined by viral tracing and electrophysiology. Immunostaining reveals a pronounced increase in presynaptic and postsynaptic marker expression in GelMA-Cad relative to Matrigel, as well as extensive co-localization of these markers, thus highlighting the biological activity of the N-cadherin peptide. Overall, given its ability to enhance iPSC-derived neuron maturity and connectivity, GelMA-Cad should be broadly useful for in vitro studies of neural circuitry in health and disease.
Siah2 integrates mitogenic and extracellular matrix signals linking neuronal progenitor ciliogenesis with germinal zone occupancy
Authors: Ong Taren , Trivedi Niraj , Wakefield Randall , Frase Sharon , Solecki David J.
Published: August 2019

Evidence is lacking as to how developing neurons integrate mitogenic signals with microenvironment cues to control proliferation and differentiation. We determined that the Siah2 E3 ubiquitin ligase functions in a coincidence detection circuit linking responses to the Shh mitogen and the extracellular matrix to control cerebellar granule neurons (CGN) germinal zone (GZ) occupancy. We found that Shh maintains Siah2 expression in CGN progenitors (GNPs) in a Ras/Mapk-dependent manner. Siah2 supports ciliogenesis in a feed-forward fashion by restraining ciliogenic targets. Efforts to identify GZ sources of Ras/Mapk signaling led us to discover that GNPs respond to laminin, but not vitronectin, in the microenvironment via integrin β1 receptors, which engages the Ras/Mapk cascade, and that this niche interaction is essential for promoting GNP ciliogenesis. As GNPs leave the GZ, differentiation is seamlessly driven by changing extracellular cues that diminish Siah2-activity leading to primary cilia retraction and attenuation of mitogenic responses.
Gαi-derived peptide binds the µ-opioid receptor
Authors: Kosson Piotr , Dyniewicz Jolanta , Lipiński Piotr F. J. , Matalinska Joanna , Misicka Aleksandra , Bojarski Andrzej J. , Mordalski Stefan
Published: August 2019

G protein-coupled receptors (GPCRs) transduce external stimuli into the cell by G proteins via an allosteric mechanism. Agonist binding to the receptor stimulates GDP/GTP exchange within the heterotrimeric G protein complex. Whereas recent structures of GPCR-G protein complexes revealed that the H5, S1 and S2 domains of Gα are involved in binding the active receptor, earlier studies showed that a short peptide analogue derived from the C-terminus (H5) of the G protein transducin (Gt) is sufficient to stabilize rhodopsin in an active form. Here, we show that a Gαi-derived peptide of 12 amino acids binds the µ-opioid receptor (µOR) and acts as an allosteric modulator. The Gαi-derived peptide increases µOR affinity for its agonist morphine in a dose-dependent way. These results indicate that the GPCR-Gα peptide interaction observed so far for only rhodopsin can be extrapolated to µOR. In addition, we show that the C-terminal peptide of the Gαisubunit is sufficient to stabilize the active conformation of the receptor. Our approach opens the possibility to investigate the GPCR-G protein interface with peptide modification.
A single CRISPR base editor to induce simultaneous C-to-T and A-to-G mutations
Authors: Sakata Rina C. , Ishiguro Soh , Mori Hideto , Tanaka Mamoru , Seki Motoaki , Masuyama Nanami , Nishida Keiji , Nishimasu Hiroshi , Kondo Akihiko , Nureki Osamu , Tomita Masaru , Aburatani Hiroyuki , Yachie Nozomu
Published: August 2019

While several Cas9-derived base editors have been developed to induce either C-to-T or A-to-G mutation at target genomic sites, the possible genome editing space when using the current base editors remains limited. Here, we present a novel base editor, Target-ACE, which integrates the abilities of both of the previously developed C-to-T and A-to-G base editors by fusing an activation-induced cytidine deaminase (AID) and an engineered tRNA adenosine deaminase (TadA) to a catalytically impaired Streptococcus pyogenes Cas9. In mammalian cells, Target-ACE enabled heterologous editing of multiple bases in a small sequence window of target sites with increased efficiency compared with a mixture of two relevant base editor enzymes, each of which may block the same target DNA molecule from the other. Furthermore, by modeling editing patterns using deep sequencing data, the editing spectra of Target-ACE and other base editors were simulated across the human genome, demonstrating the highest potency of Target-ACE to edit amino acid coding patterns. Taking these findings together, Target-ACE is a new tool that broadens the capabilities for base editing for various applications.
Aneuploidy and deregulated DNA damage response define haploinsufficiency in breast tissues of BRCA2 mutation carriers
Authors: Karaayvaz Mihriban , Silberman Rebecca E , Langenbucher Adam , Saladi Srinivas Vinod , Ross Kenneth N , Zarcaro Elena , Desmond Andrea , Yildirim Murat , Vivekanandan Varunika , Ravichandran Hiranmayi , Mylavagnanam Ravindra , Specht Michelle C , Ramaswamy Sridhar , Lawrence Michael , Amon Angelika , Ellisen Leif W
Published: August 2019

Women harboring heterozygous germline mutations of BRCA2 have a 50-80% risk of developing breast cancer, yet the early pathogenesis of these cancers is poorly understood. We sought to reveal early steps in BRCA2-associated carcinogenesis through analysis of sorted cell populations from freshly-isolated, non-cancerous breast tissues among a cohort of BRCA2 mutation carriers and matched controls. Single-cell whole-genome sequencing demonstrates that >25% of BRCA2 carrier (BRCA2mut/+) luminal progenitor (LP) cells exhibit sub-chromosomal copy number variations (CNVs), which are rarely observed in non-carriers. Correspondingly, primary BRCA2mut/+ breast epithelia exhibit spontaneous and replication stress-induced DNA damage together with attenuated replication checkpoint and apoptotic responses, associated with an age-associated expansion of the LP compartment in human carrier tissues. These phenotypes are not associated with loss of wild-type BRCA2. Collectively, these findings provide evidence for BRCA2 haploinsufficiency and associated DNA damage in vivo that precede histologic abnormalities. These results provide unanticipated opportunities for new cancer risk assessment and prevention strategies in high-risk patients.
Integrated single cell and bulk multi-omics reveals heterogeneity and early changes in pathways associated with cetuximab resistance in HNSCC sensitive cell lines
Authors: Kagohara Luciane Tsukamoto , Zamuner Fernando , Considine Michael , Allen Jawara , Yegnasubramanian Srinivasan , Gaykalova Daria A , Fertig Elana J
Published: August 2019

Identifying potential mechanisms of resistance while tumor cells still respond to therapy is critical to delay acquired resistance. We generated the first comprehensive multi-omics, bulk and single cell data in sensitive head and neck squamous cell carcinoma (HNSCC) cells to identify immediate responses to cetuximab. Two pathways potentially associated with resistance were focus of the study: regulation of receptor tyrosine kinases through the transcription factor TFAP2A, and epithelial-to-mesenchymal transition (EMT) process. Single cell RNA-seq demonstrates heterogeneity, with cell specific TFAP2A and VIM expression profiles in response to treatment. RNA-seq and ATAC-seq reveal global changes within five days of cetuximab therapy, suggesting early onset of mechanisms of resistance; and corroborates cell line heterogeneity, with different TFAP2A targets or EMT markers affected by therapy. Lack of TFAP2A reduces HNSCC growth and is enhanced by cetuximab and JQ1. Regarding the EMT process, short term cetuximab therapy has the strongest effect on inhibiting migration. TFAP2A silencing does not affect cell migration, supporting an independent role for both mechanisms in resistance. Overall, we show that immediate adaptive transcriptional and epigenetic changes induced by cetuximab are heterogeneous and cell type dependent; and independent mechanisms of resistance arise while tumor cells are still sensitive to therapy.
Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy
Authors: Horst Benjamin G. , Yokom Adam L. , Rosenberg Daniel J. , Morris Kyle L. , Hammel Michal , Hurley James H. , Marletta Michael A.
Published: August 2019

Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-lengthManduca sextasGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.
The microstructure investigation of plant architecture with X-ray microscopy
Authors: Zhang Wenting , Guo Tao , Chen Ke , La Ting , Bastians Philipp Alexander , Cao Chunjie
Published: August 2019

Background

In recent years, the plant morphology has been well studied by multiple approaches at cellular and subcellular levels. Two-dimensional (2D) microscopy techniques offer imaging of plant structures on a wide range of magnifications for researchers. However, subcellular imaging is still challenging in plant tissues like roots and seeds.

Results

Here we use a three-dimensional (3D) imaging technology based on the ZEISS X-ray microscope (XRM) Versa and analyze several plant tissues from different plant species. The XRM provides new insights into plant structures using non-destructive imaging at high-resolution and high contrast. We also developed a workflow aiming to acquire accurate and high-quality images in the context of the whole specimen. Multiple plant samples including rice, tobacco, Arabidopsis and maize were used to display the differences of phenotypes, which indicates that the XRM is a powerful tool to investigate plant microstructure.

Conclusions

Our work provides a novel observation method to evaluate and quantify tissue specific differences for a range of plant species. This new tool is suitable for non-destructive seed observation and screening.
Cell-scale biophysical determinants of cell competition in epithelia
Authors: Gradeci Daniel , Bove Anna , Vallardi Giulia , Lowe Alan R. , Banerjee Shiladitya , Charras Guillaume
Published: August 2019

How cells with different genetic makeups compete in tissues is an outstanding question in developmental biology and cancer research. Studies in recent years have revealed that cell competition can either be driven by short-range biochemical signalling or by long-range mechanical stresses in the tissue. To date, cell competition has generally been characterised at the population-scale, leaving the single-cell level mechanisms of competition elusive. Here, we use high time-resolution experimental data to construct a multi-scale agent-based model for epithelial cell competition, and use it to gain a conceptual understanding of the cellular factors that governs competition in cell populations within tissues. We find that a key determinant of mechanical competition is the difference in homeostatic density between winners and losers, while differences in growth rates and tissue organisation do not affect competition end-result. In contrast, the outcome and kinetics of biochemical competition is strongly influenced by local tissue organisation. Indeed, when loser cells are homogenously mixed with winners at the onset of competition, they are eradicated; however, when they are spatially separated, winner and loser cells coexist for long times. These findings suggest distinct biophysical origins for mechanical and biochemical modes of cell competition.
A neurophysiological study of noun-adjective agreement in Arabic: The impact of animacy and diglossia on the dynamics of language processing
Authors: Idrissi Ali , Mustafawi Eiman , Khwaileh Tariq , Muralikrishnan R.
Published: August 2019

We used event-related brain potentials to identify the neurophysiological responses of Arabic speakers to processing full and deflected agreement in plural noun-adjective constructions in Standard Arabic. Under full agreement, an adjective fully agrees in number and gender with a preceding plural noun, but only when this noun is human, while it is systematically marked feminine singular when the noun is non-human under deflected agreement. We recorded grammaticality judgment and ERP responses from 32 speakers of Arabic to sentences violating full and deflected agreement and their well-formed counterparts. The participants were relatively fast and accurate in judgingallthe sentences, although violations, especially deflected agreement violations, were not always deemed ungrammatical. However, the ERP responses show a differential processing of human versus non-human violations. Violations of full agreement involving human nouns elicited larger N400 and P600 components than violations of deflected agreement involving non-human nouns, whose ERP signatures were hardly distinguishable from those of their acceptable counterparts. Our results present evidence for animacy (more specifically, humanness) and inter-dialect effects on language processing. We argue that violations of Standard Arabic deflected agreement are not treated as outright violations because non-human referents permit both full and deflected agreement in Spoken Arabic. We discuss these results in light of the ERP literature on agreement processing and the role of animacy/humanness in grammar, and highlight the potential effect of diglossia on the architecture of the mental grammar of Arabic speakers.
Social Perception and Interaction Database – a novel tool to study social cognitive processes with point-light displays
Authors: Okruszek Ł. , Chrustowicz M.
Published: August 2019

Introduction

The ability to detect and interpret third-party encounters (TPE) is one of the crucial skills enabling people to operate in the social world. Multiple lines of evidence converge towards the preferential processing of TPE when compared to the individual actions of multiple agents, even if the actions of agents were visually degraded to minimalistic point-light displays (PLDs). Here, we present a novel PLD dataset (Social Perception and Interaction Database; SoPID) that may be used for studying multiple levels of social information processing.

Methods

During a motion-capture session, two pairs of actors were asked to perform a wide range of dyadic 3-second actions, including: (1) neutral, gesture-based communicative interactions (COM); (2) emotional exchanges (Happy/Angry); (3) synchronous physical activity of actors (SYNC); and (4) independent actions of agents, either object-related (ORA) or non-object related (NORA). The stimuli were then transformed into PLDs. Two validation studies (each with 20 healthy individuals) were then performed to establish the recognizability of the SoPID vignettes.

Results

The first study showed a ceiling level accuracy for discrimination of communicative vs. individual actions (93% +/- 5%) and high accuracy for interpreting specific types of actions (85 +/- 4%) from the SoPID. In the second study, a robust effect of scrambling on the recognizability of SoPID vignettes was observed in an independent sample of healthy individuals.

Discussion

These results suggest that the SoPID may be effectively used to examine processes associated with communicative interactions and intentions processing. The database can be accessed via Open Science Framework (https://osf.io/dcht8/).
Human oral microbiome characterization and its association with environmental microbiome revealed by the Earth Microbiome Project
Authors: Wang Jinlan , Li Dandan , Wang Jianing , Zhang Zheng
Published: August 2019

The oral cavity is an important window for the microbial communication between environment and the human body. The oral microbiome plays an important role in human health. Here, we analyzed 447 datasets from human oral samples published by the Earth Microbiome Project (EMP). The microbes in these human oral samples were taxonomically assigned to at least 266 genera of 18 bacterial and archaeal phyla. Among them, 11 genera with the relative abundance more than 1% were identified as 5 different bacterial phyla. Compared with 815 samples from human gut, nose/pharynx and skin, the oral microbiome showed significantly lower diversity and possessed fewer unknown species than those of other body parts, and had distinct differences in species composition from other body parts. In addition, the oral microbiome showed significant differences in the populations of different countries, which may be determined by the living environment and lifestyle/dietary habits. Finally, the correlation analysis showed highly similarity between the oral microbiome and the microbiomes of Aerosol (non-saline) and Surface (non-saline), two types of environmental microbial habitats related closely to human. Together, these findings expand our understanding to the human oral microbiome.
Loss of FBXO9 enhances proteasome activity and promotes aggressiveness in acute myeloid leukemia
Authors: Hynes-Smith R. Willow , Swenson Samantha A. , Vahle Heather , Wittorf Karli J. , Caplan Mika , Amador Catalina , Hyde R. Katherine , Buckley Shannon M.
Published: August 2019

The hematopoietic system is maintained throughout life by hematopoietic stem cells that are capable of differentiating into all hematopoietic lineages. An intimate balance between self-renewal, differentiation, and quiescence is required to maintain hematopoiesis. Disruption of this balance can result in hematopoietic malignancy, including acute myeloid leukemia (AML). FBXO9, from the F-box E3 ubiquitin ligases, is down-regulated in patients with AML compared to normal bone marrow. FBXO9 is the substrate recognition component of the Skp1-Cullin-F-box (SCF)-type E3 ligase complex. FBXO9 is highly expressed in hematopoietic stem and progenitor populations, which contain the tumor-initiating population in AML. In AML patients, decrease in FBXO9 expression is most pronounced in patients with the inversion of chromosome 16 (inv(16)), a rearrangement that generates the transcription factor fusion gene, CBFB-MYH11. To study FBXO9 in malignant hematopoiesis, we generated a conditional knockout mouse model using a novel CRISPR/Cas9 strategy. Our data show that deletion of Fbxo9 in mice expressing Cbfb-MYH11 leads to markedly accelerated and aggressive leukemia development. In addition, we find loss of FBXO9 leads to increased proteasome expression and tumors are more sensitive to bortezomib suggesting that FBXO9 expression may predict patient response to bortezomib treatment.
A sulfur coordination polymer with wide bandgap semiconductivity formed from zinc(II) and 5-methylsulfanyl-1,3,4-thiadiazole-2-thione
Authors: Zhang Jun , Ma Xiaofan , Kong Weili , Xie Fazhi , Yuan Shizhen , Song Xiaojie , Lu Zhansheng , Xuan Xiaopeng
Published: August 2019

The sulfur coordination polymer catena-poly[zinc(II)-μ2-bis[5-(methylsulfanyl)-2-sulfanylidene-2,3-dihydro-1,3,4-thiadiazol-3-ido-κ2
N
3:S]], [Zn(C3H3N2S3)2]
n
or [Zn2MTT4]
n
, constructed from Zn2+ ions and 5-methylsulfanyl-1,3,4-thiadiazole-2-thione (HMTT), was synthesized successfully and structurally characterized. [Zn2MTT4]
n
crystallizes in the tetragonal space group I\overline{4} (No. 82). Each MTT− ligand (systematic name: 5-methylsulfanyl-2-sulfanylidene-2,3-dihydro-1,3,4-thiadiazol-3-ide) coordinates to two different ZnII ions, one via the thione group and the other via a ring N atom, with one ZnII atom being in a tetrahedral ZnS4 and the other in a tetrahedral ZnN4 coordination environment. These tetrahedral ZnS4 and ZnN4 units are alternately linked by the organic ligands, forming a one-dimensional chain structure along the c axis. The one-dimensional chains are further linked via C—H...N and C—H...S hydrogen bonds to form a three-dimensional network adopting an ABAB-style arrangement that lies along both the a and b axes. The three-dimensional Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots confirm the major interactions as C—H...S hydrogen bonds with a total of 35.1%, while 7.4% are C—H...N hydrogen-bond interactions. [Zn2MTT4]
n
possesses high thermal and chemical stability and a linear temperature dependence of the bandgap from room temperature to 270 °C. Further investigation revealed that the bandgap changes sharply in ammonia, but only fluctuates slightly in other solvents, indicating its promising application as a selective sensor.
Back scattering response from single, finite and infinite array of nonlinear antennas based on intelligent water drops algorithm
Authors: Bahrami Amir , Ostadzadeh Saeed Reza
Published: August 2019

Purpose

The purpose of this paper is to calculate the back scattering response from single, finite and infinite arrays of nonlinear antennas like the case where the antennas are exposed to high-value signals such as lightning strokes.

Design/methodology/approach

In this paper, the authors have used a recently introduced optimization technique called intelligent water drop.

Findings

The results exhibit that the method used by the authors is faster and more accurate than other conventional optimization algorithms, i.e. particle swarm optimization and genetic algorithm.

Originality/value

A new optimization algorithm is used to solve nonlinear problem accurately and sufficiently. Although the technique is not confined to the mentioned examples in the paper, it can be applied to other nonlinear circuits.