bluuebunny/crossref_metadata_2025 huggingface dataset:
Sex-dependent macromolecule and nanoparticle delivery in experimental brain injury
Authors: Bharadwaj Vimala N. , Copeland Connor , Mathew Ethan , Newbern Jason , Anderson Trent R. , Lifshitz Jonathan , Kodibagkar Vikram D. , Stabenfeldt Sarah E.
Published: October 2019

Development of effective therapeutics for brain disorders is challenging, in particular, the blood-brain barrier (BBB) severely limits access of the therapeutics into the brain parenchyma. Traumatic brain injury (TBI) may lead to transient BBB permeability that affords a unique opportunity for therapeutic delivery via intravenous administration ranging from macromolecules to nanoparticles (NP) for developing precision therapeutics. In this regard, we address critical gaps in understanding the range/size of therapeutics, delivery window(s), and moreover the potential impact of biological factors for optimal delivery parameters. Here we show, for the first time, to the best of our knowledge, that 24 h post-focal TBI female mice exhibit a heightened macromolecular tracer and NP accumulation compared to male mice, indicating sex-dependent differences in BBB permeability. Furthermore, we report for the first time the potential to deliver NP-based therapeutics within 3 d after focal injury in both female and male mice. The delineation of injury-induced BBB permeability with respect to sex and temporal profile is essential to more accurately tailor time-dependent precision and personalized nanotherapeutics.
Cumulative effects of social stress on reward-guided actions and prefrontal cortical activity
Authors: Barthas Florent , Hu Melody Y. , Siniscalchi Michael J. , Ali Farhan , Mineur Yann S. , Picciotto Marina R. , Kwan Alex C.
Published: October 2019

When exposed to chronic social stress, animals display behavioral changes that are relevant to depressive-like phenotypes. However, the cascading relationship between incremental stress exposure and neural dysfunctions over time remains incompletely understood. Here we characterize the longitudinal effect of social defeat on goal-directed actions and prefrontal cortical activity in mice, using a head-fixed sucrose preference task and two-photon calcium imaging. Behaviorally, stress-induced loss of reward sensitivity intensifies over days. Motivational anhedonia, the failure to translate positive reinforcements into future actions, requires multiple sessions of stress exposure to become fully established. For neural activity, individual layer 2/3 pyramidal neurons in the Cg1 and M2 subregions of the medial prefrontal cortex have heterogeneous responses to stress. Changes in ensemble activity differ significantly between susceptible and resilient animals after the first defeat session, and continue to diverge following successive stress episodes before reaching persistent abnormal levels. Collectively, these results demonstrate that the cumulative impact of an ethologically relevant stress can be observed at the level of cellular activity of individual prefrontal neurons. The distinct neural responses associated with resilience versus susceptibility raises the hypothesis that the negative impact of social stress is neutralized in resilient animals, in part through an adaptive reorganization of prefrontal cortical activity.
Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3
Authors: Hagemann-Jensen Michael , Ziegenhain Christoph , Chen Ping , Ramsköld Daniel , Hendriks Gert-Jan , Larsson Anton J.M. , Faridani Omid R. , Sandberg Rickard
Published: October 2019

Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states1. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells2,3. Here, we introduce Smart-seq3 that combines full-length transcriptome coverage with a 5’ unique molecular identifier (UMI) RNA counting strategy that enabled in silico reconstruction of thousands of RNA molecules per cell. Importantly, a large portion of counted and reconstructed RNA molecules could be directly assigned to specific isoforms and allelic origin, and we identified significant transcript isoform regulation in mouse strains and human cell types. Moreover, Smart-seq3 showed a dramatic increase in sensitivity and typically detected thousands more genes per cell than Smart-seq2. Altogether, we developed a short-read sequencing strategy for single-cell RNA counting at isoform and allele-resolution applicable to large-scale characterization of cell types and states across tissues and organisms.
Genetic diversity and taxonomic issues inGastridiumP.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis
Authors: Scoppola Anna , Cardoni Simone , Pellegrino Mariangela , López-Tirado Javier , Simeone Marco Cosimo
Published: October 2019

Incomplete taxonomic knowledge may seriously hamper biodiversity conservation efforts that are crucial in a context of global change.GastridiumP.Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, inhabiting ephemeral grass habitats, whose species number and diversity are still imperfectly known. In order to progress towards a comprehensive taxonomic treatment of this genus, we examined patterns of DNA diversity in the four taxa (Gastridium lainzii,G. phleoides,G. scabrum, andG. ventricosum) that have been recently advanced by different authors, based on new morpho-ecological descriptors. We explored nucleotide sequence variation at two plastid (trnH-psbA, trnL-F) and one nuclear (ITS) DNA markers in 44 total individuals. Diversity data were treated with multiple statistical and phylogenetic tools, and integrated with available GenBank sequences ofGastridiumand other closely related genera. Despite the limited variability detected, evidence of within-taxon genetic cohesion and estimates of molecular divergence comparable with those of species in the same subtribal lineage (Agrostidinae) were recovered. The identified plastid genealogies appeared congruent with a subdivision of the genus into (at least) three distinct entities, and coherent with collected morphological descriptors. Phylogenetic reconstructions with ITS were less corresponding to taxa identities, likely due to reticulation and polyploidization. Once placed in a broader taxonomic context, the investigated dataset produced plastid and nuclear tree topologies consistent with previous assessments, highlighting the overall little resolution of species and genera within Agrostidinae. In the plastid tree, a sister relationship betweenGastridiumandTriplachnewas weakly supported. In the ITS tree, relationships among these genera were unresolved. The hypothesis of closely related but separately evolving lineages withinGastridiumis discussed, suggesting a re-evaluation of its current assessment in taxonomic authorities to enhance our knowledge of the grass family, and assist future biodiversity surveys of key Mediterranean grassland ecosystems.
A comprehensive human minimal gut metagenome extends the host’s metabolic potential
Authors: Parras-Moltó Marcos , Aguirre de Cárcer Daniel
Published: October 2019

Accumulating evidence suggests that humans should be considered as holobionts in which the gut microbiota plays essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis, and present in all healthy individuals. Despite its interest, this concept has received little attention following its initial description in terms of various ubiquitous pathways in Western cohorts. This study analyzes the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3,412 gene clusters, mapping to 1,856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.
Genome-wide identification of accessible chromatin regions in bumblebee (Bombus terrestris) by ATAC-seq
Authors: Zhao Xiaomeng , Xu Weilin , Schaack Sarah , Sun Cheng
Published: October 2019

Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To date, while the protein-coding sequences of bumblebees have been extensively annotated, regulatory elements, such as promoters and enhancers, have been poorly annotated in the bumblebee genome. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) for B. terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and the accessible chromatin regions of bumblebee were identified and characterized by using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology. The ATAC-seq data generated in this study has been deposited in NCBI GEO (accession#: GSE131063).
Glutathione Peroxidase 8 (GPX8)-IL6 axis is essential in maintaining breast cancer mesenchymal stem-like state and aggressive phenotype
Authors: Khatib Anees , Balakrishnan Solaimuthu , Ben-Yosef Michal , Oren Gidi , Abu Rmaileh Areej , Schlesinger Michal , Axelrod Jonathan H. , Lichtenstein Michal , Shaul Yoav D.
Published: October 2019

Metabolic reprogramming as a downstream result of oncogenic signaling pathways has been described as a hallmark of cancer. Here, we describe a reverse scenario in which a metabolic enzyme regulates cancer cell behavior by triggering a signaling pathway. We find that glutathione peroxidase 8 (GPX8), a poorly characterized redox enzyme that resides in the endoplasmic reticulum, is upregulated during the epithelial-to-mesenchymal (EMT) program in HMLE and A549 cells. In cancer patients, high tumor levels of GPX8 correlate with mesenchymal markers and poor patient outcome. Strikingly, GPX8 knockout in mesenchymal-like cells results in an epithelial-like morphology, downregulation of EMT characteristics, loss of cancer stemness features, and impeded tumor initiation in mice. We determine the mechanism governing this reduction in cancer aggressiveness is through the repression of crucial autocrine factors, in particular, interleukin-6 (IL-6). Specifically, GPX8 knockout impairs IL-6-driven activation of the JAK-STAT3 signaling pathway, a critical regulator of a cancer-aggressive state. Altogether, we uncover the GPX8-IL-6 axis as a novel metabolic-inflammatory pathway that acts as a robust EMT activator and program to induce aggressive cancer cell characteristics.
Single-cell dissection of a rare human prostate basal cell carcinoma
Authors: Su Xianbin , Long Qi , Bo Juanjie , Shi Yi , Zhao Li-Nan , Lin Yingxin , Luo Qing , Ghazanfar Shila , Zhang Chao , Liu Qiang , Wang Lan , He Kun-Yan , He Jian , Cui Xiao-Fang , Yang Jean Y. H. , Han Ze-Guang , Sha Jian-Jun , Yang Guoliang
Published: October 2019

As a rare subtype of prostate carcinoma, basal cell carcinoma (BCC) has not been studied extensively and thus lacks systematic molecular characterization. Here we applied single-cell genomic amplification and RNA-Seq to a specimen of human prostate BCC (CK34βE12+/P63+/PAP−/PSA−). The mutational landscape was obtained via whole exome sequencing of the amplification mixture of 49 single cells, and the 5 putative driver genes mutated areCASC5,NUTM1,PTPRC,KMT2CandTBX3. The top 3 nucleotide substitutions are C>T, T>C and C>A, similar to common prostate cancer. The distribution of the variant allele frequency values indicated these single cells are from the same tumor clone. The transcriptomes of 69 single cells were obtained, and they were clustered into tumor, stromal and immune cells based on their global transcriptomic profiles. The tumor cells specifically express basal cell markers likeKRT5,KRT14andKRT23, and epithelial markersEPCAM,CDH1andCD24. The transcription factor (TF) co-variance network analysis showed that the BCC tumor cells have distinct regulatory networks. By comparison with current prostate cancer datasets, we found that some of the bulk samples exhibit basal-cell signatures. Interestingly, at single-cell resolution the gene expression patterns of prostate BCC tumor cells show uniqueness compared with that of common prostate cancer-derived circulating tumor cells. This study, for the first time, discloses the comprehensive mutational and transcriptomic landscapes of prostate BCC, which lays a foundation for the understanding of its tumorigenesis mechanism and provides new insights into prostate cancers in general.
Synthesis and Characterisation of Aqueous Haemoglobin-based Microcapsules Coated by Genipin-Cross-Linked Albumin
Authors: Schakowski Kai Melvin , Linders Jürgen , Ferenz Katja Bettina , Kirsch Michael
Published: October 2019

Bovine serum albumin (BSA)-coated haemoglobin (Hb)-microcapsules prepared by co-precipitation of Hb and MnCO3may present an alternative type of artificial blood substitute. Prepared microcapsules were analysed by Scanning electron microscopy (SEM) and Respirometry, cytotoxicity was evaluated by addition of microcapsules to murine fibroblast-derived cell line L929 (American Type Culture Collection, NCTC clone 929 of strain L). The capsules come along with a mean diameter of approximately 0.6 μm and a mean volume of 1.13 ∙ 10−19L, thus an average human red blood cell with a volume of 9 ∙ 10−14L is about 800,000 times bigger. Hb-microcapsules are fully regenerable by ascorbic acid and maintain oxygen affinity because oxygen is able to pass the BSA wall of the capsules and thereby binding to the ferrous iron of the haemoglobin entity. Therefore, these microcapsules present a suitable type of potential artificial haemoglobin-based oxygen carrier (HbOC).
Respiratory supercomplexes provide metabolic efficiency in zebrafish
Authors: García-Poyatos Carolina , Cogliati Sara , Calvo Enrique , Hernansanz-Agustín Pablo , Lagarrigue Sylviane , Magni Ricardo , Botos Marius , Langa Xavier , Amati Francesca , Vázquez Jesús , Mercader Nadia , Enriquez José Antonio
Published: October 2019

The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the respiratory complexes coexist with super-assembled quaternary structures called supercomplexes (SCs). The physiological role of SCs is still disputed. Here we used zebrafish to study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-independent proteomics to characterize these structures and found similar SCs to those described in mice, as well as novel SCs including III2+IV2, I+IV and I+III2+IV2. To study the physiological role of SCs, we generated two null allele zebrafish lines for supercomplex assembly factor 1 (SCAF1). SCAF1-/- fish displayed altered OXPHOS activity due to the disrupted interaction of complex III and IV. SCAF1-/- fish were smaller in size, and showed abnormal fat deposition and decreased female fertility. These physiological phenotypes were rescued by doubling the food supply, which correlated with improved bioenergetics and alterations in the metabolic gene expression program. These results reveal that SC assembly by SCAF1 modulates OXPHOS efficiency and allows for the optimization of metabolic resources.
The Toxin Cercosporin is a Virulence Factor for Infection of Coffee byCercospora coffeicola
Authors: Souza A. G. C. , Herrero S. , Daub M. E.
Published: October 2019

Brown eye spot, caused byCercospora coffeicola, causes significant losses in both quality and quantity of coffee production. As manyCercosporaspp. produce the photoactivated toxin cercosporin, this study aimed to determine the role of cercosporin inC. coffeicolapathogenesis by creating disruption mutants unable to produce the toxin. SixC. coffeicolaisolates from Brazilian fields, representing organic and conventional production systems in the Minas Gerais state, were evaluated for their ability to produce cercosporinin vitro. Toxin production varied among isolates, ranging from 3.5 – 25.3 µM/ 5 mm mycelial plug; production was undetectable in one isolate. TheC. coffeicolahomolog of the polyketide synthase gene (CTB1) involved in cercosporin production was amplified using a degenerate primer strategy. The 7044 ntccCTB1gene sequence was 90.3% identical to thecnCTB1gene inCercospora nicotianaeand encoded a putative protein of 2196 amino acids with 98.2% similarity and 97.5% identity to its counterpart inC. nicotianae. Transformation of two isolates ofC. coffeicolawith aCTB1disruption construct resulted in the recovery of sixctb1disruption mutants. All of thectb1disruptants were deficient in cercosporin production. Disruption mutants did not differ significantly from the wild type for either growth or sporulation, but were significantly altered in virulence on coffee. As compared to wild type, time to lesion development was significantly increased and numbers of lesions were significantly decreased in coffee plants inoculated withctb1disruption mutants. These results show that cercosporin toxin is a virulence factor forC. coffeicolainfection of coffee.
Machine Learning Approaches Identify Genes Containing Spatial Information from Single-Cell Transcriptomics Data
Authors: Loher Phillipe , Karathanasis Nestoras
Published: October 2019

Motivation

We participated in the DREAM Single Cell Transcriptomics Challenge. The challenge’s focus was two-fold; a) to identify the top 60, 40 and 20 genes that contain the most spatial information, and b) to reconstruct the 3-D arrangement of the D. melanogaster embryo using information from those genes.

Results

We developed two independent approaches, leveraging machine learning models from Lasso and Deep Neural Networks, that we successfully apply to high-dimensional single-cell sequencing data. Our methods allowed us to achieve top performance when compared to the ground truth. Among ~40 participating teams, the resulting solutions placed 10th, 6th, and 4th in the three DREAM sub-challenges #1, #2 and #3, respectively. Notably, for the Lasso approach we introduced a feature selection technique, Lasso-TopX, that allows a user to define a specific number of features they are interested in and the Neural Network approach utilizes weak supervision for linear regression to accommodate for uncertain or probabilistic training labels. Furthermore, we identified novel D. melanogaster genes that carry important positional information and were not previously suspected. Lastly, we show how the indirect use of the full datasets’ information can lead to data leakage and generate bias in overestimating the model’s performance.

Availability

https://github.com/TJU-CMC-Org/SingleCell-DREAM/.

Contact

Nestoras.Karathanasis@jefferson.edu
Neural representation of bat predation risk and evasive flight in moths: a modelling approach
Authors: Goerlitz Holger R. , ter Hofstede Hannah M. , Holderied Marc W.
Published: October 2019

Most animals are at risk from multiple predators and can vary anti-predator behaviour based on the level of threat posed by each predator. Animals use sensory systems to detect predator cues, but the relationship between the tuning of sensory systems and the sensory cues related to predator threat are not well-studied at the community level. Noctuid moths have ultrasound-sensitive ears to detect the echolocation calls of predatory bats. Here, combining empirical data and mathematical modelling, we show that moth hearing is adapted to provide information about the threat posed by different sympatric bat species. First, we found that multiple characteristics related to the threat posed by bats to moths correlate with bat echolocation call frequency. Second, the frequency tuning of the most sensitive auditory receptor in noctuid moth ears provides information allowing moths to escape detection by all sympatric bats with similar safety margin distances. Third, the least sensitive auditory receptor usually responds to bat echolocation calls at a similar distance across all moth species for a given bat species. If this neuron triggers last-ditch evasive flight, it suggests that there is an ideal reaction distance for each bat species, regardless of moth size. This study shows that even a very simple sensory system can adapt to deliver information suitable for triggering appropriate defensive reactions to each predator in a multiple predator community.
Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR
Authors: Shu Bo , Kirby Marie K. , Warnes Christine , Sessions Wendy M. , Davis William G. , Liu Ji , Wilson Malania M. , Wentworth David E. , Barnes John R.
Published: October 2019

Influenza B viruses have two genetically and antigenically distinct lineages, B/Victoria/2/1987-like (VIC) and B/Yamagata/16/1988-like (YAM) viruses, that emerged in the 1980s and co-circulate annually during the influenza season. During the 2016-2017 influenza season, influenza B/VIC lineage variant viruses emerged with two (K162N163) or three (K162N163D164) amino acid (AA) deletions in the hemagglutinin protein. Hemagglutination inhibition assays demonstrate that these deletion variant influenza B/VIC viruses are antigenically distinct from each other and from the progenitor B/VIC virus that lacks the deletion. Therefore, there are currently four antigenically distinct HA proteins expressed by influenza B co-circulating: B/YAM, B/VIC V1A (no deletion), B/VIC V1A.1 (two-AA deletion), and B/VIC V1A.2 and V1A.3 (three-AA deletion). The prevalence of these viruses differs across geographic regions, making it critical to have a sensitive, rapid diagnostic assay(s) that detect and distinguish these Influenza B variant viruses during surveillance. Here, we present a real time RT-PCR assay that targets the influenza B/VIC deletion region in the HA gene and detects and distinguishes the influenza B/VIC V1A, B/VIC V1A.1, B/VIC V1A.2 and B/VIC V1A.3 variant viruses, with no cross-reactivity. This assay can be run as a multiplex reaction, allowing for increased testing efficiency and reduced cost. Coupling this assay with the CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel Influenza B Lineage Genotyping Kit results in rapid detection and characterization of circulating influenza B viruses. Having accurate and detailed surveillance information on these distinct Influenza B variant viruses will provide insight into the prevalence and geographic distribution and could aid in vaccine recommendations.
A theophylline-responsive riboswitch regulates expression of nuclear-encoded genes in Arabidopsis
Authors: Shanidze Nana , Lenkeit Felina , Hartig Jörg S. , Funck Dietmar
Published: October 2019

Ligand-responsive synthetic riboswitches are versatile and innovative tools for external gene regulation in pro- and eukaryotes. Riboswitches are smallcis-regulatory RNA elements that regulate gene expression by conformational changes in response to ligand binding. In plants, synthetic riboswitches were used to regulate gene expression in plastids, but the application of synthetic riboswitches for the regulation of nuclear-encoded genesin plantahas not been reported so far. Here we characterize the properties of a theophylline-responsive synthetic aptazyme for control of nuclear-encoded transgenes in Arabidopsis (Arabidopsis thaliana). Activation of the aptazyme, inserted in the 3-UTR of the target gene, resulted in rapid self-cleavage and subsequent decay of the mRNA. This riboswitch allowed reversible, theophylline-dependent downregulation of theGreen Fluorescent Protein(GFP) reporter gene in a dose- and time- dependent manner. Insertion of the riboswitch into theOne Helix Protein 1(OHP1) gene allowed complementation ofohp1mutants and induction of the mutant phenotype by theophylline.GFPorOHP1transcript levels were downregulated by maximally 90%, and GFP protein levels by 95%. These results establish artificial riboswitches as tools for externally controlled gene expression in synthetic biology in plants or functional crop design.

One sentence summary

Artificial, ligand-responsive RNA aptazymes are an efficient tool for dose- and time-dependent external control of nuclear gene expression in plants.
Genome assembly of the common pheasantPhasianus colchicus, a model for speciation and ecological genomics
Authors: Liu Yang , Liu Simin , Zhang Nan , Chen De , Que Pinjia , Liu Naijia , Höglund Jacob , Zhang Zhengwang , Wang Biao
Published: October 2019

The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspeciestorquatusof the common pheasant with the Illumina Hiseq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05 % of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented dataset, we uncover the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.
Somatosensory corticospinal tract axons sprout within the cervical cord following a dorsal root/dorsal column spinal injury in the rat
Authors: McCann Margaret M. , Fisher Karen M. , Ahloy-Dallaire Jamie , Darian-Smith Corinna
Published: October 2019

The corticospinal tract (CST) is the major descending pathway controlling voluntary hand function in primates, and though less dominant, it mediates voluntary paw movements in rats. As with primates, the CST in rats originates from multiple (albeit fewer) cortical sites, and functionally different motor and somatosensory subcomponents terminate in different regions of the spinal gray matter. We recently reported in monkeys that following a combined cervical dorsal root/dorsal column lesion (DRL/DCL), both motor and S1 CSTs sprout well beyond their normal terminal range. The S1 CST sprouting response is particularly dramatic, indicating an important, if poorly understood, somatosensory role in the recovery process. As rats are used extensively to model spinal cord injury (SCI), we asked if the S1 CST response is conserved in rodents. Rats were divided into sham controls, and two groups surviving post-lesion for ~6 and 10 weeks. A DRL/DCL was made to partially deafferent one paw. Behavioral testing showed a post-lesion deficit and recovery over several weeks. Three weeks prior to ending the experiment, S1 cortex was mapped electrophysiologically, for tracer injection placement to determine S1 CST termination patterns within the cord. Synaptogenesis was also assessed for labeled S1 CST terminals within the dorsal horn. Our findings show that the affected S1 CST sprouts well beyond its normal range in response to a DRL/DCL, much as it does in macaque monkeys. This, along with evidence for increased synaptogenesis post-lesion, indicates that CST terminal sprouting following a central sensory lesion, is a robust and conserved response.
Deformability based sorting of stored red blood cells reveals donor-dependent aging curves
Authors: Islamzada Emel , Matthews Kerryn , Guo Quan , Santoso Aline T. , Duffy Simon P. , Scott Mark D. , Ma Hongshen
Published: October 2019

A fundamental challenge in the transfusion of red blood cells (RBCs) is that a subset of donated RBC units may not provide optimal benefit to transfusion recipients. This variability stems from the inherent ability of donor RBCs to withstand the physical and chemical insults of cold storage, which ultimately dictate their survival in circulation. The loss of RBC deformability during cold storage is well-established and has been identified as a potential biomarker for the quality of donated RBCs. While RBC deformability has traditionally been indirectly inferred from rheological characteristics of the bulk suspension, there has been considerable interest in directly measuring the deformation of RBCs. Microfluidic technologies have enabled single cell measurement of RBC deformation but have not been able to consistently distinguish differences between RBCs between healthy donors. Using the microfluidic ratchet mechanism, we developed a method to sensitively and consistently analyze RBC deformability. We found that the aging curve of RBC deformability varies significantly across donors, but is consistent for each donor over multiple donations. Specifically, certain donors seem capable of providing RBCs that maintain their deformability during two weeks of cold storage in standard test tubes. The ability to distinguish between RBC units with different storage potential could provide a valuable opportunity to identify donors capable of providing RBCs that maintain their integrity, in order to reserve these units for sensitive transfusion recipients.
Oxygenation properties of hemoglobin and the evolutionary origins of isoform multiplicity in an amphibious air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris)
Authors: Storz Jay F. , Natarajan Chandrasekhar , Grouleff Magnus K. , Vandewege Michael , Hoffmann Federico G. , You Xinxin , Venkatesh Byrappa , Fago Angela
Published: October 2019

Among the numerous lineages of teleost fish that have independently transitioned from obligate water-breathing to facultative air-breathing, evolved properties of hemoglobin (Hb)-O2transport may have been shaped by the prevalence and severity of aquatic hypoxia (which influences the extent to which fish are compelled to switch to aerial respiration) as well as the anatomical design of air-breathing structures and the cardiovascular system. Here we examine the structure and function of Hbs in an amphibious, facultative air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris). We also characterized the genomic organization of the globin gene clusters of the species and we integrated phylogenetic and comparative genomic analyses to unravel the duplicative history of the genes that encode the subunits of structurally distinct mudskipper Hb isoforms (isoHbs). TheB. pectinirostrisisoHbs exhibit high intrinsic O2-affinities, similar to those of hypoxia-tolerant, water-breathing teleosts, and remarkably large Bohr effects. Genomic analysis of conserved synteny revealed that the genes that encode the α-type subunits of the two main adult isoHbs are members of paralogous gene clusters that represent products of the teleost-specific whole-genome duplication. Experiments revealed no appreciable difference in the oxygenation properties of co-expressed isoHbs in spite of extensive amino acid divergence between the alternative α-chain subunit isoforms. It therefore appears that the ability to switch between aquatic and aerial respiration does not necessarily require a division of labor between functionally distinct isoHbs with specialized oxygenation properties.

Summary statement

The blue-spotted mudskipper routinely switches between aquatic and aerial respiration. This respiratory versatility is associated with properties of hemoglobin-oxygen transport that are similar to those found in hypoxia-adapted water-breathing fishes.
Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type
Authors: Sharrar Allison M. , Crits-Christoph Alexander , Méheust Raphaël , Diamond Spencer , Starr Evan P. , Banfield Jillian F.
Published: October 2019

Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils, and whether the genetic potential for production of these metabolites differs with soil type. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with varying vegetation and bedrock characteristics and used metagenomic sequencing and assembly to reconstruct 1,334 microbial genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi and candidate phylum Dormibactereota. Surprisingly, one genome of a Candidate Phyla Radiation bacterium encoded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.
AP-1B facilitates endocytosis during cell migration
Authors: Kell Margaret Johnson , Ang Su Fen , Pigati Lucy , Halpern Abby , Fölsch Heike
Published: October 2019

The epithelial cell-specific clathrin adaptor AP-1B has a well-established role in polarized sorting of cargos to the basolateral membrane. Here we demonstrate a novel function for AP-1B during collective cell migration of epithelial sheets. We show that AP-1B colocalized with β1 integrin in focal adhesions during cell migration using confocal microscopy and total internal reflection fluorescence (TIRF) microscopy on fixed specimens. Further, AP-1B labeling in cell protrusion was distinct from labeling for the canonical endocytic adaptor complex AP-2. Using stochastic optical reconstruction microscopy (STORM) and live TIRF imaging we identified numerous AP-1B-coated structures at or close to the plasma membrane in cell protrusions. Importantly, immuno-electron microscopy (EM) showed AP-1B in clathrin-coated pits and budding vesicles at the plasma membrane during cell migration. Our data therefore established a novel function for AP-1B in endocytosis. We further show that β1 integrin was dependent on AP-1B and its co-adaptor, autosomal recessive hypercholesterolemia protein (ARH), for sorting to the basolateral membrane. Notably, we found that expression of AP-1B (and ARH) slowed epithelial-cell migration, and qRT-PCR analysis of human epithelial-derived cell lines revealed a loss of AP-1B expression in highly metastatic cancer cells indicating that AP-1B-facilitated endocytosis during cell migration might be an anti-cancer mechanism.
Glucocorticoids mediate egg rejection in a brood parasite host
Authors: Abolins-Abols Mikus , Hauber Mark E.
Published: October 2019

Avian brood parasites and their hosts are engaged in a coevolutionary battle that can result in the evolution of sophisticated trickery by parasites and novel defence behaviours in hosts. Despite the clear evolutionary and ecological significance of host behaviour, however, we know very little about the mechanisms that regulate host defences, which limits our understanding of both inter- and intraspecific variation in host responses to parasitism. Here we tested whether corticosterone, a hormone known to be upregulated in hosts exposed to parasitism, also mediates one of the most frequent host defences – the rejection of foreign eggs. We experimentally reduced corticosterone levels in free-living brood parasite hosts, American robins Turdus migratorius, using mitotane and found that the likelihood of model egg rejection was significantly lower in the mitotane-treated birds relative to the sham-treated birds. These results demonstrate a causal link between glucocorticoids and egg rejection in hosts of avian brood parasites, but the physiological and sensory-cognitive pathways that regulate this effect remain unknown.
Cre-assisted Fine-mapping of Neural Circuits using Orthogonal Split Inteins
Authors: Luan Haojiang , Kuzin Alexander , Odenwald Ward F. , White Benjamin H.
Published: October 2019

Summary:

Genetic methods for targeting small numbers of neurons of a specific type are critical for mapping the brain circuits underlying behavior. Existing methods can provide exquisite targeting precision in favorable cases, but for many cases alternative techniques will be required. Here, we introduce a new step-wise combinatorial method for sequentially refining neuronal targeting: Depending on the restriction achieved at the first step, a second step can be easily implemented to further refine expression. For both steps, the new method relies on two independent intersections. The primary intersection targets neurons based on their developmental origins (i.e. lineage) and terminal identities, while the second intersection limits the number of lineages represented in the primary intersection by selecting lineages with overlapping activity of two distinct enhancers during neurogenesis. Our method relies critically on two libraries of 134 transgenic fly lines that express fragments of a split Cre recombinase under the control of distinct neuroblast enhancers. The split Cre fragments are fused to non-interacting pairs of split inteins, which ensure reconstitution of full-length and active Cre when all fragments are expressed in the same cell. Our split Cre system, together with its open source libraries, represent off-the-shelf components that should facilitate the targeting and characterization of brain circuits inDrosophila. Our methodology may also prove useful in other genetic model organisms.
Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity
Authors: Cheng Kuoyuan , Nair Nishanth Ulhas , Lee Joo Sang , Ruppin Eytan
Published: October 2019

Various characteristics of cancers exhibit tissue-specificity, including lifetime cancer risk, onset age and cancer driver genes. Previously, the large variation in cancer risk across human tissues was found to strongly correlate with the number of stem cell divisions and abnormal DNA methylation levels occurring in them. Here we study the role of another potentially important factor, synthetic lethality, in cancer risk. Analyzing transcriptomics data in the GTEx compendium we quantify the extent of co-inactivation of cancer synthetic lethal (cSL) gene pairs in normal tissues and find that normal tissues with more down-regulated cSL gene pairs have lower and delayed cancer risk. We also show that the tissue-specificity of numerous tumor suppressor genes is strongly associated with the expression of their cSL partner genes in the corresponding normal tissues. Overall, our findings uncover the role of synthetic lethality as a novel important factor involved in tumorigenesis.
Meta-analytic clustering dissociates brain activity and behavior profiles across reward processing paradigms
Authors: Flannery Jessica S. , Riedel Michael C. , Bottenhorn Katherine L. , Poudel Ranjita , Salo Taylor , Hill-Bowen Lauren D. , Laird Angela R. , Sutherland Matthew T.
Published: October 2019

Reward learning is a ubiquitous cognitive mechanism guiding adaptive choices and behaviors, and when impaired, can lead to considerable mental health consequences. Reward-related functional neuroimaging studies have begun to implicate networks of brain regions essential for processing various peripheral influences (e.g., risk, subjective preference, delay, social context) involved in the multifaceted reward processing construct. To provide a more complete neurocognitive perspective on reward processing that synthesizes findings across the literature while also appreciating these peripheral influences, we utilized emerging meta-analytic techniques to elucidate brain regions, and in turn networks, consistently engaged in distinct aspects of reward processing. Using a data-driven, meta-analytic,k-means clustering approach, we dissociated seven meta-analytic groupings (MAGs) of neuroimaging results (i.e., brain activity maps) from 749 experimental contrasts across 176 reward processing studies involving 13,358 healthy participants. We then performed an exploratory functional decoding approach to gain insight into the putative functions associated with each MAG. We identified a seven-MAG clustering solution which represented dissociable patterns of convergent brain activity across reward processing tasks. Additionally, our functional decoding analyses revealed that each of these MAGs mapped onto discrete behavior profiles that suggested specialized roles in predicting value (MAG-1 & MAG-2) and processing a variety of emotional (MAG-3), external (MAG-4 & MAG-5), and internal (MAG-6 & MAG-7) influences across reward processing paradigms. These findings support and extend aspects of well-accepted reward learning theories and highlight large-scale brain network activity associated with distinct aspects of reward processing.
ROS production by localized SCHENGEN receptor module drives lignification at subcellular precision
Authors: Fujita Satoshi , De Bellis Damien , Edel Kai H. , Köster Phillipp , Andersen Tonni Grube , Schmid-Siegert Emanuel , Dénervaud Tendon Valérie , Pfister Alexandre , Marhavý Peter , Ursache Robertas , Doblas Verónica G. , Daraspe Jean , Creff Audrey , Ingram Gwyneth , Kudla Jörg , Geldner Niko
Published: October 2019

Production of reactive-oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and direct cellular targets of ROS. A well-understood ROS target in plants are lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here we establish a full kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicates that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.
Genome-wide association study of cryptosporidiosis in infants implicatesPRKCA
Authors: Wojcik Genevieve L. , Korpe Poonum , Marie Chelsea , Mychaleckyj Josyf , Kirkpatrick Beth D. , Rich Stephen S. , Concannon Patrick , Faruque A. S. G. , Haque Rashidul , Petri William A. , Duggal Priya
Published: October 2019

Diarrhea is a major cause of both morbidity and mortality worldwide, especially among young children. Cryptosporidiosis is a leading cause of diarrhea in children, particularly in South Asia and Sub-Saharan Africa where it is responsible for over 200,000 deaths per year. Beyond the initial clinical presentation of diarrhea, it is associated with long term sequelae such as malnutrition and neurocognitive developmental deficits. Risk factors include poverty and overcrowding, yet not all children with these risk factors and exposure are infected, nor do all infected children develop symptomatic disease. One potential risk factor to explain these differences is their human genome. To identify genetic variants associated with symptomatic cryptosporidiosis, we conducted a genome-wide association study (GWAS) examining 6.5 million single nucleotide polymorphisms (SNPs) in 873 children from three independent cohorts in Dhaka, Bangladesh: the Dhaka Birth Cohort (DBC), the Performance of Rotavirus and Oral Polio Vaccines in Developing Countries (PROVIDE) study, and the Cryptosporidiosis Birth Cohort (CBC). Associations were estimated separately for each cohort under an additive model, adjusting for height-for-age Z-score at 12 months of age, the first two principal components to account for population substructure, and genotyping batch. The strongest meta-analytic association was with rs58296998 (P=3.73×10−8), an intronic SNP and eQTL ofPRKCA. Each additional risk allele conferred 2.4 times the odds of cryptosporidiosis in the first year of life. This genetic association suggests a role for protein kinase C alpha in pediatric cryptosporidiosis and warrants further investigation. This article was submitted to an online preprint archive.(1)

Importance

Globally, one of the major causes of pediatric morbidity and mortality remains diarrhea. The initial symptoms of diarrhea can often lead to long term consequences for the health of young children, such as malnutrition and neurocognitive developmental deficits. Despite many children having similar exposures to infectious causes of diarrhea, not all develop symptomatic disease, indicating a possible role for human genetic variation. Here we conducted a genetic study of susceptibility to symptomatic disease associated with Cryptosporidium infection (a leading cause of diarrhea) in three independent cohorts of infants from Dhaka, Bangladesh. We identified a genetic variant within protein kinase c alpha (PRKCA) associated with higher risk of cryptosporidiosis in the first year of life. These results indicate a role for human genetics in susceptibility to cryptosporidiosis and warrant further research to elucidate the mechanism.
High-Throughput Translational Profiling with riboPLATE-seq
Authors: Metz Jordan B. , Hornstein Nicholas J. , Das Sharma Sohani , Worley Jeremy , Gonzalez Christian , Sims Peter A.
Published: October 2019

Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages rRNA immunoprecipitation on whole polysomes to measure ribosome association (RA). We compare RA to its analogue in ribosome profiling and RNA sequencing, translation efficiency, and demonstrate both the performance of riboPLATE-seq and its utility in detecting translational alterations induced by specific inhibitors of protein kinases.