bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic shifts of visual and saccadic signals in prefrontal cortical regions 8Ar and FEF
Authors: Khanna Sanjeev B. , Scott Jonathan A. , Smith Matthew A. 
Published: October 2019

AbstractActive vision is a fundamental process by which primates gather information about the external world. Multiple brain regions have been studied in the context of simple active vision tasks in which a visual target’s appearance is temporally separated from saccade execution. Most neurons have tight spatial registration between visual and saccadic signals, and in areas such as prefrontal cortex (PFC) some neurons show persistent delay activity that links visual and motor epochs and has been proposed as a basis for spatial working memory. Many PFC neurons also show rich dynamics, which have been attributed to alternative working memory codes and the representation of other task variables. Our study investigated the transition between processing a visual stimulus and generating an eye movement in populations of PFC neurons in macaque monkeys performing a memory guided saccade task. We found that neurons in two subregions of PFC, the frontal eye fields (FEF) and area 8Ar, differed in their dynamics and spatial response profiles. These dynamics could be attributed largely to shifts in the spatial profile of visual and motor responses in individual neurons. This led to visual and motor codes for particular spatial locations that were instantiated by different mixtures of neurons, which could be important in PFC’s flexible role in multiple sensory, cognitive, and motor tasks.New and NoteworthyA central question in neuroscience is how the brain transitions from sensory representations to motor outputs. The prefrontal cortex contains neurons that have long been implicated as important in this transition and in working memory. We found evidence for rich and diverse tuning in these neurons, that was often spatially misaligned between visual and saccadic responses. This feature may play an important role in flexible working memory capabilities.
High quality genome sequence reveals the 12 pseudo-chromosomes of Ganoderma boninense
Authors: Utomo Condro , Tanjung Zulfikar Achmad , Aditama Redi , Nurani Buana Rika Fithri , Madu Pratomo Antonius Dony , Tryono Reno , Liwang Tony 
Published: October 2019

AbstractGanoderma boninense is the dominant fungal pathogen in causing Basal Stem Rot (BSR) disease on oil palm. The whole genome of this fungus was sequenced using PacBio RS II platforms to gain the whole-genome shotgun libraries. These libraries were smoothed with Illumina Hiseq 4000 paired end sequencing to polish the genome assembly. Subsequently, a combination of Dovetail Chicago and HiC libraries with the HiRise assembly pipeline revealed the 12 pseudo-chromosomes of G. boninense. This is the first report of chromosomal-scale genome assembly for the most important fungal pathogen on oil palm.
Identification and characterization of zebrafish Tlr4 co-receptor Md-2
Authors: Loes Andrea N. , Hinman Melissa N. , Farnsworth Dylan R. , Miller Adam C. , Guillemin Karen , Harms Michael J. 
Published: October 2019

ABSTRACTThe zebrafish (Danio rerio) is a powerful model organism for studies of the innate immune system. One apparent difference between human and zebrafish innate immunity is the cellular machinery for LPS-sensing. In amniotes, the protein complex formed by Toll-like receptor 4 and myeloid differentiation factor 2 (Tlr4/Md-2) recognizes the bacterial molecule lipopolysaccharide (LPS) and triggers an inflammatory response. It is believed that zebrafish have neither Md-2 nor Tlr4: Md-2 has not been identified outside of amniotes, while the zebrafishtlr4genes appear to be paralogs, not orthologs, of amnioteTLR4s. We revisited these conclusions. We identified a zebrafish gene encoding Md-2,ly96. Using single-cell RNA-Seq, we found thatly96is transcribed in cells that also transcribe genes diagnostic for innate immune cells, including the zebrafishtlr4-like genes. Unlike amnioteLY96, zebrafishly96expression is restricted to a small number of macrophage-like cells. In a functional assay, zebrafish Md-2 and Tlr4a form a complex that activates NF-κB signaling in response to LPS, butly96loss-of-function mutations gave little protection against LPS-toxicity in larval zebrafish. Finally, by analyzing the genomic context oftlr4genes in eleven jawed vertebrates, we found thattlr4arose prior to the divergence of teleosts and tetrapods. Thus, an LPS-sensitive Tlr4/Md-2 complex is likely an ancestral feature shared by mammals and zebrafish, rather than ade novoinvention on the tetrapod lineage. We hypothesize that zebrafish retain an ancestral, low-sensitivity Tlr4/Md-2 complex that confers LPS-responsiveness to a specific subset of innate immune cells.
Learning to learn persistently modifies an entorhinal-hippocampal excitatory-inhibitory subcircuit
Authors: Chung Ain , Jou Claudia , Grau-Perales Alejandro , Levy Eliott , Dvorak Dino , Hussain Nida , Fenton André A. 
Published: October 2019

SUMMARYCognitive control, the judicious use of relevant information while ignoring distractions, is a feature of everyday cognitive experience, but its neurobiology is understudied. We investigated whether cognitive control training (CCT) changes hippocampal neural circuit function in mice, beyond the changes caused by place learning and memory formation. Mice learned and remembered a conditioned place avoidance during CCT that required ignoring irrelevant locations of shock. They were compared to controls that learned the same place avoidance under lower cognitive control demands. Weeks after CCT, mice learn new tasks in novel environments faster than controls; they learned to learn. We investigated entorhinal cortex-to-dentate gyrus neural circuit changes and report that CCT rapidly changes synaptic circuit function, resulting in an excitatory-inhibitory subcircuit change that persists for months. CCT increases inhibition that attenuates the dentate response to medial entorhinal cortical input, and through disinhibition, potentiates the response to strong inputs, pointing to overall signal-to-noise enhancement. These neurobiological findings support a neuroplasticity hypothesis that, beyond storing item/event associations, CCT persistently optimizes neural circuit information processing.
The novel shapeshifting bacterial phylumSaltatorellota
Authors: Wiegand Sandra , Jogler Mareike , Kohn Timo , Awal Ram Prasad , Oberbeckmann Sonja , Kesy Katharina , Jeske Olga , Schumann Peter , Peeters Stijn H. , Kallscheuer Nicolai , Strauss Mike , Heuer Anja , Jetten Mike S. M. , Labrenz Matthias , Rohde Manfred , Boedeker Christian , Engelhardt Harald , Schüler Dirk , Jogler Christian 
Published: October 2019

AbstractOur current understanding of a free-living bacterium - capable of withstanding a variety of environmental stresses-is represented by the image of a peptidoglycan-armored rigid casket. The making and breaking of peptidoglycan greatly determines cell shape. The cytoplasmic membrane follows this shape, pressed towards the cell wall by turgor pressure. Consequently, bacteria are morphologically static organisms, in contrast to eukaryotic cells that can facilitate shape changes. Here we report the discovery of the novel bacterial phylumSaltatorellota, that challenges this concept of a bacterial cell. Members of this phylum can change their shape, are capable of amoeba-like locomotion and trunk-formation through the creation of extensive pseudopodia-like structures. Two independentSaltatorellotacells can fuse, and they employ various forms of cell division from budding to canonical binary fission. Despite their polymorphisms, members of theSaltatorellotado possess a peptidoglycan cell wall. Their genomes encode flagella and type IV pili as well as a bacterial actin homolog, the ‘saltatorellin’. This protein is most similar to MamK, a dynamic filament-forming protein, that aligns and segregates magnetosome organelles via treadmilling. We found saltatorellin to form filaments in both,E. coliandMagnetospirillum gryphiswaldense, leading to the hypothesis that shapeshifting and pseudopodia formation might be driven by treadmilling of saltatorellin.
Active sensing in groups: (what) do bats hear in the sonar cocktail party nightmare?
Authors: Beleyur Thejasvi , Goerlitz Holger R. 
Published: October 2019

ABSTRACTActive sensing animals perceive their surroundings by emitting probes of energy and analyzing how the environment modulates these probes. However, the probes of conspecifics can jam active sensing, which should cause problems for groups of active sensing animals. This problem was termed the cocktail party nightmare for echolocating bats: as bats listen for the faint returning echoes of their loud calls, these echoes will be masked by the loud calls of other close-by bats. Despite this problem, many bats echolocate in groups and roost socially. Here, we present a biologically parametrized framework to quantify echo detection in groups. Incorporating known properties of echolocation, psychoacoustics, spatial acoustics and group flight, we quantify how well bats flying in groups can detect each other despite jamming. A focal bat in the center of a group can detect neighbors for group sizes of up to 100 bats. With increasing group size, fewer and only the closest and frontal neighbors are detected. Neighbor detection is improved for longer call intervals, shorter call durations, denser groups and more variable flight and sonar beam directions. Our results provide the first quantification of the sensory input of echolocating bats in collective group flight, such as mating swarms or emergences. Our results further generate predictions on the sensory strategies bats may use to reduce jamming in the cocktail party nightmare. Lastly, we suggest that the spatially limited sensory field of echolocators leads to limited interactions within a group, so that collective behavior is achieved by following only nearest neighbors.SIGNIFICANCE STATEMENTClose-by active sensing animals may interfere with each other. We investigated if and what many echolocators fly in a group hear – can they detect each other after all? We modelled acoustic and physical properties in group echolocation to quantify neighbor detection probability as group size increases. Echolocating bats can detect at least one of their closest neighbors per call up to group sizes of even 100 bats. Call parameters such as call rate and call duration play a strong role in how much echolocators in a group interfere with each other. Even when many bats fly together, they are indeed able to detect at least their nearest frontal neighbors – and this prevents them from colliding into one another.
“And if you gaze long into an abyss, the abyss gazes also into thee”: four morphs of Arctic charr adapting to a depth-gradient in Lake Tinnsjøen
Authors: Østbye Kjartan , Hassve Marius Hagen , Peris Ana-Maria Tamayo , Hagenlund Mari , Vogler Thomas , Præbel Kim 
Published: October 2019

AbstractBackgroundThe origin of species is a central topic in biology aiming at understanding mechanisms, level and rate of diversification. Ecological speciation is an important driver in adaptive radiation during post-glacial intra-lacustrine niche diversification in fishes. The Arctic charrSalvelinus alpinusL. species complex in the Northern hemisphere freshwater systems display huge morphological and life history divergence in lakes with one or several morphs present, thus offering a unique opportunity to address ongoing speciation mechanisms.We studied Arctic charr in Lake Tinnsjøen by fishing in four nominal lake habitats (pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats) down to 350 meters depth. Research topics addressed were; (1) to illuminate Holarctic phylogeography and lineages colonizing Lake Tinnsjøen, (2) to estimate reproductive isolation of morphs or fish using unbiased methods, and (3) to document eco-morphological and life history trait divergence. Also, we compared Lake Tinnsjøen with four Norwegian outgroup populations of Arctic charr.ResultsFour field-assigned morphs were identified in Lake Tinnsjøen; the planktivore morph in all habitats except deep-profundal, the dwarf morph in shallow-moderate profundal, the piscivore morph in shallow-moderate profundal (less in littoral and deep-profundal), and an undescribed new morph – the abyssal morph in the deep-profundal only. The morphs displayed extensive life history variation based on age and size patterns. A moderate to high concordance was observed between field-assigned morphs and four unbiased genetic clusters obtained from microsatellite variation. MtDNA suggested the occurrence of two minor endemic clades in Lake Tinnsjøen likely originating from one widespread colonizing clade in the Holarctic. All morphs were genetically differentiated at microsatellites (FST: 0.12-0.20; with some ongoing gene flow among morphs, and for most mtDNA comparisons (FST: 0.04-0.38). Analyses of Norwegian outgroup lakes implied colonization from a river system below Lake Tinnsjøen.ConclusionOur findings suggest post-glacial adaptive radiation of one colonizing mtDNA lineage with divergent niche specialization along a depth-temperature-productivity-pressure gradient. Concordance between reproductive isolation and the realized habitat of the morphs imply that ecological speciation may be the mechanism of divergence. Particularly novel is the extensive morph diversification with depth into the often unexplored deep-water profundal habitat, suggesting we may have systematically underestimated biodiversity present in lakes.
m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB
Authors: Chu Chia-Chieh , Liu Bei , Plangger Raphael , Kreutz Christoph , Al-Hashimi Hashim M. 
Published: October 2019

AbstractN6-methyladenosine (m6A) is a ubiquitous RNA post-transcriptional modification found in coding as well as non-coding RNAs. m6A has also been found in viral RNAs where it is proposed to modulate host-pathogen interactions. Two m6A sites have been reported in the HIV-1 Rev response element (RRE) stem IIB, one of which was shown to enhance binding to the viral protein Rev and viral RNA export. However, because these m6A sites have not been observed in other studies mapping m6A in HIV-1 RNA, their significance remains to be firmly established. Here, using optical melting experiments, NMR spectroscopy, andin vitrobinding assays, we show that m6A minimally impacts the stability, structure, and dynamics of RRE stem IIB as well as its binding affinity to the Rev arginine-rich-motif (ARM). Our results indicate that if present in stem IIB, m6A is unlikely to modulate RRE-Rev interaction by altering the conformational properties of the RNA. Our results add to a growing view that the impact of m6A on RNA depends on sequence context and Mg2+.
Antagonistic activity ofBacillus amyloliquefacienssubsp.amyloliquefaciensagainst multidrug resistantSerratia rubidaea
Authors: Afrin Sadia , Islam Bhuiyan Mohammad Nazrul 
Published: October 2019

AbstractSerratia rubidaeaa member of the Enterobacteriaceae family, is a Gram-negative opportunistic pathogen, known to survive harsh environmental conditions and responsible for hospital associated infections. Specifically,S. rubidaeacan withstand desiccation and survive on hospital surfaces and equipments as well as have acquired antimicrobial resistance determinants for different commercial antibiotics. The expansion of this multidrug resistant pattern suggests that the treatment ofS. rubidaeainfections will become increasingly difficult in near future. Although some measures were taken to control this species, an inhibition mechanism is remaining unknown. To design effective means to control the dissemination ofS. rubidaea, an in-depth analysis is required. In the present study, one possible candidate was isolated from the soil of Sundarban Mangroove Forest (Bangladesh) that has important physiological effects to inhibit this pathogenic bacterium. The bacterial isolate was initially identified asBacillus amyloliquefacienssubsp.amyloliquefaciensusing BIOLOG™ identification system and confirmed to beB. amyloliquefaciensstrain through 16SrDNA sequence analysis. The growth and antagonistic activity of this potential strain was shown to be stable under wide range of pH, temperature and salinity (NaCl). Moreover, the novelB. amyloliquefaciensisolate can also inhibitStaphylococcus aureus, Escherichia coli, Pseudomonas aeruginosaand other pathogenic bacteria. These results suggest thatB. amyloliquefaciensmight have potential antimicrobial properties and further research is required for future use of this bacterium as biological controls ofS. rubidaeaor development as new drugs for pathogenic bacteria.
p53 induces senescence in the unstable progeny of aneuploid cells
Authors: Giam Maybelline , Wong Cheng Kit , Low Jun Siong , Sinelli Matteo , Dreesen Oliver , Rancati Giulia 
Published: October 2019

AbstractAneuploidy is the condition of having an imbalanced karyotype, which is strongly associated with tumor initiation, evolution, and acquisition of drug-resistant features, possibly by generating heterogeneous populations of cells with distinct genotypes and phenotypes. Multicellular eukaryotes have therefore evolved a range of extrinsic and cell-autonomous mechanisms for restraining proliferation of aneuploid cells, including activation of the tumor suppressor protein p53. However, accumulating evidence indicates that a subset of aneuploid cells can escape p53-mediated growth restriction and continue proliferating in vitro. Here we show that such aneuploid cell lines display a robust modal karyotype and low frequency of chromosomal aberrations despite ongoing chromosome instability. Indeed, while these aneuploid cells are able to survive for extended periods in vitro, their chromosomally unstable progeny remain subject to p53-induced senescence and growth restriction, leading to subsequent elimination from the aneuploid pool. This mechanism helps maintain low levels of heterogeneity in aneuploid populations and may prevent detrimental evolutionary processes such as cancer progression and development of drug resistance.
Circumvention of common labeling artifacts using secondary nanobodies
Authors: Sograte-Idrissi Shama , Schlichthaerle Thomas , Duque-Afonso Carlos J. , Alevra Mihai , Strauss Sebastian , Moser Tobias , Jungmann Ralf , Rizzoli Silvio , Opazo Felipe 
Published: October 2019

AbstractThe most common procedure to reveal the location of specific (sub)cellular elements in biological samples is via immunostaining followed by optical imaging. This is typically performed with target-specific primary antibodies (1.Abs), which are revealed by fluorophore-conjugated secondary antibodies (2.Abs). However, at high resolution this methodology can induce a series of artifacts due to the large size of antibodies, their bivalency, and their polyclonality. Here we use STED and DNA-PAINT super-resolution microscopy or light sheet microscopy on cleared tissue to show how monovalent secondary reagents based on camelid single-domain antibodies (nanobodies; 2.Nbs) attenuate these artifacts. We demonstrate that monovalent 2.Nbs have four additional advantages: 1) they increase localization accuracy with respect to 2.Abs; 2) they allow direct pre-mixing with 1.Abs before staining, reducing experimental time, and enabling the use of multiple 1.Abs from the same species; 3) they penetrate thick tissues efficiently; and 4) they avoid the artificial clustering seen with 2.Abs both in live and in poorly fixed samples. Altogether, this suggests that 2.Nbs are a valuable alternative to 2.Abs, especially when super-resolution imaging or staining of thick tissue samples are involved.
How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels
Authors: Simon Alexis , Fraïsse Christelle , Ayari Tahani El , Liautard-Haag Cathy , Strelkov Petr , Welch John J. , Bierne Nicolas 
Published: October 2019

AbstractTheMytiluscomplex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study “replicated” instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bistable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.