bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracking down the molecular architecture of the synaptonemal complex by expansion microscopy
Authors: Zwettler Fabian U. , Spindler Marie-Christin , Reinhard Sebastian , Klein Teresa , Kurz Andreas , Sauer Markus , Benavente Ricardo 
Published: October 2019

AbstractThe synaptonemal complex (SC) is a meiosis-specific nuclear multiprotein complex that is essential for proper synapsis, recombination and segregation of homologous chromosomes. We combined structured illumination microscopy (SIM) with different ExM protocols including U-ExM, proExM, and magnified analysis of the proteome (MAP) to investigate the molecular organization of the SC. Comparison with structural data obtained by single-molecule localization microscopy of unexpanded SCs allowed us to investigate ultrastructure preservation of expanded SCs. For image analysis, we developed an automatic image processing software that enabled unbiased expansion factor determination. Here, MAP-SIM provided the best results and enabled reliable three-color super-resolution microscopy of the SCs of a whole set of chromosomes in a spermatocyte with 20-30 nm spatial resolution. Our data demonstrate that post-expansion labeling by MAP-SIM improves immunolabeling efficiency and allowed us thus to unravel previously hidden details of the molecular organization of SCs.
Cohesin and condensin extrude loops in a cell-cycle dependent manner
Authors: Golfier Stefan , Quail Thomas , Kimura Hiroshi , Brugués Jan 
Published: October 2019

AbstractChromatin undergoes a dramatic reorganization during the cell cycle1–3. In interphase, chromatin is organized into compartments and topological-associating domains (TADs) that are cell-type specific4–7, whereas in metaphase, chromosomes undergo large-scale compaction, leading to the loss of specific boundaries and the shutdown of transcription8–12. Loop extrusion by structural maintenance of chromosomes complexes (SMCs) has been proposed as a mechanism to organize chromatin in interphase and metaphase13–19. However, the requirements for chromatin organization in these cell phases are very different, and it is unknown whether loop extrusion dynamics and the complexes that extrude them also differ. Here, we used Xenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes asymmetric loops in metaphase, whereas cohesin extrudes symmetric loops in interphase. Our data show that loop extrusion is a general mechanism for the organization of DNA, with dynamic and structural properties that are molecularly regulated during the cell cycle.
Motor planning of vertical arm movements in healthy older adults: does effort optimization persist with aging?
Authors: Poirier Gabriel , Papaxanthis Charalambos , Mourey France , Gaveau Jeremie 
Published: October 2019

AbstractSeveral sensorimotor modifications are known to occur with aging, possibly leading to adverse outcomes such as falls. Recently, some of those modifications have been proposed to emerge from motor planning deteriorations. Motor planning of vertical movements is thought to engage an internal model of gravity to anticipate its mechanical effects on the body-limbs and thus to genuinely produce movements that minimize muscle effort. This is supported, amongst other results, by direction-dependent kinematics where relative durations to peak accelerations and peak velocity are shorter for upward than for downward movements. The present study compares motor planning of fast and slow vertical arm reaching movements between eighteen young (24 ± 3 years old) and seventeen older adults (70 ± 5 years old). We found that older participants still exhibit directional asymmetries (i.e., differences between upward and downward movements), indicating that optimization processes during motor planning persist with healthy aging. However, the size of these differences was increased in older participants, indicating that gravity-related motor planning changes with age. We discuss this increase as the possible result of an overestimation of gravity torque or increased weight of the effort cost in the optimization process. Overall, these results support the hypothesis that feedforward processes and, more precisely, optimal motor planning, remain active with healthy aging.
6-O-galloylsalidroside, an active ingredient from Acer tegmentosum, ameliorates alcoholic steatosis and liver injury in a mouse model of chronic ethanol consumption
Authors: Kim Young Han , Woo Dong-Cheol , Ra Moonjin , Jung Sangmi , Ham Su Jung , Kim Ki Hyun , Lee Yongjun 
Published: October 2019

AbstractWe previously reported that Acer tegmentosum extract, which is traditionally used to treat liver disease in Korea, may help reduce fat accumulation, improve liver metabolism, and suppress inflammation in alcoholic liver disease. The active ingredient was found to be 6-O-galloylsalidroside, which was isolated from the methanol extract of A. tegmentosum. We hypothesized that 6-O-galloylsalidroside extracted from A. tegmentosum may help protect from liver damage and attenuate hepatic fat accumulation associated with chronic alcohol consumption. In the present study, we aimed to investigate whether 6-O-galloylsalidroside can regulate alcoholic fatty liver and liver injury in mice. For this purpose, mice were fed with Lieber-DeCarli 5% ethanol diet for 11 days to induce steatosis and liver injury. Oral 6-O-galloylsalidroside was administered once a day for 11 days. Intrahepatic lipid accumulation caused by alcohol consumption was measured using in vivo 1H magnetic resonance imaging. Hepatic steatosis was observed histologically in tissue samples stained with hematoxylin and eosin, as well as Oil Red O. The serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were measured, as well as the triglyceride content in liver homogenates. On magnetic resonance spectroscopy, 6-O-galloylsalidroside appeared to alleviate alcohol-induced steatosis, which was reflected in decreased hepatic and serum triglyceride levels despite ethanol feeding. Furthermore, 6-O-galloylsalidroside treatment was associated with decreased RNA expression of Cd36, which plays an important role in the development of alcoholic steatosis through the hepatic de novo lipogenesis pathway. Furthermore, treatment with 6-O-galloylsalidroside inhibited the expression of cytochrome P4502E1 and attenuated hepatocellular damage, reflected in reduced ALT and AST levels. These findings suggest that 6-O-galloylsalidroside extracted from A. tegmentosum might serve as a bioactive agent for treating alcoholic fatty liver and liver damage.
Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss
Authors: Legried Brandon , Molloy Erin K. , Warnow Tandy , Roch Sébastien 
Published: October 2019

AbstractPhylogenomics—the estimation of species trees from multilocus datasets—is a common step in many biological studies. However, this estimation is challenged by the fact that genes can evolve under processes, including incomplete lineage sorting (ILS) and gene duplication and loss (GDL), that make their trees different from the species tree. In this paper, we address the challenge of estimating the species tree under GDL. We show that species trees areidentifiableunder a standard stochastic model for GDL, and that the polynomial-time algorithm ASTRAL-multi, a recent development in the ASTRAL suite of methods, isstatistically consistentunder this GDL model. We also provide a simulation study evaluating ASTRAL-multi for species tree estimation under GDL. All scripts and datasets used in this study are available on the Illinois Data Bank:https://doi.org/10.13012/B2IDB-2626814_V1.
Prospective and retrospective contributions to intention awareness in voluntary action
Authors: Schultze-Kraft Matthias , Parés-Pujolràs Elisabeth , Matić Karla , Haggard Patrick , Haynes John-Dylan 
Published: October 2019

AbstractSpontaneous, voluntary actions are often accompanied by motor intentions, that is the experience of “being about to move”. The emergence of this experience is contentiously discussed, culminating in two opposing views of motor intention. While prospective theorists hold that an intention to move genuinely precedes the action, retrospective theorists suggest that an intention is reconstructed only after action execution. As such, both theories offer radically different predictions about the possibility of voluntary control over action intention. We assess here the respective contributions of prospective and retrospective factors in motor intention awareness in a real-time EEG setup. Participants performed self-paced movements with intermittent interruption by cues, signalling to either move or not to move. Cues were triggered by a brain-computer interface upon detection of either the presence or absence of a readiness potential (RP), a signal known to precede self-paced voluntary actions. Subsequently, participants reported their intention to move at the time of the cue. We found that participants were more likely to report an intention to move when the cue was followed by a movement than no movement, highlighting the effect of retrospection on awareness of intention. Interestingly, however, an intention to move was also more frequently reported when the cue was elicited by an RP, compared to when no RP was present, suggesting that awareness of intention is also informed by motor preparation processes, congruent with prospective theories. Overall, our findings show that intention awareness in voluntary action relies on both prospective and retrospective components, and we describe here how these two factors are dynamically integrated over time.
Potential soil transmission of a novel Candidatus Liberibacter strain detected in citrus seedlings grown in soil from a huanglongbing infested citrus grove
Authors: Nunes da Rocha Ulisses , Shin Keumchul , Timilsina Sujan , Jones Jeffrey B. , Singer Burton H. , Van Bruggen Ariena H. C. 
Published: October 2019

SUMMARYCandidatus Liberibacter spp. are Alphaproteobacteria associated with plants and psyllid vectors. Most cause plant diseases, including Ca Liberibacter asiaticus (Las) associated with citrus huanglongbing (HLB). Replacing HLB-infected by Las-free citrus trees results in fast re-infection despite psyllid control. To check if HLB could be soil-borne, we performed an insect-free greenhouse-experiment with 130 mandarin seedlings in two citrus-grove soils (A and B), non-autoclaved or autoclaved. Liberibacter-specific 16S-rDNA PCR primers to detect Las were used to search for Ca. Liberibacter spp. in mandarin leaves. Seven plants grown in non-autoclaved soil B showed HLB-like symptoms and tested positive after 2.5 and 8.5 months using three different primer systems: two based on the 16S-rDNA gene (primers HLBas/HLBr and OI2c/OI1) and one based on the rplA/rplJ gene (primers LAA2/LAJ5). DNA segments from these plants amplified by primers OI2c/OI1 were cloned and sequenced; they were 95.9 % similar to Las and 94.8% to Ca. Liberibacter africanus (Laf). The DNA product from Liberibacter-group specific PCR primers for the rplA/rplJ gene was 87.6% similar to that of Las and 78.2% of Laf. As the strain obtained originated from soil and was different from existing Ca. Liberibacter species, this strain may be a new species.
The CNS lymphatic system modulates the adaptive neuro-immune response in the perilesional cortex in a mouse model of traumatic brain injury
Authors: Sara Wojciechowski , Maria Vihma , Barbara Galbardi , Anaïs Virenque , Keuters Meike H. , Salli Antila , Kari Alitalo , Jari Koistinaho , Noe Francesco M. 
Published: October 2019

AbstractRationaleThe recently discovered meningeal lymphatic vessels (mLVs) have been proposed to be the missing link between the immune and the central nervous systems. The role of mLVs in modulating the neuro-immune response following a brain injury, however, has not been analyzed. Parenchymal T lymphocyte infiltration has been previously reported as part of secondary events after traumatic brain injury (TBI), suggestive of an adaptive neuro-immune response. The phenotype of these cells has remained mostly uncharacterized. In this study, we identified the subpopulations of T cells infiltrating the perilesional areas 30 days post-injury (an early-chronic time point). Furthermore, we analyzed how the lack of mLVs affects the magnitude and the type of immune response in the brain after TBI.MethodsTBI was induced in K14-VEGFR3-Ig transgenic (TG) mice or in their littermate controls (WT; wild type), applying a controlled cortical impact (CCI). One month after TBI, T cells were isolated from cortical areas ipsilateral or contralateral to the trauma and from the spleen, then characterized by flow cytometry. Lesion size in each animal was evaluated by MRI.ResultsIn both WT and TG-CCI mice, we found a prominent T cell infiltration in the brain confined to the perilesional cortex and hippocampus. The majority of infiltrating T cells were cytotoxic CD8+ expressing a CD44hiCD69+ phenotype, suggesting that these are effector resident memory T cells. K14-VEGFR3-Ig mice showed a significant reduction of infiltrating CD4+ T lymphocytes, implying that mLVs are important in establishing a proper neuro-immune response. Extension of the lesion (measured as lesion volume from MRI) did not differ between the genotypes. Finally, TBI did not relate with alterations in peripheral circulating T cells, as assessed one month after injury induction.ConclusionsOur data support the hypothesis that mLVs are pivotal for a proper and specific neuro-immune response after TBI, which is principally mediated by the resident memory CD8+ T cells.
Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color
Authors: Helgeland Hanna , Sodeland Marte , Zoric Nina , Seilø Torgersen Jacob , Grammes Fabian , Lintig Johannes von , Moen Thomas , Kjøglum Sissel , Lien Sigbjørn , Våge Dag Inge 
Published: October 2019

AbstractRed coloration of muscle tissue (flesh) is a unique trait in several salmonid genera, including Atlantic salmon. The color results from dietary carotenoids deposited in the flesh, whereas the color intensity is affected both by diet and genetic components. Herein we report on a genome-wide association study (GWAS) to identify genetic variation underlying this trait. Two SNPs on ssa26 showed strong associations to the flesh color in salmon. Two genes known to be involved in carotenoid metabolism were located in this QTL-region: beta-carotene oxygenase 1 (bco1) and beta-carotene oxygenase 1 like (bco1l). To determine whether flesh color variation is caused by one, or both, of these genes, several functional studies were carried out including mRNA and protein expression in fish with red and pale flesh color. The catalytic abilities of these two genes were also tested with different carotenoids. Our results suggest bco1l to be the most likely gene to explain the flesh color variation observed in this population.
Two strategies underlying the trade-off of hepatitis C virus proliferation: stay-at-home or leaving-home?
Authors: Iwanami Shoya , Kitagawa Kosaku , Asai Yusuke , Ohashi Hirofumi , Nishioka Kazane , Inaba Hisashi , Nakaoka Shinji , Wakita Takaji , Diekmann Odo , Iwami Shingo , Watashi Koichi 
Published: October 2019

AbstractViruses proliferate through both genome replication inside infected cells and transmission to new target cells or to new hosts. Each viral genome molecule in infected cells is used either for amplifying the intracellular genome as a template (“stay-at-home strategy”) or for packaging into progeny virions to be released extracellularly (“leaving-home strategy”). The balance between these strategies is important for both initial growth and transmission of viruses. In this study, we used hepatitis C virus (HCV) as a model system to study the functions of viral genomic RNA in both RNA replication in cells and in progeny virus assembly and release. Using viral infection assays combined with mathematical modelling, we characterized the dynamics of two different HCV strains (JFH-1, a clinical isolate, and Jc1-n, a laboratory strain), which have different viral assembly and release characteristics. We found that 1.27% and 3.28% of JFH-1 and Jc1-n intracellular viral RNAs, respectively, are used for producing and releasing progeny virions. Analysis of the Malthusian parameter of the HCV genome (i.e., initial growth rate) and the number ofde novoinfections (i.e., initial transmissibility) suggests that the leaving-home strategy provides a higher level of initial transmission for Jc1-n, while, in contrast, the stay-at-home strategy provides a higher initial growth rate for JFH-1. Thus, theoretical-experimental analysis of viral dynamics enables us to better understand the proliferation strategies of viruses. Ours is the first study to analyze stay-leave trade-offs during the viral life cycle and their significance for viral proliferation.
Tuberculosis in farm workers exposed to dairy and beef livestock in Colombia
Authors: Muñoz Catalina , Rueda Johana , Botero Luz E. , Mejía Gloria I. , Cardona Ximena , Jaramillo Manuel G. , Robledo Jaime 
Published: October 2019

SummaryThe objective of this study was to determine the frequency of tuberculosis (TB) in workers from dairy and beef livestock farms in the northern part of Colombia. Tuberculin skin test and an interferon-gamma release assay (IGRA) were used for diagnosis of latent tuberculosis; sputum samples were taken from respiratory symptomatic subjects, microbiological and molecular tests were done for diagnosis of active TB. Absolute frequencies, percentages, and crude prevalence ratios were calculated, and a robust Poisson Model with adjustment by municipality was made. In 674 farm workers, latent TB frequency was 35.8%. Variables such as having had pulmonary TB (PR 2.82, 95% CI 1.90 – 4.17), having been in contact with people with active TB (PR 1.57, 95% CI 1.24 – 1.98), and having performed some undergraduate or postgraduate study (PR 1.6, 95% CI 1.03 – 2.49), were significantly associated with latent TB. No active tuberculosis disease was confirmed in symptomatic respiratory patients. The exposure level to cattle was not significantly associated with latent TB infection. In conclusion, in the studied population exposure to cattle was not a risk factor for TB, other factors commonly found in general population exposed to human TB were demonstrated.Author summaryZoonotic TB is a disease caused by the transmission of theM. bovisbacteria that is part of the Mycobacterium tuberculosis Complex, through contact with cattle to humans, by the consumption of unpasteurized dairy products from infected animals or by inhalation of aerosols exhaled by sick animals.This study investigated the frequency of TB in human population related to cattle, in order to determine if there were risk factors related to TB infection or disease. Finding that there was no significant relationship between being exposed to cattle and having latent TB. However, the results of this study together with other research reported in the literature suggest that research on zoonotic and bovine TB should be continued, especially about epidemiology, diagnostic methods, health systems and interventions coordinated with veterinary services.
A tree-planting decision support tool for urban heat island mitigation
Authors: Werbin Zoey , Heidari Leila , Buckley Sarabeth , Brochu Paige , Butler Lindsey , Connolly Catherine , Bloemendaal Lucila Houttuijn , McCabe Tempest D. , Miller Tara , Hutyra Lucy R. 
Published: October 2019

AbstractHeat poses an urgent threat to public health in cities, as the urban heat island (UHI) effect can amplify exposures, contributing to high heat-related mortality and morbidity. Urban trees have the potential to mitigate by providing substantial cooling, as well as co-benefits such as reductions in energy consumption. The City of Boston has attempted to expand its urban canopy, yet maintenance costs and high tree mortality have hindered successful canopy expansion. Here, we present an interactive web application called “Right Place, Right Tree - Boston” that aims to support informed decision-making for planting new trees. To highlight priority regions for canopy expansion, we developed a Boston-specific Heat Vulnerability Index (HVI) and present this alongside maps of summer temperatures. We also provide information about tree pests and diseases, suitability of species for various conditions, land ownership, maintenance tips, and alternatives to tree planting.
Sediment accumulation, elevation change, and the vulnerability of tidal marshes in the Delaware Estuary and Barnegat Bay to accelerated sea level rise
Authors: Haaf LeeAnn , Watson Elizabeth Burke , Elsey-Quirk Tracy , Raper Kirk , Padeletti Angela , Maxwell-Doyle Martha , Kreeger Danielle , Velinsky David 
Published: October 2019

AbstractTidal marshes protect coastal communities from the effects of sea level rise and storms, yet they are vulnerable to prolonged inundation and submergence. Uncertainty regarding their vulnerability to sea level rise motivated the establishment of a monitoring network in the Delaware Estuary and Barnegat Bay. Using data collected through these efforts, we determined whether rates of tidal marsh sediment accumulation and elevation change exceeded local sea level rise and how these dynamics varied along geographic and environmental gradients. Marker horizons, surface elevation tables, elevation surveys, water level data, and water column suspended sediment concentrations were used to evaluate sea level rise vulnerability. Of 32 study sites, 75% had elevation change that did not keep pace with long-term rising sea levels (1969–2018) and 94% did not keep pace with recent sea level rise (2000–2018). Mean high water rose most rapidly in the freshwater tidal portion of the Delaware Estuary with rates nearing 1 cm yr-1 from 2000–2018. We noted that greater sediment accumulation rates occurred in marshes with large tidal ranges, low elevations, and high water column suspended sediment concentrations. We found correlations between rates of shallow subsidence, increasing salinity, and decreasing tidal range. Marsh elevation and water level surveys revealed significant variability in elevation capital and summer flooding patterns (12–67% inundation). However, rapid increases in mean high water over the past 19 years suggests that all marsh platforms currently sit at or below mean high water. Overall, these data suggest that tidal marshes in the Delaware Estuary and Barnegat Bay are vulnerable to submergence by current rates of sea-level rise. While we observed variability in marsh elevation capital, the absence of strong correlations between elevation trends and environmental parameters makes it difficult to identify clear patterns of sea level rise vulnerability among wetlands.