bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of a functional ribozyme from short oligomers by enhanced non-enzymatic ligation
Authors: Zhou Lijun , O’Flaherty Derek K. , Szostak Jack W. 
Published: July 2019

AbstractThe non-enzymatic replication of the primordial genetic material is thought to have enabled the evolution of the first ribozymes, leading to early forms of RNA-based life. However, the reported rate of chemical RNA ligation is extremely slow. Here we show that the rate of ligation can be greatly enhanced by employing a 3′-amino group at the 3′-end of each oligonucleotide, in combination with an N-alkyl imidazole organocatalyst. These modifications allow the rapid copying of long RNA templates by multi-step ligation of tetranucleotides, as well as the assembly of long oligonucleotides from short template splints. Our work shows that a functional RNA ligase ribozyme can be assembled from relatively short oligonucleotides, demonstrating a transition from non-enzymatic ligation to enzymatic ligation. We suggest that the genomes of primitive protocells could have consisted of relatively easily replicated oligonucleotides as short as 10 to 12 nucleotides in length.
Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping
Authors: Ramilowski Jordan A , Yip Chi Wai , Agrawal Saumya , Chang Jen-Chien , Ciani Yari , Kulakovskiy Ivan V , Mendez Mickaël , Ooi Jasmine Li Ching , Ouyang John F , Parkinson Nick , Petri Andreas , Roos Leonie , Severin Jessica , Yasuzawa Kayoko , Abugessaisa Imad , Akalin Altuna , Antonov Ivan V , Arner Erik , Bonetti Alessandro , Bono Hidemasa , Borsari Beatrice , Brombacher Frank , Cameron Chris JF , Cannistraci Carlo Vittorio , Cardenas Ryan , Cardon Melissa , Chang Howard , Dostie Josée , Ducoli Luca , Favorov Alexander , Fort Alexandre , Garrido Diego , Gil Noa , Gimenez Juliette , Guler Reto , Handoko Lusy , Harshbarger Jayson , Hasegawa Akira , Hasegawa Yuki , Hashimoto Kosuke , Hayatsu Norihito , Heutink Peter , Hirose Tetsuro , Imada Eddie L , Itoh Masayoshi , Kaczkowski Bogumil , Kanhere Aditi , Kawabata Emily , Kawaji Hideya , Kawashima Tsugumi , Kelly S. Thomas , Kojima Miki , Kondo Naoto , Koseki Haruhiko , Kouno Tsukasa , Kratz Anton , Kurowska-Stolarska Mariola , Kwon Andrew Tae Jun , Leek Jeffrey , Lennartsson Andreas , Lizio Marina , López-Redondo Fernando , Luginbühl Joachim , Maeda Shiori , Makeev Vsevolod J , Marchionni Luigi , Medvedeva Yulia A , Minoda Aki , Müller Ferenc , Muñoz-Aguirre Manuel , Murata Mitsuyoshi , Nishiyori Hiromi , Nitta Kazuhiro R , Noguchi Shuhei , Noro Yukihiko , Nurtdinov Ramil , Okazaki Yasushi , Orlando Valerio , Paquette Denis , Parr Callum JC , Rackham Owen JL , Rizzu Patrizia , Martinez Diego Fernando Sánchez , Sandelin Albin , Sanjana Pillay , Semple Colin AM , Shibayama Youtaro , Sivaraman Divya M , Suzuki Takahiro , Szumowski Suzannah C , Tagami Michihira , Taylor Martin S , Terao Chikashi , Thodberg Malte , Thongjuea Supat , Tripathi Vidisha , Ulitsky Igor , Verardo Roberto , Vorontsov Ilya , Yamamoto Chinatsu , Young Robert S , Baillie J Kenneth , Forrest Alistair RR , Guigó Roderic , Hoffman Michael M , Hon Chung Chau , Kasukawa Takeya , Kauppinen Sakari , Kere Juha , Lenhard Boris , Schneider Claudio , Suzuki Harukazu , Yagi Ken ,   FANTOM consortium, de Hoon Michiel , Shin Jay W , Carninci Piero 
Published: July 2019

AbstractLong non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNA exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest to-date lncRNA knockdown dataset with molecular phenotyping (over 1,000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
Heritability of the Mouse Brain Connectome
Authors: Wang Nian , Anderson Robert J , Ashbrook David G , Gopalakrishnan Vivek , Park Youngser , Priebe Carey E , Qi Yi , Vogelstein Joshua T , Williams Robert W , Johnson G Allan 
Published: July 2019

SUMMARYGenome-wide association studies have demonstrated significant links between human brain structure and common DNA variants. Similar studies with rodents have been challenging because of smaller brain volumes. Using high field MRI (9.4T) and compressed sensing, we have achieved microscopic resolution and sufficiently high throughput for rodent population studies. We generated whole brain structural MRI and diffusion connectomes for four diverse isogenic lines of mice (C57BL/6J, DBA/2J, CAST/EiJ, and BTBR) at spatial resolution 20,000 times higher than human connectomes. We derived volumes, scalar diffusion metrics, and estimates of residual technical error for 166 regions in each hemisphere and connectivity between the regions. Volumes of discrete brain regions had the highest mean heritability (0.71 ± 0.23 SD, n = 332), followed by fractional anisotropy (0.54 ± 0.26), radial diffusivity (0.34 ± 0.022), and axial diffusivity (0.28 ± 0.19). Connection profiles were statistically different in 280 of 322 nodes across all four strains. Nearly 150 of the connection profiles were statistically different between the C57BL/6J, DBA/2J, and CAST/EiJ lines.
Warm nights disrupt global transcriptional rhythms in field-grown rice panicles
Authors: Desai Jigar S. , Lawas Lovely Mae F. , Valente Ashlee M. , Leman Adam R. , Grinevich Dmitry O. , Jagadish S.V. Krishna , Doherty Colleen J. 
Published: July 2019

ABSTRACTIn rice, a small increase in nighttime temperatures reduces grain yield and quality. How warm nighttime temperatures (WNT) produce these detrimental effects is not well understood, especially in field conditions where the normal day to night temperature fluctuation exceeds the mild increase in nighttime temperature. We observed genome-wide disruption of gene expression timing during the reproductive phase on field-grown rice panicles acclimated to 2-3°C WNT. Rhythmically expressed transcripts were more sensitive to WNT than non-rhythmic transcripts. The system-wide transcriptional perturbations suggest that WNT disrupts the tight temporal coordination between internal molecular events and the environment resulting in reduced productivity. We identified transcriptional regulators whose predicted targets are enriched for sensitivity to WNT. The affected transcripts and candidate regulators identified through our network analysis explain molecular mechanisms driving sensitivity to WNT and candidates that can be targeted to enhance tolerance to WNT.
Biotransformation of D-xylose to D-xylonic acid coupled to medium chain length polyhydroxyalkanoate production in cellobiose-grownPseudomonas putidaEM42
Authors: Dvořák Pavel , Kováč Jozef , de Lorenzo Víctor 
Published: July 2019

SummaryCo-production of two or more desirable compounds from low-cost substrates by a single microbial catalyst could greatly improve the economic competitiveness of many biotechnological processes. However, reports demonstrating the adoption of such co-production strategy are still scarce. In this study, the ability of genome-edited strainPsudomonas putidaEM42 to simultaneously valorise D-xylose and D-cellobiose -two important lignocellulosic carbohydrates -by converting them into the platform chemical D-xylonic acid and medium chain length polyhydroxyalkanoates, respectively, was investigated. Biotransformation experiments performed withP. putidaresting cells showed that promiscuous periplasmic glucose oxidation route can efficiently generate extracellular xylonate with high yield reaching 0.97 g per g of supplied xylose. Xylose oxidation was subsequently coupled to the growth ofP. putidawith cytoplasmic β-glucosidase BglC fromThermobifida fuscaon D-cellobiose. This disaccharide turned out to be a better co-substrate for xylose-to-xylonate biotransformation than monomeric glucose. This was because unlike glucose, cellobiose did not block oxidation of the pentose by periplasmic glucose dehydrogenase Gcd, but, similarly to glucose, it was a suitable substrate for polyhydroxyalkanoate formation inP. putida. Co-production of extracellular xylose-born xylonate and intracellular cellobiose-born medium chain length polyhydroxyalkanoates was established in proof-of-concept experiments withP. putidagrown on the disaccharide. This study highlights the potential ofP. putidaEM42 as a microbial platform for the production of xylonic acid, identifies cellobiose as a new substrate for mcl-PHA production, and proposes a fresh strategy for the simultaneous valorisation of xylose and cellobiose.
Whole-chromosome hitchhiking driven by a male-killing endosymbiont
Authors: Martin Simon H. , Singh Kumar Saurabh , Gordon Ian J. , Omufwoko Kennedy Saitoti , Collins Steve , Warren Ian A. , Munby Hannah , Brattström Oskar , Traut Walther , Martins Dino J. , Smith David A. S. , Jiggins Chris D. , Bass Chris , ffrench-Constant Richard H. 
Published: July 2019

AbstractNeo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterflyDanaus chrysippuspresents an intriguing case study because it is restricted to a single ‘contact zone’ population, involves a putative colour patterning supergene, and co-occurs with infection by the the male-killing endosymbiontSpiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the ‘BC supergene’, a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genesyellowandarrowin this region control the forewing colour pattern differences betweenD. chrysippussubspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within ∼2200 years. We also assembled the genome of the male-killingSpiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene, and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the unlinked genomes of host and endosymbiont, with dramatic consequences.
Gene expression of endangered coral (Orbicella spp.) in the Flower Garden Banks National Marine Sanctuary after Hurricane Harvey
Authors: Wright Rachel M. , Correa Adrienne M.S. , Quigley Lucinda A. , Davies Sarah W. 
Published: July 2019

AbstractAbout 160 km south of the Texas–Louisiana border, the East and West Flower Garden Banks (FGB) have maintained >50% coral cover with infrequent and minor incidents of disease or bleaching since monitoring began in the 1970s. However, a storm that generated coastal flooding, which ultimately interacted with the reef system, triggered a mortality event in 2016 that killed 2.6% of the East FGB. To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB corals at two times: September 2017, when salinity was reduced; and one month later when salinity had returned to typical levels (~36 ppt in October 2017). Tissue samples (N = 47) collected midday were immediately preserved for gene expression profiling from two congeneric coral species (Orbicella faveolata and Orbicella franksi) from the East and West FGB to determine the physiological consequences of storm-derived runoff. In the coral, differences between host species and sampling time points accounted for the majority of differentially expressed genes. Gene ontology enrichment for genes differentially expressed immediately after Hurricane Harvey indicated increases in cellular oxidative stress responses. Although tissue loss was not observed on FGB reefs following Hurricane Harvey, our results suggest that poor water quality following this storm caused FGB corals to experience sub-lethal stress. We also found dramatic expression differences across sampling time points in the coral’s algal symbiont, Breviolum minutum. Some of these differentially expressed genes may be involved in the symbionts’ response to changing environments, whereas a group of differentially expressed post-transcriptional RNA modification genes also suggest a critical role of post-transcriptional processing in symbiont acclimatization. In this study, we cannot disentangle the effects of reduced salinity from the collection time point, so these expression patterns may also be related to seasonality. These findings highlight the urgent need for continued monitoring of these reef systems to establish a baseline for gene expression of healthy corals in the FGB system across seasons, as well as the need for integrated solutions to manage stormwater runoff in the Gulf of Mexico.
Intrinsic activity temporal structure reactivity to behavioural state change is correlated with depressive symptoms
Authors: Duncan Niall W. , Hsu Tzu-Yu , Cheng Paul Z. , Wang Hsin-Yi , Lee Hsin-Chien , Lane Timothy J. 
Published: July 2019

AbstractThe brain’s intrinsic activity plays a fundamental role in its function. In normal conditions this activity is responsive to behavioural context, changing as an individual switches between directed tasks and task-free conditions. A key feature of such changes is the movement of the brain between corresponding critical and sub-critical states, with these dynamics supporting efficient cognitive processing. Breakdowns in processing efficiency can occur, however, in brain disorders such as depression. It was therefore hypothesised that depressive symptoms would be related to reduced intrinsic activity responsiveness to changes in behavioural state. This was tested in a mixed group of major depressive disorder patients (n = 26) and healthy participants (n = 37) by measuring intrinsic EEG activity temporal structure, quantified with detrended fluctuation analysis (DFA), in eyes-closed and eyes-open task-free states and contrasting between the conditions. The degree to which DFA values changed between the states was found to be negatively correlated with depressive symptoms. DFA values did not differ between states at all in those with high symptom levels, meaning that the brain remained in a less flexible sub-critical condition. This sub-critical condition in the eyes-closed state was further found to correlate with levels of maladaptive rumination. This may reflect a general cognitive inflexibility resulting from a lack in neural activity reactivity that may predispose people to overly engage in self-directed attention. These results provide an initial link between intrinsic activity reactivity and psychological features found in psychiatric disorders.
Gut microbiota structure differs between honey bees in winter and summer
Authors: Kešnerová Lucie , Emery Olivier , Troilo Michaël , Liberti Joanito , Erkosar Berra , Engel Philipp 
Published: July 2019

AbstractAdult honey bees harbor a specialized gut microbiota of relatively low complexity. While seasonal differences in community composition have been reported, previous studies have focused on compositional changes rather than differences in absolute bacterial loads. Moreover, little is known about the gut microbiota of winter bees, which live much longer than bees during the foraging season, and which are critical for colony survival. We quantified seven core members of the bee gut microbiota in a single colony over two years and characterized the community composition in 14 colonies during summer and winter. Our data shows that total bacterial loads substantially differ between foragers, nurses, and winter bees. Long-lived winter bees had the highest bacterial loads and the lowest community α-diversity, with a characteristic shift towards high levels of Bartonella and Commensalibacter, and a reduction of opportunistic colonizers. Using gnotobiotic bee experiments, we show that diet is a major contributor to the observed differences in bacterial loads. Overall, our study reveals that the gut microbiota of winter bees is remarkably different from foragers and nurses. Considering the importance of winter bees for colony survival, future work should focus on the role of the gut microbiota in winter bee health and disease.
Triple visual hemifield maps in optic chiasm hypoplasia
Authors: Ahmadi Khazar , Fracasso Alessio , Puzniak Robert J. , Gouws Andre D. , Yakupov Renat , Speck Oliver , Kaufmann Joern , Pestilli Franco , Dumoulin Serge O. , Morland Antony B. , Hoffmann Michael B. 
Published: July 2019

AbstractIn humans, each hemisphere comprises an overlay of two visuotopic maps of the contralateral visual field, one from each eye. Is the capacity of the visual cortex limited to these two maps or are plastic mechanisms available to host more maps? Using an integrative approach of submillimeter fMRI, diffusion-weighted imaging and population receptive field mapping, we found three hemiretinal inputs to converge onto the left hemisphere in a rare individual with chiasma hypoplasia. This generates extremely atypical responses in striate and extrastriate cortices, specifically an overlay of three hemifield representations. Unexpectedly, the effects of this large abnormality on visual function in daily life are not easily detected. We conclude that developmental plasticity including the re-wiring of local intra- and cortico-cortical connections is pivotal to support the coexistence and functioning of three hemifield maps within one hemisphere.
Identification of Polycomb Repressive Complex 1 and 2 Core Components in Hexaploid Bread Wheat
Authors: Strejčková Beáta , Čegan Radim , Pecinka Ales , Milec Zbyněk , Šafář Jan 
Published: July 2019

ABSTRACTPolycomb repressive complex 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3, while Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Although these biochemical functions are evolutionarily conserved, studies in animals and plants, mainly Arabidopsis thaliana, showed that specific subunits have evolved into small gene families, with individual members acting at different developmental stages or responding to specific environmental stimuli. However, the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization in commonly grown winter wheat.
HIPK4 is essential for murine spermiogenesis
Authors: Crapster J. Aaron , Rack Paul G. , Hellmann Zane J. , Elias Joshua E. , Perrino John J. , Behr Barry , Li Yanfeng , Lin Jennifer , Zeng Hong , Chen James K. 
Published: July 2019

ABSTRACTMammalian spermiogenesis is a remarkable cellular transformation, during which round spermatids elongate into chromatin-condensed spermatozoa. The signaling pathways that coordinate this process are not well understood, and we demonstrate here that homeodomain-interacting protein kinase 4 (HIPK4) is essential for spermiogenesis and male fertility in mice. HIPK4 is predominantly expressed in round and early elongating spermatids, and Hipk4 knockout males are sterile, exhibiting phenotypes consistent with oligoasthenoteratozoospermia. Hipk4 mutant sperm have reduced oocyte binding and are incompetent for in vitro fertilization, but they can still produce viable offspring via intracytoplasmic sperm injection. Ultrastructural analyses of HIPK4-null male germ cells reveal defects in the filamentous actin (F-actin)-scaffolded acroplaxome during spermatid elongation and abnormal head morphologies in mature spermatozoa. We further observe that HIPK4 overexpression induces branched F-actin structures in cultured fibroblasts, supporting a role for this kinase in cytoskeleton remodeling. Our findings establish HIPK4 as an essential regulator of sperm head shaping and potential target for male contraception.
Decreased Directed Functional Connectivity in the Psychedelic State
Authors: Barnett Lionel , Muthukumaraswamy Suresh D. , Carhart-Harris Robin L. , Seth Anil K. 
Published: July 2019

AbstractNeuroimaging studies of the psychedelic state offer a unique window onto the neural basis of conscious perception and selfhood. Despite well understood pharmacological mechanisms of action, the large-scale changes in neural dynamics induced by psychedelic compounds remain poorly understood. Using source-localised, steady-state MEG recordings, we describe changes in functional connectivity following the controlled administration of LSD, psilocybin and low-dose ketamine, as well as, for comparison, the (non-psychedelic) anticonvulsant drug tiagabine. We compare both undirected and directed measures of functional connectivity between placebo and drug conditions. We observe a general decrease in directed functional connectivity for all three psychedelics, as measured by Granger causality, throughout the brain. These data support the view that the psychedelic state involves a breakdown in patterns of functional organisation or information flow in the brain. In the case of LSD, the decrease in directed functional connectivity is coupled with an increase in undirected functional connectivity, which we measure using correlation and coherence. This surprising opposite movement of directed and undirected measures is of more general interest for functional connectivity analyses, which we interpret using analytical modelling. Overall, our results uncover the neural dynamics of information flow in the psychedelic state, and highlight the importance of comparing multiple measures of functional connectivity when analysing time-resolved neuroimaging data.