bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution
Authors: Ren Minglei , Feng Xiaoyuan , Huang Yongjie , Wang Hui , Hu Zhong , Clingenpeel Scott , Swan Brandon K , Fonseca Miguel M , Posada David , Stepanauskas Ramunas , Hollibaugh James T , Foster Peter G , Woyke Tanja , Luo Haiwei 
Published: April 2019

Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635–560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood–Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.
A new widespread subclass of carbonic anhydrase in marine phytoplankton
Authors: Jensen Erik L , Clement Romain , Kosta Artemis , Maberly Stephen C , Gontero Brigitte 
Published: April 2019

Abstract
Most aquatic photoautotrophs depend on CO2-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO2, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn2+ to Zn2+ as a cofactor, which is potentially of ecological relevance since Mn2+ is more abundant than Zn2+ in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO2. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.
UHRF genes regulate programmed interdigital tissue regression and chondrogenesis in the embryonic limb
Authors: Sanchez-Fernandez Cristina , Lorda-Diez Carlos I. , García-Porrero Juan A. , Montero Juan A. , Hurlé Juan M. 
Published: April 2019

AbstractThe primordium of the limb contains a number of progenitors far superior to those necessary to form the skeletal components of this appendage. During the course of development, precursors that do not follow the skeletogenic program are removed by cell senescence and apoptosis. The formation of the digits provides the most representative example of embryonic remodeling via cell degeneration. In the hand/foot regions of the embryonic vertebrate limb (autopod), the interdigital tissue and the zones of interphalangeal joint formation undergo massive degeneration that accounts for jointed and free digit morphology. Developmental senescence and caspase-dependent apoptosis are considered responsible for these remodeling processes. Our study uncovers a new upstream level of regulation of remodeling by the epigenetic regulators Uhrf1 and Uhrf2 genes. These genes are spatially and temporally expressed in the pre-apoptotic regions. UHRF1 and UHRF2 showed a nuclear localization associated with foci of methylated cytosine. Interestingly, nuclear labeling increased in cells progressing through the stages of degeneration prior to TUNEL positivity. Functional analysis in cultured limb skeletal progenitors via the overexpression of either UHRF1 or UHRF2 inhibited chondrogenesis and induced cell senescence and apoptosis accompanied with changes in global and regional DNA methylation. Uhrfs modulated canonical cell differentiation factors, such as Sox9 and Scleraxis, promoted apoptosis via up-regulation of Bak1, and induced cell senescence, by arresting progenitors at the S phase and upregulating the expression of p21. Expression of Uhrf genes in vivo was positively modulated by FGF signaling. In the micromass culture assay Uhrf1 was down-regulated as the progenitors lost stemness and differentiated into cartilage. Together, our findings emphasize the importance of tuning the balance between cell differentiation and cell stemness as a central step in the initiation of the so-called “embryonic programmed cell death” and suggest that the structural organization of the chromatin, via epigenetic modifications, may be a precocious and critical factor in these regulatory events.
MIReAD, a minimum information standard for reporting arthropod abundance data
Authors: Rund Samuel S. C. , Braak Kyle , Cator Lauren , Copas Kyle , Emrich Scott J. , Giraldo-Calderón Gloria I. , Johansson Michael A. , Heydari Naveed , Hobern Donald , Kelly Sarah A. , Lawson Daniel , Lord Cynthia , MacCallum Robert M. , Roche Dominique G. , Ryan Sadie J. , Schigel Dmitry , Vandegrift Kurt , Watts Matthew , Zaspel Jennifer M. , Pawar Samraat 
Published: April 2019

AbstractArthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the “FAIR,” (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.
Solid-phase microextraction and on-fiber derivatization for assessment of mammalian and vegetable milks with emphasis on the content of major phytoestrogens
Authors: Aresta Antonella , Cotugno Pietro , Zambonin Carlo 
Published: April 2019

AbstractA new solvent-free method for the simultaneous determination of some major phytoestrogens (equol, enterodiol, daidzein, genistein, glycitein) in different commercial milks (cow, goat and soy-rice) was developed. After solid phase microextraction, performed by direct immersion of a 65 μm-polydimethylsiloxane–divinylbenzene fiber in diluted (1:100 with 0.2% formic acid - 30% sodium chloride) milk samples (18 °C for 20 min under stirring), a direct on-fiber silylation with N,O-bis (trimethylsilyl)trifluoroacetamide) containing 1% trimethylchlorosilane (70 °C for 20 min) was performed prior to gas chromatography–mass spectrometry analysis. Since the target compounds were determined as aglycones, the hydrolytic removal of the aglycone from the glycosides was performed. The method permitted the determination of the target analytes in all the considered milk samples as well as the detection of some major amphipathic fats indicating that the approach could potentially be applied in the future for further applications, such as milk profiling.
Early Synaptic Alterations and Selective Adhesion Signaling in Hippocampal Dendritic Zones Following Organophosphate Exposure
Authors: Farizatto Karen L. G. , Almeida Michael F. , Long Ronald T. , Bahr Ben A. 
Published: April 2019

AbstractOrganophosphates account for many of the world’s deadliest poisons. They inhibit acetylcholinesterase causing cholinergic crises that lead to seizures and death, while survivors commonly experience long-term neurological problems. Here, we treated brain explants with the organophosphate compound paraoxon and uncovered a unique mechanism of neurotoxicity. Paraoxon-exposed hippocampal slice cultures exhibited progressive declines in synaptophysin, synapsin II, and PSD-95, whereas reduction in GluR1 was slower and NeuN and Nissl staining showed no indications of neuronal damage. The distinctive synaptotoxicity was observed in dendritic zones of CA1 and dentate gyrus. Interestingly, declines in synapsin II dendritic labeling correlated with increased staining for β1 integrin, a component of adhesion receptors that regulate synapse maintenance and plasticity. The paraoxon-induced β1 integrin response was targeted to synapses, and the two-fold increase in β1 integrin was selective as other synaptic adhesion molecules were unchanged. Additionally, β1 integrin–cofilin signaling was triggered by the exposure and correlations were found between the extent of synaptic decline and the level of β1 integrin responses. These findings identified organophosphate-mediated early and lasting synaptotoxicity which can explain delayed neurological dysfunction later in life. They also suggest that the interplay between synaptotoxic events and compensatory adhesion responses influences neuronal fate in exposed individuals.
Integration of lodging resistance QTL in soybean
Authors: Hwang Sadal , Lee Tong Geon 
Published: April 2019

AbstractPoor lodging resistance could limit increases in soybean yield. Previously, a considerable number of observations of quantitative trait loci (QTL) for lodging resistance have been reported by independent studies. The integration of these QTL into a consensus map will provide further evidence of their usefulness in soybean improvement. To improve informative QTL in soybean, a mapping population from a cross between the Harosoy and Clark cultivars, which inherit major U.S. soybean genetic backgrounds, was used along with previous mapping populations to identify QTL for lodging resistance. Together with 78 QTL for lodging collected from eighteen independent studies, a total of 88 QTL were projected onto the soybean consensus map. A total of 16 significant QTL clusters were observed; fourteen of them were confirmed in either two or more mapping populations or a single population subjected to different environmental conditions. Four QTL (one on chromosome 7 and three on 10) were newly identified in the present study. Further, meta-analysis was used to integrate QTL across different studies, resulting in two significant meta-QTL each on chromosomes 6 and 19. Our results provide deeper knowledge of valuable lodging resistance QTL in soybean, and these QTL could be used to increase lodging resistance.
Differential impacts of pesticides on Euschistus heros (Hem.: Pentatomidae) and its parasitoid Telenomus podisi (Hym.: Platygastridae)
Authors: Pazini Juliano de Bastos , Padilha Aline Costa , Cagliari Deise , Bueno Flávio Amaral , Rakes Matheus , Zotti Moisés João , Martins José Francisco da Silva , Grützmacher Anderson Dionei 
Published: April 2019

AbstractEuschistus heros (Fabricius) (Hemiptera: Pentatomidae) primarily attack the pods and seeds of soybean plants, causing severe economic losses in Neotropical Region, and chemical control is essential to avoid these losses. Thus, insecticides more effective against this pest and less toxic to Telenomus podisi Ashmead (Hymenoptera: Platygastridae) - the main biological control agent of E. heros - should be used. In this report, we studied the differential acute impacts of pesticides used in Brazilian soybean against E. heros and T. podisi and evaluated their sublethal effects on the parasitoid to identify effective pesticides towards the pest with less harmful effect to the natural enemy. The LC50 of the insecticides to E. heros ranged from 1.20 to 533.74 ng a.i./cm2; the order of toxicity was thiamethoxam + lambda-cyhalothrin > acetamiprid + fenpropathrin > zeta-cypermethrin > acephate > imidacloprid. All pesticides were classified as slightly to moderately toxic to T. podisi based on the risk quotient. The exposure of T. podisi females to imidacloprid and the insecticide pre-formulated mixtures reduced the emergence of the offspring parasitoids by up to 40% whereas zeta-cypermethrin and the insecticides pre-formulated mixtures reduced offspring survival. The preferred order of choice of insecticides for the management of E. heros according to agronomic, toxicological, and environmental feasibility was the following: thiamethoxam + lambda-cyhalothrin > zeta-cypermethrin > acetamiprid + fenpropathrin > acephate > imidacloprid. Our study provides important and pioneer information to select insecticides for effective control of E. heros with lower impacts on T. podisi.
Reference genes for gene expression studies by RT-qPCR in Brevipalpus yothersi (Acari: Tenuipalpidae), the mite vector of citrus leprosis virus
Authors: Rogerio Luana Aparecida , Galdeano Diogo Manzano , Arena Gabriella Dias , Nunes Maria Andreia , Machado Marcos Antonio , Novelli Valdenice Moreira 
Published: April 2019

AbstractQuantitative reverse transcription PCR (RT-qPCR) is a high-throughput method to analyze the transcriptional expression of genes. Currently, no reference genes have been described for evaluating gene expression in Brevipalpus yothersi, the false spider mite, a polyphagous that act as vector of the citrus leprosis virus C (CiLV-C), an important citrus disease. This study aimed to identify the most stable reference genes in B. yothersi. The RT-qPCR expression data for selected genes were evaluated from three conditions: different developmental stages, plant hosts and acquisition of CiLV-C. To analyze the stability of the candidate reference genes we used ΔCq method, GeNorm, NormFinder, BestKeeper and RefFinder. Ubiq and GAPDH are best suited for normalizing gene expression data in viruliferous and non-viruliferous mites. Ubiq, EF1α and GAPDH are the most stable for different developmental stages. RPL13 and RPL32 are the best reference genes for approaches to B. yothersi in different host plants. Considering all the experimental conditions, Ubiq, EF1α, and GAPDH were the most stable genes. Here we developed an accurate and comprehensive RT-qPCR strategy for use in B. yothersi gene expression analysis. These results will improve the understanding of the biology of the false spider mites and their role as virus vectors.
Vitamin K2 cannot substitute Coenzyme Q10 as electron carrier in the mitochondrial respiratory chain of mammalian cells
Authors: Cerqua Cristina , Casarin Alberto , Pierrel Fabien , Vazquez Fonseca Luis , Viola Giampiero , Salviati Leonardo , Trevisson Eva 
Published: April 2019

AbstractCoenzyme Q10 (CoQ10) deficiencies are a group of heterogeneous conditions that respond to ubiquinone administration if treated soon after the onset of symptoms. However, this treatment is only partially effective due to its poor bioavailability. We tested whether vitamin K2, which was reported to act as a mitochondrial electron carrier in D. melanogaster, could mimic ubiquinone function in human CoQ10 deficient cell lines, and in yeast carrying mutations in genes required for coenzyme Q6 (CoQ6) biosynthesis. We found that vitamin K2, despite entering into mitochondria, restored neither electron flow in the respiratory chain, nor ATP synthesis. Conversely, coenzyme Q4 (CoQ4), an analog of CoQ10 with a shorter isoprenoid side chain, could efficiently substitute its function. Given its better solubility, CoQ4 could represent an alternative to CoQ10 in patients with both primary and secondary CoQ10 deficiencies.
Associated Factors and Clinical Implication of Cutaneous Allodynia in Patients with Cluster Headache: A Prospective Multicentre Study
Authors: Kim Byung-Su , Park Jeong Wook , Sohn Jong-Hee , Lee Mi Ji , Kim Byung-Kun , Chu Min Kyung , Ahn Jin-Young , Choi Yun-Ju , Song Tae-Jin , Chung Pil-Wook , Oh Kyungmi , Lee Kwang-Soo , Kim Soo-Kyoung , Park Kwang-Yeol , Chung Jae Myun , Moon Heui-Soo , Chung Chin-Sang , Cho Soo-Jin 
Published: April 2019

AbstractCutaneous allodynia (CA) is an abnormal pain in response to non-painful stimuli. In the present study, we sought to investigate the presence of CA, its associated factors, and its clinical implications in patients with cluster headache (CH). In this cross-sectional study, we analysed data from a prospective multicentre registry enrolling consecutive patients with CH. We identified CA during and between headache attacks using the 12-item Allodynia Symptom Checklist (ASC) administered during the CH bout period. Comorbid depression and anxiety were ascertained using the Patient Health Questionnaire (PHQ-9) and the Generalized Anxiety Disorder (GAD-7) scales. Headache impact was evaluated using the Headache Impact Test-6 (HIT-6). Of 119 eligible patients, 48 and two (40.3% and 1.7%) had CA during and between headache attacks, respectively. In univariable analyses, total CH duration, major depressive disorder (MDD), and generalized anxiety disorder (GAD) were associated with CA during headache attack. They remained significantly associated with CA during headache attack in multivariable analyses. Patients with CA during headache attack had higher headache impact (P = 0.002). A “50% responder” analysis showed no difference in outcome of acute and preventive treatment between patients with and without CA during headache attack. Patients with CH commonly experienced CA during headache attack, but not between headache attacks. CA during headache attack was associated with disease duration, depression, and anxiety.
Effects of boat noise on fish fast-start escape response depend on engine type
Authors: McCormick Mark I. , Fakan Eric P. , Nedelec Sophie L. , Allan Bridie J. M. 
Published: April 2019

AbstractVessel noise represents a relatively recent but rapidly increasing form of pollution, which affects the many organisms that use sound to inform their behavioural decisions. Recent research shows that anthropogenic noise can lead to reduced responsiveness to risk and higher mortality. The current laboratory experiment determined whether the playback of noise from motorboats powered by two- or four-stroke outboard engines affected the kinematics of the fast-start response in a juvenile coral reef fish, and the time scale over which the effects may occur. Results show that the two engine types produce slightly different sound spectra, which influence fish differently. Playback of 2-stroke engines had the greatest effect on activity, but only for a brief period (45 s). While noise from 4-stroke outboard engines affected fast-start kinematics, they had half the impact of noise from 2-stroke engines. Two-stroke engine noise affected routine swimming more than 4-stroke engines, while 4-stroke noise had a greater effect on the speed at which fish responded to a startle. Evidence suggests that the source of the noise pollution will have a major influence on the way marine organisms will respond, and this gives managers an important tool whereby they may reduce the effects of noise pollution on protected communities.
Emodin inhibits zinc-induced neurotoxicity in neuroblastoma SH-SY5Y cells
Authors: Liu Wenzhou , Fan Zhen , Gao Feng , Ou Li , Li Min , Zhou Xin , Luo Wenjia , Wei Peifeng , Miao Feng 
Published: April 2019

Abstract
Emodin is a natural anthraquinone derivative with numerous beneficial effects, including antioxidant properties, anti-tumor activities, and protecting the nerves. Zinc-induced neurotoxicity plays a crucial role in the pathogenesis of vascular dementia (VD) and Parkinson’s disease (PD). Here, the protective activity of emodin inhibiting zinc-induced neurotoxicity and its molecular mechanisms such as cellular Zn2+ influx and zinc-induced gene expression were examined using human neuroblastoma cells (SH-SY5Y cells). Our findings showed that emodin obviously enhanced cell viability and reduced cell apoptosis and lactate dehydrogenase release. Bedsides, we detected a decrease of intracellular Zn2+ concentration after SH-SY5Y cells were pretreated with emodin. Simultaneously, the expression of zinc transporter-1, metallothionein-1, and metallothionein-2 were weakened in emodin-pretreated SH-SY5Y cells. In addition, emodin prevented the depletion of NAD+ and ATP induced by zinc. Emodin also reduced intracellular reactive oxygen species and endoplasmic reticulum-stress levels. Strikingly, emodin elevated SH-SY5Y cell viability and inhibited cell apoptosis caused by AMP-activated protein kinase signaling pathway activation. Thus, emodin could protect against neurotoxicity induced by Zn2+ in neuroblastoma SH-SY5Y cells. It is expected to have future therapeutic potential for VD or PD and other neurodegenerative diseases.