bluuebunny/crossref_metadata_2025 huggingface dataset:
Shortened TDP43 isoforms upregulated by neuronal hyperactivity drive TDP43 pathology in ALS
Authors: Weskamp Kaitlin , Tank Elizabeth M. , Miguez Roberto , McBride Jonathon P. , Gómez Nicolás B. , White Matthew , Lin Ziqiang , Gonzalez Carmen Moreno , Serio Andrea , Sreedharan Jemeen , Barmada Sami J.
Published: May 2019

Cortical hyperexcitability and mislocalization of the RNA-binding protein TDP43 are highly-conserved features in amyotrophic lateral sclerosis (ALS). Nevertheless, the relationship between these phenomena remains poorly defined. Here, we showed that hyperexcitability recapitulates TDP43 pathology by upregulating shortened (s) TDP43 splice isoforms. These truncated isoforms accumulated in the cytoplasm and formed insoluble inclusions that sequestered full-length TDP43 via preserved N-terminal interactions. Consistent with these findings, sTDP43 overexpression was toxic to mammalian neurons, suggesting neurodegeneration arising from complementary gain- and loss-of-function mechanisms. In humans and mice, sTDP43 transcripts were enriched in vulnerable motor neurons, and we observed a striking accumulation of sTDP43 within neurons and glia of ALS patients. Collectively, these studies uncover a pathogenic role for alternative TDP43 isoforms in ALS, and implicate sTDP43 as a key contributor to the susceptibility of motor neurons in this disorder.
DNA damage response in peripheral mouse blood leukocytesin vivoafter variable, low-dose rate exposure
Authors: Wang Qi , Pujol Monica C. , Garty Guy , Taveras Maria , Perrier Jay , Bueno-Beti Carlos , Shuryak Igor , Brenner David J. , Turner Helen C.
Published: May 2019

Environmental contamination and ingestion of the radionuclide Cesium-137 (137Cs) is a large concern in fallout from a nuclear reactor accident and improvised nuclear device and highlights the need to develop biological assays for low dose rate, internal emitter radiation. To mimic low dose rates attributable to fallout, we have developed a VAriable Dose-rate External137Cs irradiatoR (VADER), which can provide arbitrarily varying and progressive low dose rate irradiations in the range of 1.2 to 0.1 Gy/day, while circumventing the complexities of dealing with radioactively-contaminated biomaterials. We investigated the kinetics of mouse peripheral leukocytes DNA damage response in vivo after variable, low-dose rate137Cs exposure. C57BL/6 mice were placed in the VADER over 7 days with total accumulated dose up to 2.7 Gy. Peripheral blood response including the leukocytes depletion, apoptosis signal protein p53 and DNA repair biomarker γ-H2AX were measured. The results illustrated that blood leukocyte count had significantly dropped by days 7. P53 levels peaked at day 2 (total dose=0.91Gy) and then declined whereas γ-H2AX yields generally increased with accumulated dose and peaked at day 5 (total dose=2.08Gy). ROC curve analysis for γ-H2AX provided a good discrimination of accumulated dose < 2 Gy and ≥ 2 Gy, highlighting the potential of γ-H2AX as a biomarker dosimetry in a protracted, environmental exposure scenario.
Balancing selection via life-history trade-offs maintains an inversion polymorphism in a seaweed fly
Authors: Mérot Claire , Llaurens Violaine , Normandeau Eric , Bernatchez Louis , Wellenreuther Maren
Published: May 2019

How genetic diversity is maintained in natural populations is an evolutionary puzzle. Over time, genetic variation within species can be eroded by drift and directional selection, leading to the fixation or elimination of alleles. However, some loci show persistent variants at intermediate frequencies for long evolutionary time-scales, implicating a role of balancing selection, but studies are seldom set up to uncover the underlying processes. Here, we identify and quantify the selective pressures involved in the widespread maintenance of an inversion polymorphism in the seaweed fly Coelopa frigida, using an experimental evolution approach to estimate fitness associated with different allelic combinations. By precisely evaluating reproductive success and survival rates separately, we show that the maintenance of the polymorphism is governed by a life-history trade-off, whereby each inverted haplotype has opposed pleiotropic effects on survival and reproduction. Using numerical simulations, we confirm that this uncovered antagonism between natural and sexual selection can maintain inversion variation in natural populations of C. frigida. Moreover, our experimental data highlights that inversion-associated fitness is affected differently by sex, dominance and environmental heterogeneity. The interaction between these factors promotes polymorphism maintenance through antagonistic pleiotropy. Taken together, our findings indicate that combinations of natural and sexual selective mechanisms enable the persistence of diverse trait in nature. The joint dynamics of life history trade-offs and antagonistic pleiotropy documented here is likely to apply to other species where large phenotypic variation is controlled by structural variants.

Significance statement

Persistence of chromosomal rearrangements is widespread in nature and often associated with divergent life-history traits. Understanding how contrasted life-history strategies are maintained in wild populations has implications for food production, health and biodiversity in a changing environment. Using the seaweed fly Coelopa frigida, we show that a polymorphic chromosomal inversion is maintained by a trade-off between survival and reproduction, and thus provide empirical support for a role of balancing selection via antagonistic pleiotropy. This mechanism has long been overlooked because it was thought to only apply to a narrow range of ecological scenarios. These findings empirically reinforce the recent theoretical predictions that co-interacting factors (dominance, environment and sex) can lead to polymorphism maintenance by antagonistic pleiotropy and favour life-history variation.
Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Authors: Liu Daniel
Published: May 2019

Background

Unique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. Although there are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs, many tools either cannot handle substitution errors, or require expensive pairwise UMI comparisons that do not efficiently scale to larger datasets.

Results

We formulate the problem of deduplicating UMIs in a manner that enables optimizations to be made, and more efficient data structures to be used. We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 seconds.

Conclusions

We present a new formulation of the UMI deduplication problem, and show that it can be solved faster, with more sophisticated data structures.
Interpretable attention model in transcription factor binding site prediction with deep neural networks
Authors: Chen Chen , Hou Jie , Shi Xiaowen , Yang Hua , Birchler James A. , Cheng Jianlin
Published: May 2019

Due to the complexity of the biological factors that may influence the binding of transcription factors to DNA sequences, prediction of the potential binding sites remains a difficult task in computational biology. The attention mechanism in deep learning has shown its capability to learn from input features with long-range dependencies. Until now, no study has applied this mechanism in deep neural network models with input data from massively parallel sequencing. In this study, we aim to build a model for binding site prediction with the combination of attention mechanism and traditional deep learning techniques, including convolutional neural networks and recurrent neural networks. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets.

The benchmark shows that our implementation with attention mechanism (called DeepGRN) improves the performance of the deep learning models. Our model achieves better performance in at least 9 of 13 targets than any of the methods participated in the DREAM challenge. Visualization of the attention weights extracted from the trained models reveals how those weights shift when binding signal peaks move along the genomic sequence, which can interpret how the predictions are made. Case studies show that the attention mechanism helps to extract useful features by focusing on regions that are critical to successful prediction while ignoring the irrelevant signals from the input.
Auditory binaural and spatial hearing impairments in a Fragile X Syndrome mouse model
Authors: McCullagh Elizabeth A. , Poleg Shani , Greene Nathaniel T. , Huntsman Molly M. , Tollin Daniel J. , Klug Achim
Published: May 2019

The auditory brainstem compares sound-evoked excitation and inhibition from both ears to compute sound source location. Although alterations to the anatomy and physiology of the auditory brainstem have been demonstrated in Fragile X Syndrome (FXS) it is not known whether these changes cause sound localization impairments in FXS. To test the hypothesis that FXS-related alterations to brainstem circuits impair spatial hearing abilities, a reflexive prepulse inhibition (PPI) task, with sound source location as the prepulse stimulus, was used to show that Fmr1 knockout mice have decreased inhibition of their startle responses. Specifically, Fmr1 mice show decreased PPI compared to wildtype during gap detection, changes in sound source location, and spatial release from masking with no alteration to their overall startle thresholds compared to wildtype. Lastly, Fmr1 mice have increased latency to respond in these tasks suggesting additional impairments in the pathway responsible for reacting to a startling sound.
Functional synapse types via characterization of short-term synaptic plasticity
Authors: Lee Jung Hoon , Campagnola Luke , Seeman Stephanie C. , Jarsky Tim , Mihalas Stefan
Published: May 2019

The strengths of synaptic connections dynamically change depending on the history of synaptic events, which is referred to as short-term plasticity (STP). While STP’s underlying mechanisms are well researched, its exact functions remain poorly understood. This is in part due to the diverse patterns of STP experimentally reported. Recently, the Allen Institute for Brain Science has launched the synaptic physiology pipeline to characterize the diverse properties of synapses. Since this pipeline generates a large-scale survey of synapses in mouse primary visual cortex using highly standardized experimental protocols, it provides a unique opportunity to study diverse patterns of STP. Here, we develop an end-to-end workflow that can characterize STP from the Allen Institute for Brain Science pipeline data and conduct network simulations to infer STP’s functions. Employing this workflow, we find 1) that diverse patterns of STP exist even in the same synapse classes and 2) that postsynaptic neurons’ responses have distinct characteristics depending on STP.
Frontal Midline Theta Reflects Cognitive Control During Planning
Authors: Domic-Siede Marcos , Irani Martín , Valdés Joaquín , Perrone-Bertolotti Marcela , Ossandón Tomás
Published: May 2019

Neural correlates of cognitive planning are not understood well at present. Behavioral paradigms targeting this function are a current challenge in cognitive neuroscience. We recorded EEG activity while subjects were performing a novel behavioral paradigm that evaluates cognitive planning function. Participants showed longer reaction times and decreased accuracy during the planning condition compared to the control condition, suggesting that the planning condition is more time consuming, therefore reflecting higher cognitive demand. Moreover, cognitive planning induced a frontal midline theta (FMθ) frequency band originating in prefrontal cortex (PFC) as shown in previous cognitive control studies. When subjects began planning, there was a progressive and sustained increase in FMθ starting after 500 milliseconds (ms) of planning. Hence, we characterized for first time, both spatial and temporal FMθ dynamics of cognitive planning as a marker of cognitive control function.
Comparison ofEscherichia colisurface attachment methods for single-cell,in vivomicroscopy
Authors: Wang Yao-Kuan , Krasnopeeva Ekaterina , Lin Ssu-Yuan , Bai Fan , Pilizota Teuta , Lo Chien-Jung
Published: May 2019

Forin vivo, single-cell imaging bacterial cells are commonly immobilised via physical confinement or surface attachment. Different surface attachment methods have been used both for atomic force and optical microscopy (including super resolution), and some have been reported to affect bacterial physiology. However, a systematic comparison of the effects these attachment methods have on the bacterial physiology is lacking. Here we present such a comparison for bacteriumEscherichia coli, and assess the growth rate, size and intracellular pH of cells growing attached to different, commonly used, surfaces. We demonstrate thatE. coligrow at the same rate, length and internal pH on all the tested surfaces when in the same growth medium. The result suggests that tested attachment methods can be used interchangeably when studyingE. coliphysiology.
The Salmonella LysR family regulator, RipR, activates the SPI-13 encoded itaconate degradation cluster
Authors: Hersch Steven J. , Navarre William Wiley
Published: May 2019

Itaconate is a dicarboxylic acid that inhibits the isocitrate lyase enzyme of the bacterial glyoxylate shunt. Activated macrophages have been shown to produce itaconate, suggesting that these immune cells may employ this metabolite as a weapon against invading bacteria. Here we demonstrate that, in vitro, itaconate can exhibit bactericidal effects under acidic conditions similar to the pH of a macrophage phagosome. In parallel, successful pathogens including Salmonella have acquired a genetic operon encoding itaconate degradation proteins, which are induced heavily in macrophages. We characterize the regulation of this operon by the neighbouring gene, ripR, in specific response to itaconate. Moreover, we develop an itaconate biosensor based on the operon promoter that can detect itaconate in a semi-quantitative manner and, when combined with the ripR gene, is sufficient for itaconate-regulated expression in E. coli. Using this biosensor with fluorescence microscopy, we observe bacteria responding to itaconate in the phagosomes of macrophage and provide additional evidence that interferon-γ stimulates macrophage itaconate synthesis and that J774 mouse macrophages produce substantially more itaconate than the human THP-1 monocyte cell line. In summary, we examine the role of itaconate as an antibacterial metabolite in mouse and human macrophage, characterize the regulation of Salmonella’s defense against it, and develop it as a convenient itaconate biosensor and inducible promoter system.

Importance

In response to invading bacteria, immune cells can produce a molecule called itaconate, which can inhibit microbial metabolism. Here we show that itaconate can also directly kill Salmonella when combined with moderate acidity, further supporting itaconate’s role as an antibacterial weapon. We also discover how Salmonella recognizes itaconate and activates a defense to degrade it, and we harness this response to make a biosensor that detects the presence of itaconate. This biosensor is versatile, working in Salmonella enterica or lab strains of Escherichia coli, and can detect itaconate quantitatively in the environment and in immune cells. By understanding how immune cells kill bacteria and how the microbes defend themselves, we can better develop novel antibiotics to inhibit pathogens such as Salmonella.
cfrB, cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America
Authors: Stojković Vanja , Ulate María Fernanda , Hidalgo-Villeda Fanny , Aguilar Emmanuel , Monge-Cascante Camilo , Pizarro-Guajardo Marjorie , Tsai Kaitlyn , Tzoc Edgardo , Camorlinga Margarita , Paredes-Sabja Daniel , Quesada-Gómez Carlos , Fujimori Danica Galonić , Rodríguez César
Published: May 2019

Cfr is a radical S-adenosyl-L-methionine (SAM) enzyme that confers cross-resistance to all antibiotics targeting the large ribosomal subunit through hypermethylation of nucleotide A2503 of 23S rRNA. Of the four known cfr genes known to date, cfr(B) and cfr(C) have been sporadically found in C. difficile, yet functional characterization of cfr(C) is still lacking. We identified genes for putative Cfr-like enzymes among clinical C. difficile strains from Mexico, Honduras, Costa Rica, and Chile. To confirm their identity and activity, we obtained minimum inhibitory concentrations for ribosome-targeting antibiotics, annotated whole genome sequences, and performed a functional characterization of Cfr(C). The seven representative isolates analyzed displayed different levels of resistance to PhLOPSA antibiotics in the absence of the ribosome protection factor OptrA, and mutations in genes for 23S rRNAs or the ribosomal proteins L3 and L4. cfr(B) was detected in four isolates as part of a Tn6218-like transposon or an un-described mobile genetic element. In turn, cfr(C) was found integrated into an ICE-element. One isolate harbored a putative cfr-like gene that shows only 51-58% of sequence identity to Cfr and known Cfr-like enzymes. Moreover, our in vitro assays confirmed that Cfr(C) methylates E. coli and C. difficile 23S rRNA fragments. These results indicate selection of cfr-like genes in C. difficile from Latin America, suggest that the diversity of cfr-like resistance genes is larger than anticipated, and provide the first assessment of the methylation activity of Cfr(C).
PI3K activation prevents Aβ42-induced synapse loss and favors insoluble amyloid deposits formation
Authors: Arnés Mercedes , Romero Ninovska , Casas-Tintó Sergio , Acebes Ángel , Ferrús Alberto
Published: May 2019

Alzheimer’s disease is, to a large extent, a disease of the synapse triggered by the unbalanced amyloidogenic cleavage of the amyloid precursor protein APP. Excess of Aβ42 peptide in particular is considered a hallmark of the disease. Here we drive the expression of the human Aβ42 peptide to assay the neuroprotective effects of PI3K in adultDrosophila melanogaster. We show that the neuronal expression of the human peptide elicits progressive toxicity in the adult. The pathological traits include reduced axonal transport, synapse loss, defective climbing ability and olfactory perception, as well as life-span reduction. The Aβ42-dependent synapse decay does not involve transcriptional changes in the core synaptic protein encoding genes:bruchpilot,liprinandsynaptobrevin. All toxicity features, however, are suppressed by the co-expression of PI3K. Moreover, PI3K activation induces a significant increase of 6E10 and Thioflavin-positive amyloid deposits. Mechanistically, we suggest that Aβ42-Ser26 could be a candidate residue for direct or indirect phosphorylation by PI3K. Finally, along with thesein vivoexperiments we further analyze Aβ42 toxicity and its suppression by PI3K activation inin vitroassays with SH-SY5Y human neuroblastoma cell cultures, where Aβ42 aggregation into large insoluble deposits is reproduced. Taken together, these results uncover a potential novel pharmacological strategy against this disease with PI3K activation as a target.
Deep Lipidomics and Molecular Imaging of Unsaturated Lipid Isomers: A Universal Strategy Initiated by mCPBA Epoxidation
Authors: Kuo Ting-Hao , Chung Hsin-Hsiang , Chang Hsin-Yuan , Lin Chiao-Wei , Wang Ming-Yang , Shen Tang-Long , Hsu Cheng-Chih
Published: May 2019

Cellular lipidome is highly regulated through lipogenesis, rendering diverse double-bond positional isomers (C=C isomer) of a given unsaturated lipid species. In recent years, there are increasing reports indicating the physiological roles of C=C isomer compositions associated with diseases, while the biochemistry has not been fully understood due to the challenge in characterizing lipid isomers inherent to conventional mass spectrometry-based lipidomics. To address this challenge, we reported a universal, user-friendly, derivatization-based strategy, MELDI (mCPBA Epoxidation for Lipid Double-bond Identification), which enables both large-scale identification and spatial mapping of biological C=C isomers using commercial mass spectrometers without any instrument modification. With the developed liquid-chromatography mass spectrometry (LC-MS) lipidomics workflow, we elucidated more than 100 isomers among mono- and poly-unsaturated fatty acids and glycerophospholipids in both human serum, where novel isomers of low abundance were unambiguously quantified for the first time. The capability of MELDI-LC-MS in lipidome analysis was further demonstrated using the differentiated 3T3-L1 adipocytes, providing an insight into the cellular lipid reprogramming upon stearoyl-coenzyme A desaturase 1 (SCD1) inhibition. Finally, we highlighted the versatility of MELDI coupled with mass spectrometry imaging to spatially resolve cancer-associated alteration of lipid isomers in a metastatic mouse tissue section. Our results suggested that MELDI will contribute to current lipidomics pipelines with a deeper level of structural information, allowing us to investigate underlying lipid biochemistry.
Seawater salt-trappedPseudomonas aeruginosasurvives for years and gets primed for salinity tolerance
Authors: Elabed Hamouda , González-Tortuero Enrique , Ibacache-Quiroga Claudia , Bakhrouf Amina , Johnston Paul , Gaddour Kamel , Blázquez Jesús , Rodríguez-Rojas Alexandro
Published: May 2019

Background

In nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments.Pseudomonas aeruginosa, an opportunistic pathogen, after natural evaporation of seawater, was shown to be trapped in laboratory-grown halite crystals and to remain viable after entrapment for years. However, how this bacterium persists and survives in such hypersaline conditions is not understood.

Results

In this study, we aimed to understand the basis of survival, and to characterise the physiological changes required to develop salt tolerance usingP. aeruginosaas a model. Several clones ofP. aeruginosawere rescued after fourteen years in naturally evaporated marine salt crystals. Incubation of samples in nutrient-rich broth allowed re-growth and subsequent plating yielded observable colonies. Whole genome sequencing of theP. aeruginosaisolates confirmed the recovery of the original strain. The re-grown strains, however, showed a new phenotype consisting of an enhanced growth in growing salt concentration compared to the ancestor strain. The intracellular accumulation of K+was elicited by high concentration of Na+in the external medium to maintain the homeostasis. Whole transcriptomic analysis by microarray indicated that seventy-eight genes had differential expression between the parental strain and derivative clones. Sixty-one transcripts were up-regulated, while seventeen were down-regulated. Based on a collection of single-gene knockout mutants and gene ontology analysis, we suggest that the adaptive response inP. aeruginosato hyper-salinity relies on multiple gene product interactions.

Conclusions

The individual gene contributions build up the observed phenotype, but do not ease the identification of salinity-related metabolic pathways. The long-term inclusion ofP. aeruginosain salt crystals primes the bacteria, mediating a readjustment of the bacterial physiology to growth in higher salt concentrations. Our findings provide a starting point to understand howP. aeruginosa, a relevant environmental and pathogenic bacterium, survives to long-term salt stress.
Engineering bacteriocin-mediated resistance against plant pathogenic bacteria in plants
Authors: Rooney William M. , Grinter Rhys , Correia Annapaula , Parkhill Julian , Walker Daniel , Milner Joel J.
Published: May 2019

Pseudomonas syringae(Ps) and related plant pathogenic bacteria are responsible for losses in diverse crops such as tomato, kiwifruit, pepper, olive and soybean. Current solutions, involving the use of chemicals and the introduction of resistance genes, have enjoyed only limited success and may have adverse environmental impacts. Consequently, there is a pressing need to develop alternative technologies to address the problem of bacterial disease in crops. An alternative strategy is to utilise the narrow spectrum protein antibiotics (bacteriocins) used by diverse bacteria for competition against closely related species. Here, we demonstrate that active putidacin L1 (PL1) can be expressed at high levelsin plantaand expression of PL1 provides effective resistance against diverse pathovars ofPs.Furthermore, we found that strains which evolve to become insensitive to PL1; lose their O-antigen, exhibit reduced motility and are less virulent in PL1 transgenic plants. Our results provide proof-of-principle that transgene-mediated expression of a bacteriocinin plantais an effective strategy for providing disease resistance against bacterial pathogens. Genetically modified (GM) crops expressing insecticidal proteins have proved extremely successful as a strategy for pest management; expressing bacteriocins to control bacterial disease may have a similar potential. Crucially, nearly all genera of bacteria, including many plant pathogenic species, produce bacteriocins, providing an extensive source of these antimicrobial agents.

SIGNIFICANCE

With the global population to surpass 9 billion by 2050 there is a huge demand to make industrial farming as efficient as possible. A disadvantage of industrial farming is the lack of genetic diversity within crop monocultures, which make them highly susceptible to diseases caused by plant pathogenic bacteria likePseudomonas syringae. Bacteriocins are narrow spectrum protein antibiotics which are produced by all major bacterial lineages. Their main purpose is to eliminate competitor strains to establish dominance within a niche. By arming plants with bacteriocins we can increase the genetic toolbox used to engineer crops to be resistant to specific bacterial plant pathogens.
Learning may help pollinators find their host plants in polluted landscapes
Authors: Cook Brynn , Haverkamp Alexander , Hansson Bill S. , Roulston T’ai , Lerdau Manuel , Knaden Markus
Published: May 2019

Pollination strongly contributes to food production, and often relies on pollinating insects. However, atmospheric pollution may interfere with pollination by disrupting floral plumes that pollinators use to navigate to flowers.

In this study, we examine the impacts of pollution-induced elevated ozone levels on the composition of a floral blend ofNicotiana alataand examine the response of innate and trainedManduca sextato the ozone-altered blend.

Ozone exposure altered the floral blend ofN. alata, and disrupted the innate attraction of naïveM. sextato the altered blend. However, associative learning can offset this disruption in attraction. Moths that were enticed with visual cues to an artificial flower emitting an ozonated blend learned to associate this blend with a nectar reward after just one rewarded experience. More importantly, moths that were rewarded while experiencing the unozonated floral blend of their host subsequently found the ozonated floral blend of the same host attractive, most likely due to experience-based reinforcement of ozone-insensitive cues in the blend.

The attraction of moths to both unaltered and ozonated plumes is critical for tolerating polluted landscapes. At the host plant, where moths feed, floral emissions are relatively pure. As floral odors travel away from the host, however, they become degraded by pollution. Therefore, targeting the flower requires recognizing both conditions of the odor. The ability to generalize between the pure and ozone-altered scents may enable pollinators likeM. sextato maintain communication with their flowers and reduce the impact anthropogenic oxidants may have on plant-pollinator systems.
Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription
Authors: Gill Jatinder Kaur , Maffioletti Andrea , García-Molinero Varinia , Stutz Françoise , Soudet Julien
Published: May 2019

Eukaryotic genomes are almost entirely transcribed by RNA polymerase II (RNAPII). Consequently, the transcription of long noncoding RNAs (lncRNAs) often overlaps with coding gene promoters triggering potential gene repression through a poorly characterized mechanism of transcription interference. In this study, we propose a global model of chromatin-based transcription interference in Saccharomyces cerevisiae (S. cerevisiae). By using a noncoding transcription inducible strain, we analyzed the relationship between antisense elongation and coding sense repression, nucleosome occupancy and transcription-associated histone modifications using near-base pair resolution techniques. We show that antisense noncoding transcription leads to the deaceylation of a subpopulation of −1/+1 nucleosomes associated with increased H3K36 trimethylation (H3K36me3). Reduced acetylation results in decreased binding of the RSC chromatin remodeler at −1/+1 nucleosomes and subsequent sliding into the Nucleosome-Depleted Region (NDR) hindering Pre-Initiation Complex (PIC) association. Finally, we extend our model by showing that natural antisense noncoding transcription significantly represses around 20% of S. cerevisiae genes through this chromatin-based transcription interference mechanism.

Highlights

Induction of antisense noncoding transcription leads to −1/+1 nucleosome sliding that competes with sense transcription PIC deposition.

Antisense induction leads to a subpopulation of H3K36me3 nucleosomes differently positioned compared to H3K18ac nucleosomes.

RSC chromatin remodeler recruitment to −1/+1 nucleosomes is modulated by histone acetylation levels.

20% of S. cerevisiae genes are significantly repressed by this antisense-dependent chromatin-based transcription interference mechanism.
An arbitrary-spectrum spatial visual stimulator for vision research
Authors: Franke Katrin , Chagas André Maia , Zhao Zhijian , Zimmermann Maxime J.Y. , Qiu Yongrong , Szatko Klaudia , Baden Tom , Euler Thomas
Published: May 2019

Visual neuroscientists require accurate control of visual stimulation. However, few stimulator solutions simultaneously offer high spatio-temporal resolution and free control over the spectra of the light sources, because they rely on off-the-shelf technology developed for human trichromatic vision. Importantly, consumer displays fail to drive UV-shifted short wavelength-sensitive photoreceptors, which strongly contribute to visual behaviour in many animals, including mice, zebrafish and fruit flies. Moreover, many non-mammalian species feature more than three spectral photoreceptor types. Here, we present a flexible, spatial visual stimulator with up to 6 arbitrary spectrum chromatic channels. It combines a standard digital light processing engine with open source hard- and software that can be easily adapted to the experimentalist’s needs. We demonstrate the capability of this general visual stimulator experimentally in thein vitromouse retinal whole-mount and thein vivozebrafish. Hereby, we intend starting a community effort of sharing and developing a common stimulator design.
Differential sperm motility mediates the sex ratio drive shaping mouse sex chromosome evolution
Authors: Rathje CC , Johnson EEP , Drage D , Patinioti C , Silvestri G , Affara NA , Ialy-Radio C , Cocquet J , Skinner BM , Ellis PJI
Published: May 2019

The search for morphological or physiological differences between X- and Y-bearing mammalian sperm has provoked controversy for decades. Many potential differences have been proposed, but none validated, while accumulating understanding of syncytial sperm development has cast doubt on whether such differences are possible even in principle. We present the first ever mammalian experimental model to trace a direct link from a measurable physiological difference between X- and Y-bearing sperm to the resulting skewed sex ratio. We show that in mice with deletions on chromosome Yq, birth sex ratio distortion is due to a relatively greater motility of X-bearing sperm, and not to any aspect of sperm/egg interaction. Moreover, the morphological distortion caused by Yq deletion is more severe in Y-bearing sperm, providing a potential hydrodynamic basis for the altered motility. This reinforces a growing body of work indicating that sperm haploid selection is an important and underappreciated evolutionary force.
Chromosome organization by a conserved condensin-ParB system in the actinobacteriumCorynebacterium glutamicum
Authors: Böhm Kati , Giacomelli Giacomo , Schmidt Andreas , Imhof Axel , Koszul Romain , Marbouty Martial , Bramkamp Marc
Published: May 2019

Higher-order chromosome folding and segregation is tightly regulated in all domains of life. In bacteria, details on nucleoid organization regulatory mechanisms and function remains poorly characterized, especially in non-model species. Here, we investigate the role of DNA partitioning protein ParB and condensin complexes, two key players in bacterial chromosome structuring, in the actinobacteriumCorynebacterium glutamicum. Chromosome conformation capture reveals SMC-mediated long-range interactions around ten centromere-likeparSsites clustered at the replication origin (oriC). At least oneoriC-proximalparSsite is necessary for a reliable chromosome segregation. Using a combination of chromatin immunoprecipitation and photoactivated single molecule localization microscopy evidences the formation of distinct ParB-nucleoprotein subclusters in dependence ofparSnumbers. We further identified and functionally characterized two condensin paralogs. Whereas SMC/ScpAB complexes are loaded via ParB atparSsites mediating chromosomal inter-arm contacts like inBacillus subtilis, the MukBEF-like SMC complex MksBEFG does not contribute to chromosomal DNA-folding. Rather, the MksBEFG complex is involved in plasmid maintenance and interacts with the polaroriC-tethering factor DivIVA. These data complement current models of ParB-SMC/ScpAB crosstalk, while showing that some condensin complexes evolved functions uncoupled from chromosome folding.
Loss of developmental diapause as a prerequisite for social evolution in bees
Authors: Santos Priscila Karla Ferreira , Arias Maria Cristina , Kapheim Karen M.
Published: May 2019

Diapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs has been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction of the ecological and evolutionary factors associated with diapause phase. We find that social lifestyle, latitude, and voltinism are significant predictors of the life stage in which diapause occurs. Ancestral state reconstruction revealed that the most recent common ancestor of all bees likely exhibited developmental diapause and shifts to adult or reproductive diapause have occurred in the ancestors of lineages in which social behavior has evolved. These results provide fresh insight regarding the role of diapause as a prerequisite for the evolution of sociality in bees.
Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling
Authors: Edelmaier Christopher J. , Lamson Adam R. , Gergely Zachary R. , Ansari Saad , Blackwell Robert , McIntosh J. Richard , Glaser Matthew A. , Betterton Meredith D.
Published: May 2019

The essential functions required for mitotic spindle assembly and chromosome biorientation and segregation are not fully understood, despite extensive study. To illuminate the combinations of ingredients most important to align and segregate chromosomes and simultaneously assemble a bipolar spindle, we developed a computational model of fission-yeast mitosis. Robust chromosome biorientation requires progressive restriction of attachment geometry, destabilization of misaligned attachments, and attachment force dependence. Large spindle length fluctuations can occur when the kinetochore-microtubule attachment lifetime is long. The primary spindle force generators are kinesin-5 motors and crosslinkers in early mitosis, while interkinetochore stretch becomes important after biorientation. The same mechanisms that contribute to persistent biorientation lead to segregation of chromosomes to the poles after anaphase onset. This model therefore provides a framework to interrogate key requirements for robust chromosome biorientation, spindle length regulation, and force generation in the spindle.
Inducible Plasmid Self-Destruction (IPSD) assisted genome engineering in lactobacilli and bifidobacteria
Authors: Zuo Fanglei , Zeng Zhu , Hammarström Lennart , Marcotte Harold
Published: May 2019

Genome engineering is essential for application of synthetic biology in probiotics including lactobacilli and bifidobacteria. Several homologous recombination system-based mutagenesis tools have been developed for these bacteria but still, have many limitations in different species or strains. Here we developed a genome engineering method based on an inducible self-destruction plasmid delivering homologous DNA into bacteria. Excision of the replicon by induced recombinase facilitates selection of homologous recombination events. This new genome editing tool called Inducible Plasmid Self-Destruction (IPSD) was successfully used to perform gene knock-out and knock-in in lactobacilli and bifidobacteria. Due to its simplicity and universality, the IPSD strategy may provide a general approach for genetic engineering of various bacterial species.
Rats can learn a temporal task in a single session
Authors: Reyes Marcelo Bussotti , Miranda Diego Henrique de , Tunes Gabriela Chiuffa , Caetano Marcelo Salvador
Published: May 2019

Fixed interval, peak interval, and temporal bisection procedures have been used to assess cognitive functions and address questions such as how animals perceive, represent, and reproduce time intervals. They have also been extensively used to test the effects of drugs on behavior, and to describe the neural correlates of interval timing. However, those procedures usually require several weeks of training for behavior to stabilize. Here, we compared three types of training protocols and reported a procedure in which performance by the end of the very first session nearly matches the performance of long-term training. We also discuss this fast-learning protocol in terms of an information-theory approach. This one-day training protocol can be used to investigate temporal learning and may be especially useful to electrophysiological and neuropharmacological studies.
Neural trajectories in the supplementary motor area and primary motor cortex exhibit distinct geometries, compatible with different classes of computation
Authors: Russo Abigail A. , Khajeh Ramin , Bittner Sean R. , Perkins Sean M. , Cunningham John P. , Abbott Laurence F. , Churchland Mark M.
Published: May 2019

The supplementary motor area (SMA) is believed to contribute to higher-order aspects of motor control. To examine this contribution, we employed a novel cycling task and leveraged an emerging strategy: testing whether population trajectories possess properties necessary for a hypothesized class of computations. We found that, at the single-neuron level, SMA exhibited multiple response features absent in M1. We hypothesized that these diverse features might contribute, at the population level, to avoidance of ‘population trajectory divergence’ – ensuring that two trajectories never followed the same path before separating. Trajectory divergence was indeed avoided in SMA but not in M1. Network simulations confirmed that low trajectory divergence is necessary when guidance of future action depends upon internally tracking contextual factors. Furthermore, the empirical trajectory geometry – helical in SMA versus elliptical in M1 – was naturally reproduced by networks that did, versus did not, internally track context.
Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome
Authors: Dayebgadoh Gerald , Sardiu Mihaela E. , Florens Laurence , Washburn Michael P.
Published: May 2019

A hub protein in protein interaction networks will typically have a large number of diverse interactions. Determining the core interactions and the function of such a hub protein remains a significant challenge in the study of networks. Proteins with WD40 repeats represent a large class of proteins that can be hub proteins. WDR76 is a poorly characterized WD40 repeat protein with possible involvement in DNA damage repair, cell cycle progression, apoptosis, gene expression regulation, and protein quality control. WDR76 has a large and diverse interaction network that has made its study challenging. Here, we rigorously carry out a series of affinity-purification coupled to mass spectrometry (AP-MS) to map out the WDR76 interactome through different biochemical conditions. We apply AP-MS analysis coupled to size exclusion chromatography to resolve WDR76-based protein complexes. Furthermore, we also show that WDR76 interacts with the CCT complex via its WD40 repeat domain and with DNA-PK-KU, PARP1, GAN, SIRT1, and histones outside of the WD40 domain. An evaluation of the stability of WDR76 interactions led to focused and streamlined reciprocal analyses that validate the interactions with GAN and SIRT1. Overall, the approaches used to study WDR76 would be valuable to study other proteins containing WD40 repeat domains, which are conserved in a large number of proteins in many organisms
Autumn shifts in cold tolerance metabolites in overwintering adult mountain pine beetles
Authors: Thompson Kirsten M. , Huber Dezene P. W. , Murray Brent W.
Published: May 2019

The mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae) is a major forest pest of pines in western North America. Beetles typically undergo a one-year life cycle with larval cold hardening in preparation for overwintering. Two-year life cycle beetles have been observed but not closely studied. This study tracks cold-hardening and preparation for overwintering by adult MPB in their natal galleries. Adults were collected in situ between September and December (2016) for a total of nine time points during 91 days. Concentrations of 41 metabolites in these pooled samples were assessed using quantitative NMR. Levels of glycerol and proline increased significantly with lowering temperature during the autumn. Newly eclosed mountain pine beetles prepare for winter by generating the same cold-tolerance compounds found in larvae, but high on-site mortality suggested that two-year life cycle adults have a less efficacious acclimation process. This is the first documentation of cold acclimation metabolite production in overwintering new adult beetles and is evidence of physiological plasticity that would allow evolution by natural selection of alternate life cycles (shortened or lengthened) under a changing climate or during expansion into new geoclimatic areas.
Inference of Synaptic Connectivity and External Variability in Neural Microcircuits
Authors: Baker Cody , Froudarakis Emmanouil , Yatsenko Dimitri , Tolias Andreas S. , Rosenbaum Robert
Published: May 2019

A major goal in neuroscience is to estimate neural connectivity from large scale extracellular recordings of neural activity in vivo. This is challenging in part because any such activity is modulated by the unmeasured external synaptic input to the network, known as the common input problem. Many different measures of functional connectivity have been proposed in the literature, but their direct relationship to synaptic connectivity is often assumed or ignored. For in vivo data, measurements of this relationship would require a knowledge of ground truth connectivity, which is nearly always unavailable. Instead, many studies use in silico simulations as benchmarks for investigation, but such approaches necessarily rely upon a variety of simplifying assumptions about the simulated network and can depend on numerous simulation parameters. We combine neuronal network simulations, mathematical analysis, and calcium imaging data to address the question of when and how functional connectivity, synaptic connectivity, and latent external input variability can be untangled. We show numerically and analytically that, even though the precision matrix of recorded spiking activity does not uniquely determine synaptic connectivity, it is often closely related to synaptic connectivity in practice under various network models. This relation becomes more pronounced when the spatial structure of neuronal variability is considered jointly with precision.
Differential Effects of Afferent and Efferent Vagus Nerve Stimulation on Gastric Motility Assessed with Magnetic Resonance Imaging
Authors: Lu Kun-Han , Cao Jiayue , Phillips Robert , Powley Terry L , Liu Zhongming
Published: May 2019

Background

Vagus nerve stimulation (VNS) is an emerging bioelectronic therapy for regulating food intake and controlling gastric motility. However, the functional impact of different VNS parameters on postprandial gastric motility remains incompletely characterized. Moreover, while most studies focused on stimulating the motor limb (i.e. efferent VNS) of the vagovagal circuitry, the contribution of electrically activating the reflex arc of the circuitry (i.e. afferent VNS) to downstream control of gastric function has seldom been investigated.

Methods

Here, we used dynamic gastric magnetic resonance imaging (MRI) to assess antropyloric motility in anesthetized rats during which VNS was applied to the left cervical vagus. The configuration of VNS was varied in terms of directionality (i.e. afferent, efferent or combined afferent and efferent VNS) as well as parameter settings (i.e. pulse amplitude, pulse width, and frequency). The motility measurements were computed using a previously developed computer-assisted image processing pipeline.

Key Results

We found that electrical activation that favored the afferent pathway could promote gastric motility and coordination more effectively than direct activation of the efferent pathway. A reduction in antral contraction amplitude and pyloric tone under high-dose efferent VNS highlighted the inhibitory role of the efferent vagovagal circuitry.

Conclusions & Inferences

This study demonstrated the direct and reflex gastric responses to cervical VNS measured with MRI. Our findings suggest that selective stimulation of vagal afferents is potentially more favorable than stimulation of vagal efferents in facilitating coordinated antropyloric motility.

Key Points

Vagus nerve stimulation is emerging as a new bioelectronic therapy for remedying gastric symptoms. However, the effects of graded VNS settings and directionality preferences of VNS on gastric functions remain incompletely characterized.

Dynamic gastric MRI revealed that electrical activation of the afferent pathway could promote antropyloric motility more effectively than direct activation of the efferent pathway.

MRI can noninvasively characterize post-prandial gastric motility with high spatial and temporal resolution that could be used to guide the selection of VNS settings.