bluuebunny/crossref_metadata_2025_split huggingface dataset:
d-Lysergic acid diethylamide has major potential as a cognitive enhancer
Authors: Cini Felipe Augusto , Ornelas Isis , Marcos Encarni , Goto-Silva Livia , Nascimento Juliana , Ruschi Sergio , Salerno José , Karmirian Karina , Costa Marcelo , Sequerra Eduardo , de Araújo Dráulio , Tófoli Luis Fernando , Rennó-Costa César , Martins-de-Souza Daniel , Feilding Amanda , Rehen Stevens , Ribeiro Sidarta 
Published: December 2019

AbstractPsychedelic agonists of serotonin receptors induce neural plasticity and synaptogenesis, but their potential to enhance learning remains uncharted. Here we show that a single dose of d-LSD, a potent serotonergic agonist, increased novel object preference in young and adult rats several days after treatment. d-LSD alone did not increase preference in old animals, but could rescue it to young levels when followed by a 6-day exposure to enriched environment (EE). Mass spectrometry-based proteomics in human brain organoids treated with d-LSD showed upregulation of proteins from the presynaptic active zone. A computational model of synaptic connectivity in the hippocampus and prefrontal cortex suggests that d-LSD enhances novelty preference by combining local synaptic changes in mnemonic and executive regions, with alterations of long-range synapses. Better pattern separation within EE explained its synergy with d-LSD in rescuing novelty preference in old animals. These results advance the use of d-LSD in cognitive enhancement.
Deep learning enables structured illumination microscopy with low light levels and enhanced speed
Authors: Jin Luhong , Liu Bei , Zhao Fenqiang , Hahn Stephen , Dong Bowei , Song Ruiyan , Elston Tim , Xu Yingke , Hahn Klaus M. 
Published: December 2019

AbstractUsing deep learning to augment structured illumination microscopy (SIM), we obtained a fivefold reduction in the number of raw images required for super-resolution SIM, and generated images under extreme low light conditions (100X fewer photons). We validated the performance of deep neural networks on different cellular structures and achieved multi-color, live-cell super-resolution imaging with greatly reduced photobleaching.
Gut-associated bacteria invade the midgut epithelium of Aedes aegypti and stimulate innate immunity and suppress Zika virus infection in cells
Authors: Hegde Shivanand , Voronin Denis , Casas-Sanchez Aitor , Saldaña Miguel A. , Heinz Eva , Acosta-Serrano Alvaro , Popov Vsevolod L. , Chopra Ashok K. , Hughes Grant L. 
Published: December 2019

AbstractMicrobiota within mosquitoes influence nutrition, immunity, fecundity, and the capacity to transmit pathogens. Despite their importance, we have a limited understanding of host-microbiota interactions, especially at the cellular level. It is evident bacterial symbionts that are localized within the midgut also infect other organs within the mosquito; however, the route these symbionts take to colonize other tissues is unknown. Here, utilizing the gentamicin protection assay, we showed that the bacterial symbionts Cedecea and Serratia have the capacity to invade and reside intracellularly within mosquito cells. Symbiotic bacteria were found within a vacuole and bacterial replication was observed in mosquito cell by transmission electron microscopy, indicating bacteria were adapted to the intracellular milieu. Using gene silencing, we determined that bacteria exploited host factors, including actin and integrin receptors, to actively invade mosquito cells. As microbiota can affect pathogens within mosquitoes, we examined the influence of intracellular symbionts on Zika virus (ZIKV) infection. Mosquito cells harbouring intracellular bacteria had significantly less ZIKV compared to uninfected cells or cells exposed to non-invasive bacteria. Intracellular bacteria were observed to substantially upregulate the Toll and IMD innate immune pathways, providing a possible mechanism mediating these anti-viral effects. Examining mono-axenically infected mosquitoes using transmission electron and fluorescent microscopy revealed that bacteria occupied an intracellular niche in vivo. Our results provided evidence that bacteria that associate with the midgut of mosquitoes have intracellular lifestyles which likely have implications for mosquito biology and pathogen infection. This study expands our understanding of host-microbiota interactions in mosquitoes, which is important as symbiont microbes are being exploited for vector control strategies.
Forecasting the potential distribution of the invasive vegetable leafminer using ‘top-down’ and ‘bottom-up’ models
Authors: Maino James L. , Pirtle Elia I. , Ridland Peter M. , Umina Paul A. 
Published: December 2019

AbstractThe vegetable leafminer, Liriomyza sativae, is an internationally significant pest of vegetable and flower crops, that was detected for the first time on the Australian mainland in 2015. Due to the early stage of its invasion in Australia, it is unclear how climatic conditions are likely to support and potentially restrict the distribution of L. sativae as it expands into a novel range and threatens agricultural production regions. Here we predicted the future establishment potential of L. sativae in Australia, using both a novel ‘bottom-up’ process-based model and a popular ‘top-down’ correlative species distribution model (SDM), leveraging the unique strengths of each approach. Newly compiled global distribution data spanning 42 countries was used to validate the process-based model of establishment potential based on intrinsic population growth rates, as well as parameterise the correlative SDM. Both modelling approaches successfully captured the international distribution of L. sativae based on environmental variables and predicted the high suitability of non-occupied ranges, including northern regions of Australia. The largely unfilled climatic niche available to L. sativae in Australia demonstrates the early stage of its Australian invasion, and highlights locations where important vegetable and nursery production regions in Australia are highly vulnerable to L. sativae establishment.
Changing the Waddington landscape to control mesendoderm competence
Authors: Valcourt James R. , Huang Roya , Kundu Sharmistha , Venkatasubramanian Divya , Kingston Robert E. , Ramanathan Sharad 
Published: December 2019

AbstractAs pluripotent human embryonic stem cells progress towards one germ layer fate, they lose the ability to adopt alternative fates. It is unknown how the cells’ competence for these alternative fates changes along their developmental trajectory or if this competence can be modulated. Here, we show that a differentiating stem cell’s probability of adopting a mesendodermal fate when given the appropriate signal falls sharply at a specific point along the ectodermal trajectory, and we further demonstrate that this point can be moved using genetic perturbations. Using a low-dimensional reaction coordinate to monitor progression towards ectoderm, we can determine the probability that individual cells at different points along this path can transition to the mesendodermal fate upon BMP4 and Activin A signal exposure. Knowing this probability allows us to prospectively isolate and profile differentiating cells based on their mesendoderm competence. Analysis and validation of these RNA-seq and ATAC-seq profiles identified transcription factors that can independently control the cell’s mesendoderm competence and its progression along the ectodermal developmental trajectory. In the classical picture of a Waddington landscape, these effects correspond to altering the barrier between fates and changing the cell’s location on the landscape, respectively. The ability of the underlying gene regulatory network to modulate these two aspects of the developmental landscape could allow separate control of the dynamics of differentiation and tissue size proportions.
Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic
Authors: Vihani Aashutosh , Hu Xiaoyang Serene , Gundala Sivaji , Koyama Sachiko , Block Eric , Matsunami Hiroaki 
Published: December 2019

AbstractUnderstanding how genes and experiences work in concert to generate phenotypic variability will provide a better understanding of individuality. Here, we considered this in the context of the main olfactory epithelium, a chemosensory structure with over a thousand distinct cell-types, in mice. We identified a subpopulation of at least three types of olfactory sensory neurons, defined by receptor expression, whose abundances were sexually dimorphic. This subpopulation of olfactory sensory neurons was over-represented in sex-separated female mice and responded robustly to the male-specific semiochemicals 2-sec-butyl-4,5-dihydrothaizole and (methylthio)methanethiol. Sex-combined housing led to a robust attenuation of the female over-representation. Testing of Bax null mice revealed a Bax-dependence in generating the sexual dimorphism in sex-separated mice. Altogether, our results suggest a profound role of experience in influencing homeostatic neural lifespan mechanisms to generate a robust sexually dimorphic phenotype in the main olfactory epithelium.
Juvenile hormone regulation on the flight capability of Bactrocera dorsalis (Diptera: Tephritidae)
Authors: Chen Peng , Chen Min , Ye Hui , Yuan Ruiling , Du Chunhua , Ong Su Ping 
Published: December 2019

AbstractThe oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), is considered a major economic threat in many regions worldwide. In order to better understand the flight capacity of B. dorsalis and its physiological basis, the functions and regulatory roles of juvenile hormone (JH) in the flight muscle of B. dorsalis were studied under a controlled environment. JH titer of B. dorsalis varied with age and sex. Females, irrespective of age, have higher JH than males for ovarian development and maturation in addition to better flight capabilities. The flight duration and distance of both males and females increased with the gradual increase of JH titer after adult emergences. JH titer peaked in 15-d-old adult and declined subsequently with age. Flight activity stimulated the production of JH as adults flown for 24 hours on the flight mills have the highest JH titers compare to adults tethered on shorter flight durations. Furthermore, JH III-treated adults were able to perform long-duration and long-distance flights. The mutual reinforcement of JH and flight activity provides fundamental understanding on the physiological aspects of the flight capability and dispersal, which facilitates strategies for the long-term control of this destructive pest.
Effect of Assembly Method on Nanoparticle Attachment Density, Growth Rate, and Motility of Nanoscale Bacteria Enabled Autonomous Drug Delivery System (NanoBEADS)
Authors: Zhan Ying , Fergusson Austin , McNally Lacey R. , Davis Richey M. , Behkam Bahareh 
Published: December 2019

AbstractMicrobial-mediated drug delivery systems have the potential to significantly enhance the efficacy of nanomedicine for cancer therapy through improved specificity and interstitial transport. The Nanoscale Bacteria-Enabled Autonomous Drug Delivery System (NanoBEADS) is a bacteria-based bio-hybrid drug delivery system designed to carry nanotherapeutics cargo deep into poorly vascularized cancerous tissue. The effect of bacteria-nanoparticle conjugation method and NanoBEADS assembly parameters (i.e., mixing method, volume, and duration) was investigated to maximize particle attachment density. The nanoparticle attachment capacity, viability, growth rate and motility of the original NanoBEADS and an antibody-free variant NanoBEADS were characterized and compared. It is found that the assembly parameters affect the attachment outcome and the binding mechanism impacts the attachment number, the growth rate and motility of NanoBEADS. The NanoBEADS platform provides an opportunity to load nanoparticles with different materials and sizes for applications beyond cancer therapy, such as imaging agents for high-resolution medical imaging.
Controlling the speed and trajectory of evolution with counterdiabatic driving
Authors: Iram Shamreen , Dolson Emily , Chiel Joshua , Pelesko Julia , Krishnan Nikhil , Güngör Özenç , Kuznets-Speck Benjamin , Deffner Sebastian , Ilker Efe , Scott Jacob G. , Hinczewski Michael 
Published: December 2019

ABSTRACTThe pace and unpredictability of evolution are critically relevant in a variety of modern challenges: combating drug resistance in pathogens and cancer, understanding how species respond to environmental perturbations like climate change, and developing artificial selection approaches for agriculture. Great progress has been made in quantitative modeling of evolution using fitness landscapes, allowing a degree of prediction for future evolutionary histories. Yet fine-grained control of the speed and the distributions of these trajectories remains elusive. We propose an approach to achieve this using ideas originally developed in a completely different context – counterdiabatic driving to control the behavior of quantum states for applications like quantum computing and manipulating ultra-cold atoms. Implementing these ideas for the first time in a biological context, we show how a set of external control parameters (i.e. varying drug concentrations / types, temperature, nutrients) can guide the probability distribution of genotypes in a population along a specified path and time interval. This level of control, allowing empirical optimization of evolutionary speed and trajectories, has myriad potential applications, from enhancing adaptive therapies for diseases, to the development of thermotolerant crops in preparation for climate change, to accelerating bioengineering methods built on evolutionary models, like directed evolution of biomolecules.
A longitudinal study of perceived stress and cortisol responses in an undergraduate student population from India
Authors: Batabyal Anuradha , Bhattacharya Anindita , Thaker Maria , Mukherjee Shomen 
Published: December 2019

AbstractYoung adults entering into college experience immense shifts in both personal and professional environments and this may result in some of them experiencing a lot of stress and difficulty in coping with their new surroundings. Such potentially stressful events may trigger multiple psychological as well as physiological effects. The current study investigated multiple psychological parameters such as PSS14 (Perceived Stress Scale), K10 (distress scale) and positive mood measures, along with salivary cortisol levels, in a repeated measures longitudinal study of first year students (~ 19 years of age) enrolled at a residential college in India. Six salivary cortisol samples were collected over a one-year period from 20 students. On each sampling day, a questionnaire designed to evaluate (K10, PSS14 and Mood) psychological parameters was also administered.Overall, men showed a significantly lower level of salivary cortisol compared to women. Men also showed a decrease in perceived stress (PSS14) and distress (K10) with time. However, women reported similar perceived stress and distress levels all year round. Academic stress was reported by the students to be the most important stressor, whereas financial stress was reported the least number of times by all participants. Our results suggest that men seem to have a better capability to adjust to the new environment of a residential program with time. In contrast, women show an elevation in salivary cortisol at the end of the semester (the final assessment stage) in spite of a continuous assessment curricular design. This study not only provides an important glimpse into the sex differences in stress response in the first one year of joining an undergraduate program, but it also provides a valuable longitudinal dataset from the Indian undergraduate student cohort which is lacking in literature.
Polymorphisms in Human Cytomegalovirus gO Exert Epistatic Influences on Cell-Free and Cell-To-Cell Spread, and Antibody Neutralization on gH Epitopes
Authors: Day Le Zhang , Stegmann Cora , Schultz Eric P. , Lanchy Jean-Marc , Yu Qin , Ryckman Brent J. 
Published: December 2019

ABSTRACTThe human cytomegalovirus (HCMV) glycoproteins H and L (gH/gL) can be bound by either gO, or the UL128-131 proteins to form complexes that facilitate entry and spread and the complexes formed are important targets of neutralizing antibodies. Strains of HCMV vary considerably in the levels of gH/gL/gO and gH/gL/UL128-131 and this can impact infectivity and cell tropism. In this report, we investigated how natural interstrain variation in the amino acid sequence of gO influences the biology of HCMV. Heterologous gO recombinants were constructed in which 6 of the 8 alleles or genotypes (GT) of gO were analyzed in the backgrounds of strain TR and Merlin (ME). The levels of gH/gL complexes were not affected, but there were impacts on entry, spread and neutralization by anti-gH antibodies. AD169 (AD) gO (GT1a) drastically reduced cell-free infectivity of both strains on fibroblasts and epithelial cells. PHgO(GT2a) increased cell-free infectivity of TR in both cell types, but spread in fibroblasts was impaired. In contrast, spread of ME in both cell types was enhanced by Towne (TN) gO (GT4), despite similar cell-free infectivity. TR expressing TNgO(GT4) was resistant to neutralization by anti-gH antibodies AP86 and 14-4b, whereas ADgO(GT1a) conferred resistance to 14-4b, but enhanced neutralization by AP86. Conversely, ME expressing ADgO(GT1a) was more resistant to 14-4b. These results suggest; 1) mechanistically distinct roles for gH/gL/gO in cell-free and cell-to-cell spread, 2) gO isoforms can differentially shield the virus from neutralizing antibodies, and 3) effects of gO polymorphisms are epistatically dependent on other variable loci.IMPORTANCEAdvances in HCMV population genetics have greatly outpaced understanding of the links between genetic diversity and phenotypic variation. Moreover, recombination between genotypes may shuffle variable loci into various combinations with unknown outcomes. UL74(gO) is an important determinant of HCMV infectivity, and one of the most diverse loci in the viral genome. By analyzing interstrain heterologous UL74(gO) recombinants, we show that gO diversity can have dramatic impacts on cell-free and cell-to-cell spread as well as on antibody neutralization and that the manifestation of these impacts can be subject to epistatic influences of the global genetic background. These results highlight the potential limitations of laboratory studies of HCMV biology that use single, isolated genotypes or strains.
Antagonistic plants preferentially target arbuscular mycorrhizal fungi that are highly connected to mutualistic plants
Authors: Gomes Sofia IF , Fortuna Miguel A , Bascompte Jordi , Merckx Vincent SFT 
Published: December 2019

SummaryHow antagonists – mycoheterotrophic plants that obtain carbon and soil nutrients from fungi – are integrated in the usually mutualistic arbuscular mycorrhizal networks is unknown. Here, we compare mutualistic and antagonistic plant associations with arbuscular mycorrhizal fungi and use network analysis to investigate fungal association preferences in the tripartite network.We sequenced root tips from mutualistic and antagonistic plants in a tropical forest to assemble the combined tripartite network between mutualistic plants, mycorrhizal fungi, and antagonistic plants. We compared the fungal ecological similarity between mutualistic and antagonist networks, and searched for modules (an antagonistic and a mutualistic plant interacting with the same pair of fungi) to investigate whether pairs of fungi simultaneously linked to plant species from each interaction type were overrepresented throughout the network.Antagonistic plants interacted with approximately half the fungi detected in mutualistic plants. Antagonists were indirectly linked to any of the detected mutualistic plants, and fungal pairwise ecological distances were correlated in both network types. Moreover, pairs of fungi sharing the same antagonistic and mutualistic plant species occurred more often than expected by chance.We hypothesize that the maintenance of antagonistic interactions is maximized by targeting well-linked mutualistic fungi, thereby minimizing the risk of carbon supply shortages.
A new symbiotic lineage related toNeisseriaandSnodgrassellaarises from the dynamic and diverse microbiomes in sucking lice
Authors: Říhová Jana , Batani Giampiero , Rodríguez-Ruano Sonia M. , Martinů Jana , Nováková Eva , Hypša Václav 
Published: December 2019

AbstractPhylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have experienced a complex history of symbiont acquisition, loss, and replacement during their evolution. By combining metagenomics and amplicon screening across several populations of two louse genera (PolyplaxandHoplopleura) we describe a novel louse symbiont lineage related toNeisseriaandSnodgrassella, and show its’ independent origin within dynamic lice microbiomes. While the genomes of these symbionts are highly similar in both lice genera, their respective distributions and status within lice microbiomes indicate that they have different functions and history. InHoplopleura acanthopus, theNeisseria-related bacterium is a dominant obligate symbiont universally present across several host’s populations, and seems to be replacing a presumably older and more degenerated obligate symbiont. In contrast, thePolyplaxmicrobiomes are dominated by the obligate symbiontLegionella polyplacis, with theNeisseria-related bacterium co-occurring only in some samples and with much lower abundance.
The virus integrations in gut microbes associated with dysbiosis of microbial community in tumorigenesis of colorectal carcinoma
Authors: Cui Boyu , Wang Xiaodan , Xu Wenqiu , Zheng Caihong , Cai Jun 
Published: December 2019

AbstractPatients with colorectal cancer (CRC) have a different gut microbial and viral communities from healthy individuals. But little is known about the ways and functions of interaction of virus-bacteria, let alone its correlation with the aetiology of CRC. In this study we aimed to identify the association between the genetic integration of virusbacteria and the expansion of some microbial population during tumorigenesis of human colorectum. Using a gut metagenomics sequencing data of healthy controls, advanced adenoma and carcinoma patients, to our knowledge, we demonstrate for the first time that the viral genetic integrations in gut microbes tend to occur in CRC patients and are potentially associated with the carcinogenesis. We found that almost all of the genetic integrations were happened between bacteriophages and bacteria, which could be influenced by the abundance of the phage communities. Importantly, the integrations of phage-carried positive effective genes offered selective advantages to the commensal and potential pathogenic bacteria, as a result, potentially led to a microbial dysbiosis along with the increasing bacterial diversity in carcinoma patients. Consequently, our work opens a new way to understand the carcinogenicity in complex intestinal ecosystems.
Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Authors: Patrick Ralph , Humphreys David T. , Janbandhu Vaibhao , Oshlack Alicia , Ho Joshua W.K. , Harvey Richard P. , Lo Kitty K. 
Published: December 2019

AbstractHigh-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell-types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3’UTR shortening in cardiac fibroblasts. Sierra is available at https://github.com/VCCRI/Sierra.