bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forensics and DNA Barcodes – Do Identification Errors Arise in the Lab or in the Sequence Libraries?
Authors: Pentinsaari Mikko , Ratnasingham Sujeevan , Miller Scott E. , Hebert Paul D. N. 
Published: August 2019

AbstractForensic studies often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse forensic contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for the misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, forensic applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.
Protein polyglutamylation catalyzed by the bacterial Calmodulin-dependent pseudokinase SidJ
Authors: Sulpizio Alan , Minelli Marena E. , Wan Min , Burrowes Paul D. , Wu Xiaochun , Sanford Ethan , Shin Jung-Ho , Williams Byron , Goldberg Michael , Smolka Marcus B. , Mao Yuxin 
Published: August 2019

AbstractPseudokinases are considered to be the inactive counterparts of conventional protein kinases and comprise approximately 10% of the human and mouse kinomes. Here we report the crystal structure of theLegionella pneumophilaeffector protein, SidJ, in complex with the eukaryotic Ca2+-binding regulator, Calmodulin (CaM). The structure reveals that SidJ contains a protein kinase-like fold domain, which retains a majority of the characteristic kinase catalytic motifs. However, SidJ fails to demonstrate kinase activity. Instead, mass spectrometry and in vitro biochemical analysis demonstrate that SidJ modifies anotherLegionellaeffector SdeA, an unconventional phosphoribosyl ubiquitin ligase, by adding glutamate molecules to a specific residue of SdeA in a CaM-dependent manner. Furthermore, we show that SidJ-mediated polyglutamylation suppresses the ADP-ribosylation activity. Our work further implies that some pseudokinases may possess ATP-dependent activities other than conventional phosphorylation.
Higher-order chromatin organization defines Progesterone Receptor and PAX2 binding to regulate estradiol-primed endometrial cancer gene expression
Authors: La Greca Alejandro , Bellora Nicolás , Le Dily Francois , Jara Rodrigo , Oliete Javier Quilez , Villanueva José Luis , Vidal Enrique , Merino Gabriela , Fresno Cristóbal , Rieschle Inti Tarifa , Vallejo Griselda , Vicent Guillermo P. , Fernández Elmer , Beato Miguel , Saragüeta Patricia 
Published: August 2019

AbstractEstrogen (E2) and Progesterone (Pg), via their specific receptors (ER and PR respectively), are major determinants in the development and progression of endometrial malignancies. Here, we have studied how E2 and the synthetic progestin R5020 affect genomic functions in Ishikawa endometrial cancer cells. Using ChIPseq in cells exposed to the corresponding hormones, we identified cell specific binding sites for ER (ERbs) and PR (PRbs), which mostly correspond to independent sites but both adjacent to sites bound by PAX2. Analysis of long-range interactions by Hi-C showed enrichment of regions co-bound by PR and PAX2 inside TADs that contain differentially progestin-regulated genes. These regions, which we call “progestin control regions” (PgCRs), exhibit an open chromatin state prior to the exposure to the hormone. Our observations suggest that endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR together with partner transcription factors to PgCRs, compartmentalizing hormone-independent open chromatin.
Cost-free lifespan extension via optimisation of gene expression in adulthood supports the developmental theory of ageing
Authors: Lind Martin I. , Carlsson Hanne , Ivimey-Cook Edward , Maklakov Alexei A. 
Published: August 2019

SummaryClassic theory upholds that energy trade-offs between reproduction and somatic maintenance underpin the evolution of ageing and lifespan. In contrast, the developmental theory of ageing (DTA) suggests that organismal senescence is caused by dysregulated gene expression in adulthood due to decline in selection gradients with age. The DTA predicts that age-specific optimisation of gene expression can improve survival without fitness costs. Here we investigated consequences for survival, reproduction, egg size and fitness of early-life, adulthood and post-reproductive onset of RNAi knockdown of five well-described “longevity” genes involved in key biological processes inCaenorhabditis elegansnematodes: nutrient-sensing signalling via insulin/IGF-1 (age-1) and target-of-rapamycin (raga-1) pathways, global protein synthesis (ifg-1), global protein synthesis in somatic cells (ife-2) and mitochondrial respiration (nuo-6). Downregulation of these genes in adulthood and/or during post-reproductive period improves survival, while there was little evidence for a link between impaired reproduction and extended lifespan. Our findings demonstrate that hyper-function of diverse physiological processes after sexual maturation is detrimental for survival. Therefore, optimisation of gene expression in adult organisms can ameliorate ageing and increase fitness.
RIP1 kinase mediates angiogenesis by modulating macrophages in experimental neovascularization
Authors: Ueta Takashi , Ishihara Kenji , Notomi Shoji , Lee Jong-Jer , Maidana Daniel , Efstathiou Nikolaos , Murakami Yusuke , Hasegawa Eiichi , Azuma Kunihiro , Toyono Tetsuya , Paschalis Eleftherios , Aihara Makoto , Miller Joan W. , Vavvas Demetrios G. 
Published: August 2019

ABSTRACTInflammation plays an important role in pathologic angiogenesis. Receptor-interacting protein 1 (RIP1) is highly expressed in inflammatory cells and is known to play an important role in the regulation of apoptosis, necroptosis, and inflammation, however its role in angiogenesis remains elusive. Here, we show that RIP1 is abundantly expressed in infiltrating macrophages during angiogenesis, and genetic or pharmacological inhibition of RIP1 kinase activity using kinase-inactive RIP1K45A/K45Amice or necrostatin-1 attenuates angiogenesis in laser-induced choroidal neovascularization (CNV), Matrigel plug angiogenesis, and alkali injury-induced corneal neovascularization in mice. The inhibitory effect on angiogenesis was mediated by caspase activation through a kinase-independent function of RIP1 and RIP3, and simultaneous caspase inhibition with RIP1 kinase inhibition abrogated the effects of RIP1 kinase inhibition on angiogenesisin vivo. Mechanistically, infiltrating macrophages are the key target for RIP1 kinase inhibition to attenuate pathological angiogenesis, and we observed that the inhibition of RIP1 kinase activity is associated with caspase activation in infiltrating macrophages and decreased expression of pro-angiogenic M2-like markers while M1 marker expressions were sustained. Similarly,in vitro, catalytic inhibition of RIP1 down-regulated M2 marker expressions in IL-4-activated bone marrow-derived macrophages, which was blocked by simultaneous caspase inhibition. Taken together, these results suggest a novel, non-necrotic function of RIP1 kinase activity and suggest that RIP1-mediated modulation of macrophage activation may represent a therapeutic target for the control of angiogenesis-related diseases.SignificancePathological angiogenesis has been implicated in diverse pathologies. Infiltrating macrophages, especially those activated to M2-like phenotype are critically important to support angiogenesis. Whereas the role of RIP1 kinase in the regulation of apoptosis, necroptosis, and inflammation have been well established, its role in angiogenesis remains elusive despite being abundantly expressed in angiogenesis-related infiltrating macrophages. This study demonstrated for the first time that RIP1 kinase inhibition attenuates angiogenesis in multiple mouse models of pathological angiogenesisin vivo. Mechanistically, the inhibitory effect on angiogenesis depends on RIP kinase inhibition-mediated caspase activation in infiltrating macrophages that suppresses M2-like polarization, thereby attenuating pathological angiogenesis.
A cold shock protein from a thermophile bacterium promotes the high-temperature growth of bacteria and fungi through binding to diverse RNA species
Authors: Zhou Zikang , Tang Hongzhi , Wang Weiwei , Zhang Lige , Su Fei , Wu Yuanting , Bai Linquan , Li Sicong , Sun Yuhui , Tao Fei , Xu Ping 
Published: August 2019

AbstractHigh temperatures deleteriously affect cells by damaging cellular structures and changing the behavior of diverse biomolecules, and extensive research about thermophilic microorganisms has elucidated some of the mechanisms that can overcome these effects and allow thriving in high-temperature ecological niches. We here used functional genomics methods to screen out a cold-shock protein (CspL) from a high-productivity lactate producing thermophile strain (Bacillus coagulansstrain 2-6) grown at 37°C and 60°C. We subsequently made the highly striking finding that transgenic expression of CspL conferred massive increases in high temperature growth of other organisms includingE. coli(2.4-fold biomass increase at 45°C) and the eukaryoteS. cerevisiae(a 2.7-fold biomass increase at 34°C). Pursuing these findings, we used bio-layer interferometry assays to characterize the nucleotide-binding function of CspLin vitro, and used proteomics and RNA-Seq to characterize the global effects of CspL on mRNA transcript accumulation and used RIP-Seq to identifyin vivoRNA targets of this nucleotide-binding protein (e.g.rpoE, andrmf, etc.). Finally, we confirmed that a nucleotide-binding-dead variant form of CspL does not have increased growth rates or biomass accumulation effects at high temperatures. Our study thus establishes that CspL can function as a global RNA chaperone.
Intracellular Galectin-9 controls dendritic cell function by maintaining plasma membrane rigidity
Authors: Cano Laia Querol , Tagit Oya , van Duffelen Anne , Dieltjes Shannon , Buschow Sonja I. , Niki Toshiro , Hirashima Mitsuomi , Joosten Ben , van den Dries Koen , Cambi Alessandra , Figdor Carl G. , van Spriel Annemiek B. 
Published: August 2019

SummaryExtracellular Galectins constitute a novel mechanism of membrane protein organisation at the cell surface. Although Galectins are also highly expressed intracellularly, their cytosolic functions are poorly understood. Here, we investigated the role of Galectin-9 in dendritic cell (DC) surface organisation and function. By combining functional, super-resolution and atomic force microscopy experiments to analyse membrane stiffness, we identified intracellular Galectin-9 to be indispensable for plasma membrane integrity and structure in DCs. Galectin-9 knockdown studies revealed intracellular Galectin-9 to directly control cortical membrane structure via modulating Rac1 activity, providing the underlying mechanism of Galectin-9-dependent actin cytoskeleton organisation. Consequent to its role in maintaining plasma membrane structure, phagocytosis studies revealed that Galectin-9 was essential for C-type lectin receptor-mediated pathogen uptake by human DCs. This was confirmed by the impaired phagocytic capacity of Galectin-9-null murine DCs. Together, this study demonstrates a novel role for intracellular Galectin-9 in modulating DC function, which may be evolutionary conserved.
Patterns of genetic variability in genomic regions with low rates of recombination
Authors: Becher Hannes , Jackson Benjamin C. , Charlesworth Brian 
Published: August 2019

SUMMARYSurveys of DNA sequence variation have shown that the level of genetic variability in a genomic region is often strongly positively correlated with its rate of crossing over (CO) [1–3]. This pattern is caused by selection acting on linked sites, which reduces genetic variability and can also cause the frequency distribution of segregating variants to contain more rare variants than expected without selection (skew). These effects of selection may involve the spread of beneficial mutations (selective sweeps, SSWs), the elimination of deleterious mutations (background selection, BGS) or both together, and are expected to be stronger with lower rates of crossing over [1–3]. However, in a recent study of human populations, the skew was reduced in the lowest CO regions compared with regions with somewhat higher CO rates [4]. A similar pattern is seen in the population genomic studies ofDrosophila simulansdescribed here. We propose an explanation for this paradoxical observation, and validate it using computer simulations. This explanation is based on the finding that partially recessive, linked deleterious mutations can increase rather than reduce neutral variability when the product of the effective population size (Ne) and the selection coefficient against homozygous carriers of mutations (s) is ≤ 1, i.e. there is associative overdominance (AOD) rather than BGS [5]. We show that AOD can operate in a genomic region with a low rate of CO, opening up a new perspective on how selection affects patterns of variability at linked sites.
Effects of Shift Work on the Carotid Artery and Cerebral Blood Flow of Spontaneously Hypertensive Rats and Wistar-Kyoto Rats
Authors: Wang YunLei , Zhang Tong , Zhang YuGe , Yu Yan , Bai Fan , Zhang HaoJie , Chi YaFei , Gao Shan 
Published: August 2019

AbstractObjectiveThe objective was to investigate the effects of shift-work (SW) on the carotid arteries.MethodsThis study used two inverted photoperiods (inverted light:dark [ILD]16:8 and ILD12:12) to create the SW model. We recorded the rhythm and performed serological tests, carotid ultrasound, magnetic resonance imaging, and carotid biopsy.ResultsSW induced elevated blood pressure and increased angiotensin-II, apolipoprotein E, blood glucose, and triglycerides. SW increased the carotid intima-media thickness. SW led to the development of carotid arterial thrombosis, reduced cerebral blood flow, and increased the number of collagen fibers, expression of angiotensin receptor and low-density lipoprotein receptor in the carotid arteries. SW decreased 3-hydroxy-3-methylglutaryl-CoA reductase and nitric oxide. SW induced the atherosclerotic plaque in the aorta. Multiple results of SHR were worse than WKY rats.ConclusionSW can induce metabolic disorders and elevated blood pressure. SW can cause intima-media thickening of the carotid artery and aorta atherosclerosis. SW may result in carotid arterial thrombosis and affect cerebral blood flow. Hypertension can aggravate the adverse effects of SW.
Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses
Authors: Rumbou Artemis , Candresse Thierry , Marais Armelle , Svanella-Dumas Laurence , Landgraf Maria , von Bargen Susanne , Büttner Carmen 
Published: August 2019

AbstractHigh-throughput sequencing (HTS), combined with bioinformatics forde novodiscovery and assembly of plant virus or viroid genome reads, has promoted the discovery of abundant novel DNA and RNA viruses and viroids. However, the elucidation of a viral population in a single plant is rarely reported. In five birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), we identified in total five viruses, among which three are novel. The number of identified virus variants in each transcriptome ranged from one to five. The novel species are genetically - fully or partially - characterized, they belong to the generaCarlavirus, IdaeovirusandCapillovirusand they are tentatively namedbirch carlavirus,birch idaeovirus, andbirch capillovirus, respectively. The only virus systematically detected by HTS in symptomatic trees affected by the BRLD was the recently discovered birch leafroll-associated virus. The role of the new carlavirus in BLRD etiology seems at best weak, as it was detected only in one of three symptomatic trees. Continuing studies have to clarify the impact of the carlavirus to the BLRD. The role of theCapillovirusand theIdaeoviruswithin the BLRD complex and whether they influence plant vitality need to be investigated. Our study reveals the viral population in single birch trees and provides a comprehensive overview for the diversities of the viral communities they harbor.
Cannibalism as a feeding strategy for mantis shrimp Oratosquilla oratoria (De Haan, 1844) in the Tianjin coastal zone of Bohai Bay
Authors: Bo Qi-Kang , Lu Yun-Zhao , Mi Hui-Jing , Yu Yan-Guang , Gu De-Xian , You Hong-Zheng , Hao Shuang 
Published: August 2019

AbstractA representative semi-enclosed bay of China, Bohai Bay has experienced severe interference in recent decades and is under threat from rapid human development. Although the mantis shrimp Oratosquilla oratoria plays an important role in the ecosystem and fishery, its feeding ecology and the impact of habitat changes on its feeding habits are poorly known. In this study, we sought to identify the prey consumed by O. oratoria through the separation of stomach contents and to describe its trophic ecology during maturation, from March to July, in the Tianjin coastal zone of Bohai Bay. A total of 594 specimens were collected and 347 (58.59%) stomachs were found to have food remains. More than half of the O. oratoria individuals had poor feeding activity, and the degree of feeding activity of females was higher than that of males, but there was no significant difference in the visual fullness index and the fullness weight index (FWI) between sexes for each month. And the feeding activities of O. oratoria were consistent over the study months. A total of 207 prey items yielded 231 readable sequences and 24 different taxa were identified. Prey detected in O. oratoria consisted mainly of crustaceans, which accounted for 71.86 % of the clones detected; 16.02% corresponded to fishes, 8.23% corresponded to mollusks and the remaining 3.90% corresponded to other marine organisms. Cannibalism (occured frequently, 69.08%) in this study was noticeably higher than that seen in previous studies and confirmed that cannibalism may be a significant feeding strategy in the mantis shrimp O. oratoria in the Tianjin coastal zone of Bohai Bay. The ecological environment in Bohai Bay has been affected by anthropogenic activities and the macrofaunal biodiversity and abundance have noticeably declined, which might make the food scarce for the mantis shrimp O. oratoria. Then, the starvation obviously increased cannibalistic tendencies.
Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms
Authors: Fribourgh Jennifer L. , Srivastava Ashutosh , Sandate Colby R. , Michael Alicia K. , Hsu Peter L. , Rakers Christin , Nguyen Leslee T. , Torgrimson Megan R. , Parico Gian Carlo G. , Tripathi Sarvind , Zheng Ning , Lander Gabriel C. , Hirota Tsuyoshi , Tama Florence , Partch Carrie L. 
Published: August 2019

SummaryCircadian rhythms are generated by a transcription-based feedback loop where CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify a key biochemical and structural difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. While both cryptochromes bind the BMAL1 transactivation domain with similar affinity to sequester it from coactivators, CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We identify a dynamic loop in the secondary pocket that regulates differential binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2 forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1 both with and without PER2.
An advantage for targets located horizontally to the cued location
Authors: Clevenger John , Yang Pei-Ling , Beck Diane M. 
Published: August 2019

AbstractOver the years a number of researchers have reported enhanced performance of targets located horizontally to a cued location relative to those located vertically. However, many of these reports could stem from a known meridian asymmetry in which stimuli on the horizontal meridian show a performance advantage relative to those on the vertical meridian. Here we show a horizontal advantage for target and cue locations that reside outside the zone of asymmetry; that is, targets that appear horizontal to the cue, but above or below the horizontal meridian, are more accurate than those that appear vertical to the cue, but again either above or below the horizontal meridian (Experiments 1 and 4). This advantage does not extend to non-symmetrically located targets in the opposite hemifield (Experiment 2), nor horizontally located targets within the same hemifield (Experiment 3). These data raise the possibility that display designs in which the target and cue locations are positioned symmetrically across the vertical midline may be underestimating the cue validity effect.
Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS
Authors: Hsu Peter L. , Shi Hui , Leonen Calvin , Kang Jianming , Chatterjee Champak , Zheng Ning 
Published: August 2019

SUMMARYThe COMPASS complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well-known as a prerequisite histone mark for COMPASS activity, how the H2Bub-H3K4me crosstalk is catalyzed by COMPASS remains unclear. Here, we report the cryo-EM structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that auto-inhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By unmasking the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.