bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds
Authors: Waterworth Samantha C. , Isemonger Eric W. , Rees Evan R. , Dorrington Rosemary A. , Kwan Jason C. 
Published: October 2019

SUMMARYStromatolites are complex microbial mats that form lithified layers and ancient forms are the oldest evidence of life on earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline. Using assembled shotgun metagenomic data we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteriia class (Cyanobacteria phylum), with lower but notable abundances of bacteria classified as Alphaproteobacteria, Gammaproteobacteria and Bacteroidia. We identified functional gene sets in bacterial species conserved across two geographically distinct stromatolite formations, which may promote carbonate precipitation through the reduction of nitrogenous compounds and possible production of calcium ions. We propose that an abundance of extracellular alkaline phosphatases may lead to the formation of phosphatic deposits within these stromatolites. We conclude that the cumulative effect of several conserved bacterial species drives accretion in these two stromatolite formations.ORIGINALITY-SIGNIFICANCEPeritidal stromatolites are unique among stromatolite formations as they grow at the dynamic interface of calcium carbonate-rich groundwater and coastal marine waters. The peritidal space forms a relatively unstable environment and the factors that influence the growth of these peritidal structures is not well understood. To our knowledge, this is the first comparative study that assesses species conservation within the microbial communities of two geographically distinct peritidal stromatolite formations. We assessed the potential functional roles of these communities using genomic bins clustered from metagenomic sequencing data. We identified several conserved bacterial species across the two sites and hypothesize that their genetic functional potential may be important in the formation of pertidal stromatolites. We contrasted these findings against a well-studied site in Shark Bay, Australia and show that, unlike these hypersaline formations, archaea do not play a major role in peritidal stromatolite formation. Furthermore, bacterial nitrogen and phosphate metabolisms of conserved species may be driving factors behind lithification in peritidal stromatolites.
Establishing Rod-Shape from Spherical, Peptidoglycan-Deficient Bacterial Spores
Authors: Zhang Huan , Mulholland Garrett A. , Seef Sofiene , Zhu Shiwei , Liu Jun , Mignot Tâm , Nan Beiyan 
Published: October 2019

ABSTRACTChemical-induced spores of the Gram-negative bacterium Myxococcus xanthus are peptidoglycan (PG)-deficient. It is unclear how these spherical spores germinate into rod-shaped, walled cells without preexisting PG templates. We found that germinating spores first synthesize PG randomly on spherical surfaces. MglB, a GTPase-activating protein, forms a cluster that surveys the status of PG growth and stabilizes at one future cell pole. Following MglB, the Ras family GTPase MglA localizes to the second pole. MglA directs molecular motors to transport the bacterial actin homolog MreB and the Rod PG synthesis complexes away from poles. The Rod system establishes rod-shape by elongating PG at nonpolar regions. Thus, the interaction between GTPase, cytoskeletons and molecular motors provides a mechanism for the de novo establishment of rod-shape in bacteria.SignificanceSpheres and rods are among the most common shapes adopted by walled bacteria, in which the peptidoglycan (PG) cell wall largely determines cell shape. When induced by chemicals, rod-shaped vegetative cells of the Gram-negative bacterium Myxococcus xanthus thoroughly degrade their PG and shrink into spherical spores. As these spores germinate, rod-shaped cells are rebuilt without preexisting templates, which provides a rare opportunity to visualize de novo PG synthesis and bacterial morphogenesis. In this study, we investigated how spherical spores germinate into rods and elucidated a system for rod-shape morphogenesis that includes the Rod PG synthesis system, a GTPase-GAP pair, the MreB cytoskeleton and a molecular motor.
Inhibition of protein synthesis in M1 of monkeys disrupts performance of sequential movements guided by memory
Authors: Ohbayashi Machiko 
Published: October 2019

AbstractThe production of action sequences is a fundamental aspect of human motor skills. To examine whether primary motor cortex (M1) is involved in maintenance of sequential movements, we trained two monkeys (Cebus apella) to perform two sequential reaching tasks. In one task, sequential movements were instructed by visual cues, whereas in the other task, movements were generated from memory after extended practice. After the monkey became proficient with performing the tasks, we injected an inhibitor of protein synthesis, anisomycin, into M1 to disrupt information storage in this area. Injection of anisomycin in M1 had a marked effect on the performance of sequential movements that were guided by memory. In contrast, the anisomycin injection did not have a significant effect on the performance of movements guided by vision. These results suggest that M1 of non-human primates is involved in the maintenance of skilled sequential movements.
Divergent DNA methylation signatures of juvenile seedlings grafts and adult apple trees
Authors: Perrin Adrien , Daccord Nicolas , Roquis David , Celton Jean-Marc , Vergne Emilie , Bucher Etienne 
Published: October 2019

AbstractPlants are continuously exposed to environmental perturbations. Outcrossing annual plants can adapt rapidly to these changes via sexual mating and DNA mutations. However, perennial and clonally reproducing plants may have developed particular mechanisms allowing them to adapt to these changes and transmit this information to their offspring. It has been proposed that the mechanisms allowing this plasticity of response could come in the form of epigenetic marks that would evolve throughout a plant’s lifetime and modulate gene expression. To study these mechanisms, we used apple (Malus domestica) as a model perennial and clonally propagated plant. First, we investigated the DNA methylation patterns of mature trees compared to juvenile seedlings. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear changes in DNA methylation patterns localized in regions enriched in genes involved in photosynthesis. Transcriptomic analysis showed that genes involved in this pathway were overexpressed in seedlings. Secondly, we compared global DNA methylation of a newly grafted plant to its mother tree to assess if acquired epigenomic marks were transmitted via grafting. We identified clear changes, albeit showing weaker DNA methylation differences. Our results show that a majority of DNA methylation patterns from the tree are transmitted to newly grafted plants albeit with specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their mother tree.
On the asymptotic equivalence between the radon and the hough transforms of digital images
Authors: Aramini Riccardo , Delbary Fabrice , Beltrametti Mauro C , Estatico Claudio , Piana Michele , Massone Anna Maria 
Published: October 2019

ABSTRACTAlthough characterized by different mathematical definitions, both the Radon and the Hough transforms ultimately take an image as input and provide, as output, functions defined on a preassigned parameter space, i.e., the so-called either Radon or Houghsinograms. The parameters in these two spaces describe a family of curves, which represent either the integration domains considered in the Radon transform, or the kind of curves to be detected by the Hough transform.It is heuristically known that the Hough sinogram converges to the corresponding Radon sinogram when the discretization step in the parameter space tends to zero. By considering generalized functions in multi-dimensional setting, in this paper we give an analytical proof of this heuristic rationale when the input grayscale digital image is described as a set of grayscale points, that is, as a sum of weighted Dirac delta functions. On these grounds, we also show that this asymptotic equivalence may have a valuable impact on the image reconstruction problem of inverting the Radon sinogram recorded by a medical imaging scanner.
Clonal evaluation of prostate cancer molecular heterogeneity in biopsy samples by dual immunohistochemistry and dual RNA in situ hybridization
Authors: Dedigama-Arachchige Pavithra , Carskadon Shannon , Li Jia , Loveless Ian , Alhamar Mohamed , Peabody James O. , Stricker Hans , Chitale Dhananjay A. , Rogers Craig G. , Menon Mani , Bismar Tarek A. , Gupta Nilesh S. , Williamson Sean R. , Palanisamy Nallasivam 
Published: October 2019

ABSTRACTProstate cancer is frequently multifocal. Although there may be morphological variation, the genetic underpinnings of each tumor are not clearly understood. To assess the inter and intra tumor molecular heterogeneity in prostate biopsy samples, we developed a combined immunohistochemistry and RNA in situ hybridization method for the simultaneous evaluation of ERG, SPINK1, ETV1, and ETV4. Screening of 601 biopsy cores from 120 consecutive patients revealed multiple alterations in a mutually exclusive manner in 37% of patients, suggesting multifocal tumors with considerable genetic differences. Furthermore, the incidence of molecular heterogeneity was higher in African Americans patients compared to Caucasian American patients. About 47% of the biopsy cores with discontinuous tumor foci showed clonal differences with distinct molecular aberrations. ERG positivity occurred predominantly in low Gleason grade cancer, whereas ETV4 expression was observed mostly in high Gleason grade cancer. Further studies revealed correlation between the incidence of molecular markers and clinical and pathologic findings, suggesting potential implications for diagnostic pathology practice, such as defining dominant tumor nodules and discriminating juxtaposed but molecularly different tumors of different grade patterns.
Circulating glutamine and Alzheimer’s disease: a Mendelian randomization study
Authors: Adams Charleen D. 
Published: October 2019

ABSTRACTINTRODUCTIONAlzheimer’s disease is a devastating neurodegenerative disorder. Its worldwide prevalence is over 24 million and is expected to double by 2040. Finding ways to prevent its cognitive decline is urgent.METHODSA two-sample Mendelian randomization study was performed instrumenting glutamine, which is abundant in blood, capable of crossing the blood-brain barrier, and involved in a metabolic cycle with glutamate in the brain.RESULTSThe results reveal a protective effect of circulating glutamine (inverse-variance weighted method, odds ratio per 1-SD increase in circulating glutamine = 0.83; 95% CI 0.71, 0.97; P = 0.02).CONCLUSIONThese findings lend credence to the emerging story supporting the modifiability of glutamine/glutamate metabolism for the prevention of cognitive decline. More circulating glutamine might mean that more substrate is available during times of stress, acting as a neuroprotectant. Modifications to exogenous glutamine may be worth exploring in future efforts to prevent and/or treat Alzheimer’s disease.
Neuropeptide relay between SIFa signaling controls the experience-dependent mating duration of male Drosophila
Authors: Wong Kyle , Schweizer Justine , Nguyen Khoi-Nguyen Ha , Atieh Shatha , Kim Woo Jae 
Published: October 2019

SummaryDrosophila melanogaster is a suitable model for investigating how neuropeptides influence animal behaviours and physiology. We previously reported that two behavioural paradigms control mating duration of male Drosophila, called Longer-Mating-Duration (LMD) and Shorter-Mating-Duration (SMD) that are induced through socio-sexual environment prior to copulation. Understanding the molecular and cellular mechanisms by which males exhibit plasticity to different social cues remains poorly understood. Here, we show that SIFa modulates the neural circuitry for both LMD and SMD. Neuropeptide-to-neuropeptide communication, so called ‘neuropeptide relay’ plays a key role to mediate this control. We identified that 7 neuropeptides expressed in SIFa Receptor-positive cells are functionally important to regulate either LMD and/or SMD. The modulation of two independent mating duration behaviour by the different SIFa-mediated neuropeptide relay will help to further investigate how the neuropeptidergic modulation can control complex behaviours.
Experimental phasing of MicroED data using radiation damage
Authors: Martynowycz Michael W. , Hattne Johan , Gonen Tamir 
Published: October 2019

AbstractWe present an example of an experimentally phased structure using only MicroED. The structure of a seven-residue peptide is determined starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a “low-dose dataset”. The data from the second pass were similarly merged to form a “damaged dataset.” Differences between these two datasets were used to calculate a Patterson difference map and to identify a single heavy atom site, from which initial phases were generated. The structure was then completed by iterative cycles of modeling and refinement.
Stimulus blanking reveals transsaccadic feature transfer
Authors: Grzeczkowski Lukasz , Deubel Heiner , Szinte Martin 
Published: October 2019

AbstractAcross saccadic eye movements, the visual system receives two successive static images corresponding to the pre- and the postsaccadic projections of the visual field on the retina. The existence of a mechanism integrating the content of these images is today still a matter of debate. Here, we studied the transfer of a visual feature across saccades using a blanking paradigm. Participants moved their eyes to a peripheral grating and discriminated a change in its orientation occurring during the eye movement. The grating was either constantly on the screen or briefly blanked during and after the saccade. Moreover, it either was of the same luminance as the background (i.e., isoluminant) or anisoluminant with respect to it. We found that for anisoluminant grating, the orientation discrimination across saccade was improved when a blank followed the onset of the eye movement. Such effect was however abolished with isoluminant grating. Additionally, performance was also improved when an anisoluminant grating presented before the saccade was followed by an isoluminant one. These results demonstrate that a detailed representation of the presaccadic image was transferred across saccades allowing participants to perform better on the trans-saccadic orientation task. While such a transfer of visual orientation across saccade is masked in real-life anisoluminant conditions, the use of a blank and of isoluminant postsaccadic grating allowed here to reveal its existence.Significance statementStatic objects are perceived as not moving across eye movements despite their visual projection shifts on our retina. To compensate for such shifts and create a continuous perception of space, our brain may keep track of objects’ visual features across our movements. We found that shortly blanking a contrast-defined object during and after saccades allows to recover a detailed representation of its orientation. We propose that the transfer of visual content across saccades revealed with the use of a simple blank plays an important role in ensuring our continuous and stable perception of the world.
A specialized deceptive pollination system based on elaborate mushroom mimicry
Authors: Kakishima Satoshi , Tuno Nobuko , Hosaka Kentaro , Okamoto Tomoko , Ito Takuro , Okuyama Yudai 
Published: October 2019

AbstractDespite its potential effectiveness for outcrossing, few examples of pollination via mushroom mimicry have been reported. This may be because the conditions under which the strategy can evolve are limited and/or because demonstrating it is challenging. Arisaema is a plant genus that has been suggested to adopt mushroom mimicry for pollination, although no compelling evidence for this has yet been demonstrated. Here, we report that Arisaema sikokianum utilizes mostly a single genus of obligate mycophagous flies (Mycodrosophila) as pollinators, and that the insect community dominated by Mycodrosophila is strikingly similar to those found on some species of wood-decaying fungi. Comparative chemical analyses of Arisaema spp. and various mushrooms further revealed that only A. sikokianum emits a set of volatile compounds shared with some mushroom species utilized by Mycodrosophila. Meanwhile, other closely related and often sympatric Arisaema species do not possess such typical traits of mushroom mimicry or attract Mycodrosophila, thereby likely achieving substantial reproductive isolation from A. sikokianum. Our finding indicates that mushroom mimicry is an exceptional and derived state in the genus Arisaema, thus providing an unprecedented opportunity to study the mechanisms underlying the coordinated acquisition of mimicry traits that occurred during a recent speciation event.
Genetic profiling ofMycobacterium tuberculosis“modern” Beijing strains from Southwest Colombia
Authors: Nieto Ramirez Luisa Maria , Ferro Beatriz E. , Diaz Gustavo , Anthony Richard M. , de Beer Jessica , van Soolingen Dick 
Published: October 2019

AbstractBeijing strains ofMycobacterium tuberculosis(lineage2) have been associated with drug-resistance and transmission of tuberculosis worldwide. Most of the Beijing strains identified in the Colombian pacific coast exhibited a multidrug resistant (MDR) phenotype, in contrast with the phenotype observed in Beijing isolates from other South-American countries. We wanted to evaluate the clonality and genetic background of the Beijing strains isolated in Colombia that belong mostly to the spoligo-international type (SIT) 190. Out of 37 Beijing stains characterized in an 8-years period, we identified five Beijing clones; 36 that belong to the SIT190 type and only one to SIT1. Two loci in VNTR typing: MIRU 39 and QUB11b exhibited the highest level of variation among these strains. Out of the 37 Beijing strains, only one was drug susceptible, 28 represented MDR-TB, four extensively drug resistant TB (XDR-TB) and four pre-XDR-TB. The mutationsrpoBS531L andkatGS315T1 were the most common among the MDR strains as reported elsewhere. Whole genome sequencing analysis allowed us to classify them as modern lineage Beijing strains, sharing up to 76 out of the 275 SNPs described in Beijing strains, as identified worldwide by Schürchet al;including 54 non-synonymous SNPs and 23 silent mutations. We were also able to confirm the presence of 8 specific SNPs that were so far only found in the Beijing strains from Colombia. The presence of modern Beijing strains, most of them representing MDR-TB, suggests a different origin of thisM. tuberculosislineage compared to other Beijing strains found in neighboring countries, such as Peru. The specific 8-SNP signature confirmed the identity of these Colombian Beijing MDR strains. This work may serve as a genetic baseline to study the evolution and spread ofM. tuberculosisBeijing strains in Colombia, which play an important role in the control of MDR-TB.
Genetic access to functionally distinct ganglion cell types in the Somatostatin-IRES-Cre mouse retina
Authors: Fransen James W. , Borghuis Bart G. 
Published: October 2019

AbstractRetinal ganglion cells (GCs) are a functionally diverse neuron population that encodes and transmits distinct representations of the visual image on the retina to target nuclei in the brain. Independent studies of visually-evoked responses, cell morphology, and gene expression each suggest that GCs in mouse may comprise as many as forty distinct cell types. To date, only a subset of these types have been characterized in detail, and for most genetic access is still lacking. Thus, the majority of identified GC types remains inaccessible for targeted electrophysiology and functional imaging, precluding efficient studies of their response properties, and the cell-intrinsic mechanisms and presynaptic circuits that generate these properties. Here we show that an existing mouse line that is commonly used for studies of cortical inhibitory circuits – Somatostatin-IRES-Cre (Sst-Cre), consistently labels an understudied subset of four GC types with distinct visual responses. We characterized these types both anatomically and functionally using Cre-dependent reporter mouse lines and confocal fluorescence imaging, calcium imaging, and whole-cell electrophysiology. We show that one of the labeled GC types is suppressed by luminance contrast, while another matches a recently described orientation-selective GC type. Our results give new information about these two identified GC types, and establish the utility of the Sst-Cre transgenic mouse line for studies of recently identified GC circuits in the mouse retina.
Assortment of Stauntonia hexaphylla and Cornus officinalis protect against testosterone-induced benign prostatic hyperplasia through anti-inflammatory and anti-proliferative activity
Authors: Karunasagara Shanika , Hong Geum-Lan , Jung Da-Young , Kim Kyung-Hyun , Koh Eun-Jeong , Cho Kyoung-won , Park Sung-Sun , Jung Ju-Young 
Published: October 2019

AbstractBenign prostatic hyperplasia (BPH) is a progressive pathological condition associated with proliferation of prostatic tissues, prostate enlargement, and lower-urinary tract symptoms. However, the mechanism underlying the pathogenesis of BPH is not clear. The aim of this study was to investigate the protective effects of Stauntonia hexaphylla and Cornus officinalis (SC extract) on a testosterone propionate (TP)-induced BPH model. For in vitro experiments, a human prostate adenocarcinoma cell line was used to perform western blotting for androgen receptor (AR), prostate specific antigen (PSA), and 5α-reductase type 2. Male Sprague-Dawley rats were randomly divided into 8 groups as follows for the in vivo experiments: control, BPH, Fina, Saw, SC25, SC50, SC100, and SC200. To induce BPH, all rats, except those in the control group, were daily administered with subcutaneous injections of TP (5 mg/kg), and orally treated with appropriate PBS/drugs for 4 consecutive weeks. Our findings indicated that the SC treatment significantly reduced the prostate size and downregulated the serum testosterone and DHT levels in BPH rats. The histological examination revealed that SC treatment markedly recovered the TP-induced abnormalities and reduced the prostatic hyperplasia. In addition, in vitro and in vivo western blotting indicated that SC treatment significantly downregulated the AR, PSA, and 5α-reductase type 2 expression, while an immunohistochemistry examination revealed that the SC extract significantly reduced the expression of type 2 5α-reductase and proliferating cell nuclear antigen positive cell count. Collectively, our findings demonstrated that SC extract attenuates BPH through anti-proliferative and anti-inflammation activities and might be useful in the clinical treatment of BPH.