bluuebunny/crossref_metadata_2025 huggingface dataset:
Alignment-free Comparison of Metagenomics Sequences via Approximate String Matching
Authors: Chen Jian , Yang Le , Li Lu , Goodison Steve , Sun Yijun
Published: May 2020

Quantifying pairwise sequence similarities is a key step in metagenomics studies. Alignment-free methods provide a computationally efficient alternative to alignment-based methods for large-scale sequence analysis. Several neural network-based methods have recently been developed for this purpose. However, existing methods do not perform well on sequences of varying lengths and are sensitive to the presence of insertions and deletions. In this paper, we describe the development of a new method, referred to as AsMac, that addresses the aforementioned issues. We proposed a novel neural network structure for approximate string matching for the extraction of pertinent information from biological sequences and developed an efficient gradient computation algorithm for training the constructed neural network. We performed a large-scale benchmark study using real-world data that demonstrated the effectiveness and potential utility of the proposed method. The open-source software for the proposed method and trained neural-network models for some commonly used metagenomics marker genes were developed and are freely available atwww.acsu.buffalo.edu/~yijunsun/lab/AsMac.html.
Acibenzolar-S-methyl activates stomatal-based defense systemically in Japanese radish by inducing peroxidase-dependent reactive oxygen species production
Authors: Sakata Nanami , Ishiga Takako , Taniguchi Shizuku , Ishiga Yasuhiro
Published: May 2020

Acibenzolar-S-methyl (ASM) is a well-known plant activator, which is a synthetic analog of salicylic acid (SA). Recently, copper fungicides and antibiotics are major strategies for controlling bacterial diseases. However, resistant strains have already been found. Therefore, there is an increasing demand for sustainable new disease control strategies. We investigated the ASM disease control effect againstPseudomonas cannabinapv.alisalensis(Pcal), which causes bacterial blight on Japanese radish. In this study, we demonstrated that ASM effectively suppressedPcaldisease symptom development associated with reduced bacterial populations on Japanese radish leaves. Interestingly, we also demonstrated that ASM activated systemic acquired resistance (SAR), including stomatal-based defense, not only on ASM treated leaves, but also on untreated upper and lower leaves. Reactive oxidative species (ROS) are essential second messengers in stomatal-based defense. We found that ASM induced stomatal closure by inducing ROS production through peroxidase. These results indicate that stomatal closure induced by ASM treatment is effective for preventingPcalpathogen invasion into plants, and in turn reduction of disease development.
A framework forin situmolecular characterization of coral holobionts using nanopore sequencing
Authors: Carradec Quentin , Poulain Julie , Boissin Emilie , Hume Benjamin CC , Voolstra Christian R , Ziegler Maren , Engelen Stefan , Cruaud Corinne , Planes Serge , Wincker Patrick
Published: May 2020

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processedin situ, during theTaraPacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 hours. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.
Male linked genomic regions determine sex in dioeciousAmaranthus palmeri
Authors: Neves Cátia José , Matzrafi Maor , Thiele Meik , Lorant Anne , Mesgaran Mohsen B. , Stetter Markus G.
Published: May 2020

Dioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioeciousAmaranthus palmerirepresents a well suited model system to study sex determination in plants.A. palmeriis one of the most troublesome weeds in the US, has successfully colonized other regions in the world and has evolved resistance to several herbicide classes. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy inA. palmeriis currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole genome sequencing of male and female pools from two independent populations to elucidate the genetic control of dioecy inA. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex linked genes. Consequently, we employed an alignment free k-mer comparison which enabled us to identify a large number of male specific k-mers. We assembled male specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex determination system in the species. Based on our findings we suggest an intermediate evolutionary state of dioecy inA. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.
Haplotype tagging reveals parallel formation of hybrid races in two butterfly species
Authors: Meier Joana I. , Salazar Patricio A. , Kučka Marek , Davies Robert William , Dréau Andreea , Aldás Ismael , Power Olivia Box , Nadeau Nicola J. , Bridle Jon R. , Rolian Campbell , Barton Nicholas H. , McMillan W. Owen , Jiggins Chris D. , Chan Yingguang Frank
Published: May 2020

Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius eratoandH. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

One-sentence summary

Haplotagging, a novel linked-read sequencing technique that enables whole genome haplotyping in large populations, reveals the formation of a novel hybrid race in parallel hybrid zones of two co-mimickingHeliconiusbutterfly species through strikingly parallel divergences in their genomes.
LoxTnSeq: Random Transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions
Authors: Shaw Daniel , Miravet-Verde Samuel , Pinero Carlos , Serrano Luis , Lluch-Senar Maria
Published: May 2020

The removal of unwanted genetic material is a key aspect in many synthetic biology efforts, and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deep-sequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the naturally genome reduced bacteriumMycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from >50 bp to 28 Kb, which represent 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.
The effect of dispersal and preferential mating on the genetic control of mosquitoes
Authors: Khamis Doran , El Mouden Claire , Kura Klodeta , Bonsall Michael B.
Published: May 2020

Mosquito-borne diseases cause significant social and economic damage across much of the globe. New biotechnologies that utilise manipulations of the mosquito genome have been developed to combat disease. The successful implementation of genetic mosquito control technologies may depend upon ecological, evolutionary and environmental factors, as well as the specifications of the chosen technology. Understanding the influence of these external factors will help inform how best to deploy a chosen technology to control vectors of infectious diseases. We use a continuous-time stochastic spatial network model of a mosquito life-cycle coupled to population genetics models to investigate the impact of releasing seven types of genetic control technology: a self-limiting lethal gene, two underdominance threshold gene drives, two homing gene drives and twoWolbachiasystems. We apply the mathematical framework to understand control interventions of two archetypes of mosquito species: a short-range dispersingAedes aegyptiand comparatively longer-range dispersingAnopheles gambiae. We show that mosquito dispersal behaviour is an extremely important factor in determining the outcome of a release programme. Assortative mating – where the mating success of genetically modified males is lower than their wild counterparts – can facilitate the spatial containment of gene drives. The rapid evolution of strong mating preference can damage the efficacy of control efforts for all control technologies. We suggest that there cannot be a one-size-fits-all approach to regulation and implementation of vector control; there must be application-specific control plans that take account of understudied ecological, evolutionary and environmental factors.
Variation in genetic relatedness is determined by the aggregate recombination process
Authors: Veller Carl , Edelman Nathaniel B. , Muralidhar Pavitra , Nowak Martin A.
Published: May 2020

The genomic proportion that two relatives share identically by descent—their genetic relatedness— can vary depending on the history of recombination and segregation in their pedigree. This variation is important in many applications of genetics, including pedigree-based estimation of the genetic variance and heritability of traits, and estimation of pedigree relationships from sequence data. Here, we calculate the variance of genetic relatedness for general pedigree relationships, making no assumptions about the recombination process. For the specific relationships of grandparent-grandoffspring and siblings, the variance of genetic relatedness is a simple decreasing function of, the average proportion of locus pairs that recombine in meiosis. For general pedigree relationships, the variance of genetic relatedness is likewise the average of some function of pairwise recombination rates. Therefore, features of the aggregate recombination process that affectand analogs also affect variance in genetic relatedness. Such features include the number of chromosomes and heterogeneity in their size, and the number of crossovers and their location along chromosomes. Our calculations help to explain several recent observations about variance in genetic relatedness, including that it is reduced by crossover interference (which is known to increase). Our methods further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling precise statistical inference in F2-based tests for various kinds of selection.
Network bipartitioning in the anti-communicability euclidean space
Authors: Gómez-Gardeñes Jesús , Estrada Ernesto
Published: May 2020

We define the anti-communicability function for the nodes of a simple graph as the nondiagonal entries of exp (−A). We prove that it induces an embedding of the nodes into a Euclidean space. The anti-communicability angle is then defined as the angle spanned by the position vectors of the corresponding nodes in the anti-communicability Euclidean space. We prove analytically that in a givenk-partite graph, the anti-communicability angle is larger than 90° for every pair of nodes in different partitions and smaller than 90° for those in the same partition. This angle is then used as a similarity metric to detect the “best”k-partitions in networks where certain level of edge frustration exists. We apply this method to detect the “best” k-partitions in 15 real-world networks, finding partitions with a very low level of “edge frustration”. Most of these partitions correspond to bipartitions but tri- and pentapartite structures of real-world networks are also reported.
TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells
Authors: Sharma Rajiv , Dever Daniel P , Lee Ciaran M , Azizi Armon , Pan Yidan , Camarena Joab , Köhnke Thomas , Bao Gang , Porteus Matthew H , Majeti Ravindra
Published: May 2020

Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may usher in a new class of medicines to treat genetic diseases of the blood and immune system. With state-of-the-art methodologies, it is now possible to correct disease-causing mutations at high frequencies in HSPCs by combining ribonucleoprotein (RNP) delivery of Cas9 and chemically modified sgRNAs with homologous DNA donors via recombinant adeno-associated viral vector serotype six (AAV6). However, because of the precise nucleotide-resolution nature of gene correction, these current approaches do not allow for clonal tracking of gene targeted HSPCs. Here, we describeTrackingRecombinationAlleles inClonalEngraftment usingsequencing (TRACE-Seq), a novel methodology that utilizes barcoded AAV6 donor template libraries, carrying either in-frame silent mutations or semi-randomized nucleotide sequences outside the coding region, to track thein vivolineage contribution of gene targeted HSPC clones. By targeting theHBBgene with an AAV6 donor template library consisting of ∼20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution ofHBBtargeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in immunodeficient mice. We anticipate that this methodology has the potential to be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.
Content-Based Similarity Search in Large-Scale DNA Data Storage Systems
Authors: Bee Callista , Chen Yuan-Jyue , Ward David , Liu Xiaomeng , Seelig Georg , Strauss Karin , Ceze Luis
Published: May 2020

Synthetic DNA has the potential to store the world’s continuously growing amount of data in an extremely dense and durable medium. Current proposals for DNA-based digital storage systems include the ability to retrieve individual files by their unique identifier, but not by their content. Here, we demonstrate content-based retrieval from a DNA database by learning a mapping from images to DNA sequences such that an encoded query image will retrieve visually similar images from the database via DNA hybridization. We encoded and synthesized a database of 1.6 million images and queried it with a variety of images, showing that each query retrieves a sample of the database containing visually similar images are retrieved at a rate much greater than chance. We compare our results with several algorithms for similarity search in electronic systems, and demonstrate that our molecular approach is competitive with state-of-the-art electronics.

One Sentence Summary

Learned encodings enable content-based image similarity search from a database of 1.6 million images encoded in synthetic DNA.
Changes in arthropod community but not plant quality benefit a specialist herbivore on plant under reduced water availability
Authors: Lin Po-An , Liu Chia-Ming , Ou Jia-Ang , Sun Cheng-Han , Chuang Wen-Po , Ho Chuan-Kai , Kinoshita Natsuko , Felton Gary W.
Published: May 2020

Plants grow under reduced water availability can have divergent effects on insect herbivores, in some instances producing benefits to them. However, the forces mediating these positive impacts remain mostly unclear. We conducted a manipulative field study using a specialist herbivorePieris rapae, and its host plant,Rorippa indica, in two populations to identify how water availability impacts overall plant quality and multitrophic interactions. We observed thatR. indicagrowing under low water availability led to higher survival ofP. rapaelarvae. The increase in survival of eggs and larvae was related to the reduced abundance of other herbivores and natural enemies. Water availability had differential impacts on members of the herbivore community through changes in plant quality. Low water availability decreased the quality ofR. indicato most herbivores as indicated by reduced abundance in the field and decreased relative growth rate in feeding assays. In contrast, the performance ofP. rapaelarvae were not affected by differences in sympatricR. indicagrown under different water availability. These results indicate that localP. rapaepossess some physiological adaptation to overcome fluctuations in host quality. Our findings illustrate that reduced water availability is beneficial to a specialist herbivore, but detrimental to most other herbivores. Our work highlights the complex roles of the arthropod communities associated with plants in determining the impacts of water availability on insect herbivores.
Characterization of systemic genomic instability in budding yeast
Authors: Sampaio Nadia M. V. , Ajith V. P. , Watson Ruth A. , Heasley Lydia R. , Chakraborty Parijat , Rodrigues-Prause Aline , Malc Ewa P. , Mieczkowski Piotr A. , Nishant Koodali T. , Argueso Juan Lucas
Published: May 2020

Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) inSaccharomyces cerevisiae, providing support for an additional non-independent and faster mode of mutation accumulation. We initially characterized a yeast clone isolated for carrying an LOH event at a specific chromosome site, and surprisingly, found that it also carried multiple unselected rearrangements elsewhere in its genome. Whole genome analysis of over 100 additional clones selected for carrying primary LOH tracts revealed that they too contained unselected structural alterations more often than control clones obtained without any selection. We also measured the rates of coincident LOH at two different chromosomes and found that double LOH formed at rates 14-150 fold higher than expected if the two underlying single LOH events occurred independently of each other. These results were consistent across different strain backgrounds, and in mutants incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population can experience discrete episodes of systemic genomic instability, when the entire genome becomes vulnerable and multiple chromosomal alterations can form over a narrow time window. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in the cancer and genomic disorder contexts. The experimental model we describe provides a system to further dissect the fundamental biological processes responsible for punctuated bursts of structural genomic variation.

SIGNIFICANCE STATEMENT

Mutations are generally thought to accumulate independently and gradually over many generations. Here, we combined complementary experimental approaches in budding yeast to track the appearance of chromosomal changes resulting in loss-of-heterozygosity (LOH). In contrast to the prevailing model, our results provide evidence for the existence of a path for non-independent accumulation of multiple chromosomal alteration events over few generations. These results are analogous to recent reports of bursts of genomic instability in human cells. The experimental model we describe provides a system to further dissect the fundamental biological processes underlying such punctuated bursts of mutation accumulation.
Peptide recognition and dephosphorylation by the vaccinia VH1 phosphatase
Authors: Zhao Bryan M. , Hogan Megan , Lee Michael S , Dyas Beverly K. , Ulrich Robert G.
Published: May 2020

The VH1 protein encoded by the highly conserved H1 locus of orthopoxviruses is a dual-specificity phosphatase (DUSPs) that hydrolyzes phosphate groups from phosphorylated tyrosine, serine, and threonine residues of viral and host cell proteins. Because the DUSP activities are required for virus replication, VH1 is a prime target for the development of therapeutic inhibitors. However, the presentation of a shallow catalytic site has thwarted all drug development efforts. As an alternative to direct targeting of catalytic pockets, we describe surface contacts between VH1 and substrates that are essential for full activity and provide a new pathway for developing inhibitors of protein-protein interactions. Critical amino acid residues were manipulated by site-directed mutagenesis of VH1, and perturbation of peptide substrate interactions based on these mutations were assessed by high-throughput assays that employed surface plasmon resonance and phosphatase activities. Two positively-charged residues (Lys-20 and Lys-22) and the hydrophobic side chain of Met-60 appear to orient the polarity of the pTyr peptide on the VH1 surface, while additional amino acid residues that flank the catalytic site contribute to substrate recognition and productive dephosphorylation. We propose that the enzyme-substrate contact residues described here may serve as molecular targets for the development of inhibitors that specifically block VH1 catalytic activity and thus poxvirus replication.
ModelingIKZF1lesions in B-ALL reveals distinct chemosensitivity patterns and potential therapeutic vulnerabilities
Authors: Rogers Jason H. , Gupta Rohit , Reyes Jaime M. , Gundry Michael C. , Medrano Geraldo , Guzman Anna , Song Tidie , Johnson Cade , Barnes Sean , Cristobal Carlo D. D. , Brunetti Lorenzo , Goodell Margaret A. , Rau Rachel E.
Published: May 2020

IKAROS family zinc finger 1 (IKZF1) alterations represent a diverse group of genetic lesions that are associated with an increased risk of relapse in B-lymphoblastic leukemia (B-ALL). Due to the heterogeneity of concomitant lesions it remains unclear howIKZF1abnormalities directly affect cell function and therapy resistance and whether their consideration as a prognostic indicator is valuable in improving outcome. We used CRISPR/Cas9 to engineer multiple panels of isogeneic lymphoid leukemia cell lines with a spectrum ofIKZF1lesions in order to measure changes in chemosensitivity, gene expression, cell cycle, and in vivo engraftment dynamics that can be directly linked to loss of IKAROS protein.IKZF1knockout and heterozygous null cells displayed relative resistance to a number of commonly employed therapies for B-ALL including dexamethasone, vincristine, asparaginase, and daunorubicin. Transcription profiling revealed a stem/myeloid cell-like phenotype and JAK/STAT upregulation after IKAROS loss. We also used a CRISPR homology-directed repair (HDR) strategy to knock-in the dominant-negative IK6 isoform tagged with GFP into the endogenous locus and observed a similar drug resistance profile with the exception of retained sensitivity to dexamethasone. Interestingly,IKZF1knockout and IK6 knock-in cells both have significantly increased sensitivity to cytarabine, suggesting intensification of nucleoside analog therapy may be specifically effective forIKZF1-deleted B-ALL. Both types ofIKZF1lesions decreased survival time of xenograft mice, with higher numbers of circulating blasts and increased organ infiltration. Given these findings, exact specification ofIKZF1status in patients may be a beneficial addition to risk stratification and could inform therapy.

Key points

EngineeredIKZF1perturbations result in a stem-cell like expression signature, enhanced engraftment in vivo, and multi-drug resistance

Loss of IKAROS may result in new vulnerabilities due to increased sensitivity to cytarabine and upregulation of JAK/STAT and mAb targets
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales
Authors: Cai Liming , Xi Zhenxiang , Lemmon Emily Moriarty , Lemmon Alan R. , Mast Austin , Buddenhagen Christopher E. , Liu Liang , Davis Charles C.
Published: May 2020

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order alone includes nine of the top ten most unstable nodes in angiosperms, and the recalcitrant relationships along the backbone of the order have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 15%, 52%, and 32% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.
A non-linear relation between levels of adult hippocampal neurogenesis and expression of the immature neuron marker doublecortin
Authors: Mendez-David Indira , David Denis J , Deloménie Claudine , Beaulieu Jean-Martin , Gardier Alain M. , Hen René
Published: May 2020

We investigated the mechanisms underlying the effects of the antidepressant fluoxetine on behavior and adult hippocampal neurogenesis (AHN). After confirming our earlier report that the signaling molecule β2-arrestin is required for the antidepressant-like effects of fluoxetine, we found that the effects of fluoxetine on proliferation of neural progenitors and on survival of adult-born granule cells are absent in the β2-arrestin knockout (β2-Arr KO) mice. To our surprise fluoxetine induced a dramatic upregulation of doublecortin (DCX) in the β2-Arr KO mice, indicating that DCX expression can be increased even though AHN is not. We discovered two other conditions where DCX expression is regulated non linearly compared to levels of AHN: a chronic stress model where DCX is upregulated and an inflammation model where DCX is down regulated. We conclude that assessing DCX expression alone to quantify levels of AHN can be misleading and that caution should be applied when label retention techniques are not available.

HIGHLIGHTS

β2-arrestin (β-Arr2) is required for the antidepressant-like effects of fluoxetine.

A dramatic upregulation of doublecortin (DCX) is observed in the β2-Arr KO mice after antidepressant treatment whereas its effects on proliferation of neural progenitors and on survival of adult-born granule cells are absent.

DCX is more upregulated than the number of young neurons in a mouse model of depression.

DCX is more down regulated than the number of young neurons in a model of inflammation.

microRNAs (miRs) may contribute to the regulation of DCX mRNA expression.
Conscious processing of narrative stimuli synchronizes heart rate between individuals
Authors: Pérez Pauline , Madsen Jens , Banellis Leah , Türker Başak , Raimondo Federico , Perlbarg Vincent , Valente Melanie , Niérat Marie-Cécile , Puybasset Louis , Naccache Lionel , Similowski Thomas , Cruse Damian , Parra Lucas C , Sitt Jacobo D
Published: May 2020

Heart rate has natural fluctuations that are typically ascribed to autonomic function. Recent evidence suggests that conscious processing can affect the timing of the heartbeat. We hypothesized that heart rate is modulated by conscious processing and therefore dependent on attentional focus. To test this, we leverage the observation that neural processes can be synchronized between subjects by presenting an identical narrative stimulus. As predicted, we find significant inter-subject correlation of the heartbeat (ISC-HR) when subjects are presented with an auditory or audiovisual narrative. Consistent with the conscious processing hypothesis, we find that ISC-HR is reduced when subjects are distracted from the narrative, and that higher heart rate synchronization predicts better recall of the narrative. Finally, patients with disorders of consciousness who are listening to a story have lower ISC-HR, as compared to healthy individuals, and that individual ISC-HR might predict a patients’ prognosis.. We conclude that heart rate fluctuations are partially driven by conscious processing, depend on attentional state, and may represent a simple metric to assess conscious state in unresponsive patients.
Reduced reproductive success is associated with selective constraint on human genes
Authors: Gardner Eugene J. , Neville Matthew D. C. , Samocha Kaitlin E. , Barclay Kieron , Kolk Martin , Niemi Mari E. K. , Kirov George , Martin Hilary C. , Hurles Matthew E.
Published: May 2020

Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants1. While genes under the strongest selective constraint are highly enriched for associations with Mendelian disorders, most of these genes are not associated with disease and therefore the nature of the selection acting on them is not known2. Here we show that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily due to increased childlessness, with a stronger effect in males than in females. We present evidence that increased childlessness is likely mediated by genetically associated cognitive and behavioural traits, which may mean male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. While this genetic association could only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.
Nonspecific Cleavages Arising from Reconstitution of Trypsin under Mildly Acidic Conditions
Authors: Niu Ben , Martinelli Michael , Jiao Yang , Meinke Eric , Cao Mingyan , Wang Jihong
Published: May 2020

Tryptic digestion of proteins followed by liquid chromatography with tandem mass spectrometry analysis is an extensively used approach in proteomics research and biopharmaceutical product characterization, owing to the high level of cleavage fidelity produced with this technique. However, nonspecific trypsin cleavages have been frequently reported and shown to be related to a number of digestion conditions and predigestion sample treatments. In this work, we reveal that, for a number of commercial trypsins, reconstitution and storage conditions can have a significant impact on the occurrence of trypsin nonspecific cleavages. We analyzed the tryptic digestion of a variety of biotherapeutics, using trypsins reconstituted under different conditions. The results indicate that, for many commercial trypsins, commonly recommended reconstitution/storage conditions (mildly acidic, e.g., 50 mM acetic acid, 1 mM HCl) can actually promote nonspecific trypsin activities, which are time dependent and can be as high as 20% in total relative abundance. In contrast, using water for reconstitution and storage can effectively limit nonspecific cleavages to 1%. Interestingly, the performances of different commercial trypsins were found to be quite distinct in their levels of nonspecific cleavages and responses to the two reconstitution conditions. Our findings demonstrate the importance of choosing the appropriate trypsin for tryptic digestion and the necessity of assessing the impact of trypsin reconstitution and storage on nonspecific cleavages. We advocate for manufacturers of commercial trypsins to reevaluate manufacturing processes and reconstitution/storage conditions to provide good cleavage specificity.
Effects of agricultural fungicide use onAspergillus fumigatusabundance, antifungal susceptibility, and population structure
Authors: Barber Amelia E. , Riedel Jennifer , Sae-Ong Tongta , Kang Kang , Brabetz Werner , Panagiotou Gianni , Deising Holger B. , Kurzai Oliver
Published: May 2020

Antibiotic resistance is an increasing threat to human health. In the case ofAspergillus fumigatus, which is both an environmental saprobe and an opportunistic human fungal pathogen, resistance is suggested to arise from fungicide use in agriculture, as the azoles used for plant protection are almost identical to the frontline antifungals used clinically. However, limiting azole fungicide use on crop fields to preserve their activity for clinical use could threaten the global food supply via a reduction in yield. In this study we clarify the link between fungicide use on crop fields and resistance in a prototypical human pathogen through systematic soil sampling on farms in Germany and surveying fields before and after azole application. We observed a reduction in the abundance ofA. fumigatuson fields following fungicide treatment in 2017—a finding that was not observed on an organic control field applying only natural plant protection agents. However, this finding was less pronounced during our 2018 sampling, indicating that the impact of fungicides onA. fumigatuspopulation size is variable and influenced by additional factors. The overall resistance frequency among agricultural isolates is low, with only 1-3% of isolates from 2016-2018 displaying resistance to medical azoles. Isolates collected after the growing season and azole exposure show a subtle, but consistent decrease in susceptibility to medical and agricultural azoles. Whole genome sequencing indicates that, despite the alterations in antifungal susceptibility, fungicide application does not significantly affect the population structure and genetic diversity ofA. fumigatusin fields. Given the low observed resistance rate among agricultural isolates, as well the lack of genomic impact following azole application, we do not find evidence that azole use on crops is significantly driving resistance inA. fumigatusin this context.

IMPORTANCE

Antibiotic resistance is an increasing threat to human health. In the case ofAspergillus fumigatus, which is an environmental fungus that also causes life-threatening infections in humans, antimicrobial resistance is suggested to arise from fungicide use in agriculture, as the chemicals used for plant protection are almost identical to the antifungals used clinically. However, removing azole fungicides from crop fields threatens the global food supply via a reduction in yield. In this study, we survey crop fields before and after fungicide application. We find a low overall azole resistance rate among agricultural isolates, as well a lack of genomic and population impact following fungicide application, leading us to conclude azole use on crops does not significantly contribute to resistance inA. fumigatus.
Metformin increases tauroursodeoxycholic acid levels to improve insulin resistance in diet-induced obese mice
Authors: Zhang Ya , Cheng Yang , Liu Jian , He Dan , Zuo Jihui , Yan Liping , Thring Ronald W. , Wu Mingjiang , Gao Yitian , Tong Haibin
Published: May 2020

Metformin is widely used to surmount insulin resistance (IR) and type 2 diabetes. Evidence indicates that metformin improves insulin resistance associated with gut microbiota, but the underlying mechanism remains unclear. In the present study, metformin effectively improved insulin sensitivity and alleviated liver inflammation and oxidative stress in high-fat diet (HFD)-fed mice. Metabolomics analysis showed that metformin increased tauroursodeoxycholic acid (TUDCA) levels both in intestinal content and liver by reducing the production and activity of bile salt hydrolase (BSH). We further found that TUDCA was able to antagonize with KEAP1 to prevent its binding to Nrf2 and activate Nrf2/ARE pathway, thereby reducing intracellular ROS and improving insulin signaling. Moreover, metformin increased the proportion ofAkkermanisia muciniphliain the HFD-fed mice, whilein vitrogrowth curve test confirmed that it’s TUDCA, not metformin, promoted the proliferation ofA. muciniphlia. Subsequently, TUDCA administration could effectively ameliorate insulin resistance, activate hepatic Nrf2/ARE pathways, and increase the abundance of intestinalA. muciniphliainob/obmice. These findings reveal that metformin remodels the gut microbiota, reduces oxidative stress and enhances insulin sensitivity partly due to increasing the production of TUDCA. This provides a novel mechanism by which metformin alleviates diet-induced insulin resistance and improves metabolism.
An improved CRISPR/dCas9 interference tool for neuronal gene suppression
Authors: Duke Corey G. , Bach Svitlana V. , Revanna Jasmin S. , Sultan Faraz A. , Southern Nicholas T. , Davis M. Natalie , Carullo Nancy V.N. , Bauman Allison J. , Phillips Robert A. , Day Jeremy J.
Published: May 2020

The expression of genetic material governs brain development, differentiation, and function, and targeted manipulation of gene expression is required to understand contributions of gene function to health and disease states. Although recent improvements in CRISPR/dCas9 interference (CRISPRi) technology have enabled targeted transcriptional repression at selected genomic sites, integrating these techniques for use in non-dividing neuronal systems remains challenging. Previously, we optimized a dual lentivirus expression system to express CRISPR-based activation machinery in post-mitotic neurons. Here we used a similar strategy to adapt an improved dCas9-KRAB-MeCP2 repression system for robust transcriptional inhibition in neurons. We find that lentiviral delivery of a dCas9-KRAB-MeCP2 construct driven by the neuron-selective promoter human synapsin 1 enabled transgene expression in primary rat neurons. Next, we demonstrate transcriptional repression using CRISPR sgRNAs targeting diverse gene promoters, and show superiority of this system in neurons compared to existing RNA interference methods for robust transcript specific manipulation at the complex Brain-derived neurotrophic factor (Bdnf) gene. Our findings advance this improved CRISPRi technology for use in neuronal systems for the first time, potentially enabling improved ability to manipulate gene expression states in the nervous system.
Adrenergic activation modulates the signal from the Reissner fiber to cerebrospinal fluid-contacting neurons during development
Authors: Yasmine Cantaut-Belarif , Margot Penru , Adeline Orts Del’Immagine , Guillaume Pézeron , Claire Wyart , Pierre-Luc Bardet
Published: May 2020

The cerebrospinal fluid (CSF) contains an extracellular thread that is conserved in vertebrates and referred to as the Reissner fiber. Genetic ablation in the zebrafish revealed that the Reissner fiber controls body axis morphogenesis in the embryo. Yet, the signaling cascade originating from this fiber to ensure body axis straightening is not fully understood. Here, we explore the functional link between the Reissner fiber and undifferentiated spinal neurons contacting the CSF (CSF-cNs). First, we show that the Reissner fiber is required for the expression ofurp2, a neuropeptide expressed in CSF-cNs. Usingin vivocalcium imaging, we show that the Reissner fiber is also required for embryonic calcium transients in these spinal neurons. Finally, we study how local adrenergic activation directly in the CSF can substitute for the Reissner fiber-signaling pathway to CSF-cNs and rescue body axis morphogenesis. Our results suggest that the Reissner fiber acts on CSF-cNs to establish body axis morphogensis by controlling the availability of a chemical signal in the CSF.
Developmental Phase Transitions in Spatial Organization of Spontaneous Activity in Postnatal Barrel Cortex Layer 4
Authors: Nakazawa Shingo , Yoshimura Yumiko , Takagi Masahiro , Mizuno Hidenobu , Iwasato Takuji
Published: May 2020

Spatially-organized spontaneous activity is a characteristic feature of developing mammalian sensory systems. However, the transitions of spontaneous-activity spatial organization during development and related mechanisms remain largely unknown. We reported previously that layer 4 (L4) glutamatergic neurons in the barrel cortex exhibit spontaneous activity with a patchwork-type pattern at postnatal day 5 (P5), which is during barrel formation. In the current work, we revealed that spontaneous activity in barrel-cortex L4 glutamatergic neurons exhibits at least three phases during the first two weeks of postnatal development. Phase I activity has a patchwork-type pattern and is observed not only at P5, but also P1, prior to barrel formation. Phase II is found at P9, by which time barrel formation is completed, and exhibits broadly synchronized activity across barrel borders. Phase III emerges around P11 when L4-neuron activity is desynchronized. The Phase I activity, but not Phase II or III activity, is blocked by thalamic inhibition, demonstrating that the Phase I to II transition is associated with loss of thalamic dependency. Dominant-negative Rac1 expression in L4 neurons hampers the Phase II to III transition. It also suppresses developmental increases in spine density and excitatory synapses of L4 neurons in the second postnatal week, suggesting that Rac1-mediated synapse maturation could underlie the Phase II to III transition. Our findings revealed the presence of distinct mechanisms for Phase I to II and Phase II to III transition. They also highlighted the role of a small GTPase in the developmental desynchronization of cortical spontaneous activity.

Significant statement

Developing neocortex exhibits spatially-organized spontaneous activity, which plays a critical role in cortical circuit development. The features of spontaneous-activity spatial organization and the mechanisms underlying its changes during development remain largely unknown. In the present study, using two-photon in vivo imaging, we revealed three phases (Phase I, II, and III) of spontaneous activity in barrel-cortex layer 4 (L4) glutamatergic neurons during the first two postnatal weeks. We also demonstrated the presence of distinct mechanisms underlying phase transitions. Phase I to II shift arose from the switch in the L4-neuron driving source, and Phase II to III transition relied on L4-neuron Rac1 activity. These results provide new insights into the principles of developmental transitions of neocortical spontaneous-activity spatial patterns.