bluuebunny/crossref_metadata_2025_split huggingface dataset:
An assessment of adult mosquito collection techniques for studying species abundance and diversity in Maferinyah, Guinea
Authors: Cansado-Utrilla Cintia , Jeffries Claire L. , Kristan Mojca , Brugman Victor A. , Heard Patrick , Camara Gnepou , Sylla Moussa , Beavogui Abdoul H. , Messenger Louisa A. , Walker Thomas 
Published: September 2019

ABSTRACTBackgroundGuinea is a West African country with a high prevalence of vector-borne diseases where few entomological studies have been undertaken. Although several mosquito collection methods are routinely used for surveillance in vector control programmes, they target different behaviours causing bias in species diversity and abundance. Given the paucity of mosquito trap data in West Africa, we compared the performance of five trap-lure combinations and Human Landing Catches (HLCs) in Guinea.MethodsFive mosquito traps were compared in a 5×5 Latin Square design for 15 days in three villages in Guinea between June and July 2018. CDC light traps, BG sentinel 2 traps (with BG and MB5 lures), gravid traps and Stealth traps were deployed for 24-hour intervals with mosquitoes collected every 12 hours (day and night collections). HLCs were also performed for 15 nights. A Generalised Linear Mixed Model was applied to compare the effect of the traps, sites and collection times on the mosquito abundance. Species identification was confirmed using PCR-based analysis and Sanger sequencing.ResultsIn total, 10,610 mosquitoes were captured across all five traps. Significantly more mosquitoes (P<0.005) were collected by Stealth traps (7,096) compared to the rest of the traps. Stealth traps and BG sentinel 2 traps were the best at capturingAn. gambiaeandAe. aegyptimosquitoes respectively. HLCs captured predominantlyAn. coluzzii(41%) and hybrids ofAn. gambiae s.s. /An. coluzzii(36%) in contrast to the five adult traps, which captured predominantlyAn. melas(83%). Senguelen (rural) presented the highest abundance of mosquitoes and overall diversity in comparison with Fandie (semi-rural) and Maferinyah Centre One (semi-urban). To our knowledge, four species are reported for the first time in Guinea.ConclusionsStealth traps presented the best performance overall, suggesting that this trap may play an important role for mosquito surveillance in Guinea and similar sites in West Africa. We recommend the incorporation of molecular tools in entomological studies since it has helped to reveal, together with morphological identification, the presence of 25 mosquito species in this area.
Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation
Authors: Lee Chol Gyu , Kunitomo Eriko , Iida Toshiya , Nakaho Kazuhiro , Ohkuma Moriya 
Published: September 2019

AbstractAnaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. To this end, we investigated changes in the microbial community and pathogen density during a period of ASD under field conditions for 14 days in a greenhouse using three different substrates. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions, prokaryotic community analysis was conducted using unidirectional pyrosequencing, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14, but the rate of decrease differed among the substrates. The microbial communities became altered after 3 days and recovered to their original state on day 14. The dipyridyl reaction, microbial diversity, richness, and community structure were not correlated with pathogen density. The most negatively correlated operational taxonomic units with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. These results suggested that the growth of specific microbes, but not the changes in microbial community structure, might be important for ASD disinfestation efficiency.
Gene Knock Up via 3’UTR editing to study gene functionin vivo
Authors: Mätlik Kärt , Olfat Soophie , Garton Daniel R. , Montaño-Rodriguez Ana , Turconi Giorgio , Porokuokka L. Lauriina , Panhelainen Anne , Schweizer Nadine , Kopra Jaakko , Cowlishaw Mark C. , Piepponen T. Petteri , Zhang Fu-Ping , Sipilä Petra , Jakobsson Johan , Andressoo Jaan-Olle 
Published: September 2019

AbstractCurrently available genetic tools do not allow researchers to upregulate (‘Knock Up’) the levels of a given protein while retaining its cell-type-specific regulation. As a result, we have limited ability to develop overexpression-related disease models, to study the contribution of single genes in diseases caused by copy number variations and to identify disease pathways for drug targets. Here we develop two approaches for endogenous gene upregulation:conditionalKnockUp (cKU) utilizing the Cre/lox system, and CRISPR-Cas9 mediated geneKnockUp (KU) in wild-type mouse embryos and human cells. Using glial cell line derived neurotrophic factor (GDNF) as a proof of concept, we show that both approaches resulted in upregulation of endogenous GDNF levels without disturbingGdnf’s expression pattern. Furthermore, CNS-specific GDNF cKU resulted in dopaminergic abnormalities and schizophrenia-like phenotypes. Our results suggest that gene Knock Up can reveal unknown gene functions and provide novel entry points for studying neurological disease.
Resting-State Functional Networks of Different Topographic Representations in the Somatosensory Cortex of Macaque Monkeys and Humans
Authors: Thomas John , Sharma Dixit , Mohanta Sounak , Jain Neeraj 
Published: September 2019

AbstractInformation processing in the brain is mediated through a complex functional network architecture whose comprising nodes integrate and segregate themselves on different timescales. To gain an understanding of the network function it is imperative to identify and understand the network structure with respect to the underlying anatomical connectivity and the topographic organization. Here we show that the previously described resting-state network for the somatosensory area 3b comprises of distinct networks that are characteristic for different topographic representations. Seed-based resting-state functional connectivity analysis in macaque monkeys and humans using BOLD-fMRI signals from the face, the hand and rest of the medial somatosensory representations of area 3b revealed different correlation patterns. Both monkeys and humans have many similarities in the connectivity networks, although the networks are more complex in humans with many more nodes. In both the species face area network has the highest ipsilateral and contralateral connectivity, which included areas 3b and 4, and ventral premotor area. The area 3b hand network included ipsilateral hand representation in area 4.The emergent functional network structures largely reflect the known anatomical connectivity. Our results show that different body part representations in area 3b have independent functional networks perhaps reflecting differences in the behavioral use of different body parts. The results also show that large cortical areas if considered together, do not give a complete and accurate picture of the network architecture.HighlightsSomatosensory resting-state functional network is not uniform across the entire area 3b. Different body part representations have different connectivity networks.These functional connectivity networks have many similarities in the two primate species, i.e. macaque monkeys and humans, although the human network is more complex.In both the species network of the face representation is most extensive, which includes ipsilateral face motor cortex and PMv in both hemispheres.The hand representation in area 3b has connectivity with ipsilateral hand motor cortex.Bilateral connectivity with homologous and nonhomologous area 3b representations was observed only in humans.The functional connectivity networks largely reflect the underlying anatomical connectivity.
The Activome: multiplexed probing of activity of proteolytic enzymes using mass cytometry-compatible activity-based probes (TOF-probes)
Authors: Poreba Marcin , Groborz Katarzyna , Rut Wioletta , Pore Milind , Snipas Scott J. , Vizovisek Matej , Turk Boris , Kuhn Peter , Drag Marcin , Salvesen Guy S. 
Published: September 2019

AbstractThe activome can be considered as a subset of the proteome that contains enzymes in their catalytically active form and can be interrogated by using probes targeted towards individual specific enzymes. A subset of such enzymes are proteases that are frequently studied with activity-based probes, small inhibitors equipped with a detectable tag, commonly a fluorophore. Due to the spectral overlap of these commonly used fluorophores, simultaneous analysis becomes limited. To overcome this, we developed a series of protease-selective lanthanide-labeled probes compatible with mass cytometry. Using lanthanide-based tags instead of fluorophores gives us the ability to monitor the activity of multiple proteases in parallel. As proof of concept we developed a panel of cathepsin and legumain specific probes and showed that we were able to identify an activome of these proteases in two cell lines and peripheral blood mononuclear cells, providing a framework for the use of mass cytometry for multiplexed enzyme activity detection.
Coconut inflorescence sap mediated synthesis of silver nanoparticles and its diverse antimicrobial properties
Authors: Rajesh M.K. , Muralikrishna K.S. , Nair Swapna S. , Kumar B. Krishna , Subrahmanya T.M. , Sonu K.P. , Subaharan K. , Sweta H. , Prasad T.S. Keshava , Chandran Neeli , Hebbar K.B. , Karun Anitha 
Published: September 2019

ABSTRACTGreen synthesis of nanoparticles (NPs) involves the use of diverse extracts of biological origin as substrates to synthesize nanoparticles and can overcome the hazards associated with chemical methods. Coconut inflorescence sap, which is unfermented phloem sap obtained by tapping of coconut inflorescence, is a rich source of sugars and secondary metabolites. In this study, coconut inflorescence sap was used to synthesize silver nanoparticles (AgNPs). We have initially undertaken metabolomic profiling of coconut inflorescence sap from West Coast Tall cultivar to delineate its individual components. Secondary metabolites constituted the major portion of the inflorescence sap along with sugars, lipids and, peptides. The concentration of silver nitrate, inflorescence sap and incubation temperature for synthesis of AgNPs were optimized. Incubating the reaction mixture at 40°C was found to enhance AgNP synthesis. The AgNPs synthesized were characterized using UV-Visible spectrophotometry, X-Ray Diffraction (XRD), Fourier Transform Infrared spectroscopy (FTIR), Field Emission Scanning Electron Microscopy (FESEM) and Transmission Electron Microscopy (TEM). Antimicrobial property of AgNP was tested in tissue culture of arecanut (Areca catechu L.) where bacterial contamination (Bacillus pumilus) was a frequent occurrence. Significant reduction in the contamination was observed when plantlets were treated with aqueous solutions of 0.01, 0.02 and 0.03% of AgNPs for one hour. Notably, treatment with AgNPs did not affect growth and development of the arecanut plantlets. Cytotoxicity of AgNPs was quantified in HeLa cells. Viability (%) of HeLa cells declined significantly at 10 ppm concentration of AgNP and complete mortality was observed at 60 ppm. Antimicrobial properties of AgNPs synthesized from inflorescence sap were also evaluated and confirmed in human pathogenic bacteria viz., Salmonella sp., Vibrio parahaemolyticus, and Escherichia coli. The study concludes that unfermented inflorescence sap, with above neutral pH, serves as an excellent reducing agent to synthesize AgNPs from Ag+.
Graphical abstract
Epigenetic rejuvenation of the hippocampus by environmental enrichment
Authors: Zocher Sara , Overall Rupert W. , Lesche Mathias , Dahl Andreas , Kempermann Gerd 
Published: September 2019

AbstractThe decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that environmental enrichment counteracted age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is known to control neuronal functions. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the rejuvenating effects of environmental enrichment at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.
Amphipathic helices of cellular proteins can replace the helix in M2 of Influenza A virus with only small effects on virus replication
Authors: Hu Bodan , Siche Stefanie , Möller Lars , Veit Michael 
Published: September 2019

AbstractM2 of influenza virus functions as proton channel during virus entry. In addition, an amphipathic helix in its cytoplasmic tail plays a role during budding. It targets M2 to the assembly site where it inserts into the inner membrane leaflet to induce curvature that causes virus scission. Since vesicularisation of membranes can be performed by a variety of amphiphilic peptides we used reverse genetics to investigate whether they can substitute for M2’s helix.Virus could not be generated if M2’s helix was deleted or replaced by a peptide predicted not to form an amphiphilic helix. In contrast, viruses could be rescued if the M2 helix was exchanged by helices known to induce membrane curvature. Infectious virus titers were marginally reduced if M2 contains the helix of the amphipathic lipid packing sensor, from the Epsin N-Terminal Homology domain or the non-natural membrane inducer RW16. Transmission EM of infected cells did not reveal unequivocal evidence that virus budding or membrane scission was disturbed in any of the mutants. Instead, individual virus mutants exhibit other defects in M2, such as reduced surface expression, incorporation into virus particles and ion channel activity. The protein composition and specific infectivity was also altered for mutant virions. We conclude that the presence of an amphiphilic helix in M2 is essential for virus replication, but other helices can replace its basic (curvature-inducing) function.ImportanceInfluenza is unique among enveloped viruses since it does not rely on the cellular ESCRT-machinery for budding. Instead viruses encode their own scission machine, the M2 protein. M2 is targeted to the edge of the viral assembly site where it inserts an amphiphilic helix into the membrane to induce curvature. Cellular proteins utilize a similar mechanism for scission of vesicles. We show that the helix of M2 can be replaced by helices from cellular proteins with only small effects on virus replication. No evidence was obtained that budding is disturbed, but individual mutants exhibit other defects in M2 which explain the reduced virus titers. In contrast, no virus could be generated if the helix of M2 is deleted or replaced by irrelevant sequences. These experiments support the concept that M2 requires an amphiphilic helix to induce membrane curvature, but its biophysical properties are more important than the amino acid sequence.
Mating-type specific ribosomal proteins control aspects of sexual reproduction inCryptococcus neoformans
Authors: Ianiri Giuseppe , Fang Yufeng “Francis” , Dahlmann Tim A. , Applen Clancey Shelly , Janbon Guilhem , Kück Ulrich , Heitman Joseph 
Published: September 2019

AbstractTheMATlocus ofCryptococcus neoformanshas a bipolar organization characterized by an unusually large structure, spanning over 100 kb.MATgenes have been characterized by functional genetics as being involved in sexual reproduction and virulence. However, classical gene replacement failed to achieve mutants for fiveMATgenes (RPL22, RPO41, MYO2, PRT1, RPL39), indicating that they are likely essential. In the present study, targeted gene replacement was performed in a diploid strain for both the α andaalleles of the ribosomal genesRPL22andRPL39. Mendelian analysis of the progeny confirmed that bothRPL22andRPL39are essential for viability. Ectopic integration of theRPL22allele of oppositeMATidentity in the heterozygousRPL22a/rpl22αΔ orRPL22α/rpl22aΔ mutant strains failed to complement their essential phenotype. Evidence suggests that this is due to differential expression of theRPL22genes, and an RNAi-dependent mechanism that contributes to controlRPL22aexpression. Furthermore, via CRISPR/Cas9 technology theRPL22alleles were exchanged in haploidMATα andMATastrains ofC. neoformans. TheseRPL22exchange strains displayed morphological and genetic defects during bilateral mating. These results contribute to elucidate functions ofC. neoformansessential mating type genes that may constitute a type of imprinting system to promote inheritance of nuclei of both mating types.
Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils
Authors: Simonin Marie , Dasilva Cindy , Terzi Valeria , Ngonkeu Eddy L. M. , Diouf Diégane , Kane Aboubacry , Béna Gilles , Moulin Lionel 
Published: September 2019

AbstractHere, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our dataset. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.Graphical Abstract
LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately
Authors: Getman-Pickering Zoe L. , Campbell Adam T. , Aflitto Nicholas , Ugine Todd A. , Grele Ari , Davis Julie 
Published: September 2019

AbstractIn both basic and applied studies, quantification of herbivory on foliage is a key metric in characterizing plant-herbivore interactions, which underpin many ecological, evolutionary, and agricultural processes. Current methods of quantifying herbivory are slow or inaccurate. We present LeafByte, a free iOS application for measuring leaf area and herbivory. LeafByte can save data automatically, read and record barcodes, handle both light and dark colored plant tissue, and be used non-destructively.We evaluate its accuracy and efficiency relative to existing herbivory assessment tools.LeafByte has the same accuracy as ImageJ, the field standard, but is 50% faster. Other tools, such as BioLeaf and grid quantification, are quick and accurate, but limited in the information they can provide. Visual estimation is quickest, but it only provides a coarse measure of leaf damage and tends to overestimate herbivory.LeafByte is a quick and accurate means of measuring leaf area and herbivory, making it a useful tool for research in fields such as ecology, entomology, agronomy, and plant science.
Chromatin information content landscapes inform transcription factor and DNA interactions
Authors: Albanus Ricardo D’Oliveira , Kyono Yasuhiro , Hensley John , Varshney Arushi , Orchard Peter , Kitzman Jacob O. , Parker Stephen C. J. 
Published: September 2019

AbstractInteractions between transcription factors (TFs) and chromatin are fundamental to genome organization and regulation and, ultimately, cell state. Here, we use information theory to measure signatures of TF-chromatin interactions encoded in the patterns of the accessible genome, which we call chromatin information enrichment (CIE). We calculate CIE for hundreds of TF motifs across human tissues and identify two classes: low and high CIE. The 10-20% of TF motifs with high CIE associate with higher protein-DNA residence time, including different binding sites subclasses of the same TF, increased nucleosome phasing, specific protein domains, and the genetic control of both gene expression and chromatin accessibility. These results show that variations in the information content of chromatin architecture reflect functional biological variation, with implications for cell state dynamics and memory.
The presence of copy number variants in specific topologically associating domains has prognostic value in many cancer types
Authors: Li Lifei , Barth Nicolai K. H. , Pilarsky Christian , Taher Leila 
Published: September 2019

AbstractThe human genome is organized into topologically associating domains (TADs), which represent contiguous regions with a higher frequency of intra-interactions as opposed to inter-interactions. TADs contribute to gene expression regulation by restricting interactions between regulatory elements, and their disruption by genomic rearrangements can result in altered gene expression and, ultimately, in cancer. Here, we provide a proof-of-principle that mutations within TADs can be used to predict the survival of cancer patients. For this purpose, we first constructed a set of 1,467 TADs representing the three-dimensional organization of genome across 24 normal human tissues. We then used Cox regression analysis to assess the prognostic value of the TADs in different cancer types, and identified a total of 35 TADs that were prognostic for at least one of nine cancer types. Interestingly, only 46% of the prognostic TADs comprised one or more genes with a known causal association with cancer. Moreover, for those TADs encompassing such a gene, the prognostic effect of the TAD was only directed related to the presence/absence of mutations in the gene in 13% of the cases. These observations indicate that the predictive power of a large proportion of the prognostic TADs is independent of whether pan-cancer genes are mutated or not. Furthermore, 34% of the 35 prognostic TADs showed strong structural perturbations in the cancer genome, which might mediate cancer development and progression. This study has important implications for the interpretation of cancer-related non-coding mutations and offer insights to new strategies for personalizing cancer medicine.