bluuebunny/crossref_metadata_2025 huggingface dataset:
State–merchant relations and economic thought: the Dutch Republic and England, 1580–1720
Authors: Erikson Emily
Published: August 2020

The commercially and financially dynamic early modern Dutch Republic experienced a broad expansion of the public sphere and print industry. One topic was largely absent from this boom: trade, commerce and finance. This absence is particularly notable given that the Dutch Republic was widely considered to be the most accomplished site of expertise in those matters. Instead, a discourse attempting to understand the causes and consequences of market processes emerged in England. A comparison between the two emerging nations suggests that the tight integration between the commercial and political worlds in the Netherlands discouraged the development of a public discourse on economic matters. High levels of merchant representation in the offices of state depressed the need for the type of public debate that stimulated advances in the English context. The results suggest that there is an important relational component to the formation and development of economic thought.
Right Lateralized Brain Reserve Offsets Age-Related Deficits in Ignoring Distraction
Authors: Shalev Nir , Brosnan Méadhbh B , Chechlacz Magdalena
Published: August 2020

Age-related deterioration of attention decreases the ability to stay focused on the task at hand due to less efficient selection of relevant information and increased distractibility in the face of irrelevant, but salient stimuli. While older (compared with younger) adults may have difficulty suppressing salient distractors, the extent of these challenges differs vastly across individuals. Cognitive reserve measured by proxies of cognitively enriching life experiences, such as education, occupation, and leisure activities, is thought to mitigate the effects of the aging process and account for variability in trajectories of cognitive decline. Based on combined behavioral and neuroimaging (voxel-based morphometry) analyses of demographic, cognitive, and neural markers of aging and cognitive reserve proxy measures, we examine here predictors of variability in the age-related changes in attention function, indexed by ability to suppress salient distraction. Our findings indicate that in healthy (neurotypical), aging gray matter volume within several right lateralized fronto-parietal brain regions varies according to both levels of cognitive reserve (education) and the capacity to effectively select visual stimuli amid salient distraction. Thus, we provide here novel experimental evidence supporting Robertson’s theory of a right lateralized neural basis for cognitive reserve.
Sharp Wave-Ripples in Human Amygdala and Their Coordination with Hippocampus during NREM Sleep
Authors: Cox Roy , Rüber Theodor , Staresina Bernhard P , Fell Juergen
Published: August 2020

Cooperative interactions between the amygdala and hippocampus are widely regarded as critical for overnight emotional processing of waking experiences, but direct support from the human brain for such a dialog is absent. Using overnight intracranial recordings in 4 presurgical epilepsy patients (3 female), we discovered ripples within human amygdala during nonrapid eye movement (NREM) sleep, a brain state known to contribute to affective processing. Like hippocampal ripples, amygdala ripples are associated with sharp waves, linked to sleep spindles, and tend to co-occur with their hippocampal counterparts. Moreover, sharp waves and ripples are temporally linked across the 2 brain structures, with amygdala ripples occurring during hippocampal sharp waves and vice versa. Combined with further evidence of interregional sharp-wave and spindle synchronization, these findings offer a potential physiological substrate for the NREM-sleep-dependent consolidation and regulation of emotional experiences.
In-Depth Characterization of Layer 5 Output Neurons of the Primary Somatosensory Cortex Innervating the Mouse Dorsal Spinal Cord
Authors: Frezel N , Platonova E , Voigt F F , Mateos J M , Kastli R , Ziegler U , Karayannis T , Helmchen F , Wildner H , Zeilhofer H U
Published: August 2020

Neuronal circuits of the spinal dorsal horn integrate sensory information from the periphery with inhibitory and facilitating input from higher central nervous system areas. Most previous work focused on projections descending from the hindbrain. Less is known about inputs descending from the cerebral cortex. Here, we identified cholecystokinin (CCK) positive layer 5 pyramidal neurons of the primary somatosensory cortex (CCK + S1-corticospinal tract [CST] neurons) as a major source of input to the spinal dorsal horn. We combined intersectional genetics and virus-mediated gene transfer to characterize CCK+ S1-CST neurons and to define their presynaptic input and postsynaptic target neurons. We found that S1-CST neurons constitute a heterogeneous population that can be subdivided into distinct molecular subgroups. Rabies-based retrograde tracing revealed monosynaptic input from layer 2/3 pyramidal neurons, from parvalbumin positive cortical interneurons, and from thalamic relay neurons in the ventral posterolateral nucleus. Wheat germ agglutinin-based anterograde tracing identified postsynaptic target neurons in dorsal horn laminae III and IV. About 60% of these neurons were inhibitory and about 60% of all spinal target neurons expressed the transcription factor c-Maf. The heterogeneous nature of both S1-CST neurons and their spinal targets suggest complex roles in the fine-tuning of sensory processing.
Morphologic Diversity of Merkel Cell Carcinoma
Authors: Ogawa Toru , Donizy Piotr , Wu Cheng-Lin , Cornejo Kristine M. , Ryś Janusz , Hoang Mai P.
Published: August 2020

Merkel cell carcinoma (MCC) is a rare and highly aggressive neuroendocrine carcinoma of unknown origin. We performed a retrospective histologic review of primary cutaneous MCCs diagnosed from 1997 to 2018 in several clinical institutions and literature review to determine the frequency of various unusual morphologic appearances of MCC. Of the 136 primary MCCs identified, intraepidermal carcinoma or epidermotropism was noted in 11/136 (8%) cases. An association with pilar cyst in 1/136 (0.7%) case, with actinic keratosis in 2/136 (1.5%) cases, with either invasive or in situ squamous cell carcinoma (SCC) in 14/136 (10%) cases, with poroma in 1/136 (0.7%), and with basal cell carcinoma in 1/136 (0.7%) case was noted. Trabecular pattern and rosettes were noted in 7/136 (5%) and 3/136 (2%) cases, respectively. There was one case of metastatic MCC in a lymph node with chronic lymphocytic leukemia and one rare case of metastatic MCC and SCC in a lymph node. Although uncommon, differentiation toward other cell lineage can be observed in both primary and metastatic MCCs. The tumor can assume a variety of histologic appearances including association with SCC, basal cell carcinoma, melanocytic neoplasm, and follicular cyst; as well as exhibit glandular, sarcomatous, and mesenchymal differentiation. This diversity of morphologic appearance of MCC reflects the complexity of its underlying pathogenesis.
Fifty Years of Surgery for Pancreatic Cancer
Authors: Hackert Thilo , Klaiber Ulla , Pausch Thomas , Mihaljevic André L. , Büchler Markus W.
Published: August 2020

The surgical treatment of pancreatic cancer (PDAC) has seen sweeping changes during the past 5 decades. Up to the middle of the 20th century resection rates were below 5%, but the numbers of curative resections for PDAC are now continuously increasing due to improved neoadjuvant treatment concepts as well as progress in surgical techniques and perioperative management. During the same period, mortality rates after pancreatic surgery have decreased considerably and are now less than 5%. One of the most important cornerstones of reduced mortality has been the concentration of PDAC surgery in specialized centers. In addition, the management of postoperative complications has improved greatly as a result of optimized interdisciplinary teamwork. Adjuvant chemotherapy has become the reference treatment in resected PDAC, achieving significantly prolonged survival. Moreover, the concept of borderline resectable PDAC has emerged to characterize tumors with increased risk for tumor-positive resection margins or worse outcome. The best treatment strategy for borderline resectable PDAC is currently under debate, whereas neoadjuvant therapy has become established as a beneficial treatment option for patients with locally advanced PDAC, enabling conversion surgery in up to 60% of cases. This review article summarizes the principal changes in PDAC surgery during the past 50 years.
Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau
Authors: Gao Peixin , Lu Huibin , Xing Peng , Wu Qinglong L.
Published: August 2020

Two novel Gram-stain-negative, aerobic and non-motile rods bacteria, designated TQ8ST and ZH2ST, were isolated from salt marsh sediment collected from the Tibetan Plateau. Strain TQ8ST was found to grow at 10–40 °C (optimum, 30 °C), pH 6.0–11.0 (optimum, pH 8.0–9.0) and in the presence of 2–12 % (w/v) NaCl (optimum, 6–8 %). Strain ZH2ST was found to grow at 15–40 °C (optimum, 30 °C), pH 7.0–10.0 (optimum pH 9.0) and in the presence of 2–10 % (w/v) NaCl (optimum, 4–6 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains TQ8ST and ZH2ST shared 99.07 % sequence similarity between each other and were affiliated with the genus

Halomonas

, sharing 97.48 % and 97.41 % of sequence similarity to their closest neighbour

Halomonas sulfidaeris

Esulfide1T, respectively. DNA–DNA hybridization analyses showed 61.0 % relatedness between strains TQ8ST and ZH2ST. The average nucleotide identity and the average amino acid identity values between the two genomes were 92.33 and 92.84 %, respectively. The values between the two strains and their close phylogenetic relatives were all below 95 %. The major respiratory quinones of strain TQ8ST were Q-9 and Q-8, while that of ZH2ST was Q-9. The main fatty acids shared by the two strains were C18 : 1
 ω6c and/or C18 : 1
 ω7c, C16 : 1
 ω6c and/or C16 : 1
 ω7c, C16 : 0 and C12 : 0 3-OH. Strain ZH2ST can be distinguished from TQ8ST by a higher proportion of C19 : 0 cyclo ω8c. The G+C content of the genomic DNA of strains TQ8ST and ZH2ST were 57.20 and 57.14 mol%, respectively. On the basis of phenotypic distinctiveness and phylogenetic divergence, the two isolates are considered to represent two novel species of the genus

Halomonas

, for which the names Halomonas rituensis sp. nov (type strain TQ8ST=KCTC 62530T=CICC 24572T) and Halomonas zhuhanensis sp. nov (type strain ZH2ST=KCTC 62531T=CICC 24505T) are proposed.
Air pollution, SARS-CoV-2 transmission, and COVID-19 outcomes: A state-of-the-science review of a rapidly evolving research area
Authors: Bhaskar A , Chandra J , Braun D , Cellini J , Dominici F
Published: August 2020

Background

As the coronavirus pandemic rages on, 692,000 (August 7, 2020) human lives and counting have been lost worldwide to COVID-19. Understanding the relationship between short- and long-term exposure to air pollution and adverse COVID-19 health outcomes is crucial for developing solutions to this global crisis.

Objectives

To conduct a scoping review of epidemiologic research on the link between short- and long-term exposure to air pollution and COVID-19 health outcomes.

Method

We searched PubMed, Web of Science, Embase, Cochrane, MedRxiv, and BioRxiv for preliminary epidemiological studies of the association between air pollution and COVID-19 health outcomes. 28 papers were finally selected after applying our inclusion/exclusion criteria; we categorized these studies as long-term studies, short-term time-series studies, or short-term cross-sectional studies. One study included both short-term time-series and a cross-sectional study design.

Results

27 studies of the 28 reported evidence of statistically significant positive associations between air pollutant exposure and adverse COVID-19 health outcomes; 11 of 12 long-term studies and all 16 short-term studies reported statistically significant positive associations. The 28 identified studies included various confounders, spatial and temporal resolutions of pollution concentrations, and COVID-19 health outcomes.

Discussion

We discuss methodological challenges and highlight additional research areas based on our findings. Challenges include data quality issues, ecological study design limitations, improved adjustment for confounders, exposure errors related to spatial resolution, geographic variability in testing, mitigation measures and pandemic stage, clustering of health outcomes, and a lack of publicly available data and code.
RNA-Based COVID-19 Vaccine BNT162b2 Selected for a Pivotal Efficacy Study
Authors: Walsh Edward E. , Frenck Robert , Falsey Ann R. , Kitchin Nicholas , Absalon Judith , Gurtman Alejandra , Lockhart Stephen , Neuzil Kathleen , Mulligan Mark J. , Bailey Ruth , Swanson Kena A. , Li Ping , Koury Kenneth , Kalina Warren , Cooper David , Fontes-Garfias Camila , Shi Pei-Yong , Türeci Özlem , Tompkins Kristin R. , Lyke Kirsten E. , Raabe Vanessa , Dormitzer Philip R. , Jansen Kathrin U. , Şahin Uğur , Gruber William C.
Published: August 2020

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and the resulting disease, coronavirus disease 2019 (COVID-19), have spread to millions of people globally. Multiple vaccine candidates are under development, but no vaccine is currently available.

Methods

Healthy adults 18–55 and 65–85 years of age were randomized in an ongoing, placebo-controlled, observer-blinded dose-escalation study to receive 2 doses at 21-day intervals of placebo or either of 2 lipid nanoparticle–formulated, nucleoside-modified RNA vaccine candidates: BNT162b1, which encodes a secreted trimerized SARS-CoV-2 receptor-binding domain, or BNT162b2, which encodes a prefusion stabilized membrane-anchored SARS-CoV-2 full-length spike. In each of 13 groups of 15 participants, 12 received vaccine and 3 received placebo. Groups were distinguished by vaccine candidate, age of participant, and vaccine dose level. Interim safety and immunogenicity data of BNT162b1 in younger adults have been reported previously from US and German trials. We now present additional safety and immunogenicity data from the US Phase 1 trial that supported selection of the vaccine candidate advanced to a pivotal Phase 2/3 safety and efficacy evaluation.

Results

In both younger and older adults, the 2 vaccine candidates elicited similar dose- dependent SARS-CoV-2-neutralizing geometric mean titers (GMTs), comparable to or higher than the GMT of a panel of SARS-CoV-2 convalescent sera. BNT162b2 was associated with less systemic reactogenicity, particularly in older adults.

Conclusion

These results support selection of the BNT162b2 vaccine candidate for Phase 2/3 large-scale safety and efficacy evaluation, currently underway.
DNA oxidation induced by fetal exposure to BPA agonists impairs female meiosis
Authors: Abdallah Sonia , Moison Delphine , Wieckowski Margaux , Messiaen Sébastien , Martini Emmanuelle , Campalans Anna , Radicella J. Pablo , Habert René , Livera Gabriel , Rouiller-Fabre Virginie , Guerquin Marie-Justine
Published: August 2020

Many endocrine disruptors have been proven to impair the meiotic process that is mandatory to produce healthy gametes. Bisphenol A is emblematic as it impairs meiotic prophase I and causes oocyte aneuploidy followingin uteroexposure. However, the mechanisms underlying these deleterious effects remain poorly understood. Furthermore, the increasing uses of BPA analogs raise concerns for public health. Here, we investigated the effect on oogenesis in mouse of fetal exposure to two BPA analogs, Bisphenol A Diglycidyl Ether (BADGE) or Bisphenol AF (BPAF). These analogs delay meiosis initiation, increase MLH1 focipercell and induce oocyte aneuploidy. We further demonstrate that these defects are accompanied by a deregulation of gene expression and aberrant mRNA splicing in fetal premeiotic germ cells. Interestingly, we observed an increase in DNA oxidation after exposure to BPA analogs. Specific induction of oxidative DNA damages during fetal germ cell differentiation causes similar defects during oogenesis, as observed in 8-Oxoguanine DNA Glycosylase (OGG1) deficient mice or afterin uteroexposure to potassium bromate (KBrO3), an inducer of oxidative DNA damages. Moreover, the supplementation of N-acetylcysteine (NAC) with BPA analogs counteracts the bisphenol-induced meiotic effect. Together our results position oxidative stress as a central event that negatively impacts the female meiosis with major consequences on oocyte quality. This could be a common mechanism of action for so called endocrine disruptors pollutants and it could lead to novel strategies for reprotoxic compounds.
Correlated decision making across multiple phases of olfactory guided search in Drosophila
Authors: van Breugel Floris
Published: August 2020

All motile organisms must search for food, often requiring the exploration of heterogeneous environments across a wide range of spatial scales. Recent field and laboratory experiments with the fruit fly,Drosophila, have revealed that they employ different strategies across these regimes, including kilometer scale straight-path flights between resource clusters, zig-zagging trajectories to follow odor plumes, and local search on foot after landing. However, little is known about the extent to which experiences in one regime might influence decisions in another. To determine how a flies’ odor plume tracking during flight is related to their behavior after landing, I tracked the behavior of individually labelled fruit flies as they explored an array of three odor emitting, but food-barren, objects. The distance flies travelled on the objects in search of food was correlated with the time elapsed between their visits, suggesting that their in-flight plume tracking and on-foot local search behaviors are interconnected through a lossy memory-like process.
A Practical Alzheimer Disease Classifier via Brain Imaging-Based Deep Learning on 85,721 Samples
Authors: Lu Bin , Li Hui-Xian , Chang Zhi-Kai , Li Le , Chen Ning-Xuan , Zhu Zhi-Chen , Zhou Hui-Xia , Li Xue-Ying , Wang Yu-Wei , Cui Shi-Xian , Deng Zhao-Yu , Fan Zhen , Yang Hong , Chen Xiao , Thompson Paul M. , Castellanos Francisco Xavier , Yan Chao-Gan ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2020

Beyond detecting brain lesions or tumors, comparatively little success has been attained in identifying brain disorders such as Alzheimer’s disease (AD), based on magnetic resonance imaging (MRI). Many machine learning algorithms to detect AD have been trained using limited training data, meaning they often generalize poorly when applied to scans from previously unseen populations. Therefore, we built a practical brain MRI-based AD diagnostic classifier using deep learning/transfer learning on a dataset of unprecedented size and diversity. A retrospective MRI dataset pooled from more than 217 sites/scanners constituted one of the largest brain MRI samples to date (85,721 scans from 50,876 participants) between January 2017 and August 2021. Next, a state-of-the-art deep convolutional neural network, Inception-ResNet-V2, was built as a sex classifier with high generalization capability. The sex classifier achieved 94.9% accuracy and served as a base model in transfer learning for the objective diagnosis of AD. After transfer learning, the model fine-tuned for AD classification achieved 90.9% accuracy in leave-sites-out cross-validation on the Alzheimer’s Disease Neuroimaging Initiative (ADNI, 6,857 samples) dataset and 94.5%/93.6%/91.1% accuracy for direct tests on three unseen independent datasets (AIBL, 669 samples / MIRIAD, 644 samples / OASIS, 1,123 samples). When this AD classifier was tested on brain images from unseen mild cognitive impairment (MCI) patients, MCI patients who converted to AD were 3 times more likely to be predicted as AD than MCI patients who did not convert (65.2% vs 20.6%). Predicted scores from the AD classifier showed significant correlations with illness severity. In sum, the proposed AD classifier offers a medical-grade marker that has potential to be integrated into AD diagnostic practice.
Myanmar’s terrestrial ecosystems: status, threats and conservation opportunities
Authors: Murray Nicholas J. , Keith David A. , Duncan Adam , Tizard Robert , Ferrer-Paris Jose R. , Worthington Thomas A. , Armstrong Kate , Hlaing Nyan , Htut Win Thuya , Oo Aung Htat , Ya Kyaw Zay , Grantham Hedley
Published: August 2020

Myanmar is highly biodiverse, with more than 16,000 plant, 314 mammal, 1131 bird, 293 reptile, and 139 amphibian species. Supporting this biodiversity is a variety of natural ecosystems—mostly undescribed—including tropical and subtropical forests, savannas, seasonally inundated wetlands, extensive shoreline and tidal systems, and alpine ecosystems. Although Myanmar contains some of the largest intact natural ecosystems in Southeast Asia, remaining ecosystems are under threat from accelerating land use intensification and over-exploitation. In this period of rapid change, a systematic risk assessment is urgently needed to estimate the extent and magnitude of human impacts and identify ecosystems most at risk to help guide strategic conservation action. Here we provide the first comprehensive conservation assessment of Myanmar’s natural terrestrial ecosystems using the IUCN Red List of Ecosystems categories and criteria. We identified 64 ecosystem types for the assessment, and used models of ecosystem distributions and syntheses of existing data to estimate declines in distribution, range size, and functioning of each ecosystem. We found that more than a third (36.9%) of Myanmar’s area has been converted to anthropogenic ecosystems over the last 2-3 centuries, leaving nearly half of Myanmar’s ecosystems threatened (29 of 64 ecosystems). A quarter of Myanmar’s ecosystems were identified as Data Deficient, reflecting a paucity of studies and an urgency for future research. Our results show that, with nearly two-thirds of Myanmar still covered in natural ecosystems, there is a crucial opportunity to develop a comprehensive protected area network that sufficiently represents Myanmar’s terrestrial ecosystem diversity.
Design of synthetic human gut microbiome assembly and function
Authors: Clark Ryan L. , Connors Bryce M. , Stevenson David M. , Hromada Susan E. , Hamilton Joshua J. , Amador-Noguez Daniel , Venturelli Ophelia S.
Published: August 2020

The assembly of microbial communities and functions emerge from a complex and dynamic web of interactions. A major challenge in microbiome engineering is identifying organism configurations with community-level behaviors that achieve a desired function. The number of possible subcommunities scales exponentially with the number of species in a system, creating a vast experimental design space that is challenging to even sparsely traverse. We develop a model-guided experimental design framework for microbial communities and apply this method to explore the functional landscape of the health-relevant metabolite butyrate using a 25-member synthetic human gut microbiome community. Based on limited experimental measurements, our model accurately forecasts community assembly and butyrate production at every possible level of complexity. Our results elucidate key ecological and molecular mechanisms driving butyrate production including inter-species interactions, pH and hydrogen sulfide. Our model-guided iterative approach provides a flexible framework for understanding and predicting community functions for a broad range of applications.
MTCL2 promotes asymmetric microtubule organization by crosslinking microtubules on the Golgi membrane
Authors: Matsuoka Risa , Miki Masateru , Mizuno Sonoko , Ito Yurina , Yamada Chihiro , Suzuki Atsushi
Published: August 2020

The Golgi complex plays an active role in organizing asymmetric microtubule arrays essential for polarized vesicle transport. The coiled-coil protein MTCL1 stabilizes microtubules nucleated from the Golgi membrane. Here, we report an MTCL1 paralog, MTCL2, which preferentially acts on the perinuclear microtubules accumulated around the Golgi. MTCL2 associates with the Golgi membrane through the N-terminal coiled- coil region and directly binds microtubules through the conserved C-terminal domain without promoting microtubule stabilization. Knockdown of MTCL2 significantly impaired microtubule accumulation around the Golgi as well as the compactness of the Golgi ribbon assembly structure. Given that MTCL2 forms parallel oligomers through homo-interaction of the central coiled-coil motifs, our results indicate that MTCL2 promotes asymmetric microtubule organization by crosslinking microtubules on the Golgi membrane. Results ofin vitrowound healing assays further suggest that this function of MTCL2 enables integration of the centrosomal and Golgi-associated microtubules on the Golgi membrane, supporting directional migration. Additionally, the results demonstrated the involvement of CLASPs and giantin in mediating the Golgi association of MTCL2.
Belowground plant-plant signaling of root infection by nematodes
Authors: Zhang Peihua , Bonte Dries , De Deyn Gerlinde B. , Vandegehuchte Martijn L.
Published: August 2020

Communication between plants mediated by herbivore-induced volatile organic compounds has been extensively studied aboveground. However, the role of root herbivory in belowground plant-plant communication is much less understood. We here investigated whether root herbivores can trigger plant roots to emit warning signals to neighbouring plants that are not yet in direct contact with them.

We used a split-root system and infected half of the roots ofAgrostis stoloniferaplants with root-knot nematodes (Meloidogyne minor) and left the other half uninfected. As a control, we grew plants without nematodes in separate pots. Leachates from each split-root soil compartment and from soils with control plants were applied to separate pots withA. stoloniferaplants, of which biomass allocation and morphological traits were measured one month after leachate addition.

Plants receiving leachates from the soil with the nematode-free roots of the nematode-infected plants showed a significantly larger total biomass, more root branches, and deeper rooting than plants receiving leachates from the soil with the nematode-infected roots or from soil with control plants. Plants were taller and the root/shoot ratio was higher in plants receiving leachates from soil with the nematode-free roots than in plants receiving leachates from soil with nematode-infected roots. Shoot tiller number was higher in plants receiving leachates from either soil of the nematode-infected plants than in plants receiving control leachates.

Our results suggest that an overcompensation response was triggered by systemically induced root-derived compounds from nematode-free roots of a plant locally infected with root-feeding nematodes. Signals from directly attacked roots of the same nematode-infected plant only caused receiver plants to develop more shoot tillers, possibly for future stolon development to grow away from the infected area. This may indicate an anticipatory tolerance response to root feeders that are still distant and an additional generalized escape response to root feeding.
Curing genetic skin disease through altered replication stress response
Authors: Miyauchi Toshinari , Suzuki Shotaro , Takeda Masae , Peh Jin Teng , Aiba Masayuki , Natsuga Ken , Fujita Yasuyuki , Takeichi Takuya , Sakamoto Taiko , Akiyama Masashi , Shimizu Hiroshi , Nomura Toshifumi
Published: August 2020

Revertant mosaicism, or ‘natural gene therapy’, refers to the spontaneousin vivoreversion of an inherited mutation in a somatic cell1. Only ∼50 human genetic disorders exhibit revertant mosaicism, implicating a distinctive role played by mutant proteins in somatic correction of a pathogenic germline mutation2. However, the process by which mutant proteins induce somatic genetic reversion in these diseases remains unknown. Here we show that heterozygous pathogenicCARD14mutations causing autoinflammatory skin diseases, including psoriasis and pityriasis rubra pilaris, are repaired mainly via homologous recombination. Rather than altering the DNA damage response to exogenous stimuli such as X-irradiation or etoposide treatment, mutant CARD14 increased DNA double-strand breaks under conditions of replication stress. Furthermore, mutant CARD14 suppressed new origin firings without promoting crossover events in the replication stress state. Together, these results suggest that mutant CARD14 alters the replication stress response and preferentially drives break-induced replication (BIR), which is generally suppressed in eukaryotes3. Our results highlight the involvement of BIR in reversion events, thus revealing a previously undescribed role of BIR that could potentially be exploited to develop therapeutics for currently intractable genetic diseases.
Engineered Terpenoid Production inSynechocystissp. PCC 6803 Under Different Growth Conditions
Authors: Herold Ryan A. , Bryan Samantha J.
Published: August 2020

Terpenoids are the largest class of natural products and have applications in a wide variety of industries. Many terpenoids can be chemically synthesized or extracted from plants, but this is often uneconomical or unsustainable. An alternative production method relies on the heterologous expression of terpene synthase enzymes in cyanobacteria, producing the desired compounds directly from carbon dioxide. In this work, a patchoulol synthase enzyme fromPogostemon cablin(patchouli) was expressed in the cyanobacteriumSynechocystissp. PCC 6803 under four different growth conditions. Final yields of patchoulol from each growth condition were as follows: 249 μg L−1, photoautotrophic growth; 6.5 μg L−1, mixotrophic growth; 27.6 μg L−1, bicarbonate low light; 31.7 μg L−1, bicarbonate high light. By comparing patchoulol production across growth conditions, we identified a significant positive correlation between the production of photopigments (chlorophyll and carotenoids) and the production of patchoulol. Importantly, this relationship was found to be stronger than the correlation between cell density and patchoulol production across growth conditions, which was not statistically significant. The relationship between photopigments and patchoulol should be generalizable to the production of other terpenoids that rely on expression of the endogenous methylerythritol phosphate (MEP) pathway in cyanobacteria. Based on the results of this work, we propose a strategy for maximizing terpenoid production in cyanobacteria by optimizing growth conditions for photopigment production, resulting in increased flux through the MEP pathway. This strategy has the advantage of facile photopigment quantification using simple spectroscopic methods, and optimized growth conditions can be utilized in partnership with conventional terpenoid production strategies to further improve yields.
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes inArabidopsis thaliana
Authors: Li Yichao , Mullin Maxwell , Zhang Yingnan , Drews Frank , Welch Lonnie , Showalter Allan
Published: August 2020

Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized HRGP superfamily into three family members: the hyperglycosylated arabinogalactan-proteins, the moderately glycosylated extensins, and the lightly glycosylated proline-rich proteins. However, the mechanism of pollen-specific HRGP expression remains untouched. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences that identified 15 transcriptional cis-regulatory motifs responsible for pollen-specific expression of HRGP inArabidopsis Thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery with various filters identified 15 conserved promoter elements betweenThalianaandLyrata. Known motif analysis revealed pollen related transcription factors of GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Lastly, we performed a machine learning regression analysis and demonstrated that the identified 15 motifs well captured the HRGP gene expression in pollen (R=0.61). In conclusion, we performed the integrative analysis as the first-of-its-kind study to identify cis-regulatory motifs in pollen-specific HRGP genes and shed light on its transcriptional regulation in pollen.
Brassica napusL. dwarfing gene: Determining candidate intervals of dwarfing genes by BSA and SNP typing
Authors: Jing Luo , Chao Li , Ruimao Zhang , Zhineng Chen , Xianqiang Zhang , Zhihong Gao , Lei Lei , Pan Li
Published: August 2020

The plant height of rapeseed is one of the important factors that affects the production of rapeseed. If the plant height of rapeseed is too high, on the one hand, it will cause rapeseed to lodge and affect the yield, on the other hand, it will also affect the mechanized harvesting of rapeseed. In this research, the high-stalked line (YY50) and the dwarfed line (DW871) are crossed to obtain an F2 rapeseed population which was used to build pools, and then we used this to mine the main dwarfing genes. In the pools composed of tall and short stalks, we obtained 192.80Mb clean reads, which can be used for BSA (bulked segregant analysis). Preliminary positioning around the candidate section identified 23 SNP markers. Then 17 polymorphic SNP markers were obtained through polymorphism screening. Further we narrowed the candidate interval, and finally determined between 15.51-16.60Mb of ChrA10. Through identifying 231 genes from the above interval, it’s predicted that the production of dwarf traits may be related to lignin synthesis and limited inflorescence. It provides a basis for further mapping and cloning of the dwarfing gene DW871.
Aquaporin-3 regulates endosome-to-cytosol transfer via lipid peroxidation for cross presentation
Authors: Nalle Sam C. , da Silva Rosa Barreira , Zhang Hua , Decker Markus , Chalouni Cecile , Xu Min , Posthuma George , de Mazière Ann , Klumperman Judith , Baz Morelli Adriana , Fleire Sebastian J. , Verkman Alan S. , Trombetta E. Sergio , Albert Matthew L. , Mellman Ira
Published: August 2020

Antigen cross presentation, whereby exogenous antigens are presented by MHC class I molecules to CD8+ T cells, is essential for generating adaptive immunity to pathogens and tumor cells (1). Following endocytosis, it is widely understood that protein antigens must be transferred from endosomes to the cytosol where they are subject to ubiquitination and proteasome degradation prior to being translocated into the endoplasmic reticulum (ER), or possibly endosomes, via the TAP1/TAP2 complex (2, 3). Revealing how antigens egress from endocytic organelles (endosome-to-cytosol transfer, ECT), however, has proved vexing. Here, we used two independent screens to identify the hydrogen peroxide-transporting channel aquaporin-3 (AQP3) as a regulator of ECT. AQP3 overexpression increased ECT, whereas AQP3 knockout or knockdown decreased ECT. Mechanistically, AQP3 appears to be important for hydrogen peroxide entry into the endosomal lumen where it affects lipid peroxidation and subsequent antigen release. AQP3-mediated regulation of ECT was functionally significant, as AQP3 modulation had a direct impact on the efficiency of antigen cross presentationin vitro. Finally,AQP3-/-mice exhibited a reduced ability to mount an anti-viral response and cross present exogenous extended peptide. Together, these results indicate that the AQP3-mediated transport of hydrogen peroxide can regulate endosomal lipid peroxidation and suggest that compromised membrane integrity and coordinated release of endosomal cargo is a likely mechanism for ECT.
MicroRNA-1 promotes the development of and prolongs engorgement time inHyalomma anatolicum anatolicum(Acari: Ixodidae) ticks
Authors: Luo Jin , Ren Qiaoyun , Liu Wenge , Qiu Xiaofei , Zhang Gaofeng , Tan Yangchun , Cao Runlai , Yin Hong , Luo Jianxun , Li Xiangrui , Liu Guangyuan
Published: August 2020

MicroRNAs act as mRNA posttranscriptional regulators, playing important roles in cell differentiation, transcriptional regulation, growth and development. In this study, microRNA expression profiles ofHyalomma anatolicum anatolicumticks at different developmental stages were detected by high-throughput sequencing and functionally assessed. In total, 2,585,169, 1,252,678, 1,558,217 and 1,155,283 unique reads were obtained from eggs, larvae, nymphs and adults, respectively, with 42, 46, 45 and 41 conserved microRNAs in these stages, respectively. Using eggs as a control, 48, 43 and 39 microRNAs were upregulated and 3, 10 and 9 downregulated in larvae, nymphs and adults, respectively. microRNA-1 (miR-1) was expressed in high abundance throughoutHa. anatolicumdevelopment, with an average of nearly one million transcripts, and it is highly conserved among tick species. Quantitative real-time PCR (qPCR) showed that miR-1 expression gradually increased with tick development, reaching the highest level at engorgement. Differential tissue expression was detected, with significantly higher levels in the salivary glands and epidermis than in the midgut. Inhibition assays showed no significant change in body weight or spawning time or amount between experimental and control groups, but there was a significant difference (p<0.01) in engorgement time. With miR-1 inhibition, ticks displayed obvious deformities during later development. To more fully explain the microRNA mechanism of action, the miR-1 family was analyzed regarding target gene; members acting on Hsp60 include miR-5, miR-994, miR-969, and miR-1011, which jointly play a role. Therefore, microRNAs are critical for normal tick development, and the primary structure of the mature sequence of miR-1 is highly conserved. Nonetheless, different developmental stages and tissues show different expression patterns, with a certain role in prolonging feeding. miR-1, together with other family members, regulates mRNA function and may be used as a molecular marker for species origin and evolution analysis and internal reference gene selection.
Poliovirus-nonsusceptible Vero cell line for the World Health Organization global action plan
Authors: Okemoto-Nakamura Yuko , Someya Kenji , Yamaji Toshiyuki , Saito Kyoko , Takeda Makoto , Hanada Kentaro
Published: August 2020

Polio or poliomyelitis is a disabling and life-threatening disease caused by poliovirus (PV). As a consequence of global polio vaccination efforts, wild PV serotype 2 has been eradicated, and wild PV serotypes 1- and 3-transmitted cases have been largely eliminated except for in limited regions around the world. However, vaccine-derived PV, pathogenically reverted live PV vaccine strains in vaccinated humans, has become a serious issue. For the global eradication of polio, the World Health Organization is conducting the third edition of the Global Action Plan, which is requesting stringent control of potentially PV-infected materials. To facilitate the mission, we generated a PV-nonsusceptible Vero cell subline, which may serve as an ideal replacement of standard Vero cells to isolate emerging/re-emerging viruses without the risk of generating PV-infected materials.
Vascular control of the CO2/H+dependent drive to breathe
Authors: Cleary CM , Moreira TS , Takakura AC , Nelson MT , Longden TA , Mulkey DK
Published: August 2020

Respiratory chemoreceptors regulate breathing in response to changes in tissue CO2/H+. Blood flow is a fundamental determinant of tissue CO2/H+, yet little is known regarding how regulation of vascular tone in chemoreceptor regions contributes to respiratory behavior. Previously, we showed in rat that CO2/H+-vasoconstriction in the retrotrapezoid nucleus (RTN) supports chemoreception by a purinergic-dependent mechanism (Hawkins et al. 2017). Here, we show in mice that CO2/H+dilates arterioles in other chemoreceptor regions, thus demonstrating CO2/H+vascular reactivity in the RTN is unique. We also identify P2Y2receptors in RTN smooth muscle cells as the substrate responsible for this response. Specifically, pharmacological blockade or genetic deletion of P2Y2from smooth muscle cells blunted the ventilatory response to CO2, and re-expression of P2Y2receptors only in RTN smooth muscle cells fully rescued the CO2/H+chemoreflex. These results identify P2Y2receptors in RTN smooth muscle cells as requisite determinants of respiratory chemoreception.

Significance Statement

Disruption of vascular control as occurs in cardiovascular disease leads to compromised chemoreceptor function and unstable breathing. Despite this, virtually nothing is known regarding how regulation of vascular tone in chemoreceptor regions contributes to respiratory behavior. Here, we identify P2Y2receptors in RTN vascular smooth muscle cells as a novel vascular element of respiratory chemoreception. Identification of this mechanism may facilitate development of treatments for breathing problems including those associated with cardiovascular disease.
The Response of Bacterial Flagellar Motor to Stepwise Increase in NaCl Concentration
Authors: Soman V. , Kumari S. , Nath S. , Elangovan R.
Published: August 2020

Many species of bacteria use flagella to navigate in its environment. The flagellum is a 7-10 μm long helical filament with a rotary motor at its base embedded in the cell membrane and almost a dozen stator complexes. Proton motive force across the cell membrane powers the flagellar motors ofE.coliandSalmonella. The motor stochastically switches between clockwise and counter-clockwise direction. A chemotaxis system causes the motor to change its direction, but the process is more complex as the switch is sensitive to load and proton motive force as well. NaCl is significant with regard to the flagellar motor as it affects the stator dynamics, proton motive force, and osmotaxis at higher concentration. Chemotaxis helps the bacteria for its growth and survival.E.coli’s natural habitat has high osmolarity and the organism uses use various mechanisms for osmoregulation. However, the role of flagellar motor to adapt to the changes in osmolarity, or osmotaxis, is not well studied. In this work, we dissipated the membrane potential of bacteria in pH 7 using step-wise increase in concentration of NaCl in motility buffer and studied the output of E.coli’s flagellar motor using tethered bead assay and swimming Salmonella enteritidis cells. We observed decrease in motor speed and switching rates with stepwise increase in NaCl concentration in the motility buffer. The mean speed of the motors decreased with NaCl concentration. The population of swimming cells tumbled more with increase in concentration of NaCl. At the single motor level, the motors biased to CCW rotation with decrease in membrane potential. In this study, we present our observations of the flagellar motor in high NaCl concentration, and explore how NaCl can be used to study various aspects of the bacterial flagellar motor.

Statement of significance

Sodium ion has been significant in the both the cellular energetics and the function of bacterial flagellar motor. Growing evidence show that the effect of sodium ions was not what hitherto thought it would be. It is involved in the sodium energetics, dissipate membrane potential, affect the flagellar stator dynamics of bacteria. Being an osmolyte, it influences the osmotaxis of bacteria. In this work, we studied the effect of NaCl on the response of the single bacterial flagellar motor ofE.coliand swimming cells ofSalmonella enteritidis. We observed that the effect of NaCl on the output of the flagellar motor was significant and it may affect the cells in various ways.
Collaboration of multiple pathways in making a compound leaf
Authors: Israeli Alon , Ben-Herzel Ori , Burko Yogev , Shwartz Ido , Ben-Gera Hadas , Harpaz-Saad Smadar , Bar Maya , Efroni Idan , Ori Naomi
Published: August 2020

The variability in leaf form in nature is immense. Leaf patterning occurs by differential growth that occurs during a limited window of morphogenetic activity at the leaf marginal meristem. While many regulators have been implicated in the designation of the morphogenetic window and in leaf patterning, how these effectors interact to generate a particular form is still not well understood.

We addressed the interaction among different effectors of tomato compound leaf development, using genetic and molecular analyses.

Mutations in the tomato auxin response factor SlARF5/SlMP, which promotes leaflet formation, suppressed the increased leaf complexity of mutants with extended morphogenetic window. Impaired activity of the NAC/CUC transcription factor GOBLET (GOB), which specifies leaflet boundaries, also reduced leaf complexity in these backgrounds. Analysis of genetic interactions showed that the patterning factors SlMP, GOBand the MYB transcription factor LYRATE (LYR) act in parallel to promote leaflet formation.

This work places an array of developmental regulators in a morphogenetic context. It reveals how organ-level differentiation rate and local growth are coordinated to sculpture an organ. These concepts and findings are applicable to other plant species and developmental processes that are regulated by patterning and differentiation.
What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?
Authors: Peng Foen , Ballare Kimberly M. , Woodard S. Hollis , den Haan Stijn , Bolnick Daniel I.
Published: August 2020

Major Histocompatibility Complex (MHC) genes encode for proteins that recognize foreign protein antigens to initiate T-cell mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity is still an unsettled issue. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey in a stickleback metapopulation to test predictions derived from each of these hypotheses. We identify over a thousand MHCIIβ alleles and find that many of them covary positively or negatively with parasite load, suggesting that these genes contribute to resistance or susceptibility. However, despite our large sample-size, we find no evidence for the widely-cited stabilizing selection on MHC heterozygosity, in which individuals with an intermediate number of MHC alleles have the lowest parasite burden. Nor do we observe a rare-allele advantage, or widespread fluctuating selection across populations. In contrast, we find that MHC diversity is best predicted by neutral genome-wide heterozygosity and between-population genomic divergence, suggesting neutral processes are important in shaping the pattern of metapopulation MHC diversity. Thus, although MHCIIβ is highly diverse and relevant to the type and intensity of macroparasite infection in these populations of stickleback, the main models of MHC evolution still provide little explanatory power in this system.