bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and antimicrobial properties of bacteria isolated from naturally decaying wood
Authors: Scheublin Tanja R. , Kielak Anna M. , van den Berg Marlies , van Veen Johannes A. , de Boer Wietse 
Published: January 2020

AbstractResearch on wood decay in forest ecosystems has traditionally focused on wood-rot fungi, which lead the decay process through attack of the lignocellulose complex. The role of bacteria, which can be highly abundant, is still unclear. Wood-inhabiting bacteria are thought to be nutritionally dependent on decay activities of wood-rot fungi. Therefore, we hypothesized that these bacteria are not antagonistic against wood-rot fungi whereas antagonistic activity against other bacteria may be high (resource competition). This was examined for decaying wood in temperate forests. We found that the abundance of cultivable bacteria in decaying wood can be highly variable. The general pattern is an increase of bacteria with progressive decay, but we also identified several fungi that were apparently able to exclude bacteria from their woody territory. We established a bacterial collection which is highly representative for decaying wood with typical wood-inhabiting taxa:Xanthomonadaceae,Acetobacteraceae,Caulobacteraceae,Methylovirgula,Sphingomonas,BurkholderiaandGranulicella.In vitroantagonistic activity against other bacteria and fungi was evaluated. In contrast to our hypothesis, we found surprisingly low antagonistic activity against bacteria (<2% of isolates), while antagonism against fungi was more prevalent. These results may point at a prominent role of mycophagy (growth at the expense of living fungi) among wood-inhabiting bacteria.
Geminin is required for Hox gene regulation to pattern the developing limb
Authors: Lewis Emily M.A. , Sankar Savita , Tong Caili , Patterson Ethan , Waller Laura E. , Gontarz Paul , Zhang Bo , Ornitz David M. , Kroll Kristen L. 
Published: January 2020

AbstractDevelopment of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5’ Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5’ Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.SummaryThis work identifies a new role for Geminin in mouse limb development. Geminin is a nuclear protein that regulates gene expression to control several other aspects of vertebrate development.
Brain-wide mapping of water flow perception in zebrafish
Authors: Vanwalleghem Gilles , Schuster Kevin , Taylor Michael A. , Favre-Bulle Itia A. , Scott Ethan K. 
Published: January 2020

AbstractInformation about water flow, detected by lateral line organs, is critical to the behavior and survival of fish and amphibians. While certain specific aspects of water flow processing have been revealed through electrophysiology, we lack a comprehensive description of the neurons that respond to water flow and the network that they form. Here, we use brain-wide calcium imaging in combination with microfluidic stimulation to map out, at cellular resolution, all neurons involved in perceiving and processing water flow information in larval zebrafish. We find a diverse array of neurons responding to forward flow, reverse flow, or both. Early in this pathway, in the lateral line ganglia, these are almost exclusively neurons responding to the simple presence of forward or reverse flow, but later processing includes neurons responding specifically to flow onset, representing the accumulated volume of flow during a stimulus, or encoding the speed of the flow. The neurons reporting on these more nuanced details are located across numerous brain regions, including some not previously implicated in water flow processing. A graph theory-based analysis of the brain-wide water flow network shows that a majority of this processing is dedicated to forward flow detection, and this is reinforced by our finding that details like flow velocity and the total volume of accumulated flow are only encoded for the simulated forward direction. The results represent the first brain-wide description of processing for this important modality, and provide a departure point for more detailed studies of the flow of information through this network.Significance statementIn aquatic animals, the lateral line is important for detecting water flow stimuli, but the brain networks that interpret this information remain mysterious. Here, we have imaged the activity of individual neurons across the entire brains of larval zebrafish, revealing all response types and their brain locations as water flow processing occurs. We find some neurons that respond to the simple presence of water flow, and others that are attuned to the flow’s direction, speed, duration, or the accumulated volume of water that has passed during the stimulus. With this information, we modeled the underlying network, describing a system that is nuanced in its processing of water flow simulating forward motion but rudimentary in processing flow in the reverse direction.
Strigolactone defective mutants ofArabidopsisexhibit delayed sepal senescence
Authors: Xu Xi , Jibran Rubina , Wang Yanting , Dong Lemeng , Flokova Kristyna , Esfandiari Azadeh , McLachlan Andrew , Heiser Axel , Sutherland-Smith Andrew , Bouwmeester Harro , Dijkwel Paul , Hunter Donald 
Published: January 2020

AbstractFlower sepals are critical for flower development and vary greatly in lifespan depending on their function postpollination. However, very little is known on what controls sepal longevity. Using a sepal senescence mutant screen, we directly connected strigolactones (SL) with sepal longevity. We identified twoArabidopsismutants that harbour novel mutations in the SL biosynthetic geneMORE AXILLARY GROWTH1(MAX1) and receptorDWARF14(AtD14). The mutation inAtD14caused a substitution of the catalytic Ser-97 to Phe in the enzyme active site. The lesion inMAX1changed a highly conserved Gly-469 to Arg in the haem-iron ligand signature of the cytochrome P450 protein, which caused loss-of-function of MAX1. nCounter-based transcriptional analysis suggested an interaction between SL and sugar signalling in controlling dark-induced inflorescence senescence. The results uncover an important function for SL in regulating floral organ senescence in addition to its other diverse functions in plant development and stress response.One-sentence summaryTwo novel mutants in the strigolactone pathway demonstrate a role for the hormone in sepal senescence, and transcriptional analysis highlights interaction between strigolactones and sugar signalling.
Genome wide association study pinpoints key agronomic QTLs in African riceOryza glaberrima
Authors: Cubry Philippe , Pidon Hélène , Ta Kim Nhung , Tranchant-Dubreuil Christine , Thuillet Anne-Céline , Holzinger Maria , Adam Hélène , Kam Honoré , Chrestin Harold , Ghesquière Alain , François Olivier , Sabot François , Vigouroux Yves , Albar Laurence , Jouannic Stefan 
Published: January 2020

AbstractBackgroundAfrican rice,Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species.ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance toRice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (includingRymv1for resistance andSP1,Ghd7.1,APO1andOsMADS1for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations.ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within theO. glaberrimagenome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.
Information theory tests critical predictions of plant defense theory for specialized metabolism
Authors: Li Dapeng , Halitschke Rayko , Baldwin Ian T. , Gaquerel Emmanuel 
Published: January 2020

AbstractDifferent plant defense theories have provided important theoretical guidance in explaining patterns in plant specialized metabolism, but their critical predictions remain to be tested. Here, we systematically explored the metabolomes ofNicotiana attenuata, from single plants to populations, as well as of closely-related species, using unbiased MS/MS analyses and processed the abundances of compound-spectrum-based MS features within an information theory framework to test critical predictions of Optimal Defense (OD) and Moving Target (MT) theories. Information components of herbivory-elicited plant metabolomes were fully consistent with the OD theory predictions and contradicted the main prediction of the MT theory. From micro- to macro-evolutionary scales, jasmonate signaling was identified as the master determinant of OD while ethylene signaling provided fine-tuning for herbivore-specific responses annotated via MS/MS molecular networks.One-sentence summaryInformation theory tests defense theory predictions by providing a common currency for comparison of specialized metabolomes
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: January 2020

AbstractCooperative 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 intracranial recordings in four pre-surgical epilepsy patients (two male, two female), we discovered ripples within human amygdala during non-rapid eye movement (NREM) sleep. Like hippocampal ripples, amygdala ripples are strongly associated with sharp waves, are linked to sleep spindles, and tend to co-occur with their hippocampal counterparts. Moreover, sharp waves and ripples are temporally linked across the two brain structures, with amygdala ripples occurring during hippocampal sharp waves andvice 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.
Basal-like and Classical cells coexistence in pancreatic cancer revealed by single cell analysis
Authors: Juiz Natalia , Elkaoutari Abdessamad , Bigonnet Martin , Gayet Odile , Roques Julie , Nicolle Rémy , Iovanna Juan , Dusetti Nelson 
Published: January 2020

SummaryPancreatic ductal adenocarcinoma (PDAC) is composed of stromal, immune and epithelial cells. Transcriptomic analysis of the epithelial compartment allows a binary classification into mainly two phenotypic subtypes, classical and basal-like. However, little is known about the intra-tumor heterogeneity of the epithelial component. Growing evidences suggest that this two side phenotypic segregation is not so clear and that both could coexist in a single tumor. In order to elucidate this hypothesis, we performed single-cell transcriptomic analyses using combinational barcoding on epithelial cells from 6 different classical PDAC obtained by Endoscopic Ultrasound (EUS) with Fine Needle Aspiration (FNA). In order to purify the epithelial compartment, PDAC were grown as Biopsy Derived Pancreatic Cancer Organoids. Single cell transcriptomic analysis allowed the identification of 4 main cell clusters present in different proportions in all tumors. Remarkably, although these tumors were classified as Classical, one of the clusters corresponded to a basal-like. These results depict the unanticipated high heterogeneity of pancreatic cancers and demonstrated that basal-like cells with a high aggressive phenotype are more widespread than expected.
Human papillomavirus 16 positive cervical cancer in Guatemala: The D2 and D3 sublineages differ in integration rate and age of diagnosis
Authors: Lou Hong , Boland Joseph F. , Torres-Gonzalez Edmundo , Albanez Anaseidy , Zhou Weiyin , Steinberg Mia , Diaw Lena , Mitchell Jason , Roberson David , Cullen Michael , Garland Lisa , Bass Sara , Burk Robert , Yeager Meredith , Wentzensen Nicolas , Schiffman Mark , Alvirez Enrique , Gharzouzi Eduardo , Mirabello Lisa , Dean Michael 
Published: January 2020

AbstractHuman papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, D) have been described, as well as multiple sub-lineages. To identify molecular events associated with HPV16 carcinogenesis we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 64% (60/94) of the samples had integrated HPV16 sequences, and integration was associated with an earlier age of diagnosis (P=0.0007) and pre-menopausal disease. HPV16 integration sites were broadly distributed in the genome but in one tumor, HPV16 integrated into the promoter of the interferon regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the interferon response to viral infection. The HPV16 D2 and D3 sub-lineages were found in 23% and 30% of the tumors, respectively and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration (P=0.011), earlier age of diagnosis (P=0.012), and a lower rate of somatic mutation (P=0.03). Whereas D3-positive tumors are less likely to integrate, have later age-of-diagnosis, and a higher rate of somatic mutation. In conclusion, Guatemalan cervical tumors have a high frequency of the very high-risk HPV16 D2 and D3 sub-lineages and cervical cancer patients with these variants of HPV16 differ in histology, age of- diagnosis, integration, and somatic mutation frequency. In summary, related lineages of HPV16 have different features of oncogenicity.
SparkINFERNO: A scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants
Authors: Kuksa Pavel P. , Lee Chien-Yueh , Amlie-Wolf Alexandre , Gangadharan Prabhakaran , Mlynarski Elizabeth E. , Chou Yi-Fan , Lin Han-Jen , Issen Heather , Greenfest-Allen Emily , Valladares Otto , Leung Yuk Yee , Wang Li-San 
Published: January 2020

AbstractSummaryWe report SparkINFERNO (Spark-based INFERence of the molecular mechanisms of NOn-coding genetic variants), a scalable bioinformatics pipeline characterizing noncoding GWAS association findings. SparkINFERNO prioritizes causal variants underlying GWAS association signals and reports relevant regulatory elements, tissue contexts, and plausible target genes they affect. To achieve this, the SparkINFERNO algorithm integrates GWAS summary statistics with large-scale collection of functional genomics datasets spanning enhancer activity, transcription factor binding, expression quantitative trait loci, and other functional datasets across more than 400 tissues and cell types. Scalability is achieved by an underlying API implemented using Apache Spark and Giggle-based genomic indexing. We evaluated SparkINFERNO on large GWAS studies and show that SparkINFERNO is more than 60-times efficient and scales with data size and amount of computational resources.AvailabilitySparkINFERNO runs on clusters or a single server with Apache Spark environment, and is available athttps://bitbucket.org/wanglab-upenn/SparkINFERNOorhttps://hub.docker.com/r/wanglab/spark-inferno.Contactlswang@pennmedicine.upenn.edu
Role of Sulphate Transporter(PiSulT)of Endophytic FungusSerendipita indicain Plant Growth and Development
Authors: Narayan Om Prakash , Verma Nidhi , Jogawat Abhimanyu , Dua Meenakshi , Johri Atul Kumar 
Published: January 2020

ABSTRACTSulfur is an important macronutrient required for the growth, development of plants and is a key component of many metabolic pathways. We have functionally characterized a high-affinity sulphate transporter (PiSulT) from an endophytic fungusSerendipita indica. ThePiSulTbelongs to the major facilitator superfamily (MFS) of membrane transporter. ThePiSulTfunctionally complements the yeast sulphate transporter mutant HK14.PiSulTis a high-affinity sulphate transporter, havingKm15μM. We found enhanced expression ofPiSulTin external fungal hyphae which helps the fungus in the acquisition of sulphate from the soil. When knockdown (KD)-PiSulT-P.indicacolonized with the plant, it results in an 8-fold reduction in the transfer of sulphate to the colonized plants as compared to the plants colonized with the WTS. indica, which suggests thatPiSulTis playing a role in sulphate transfer from soil to host plant. Further, plants colonized with the WTS. indicawere found to be healthy in comparison to the plants colonized with the KD-PiSulT-P.indica. Additionally,S. indicacolonization provides a positive effect on total sulfur content and on plant metabolites like sulfate ions and glutathione, particularly under low sulphate condition. We observed that the expression of sulfur assimilation pathway genes ofS. indicaand plant is dependent on the availability of sulphate and on the colonization with the plant. Our study highlights the importance ofPiSulTin the improvement of sulfur nutrition of host plant particularly under low sulphate condition and in plant growth development. This study will open new vistas to useS. indicaas a bio-fertilizer in the sulphate deficient field to improve crop production.One-Sentence SummaryHigh-affinity sulphate transporter ofSerendipita indica(PiSulT) transfer sulphate from soil to plant under low sulphate condition and improve plant growth and development.
The copy-number and varied strengths of MELT motifs in Spc105 balance the strength and responsiveness the Spindle Assembly Checkpoint
Authors: Roy Babhrubahan , Han Simon JY , Fontan Adrienne N. , Joglekar Ajit P. 
Published: January 2020

SummaryThe Spindle Assembly Checkpoint (SAC) maintains genome stability while enabling timely anaphase onset. To maintain genome stability, the SAC must be strong so that it delays cell division even if one chromosome is unattached, but for timely anaphase onset, it must be responsive to silencing mechanisms. How it meets these potentially antagonistic requirements is unclear. Here we show that the balance between SAC strength and responsiveness is determined by the number of ‘MELT’ motifs in the kinetochore protein Spc105/KNL1 and their Bub3-Bub1 binding affinities. Spc105/KNL1 must contain many strong MELT motifs to prevent chromosome missegregation, but not too many, because this delays SAC silencing and anaphase onset. We demonstrate this by constructing a Spc105 variant that trades SAC responsiveness for significantly improved chromosome segregation accuracy. We propose that the necessity of balancing SAC strength with responsiveness drives the evolutionary trend of MELT motif number amplification and degeneration of their functionally optimal amino acid sequence.
The transcription regulatory code of a plant leaf
Authors: Tu Xiaoyu , Mejía-Guerra María Katherine , Franco Jose A Valdes , Tzeng David , Chu Po-Yu , Dai Xiuru , Li Pinghua , Buckler Edward S , Zhong Silin 
Published: January 2020

AbstractThe transcription regulatory network underlying essential and complex functionalities inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex regulatory netowrk. Here, we used ChIP-seq to determine the binding profiles of 104 TF expressed in the maize leaf. With this large dataset, we could reconstruct a transcription regulatory network that covers over 77% of the expressed genes, and reveal its scale-free topology and functional modularity like a real-world network. We found that TF binding occurs in clusters covering ∼2% of the genome, and shows enrichment for sequence variations associated with eQTLs and GWAS hits of complex agronomic traits. Machine-learning analyses were used to identify TF sequence preferences, and showed that co-binding is key for TF specificity. The trained models were used to predict and compare the regulatory networks in other species and showed that the core network is evolutionarily conserved. This study provided an extensive description of the architecture, organizing principle and evolution of the transcription regulatory network inside the plant leaf.