bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel pathway controlling cambium initiation and - activity via cytokinin biosynthesis in Arabidopsis
Authors: Rahimi Arezoo , Karami Omid , Lestari Angga Dwituti , Shi Dongbo , Greb Thomas , Offringa Remko 
Published: June 2020

AbstractPlant secondary growth, also referred to as wood formation, includes the production of secondary xylem, which is derived from meristematic cambium cells embedded in vascular tissues. Despite the importance of secondary xylem in plant growth and wood formation, the molecular mechanism of secondary growth is not yet well understood. Here we identified an important role for theArabidopsis thaliana(Arabidopsis)AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15)gene, encoding for a putative transcriptional regulator, in controlling vascular cambium activity and secondary xylem formation. Secondary xylem development was significantly reduced in inflorescence stems of the Arabidopsisahl15loss-of-function mutant, whereasAHL15overexpression led to extensive secondary xylem formation.AHL15expression under a vascular meristem-specific promoter also enhanced the amount of interfascicular secondary xylem. Moreover,AHL15appeared to be required for the enhanced secondary xylem formation in the Arabidopsis double loss-of-function mutant of theSUPPRESSOR OF OVEREXPRESSION OF CO 1(SOC1) andFRUITFULL(FUL) genes. A well-known central regulator of cambial activity is the plant hormone cytokinin. We showed that the expression of two cytokinin biosynthesis genes (ISOPENTENYL TRANSERASE (IPT) 3and7) is decreased inahl15loss-of-function mutant stems, whereas the secondary xylem deficiency in these mutant stems can be resorted by cambium-specific expression of theAgrobacterium tumefaciens IPTgene, indicating thatAHL15acts through the cytokinin pathway. These findings support a model wherebyAHL15acts as a central factor inducing vascular cambium activity downstream ofSOC1andFULand upstream ofIPT3,IPT7andLOG4, LOG5governing the rate of secondary xylem formation in Arabidopsis inflorescence stems.
Discovery of protein modifications using high resolution differential mass spectrometry proteomics
Authors: Cifani Paolo , Li Zhi , Luo Danmeng , Grivainis Mark , Intlekofer Andrew M. , Fenyö David , Kentsis Alex 
Published: June 2020

SummaryRecent studies have revealed diverse amino acid, post-translational and non-canonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for Spectral Alignment-based Modified PEptide Identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate its high specificity and sensitivity for the discovery of sub-stoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI’s robust parameterization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules. SAMPEI is implemented as a Python package, and is available open-source from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).
Does rhythmic priming improve grammatical processing in Hungarian-speaking children with and without Developmental Language Disorder?
Authors: Ladányi Enikő , Lukács Ágnes , Gervain Judit 
Published: June 2020

AbstractResearch has described several features shared between musical rhythm and speech or language, and experimental studies consistently show associations between performance on tasks in the two domains as well as impaired rhythm processing in children with language disorders. Motivated by these results, in the current study our first aim was to explore whether the activation of the shared system underlying rhythm and language processing with a regular musical rhythm can improve subsequent grammatical processing in preschool-aged Hungarianspeaking children with and without Developmental Language Disorder (DLD). Second, we investigated whether rhythmic priming is specific to grammar processing by assessing priming in two additional domains: a linguistic but non-grammatical task (picture naming) and a non-linguistic task (nonverbal Stroop task). Third, to confirm that the rhythmic priming effect originates from the facilitating effect of the regular rhythm and not the negative effect of the control condition, we added a third condition, silence, for all the three tasks. Both groups of children showed better performance on the grammaticality judgment task in the regular compared to both the irregular and the silent conditions but no such effect appeared in the non-grammatical and non-linguistic tasks. These results suggest that 1) rhythmic priming can improve grammatical processing in Hungarian, a language with complex morphosyntax, both in children with and without DLD, 2) the effect is specific to grammar and 3) is a result of the facilitating effect of the regular rhythm.Research Highlights6-year-old Hungarian-speaking children with and without Developmental Language Disorder perform better on a grammatical task subsequent to exposure to a regular rhythm vs. an irregular rhythm/silenceThe effect of regular rhythm is specific: it improves performance on a grammatical task but not on a word retrieval or a non-linguistic taskDifference between performance following regular vs. irregular rhythm originates from the facilitating effect of the regular rhythm (not the negative effect of the irregular rhythm)The results highlight the importance of rhythm in speech processing, and point towards a possible intervention tool in language disorders
Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion
Authors: Wangsanuwat Chatarin , Heom Kellie A. , Liu Estella , O’Malley Michelle A. , Dey Siddharth S. 
Published: June 2020

AbstractRNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic cells, mRNA sequencing of bacterial samples is more challenging due to the absence of a poly-A tail that typically enables efficient capture and enrichment of mRNA from the abundant rRNA molecules in a cell. Moreover, bacterial cells frequently contain 100-fold lower quantities of RNA compared to mammalian cells, which further complicates mRNA sequencing from non-cultivable and non-model bacterial species. To overcome these limitations, we report EMBR-seq (Enrichment of mRNA by Blocked rRNA), a method that efficiently depletes 5S, 16S and 23S rRNA using blocking primers to prevent their amplification, resulting in greater than 80% of the sequenced RNA molecules from anE. coliculture deriving from mRNA. We demonstrate that this increased efficiency provides a deeper view of the transcriptome without introducing technical amplification-induced biases. Moreover, compared to recent methods that employ a large array of oligonucleotides to deplete rRNA, EMBR-seq uses a single oligonucleotide per rRNA, thereby making this new technology significantly more cost-effective, especially when applied to varied bacterial species. Finally, compared to existing commercial kits for bacterial rRNA depletion, we show that EMBR-seq can be used to successfully quantify the transcriptome from more than 500-fold lower starting total RNA. Thus, EMBR-seq provides an efficient and cost-effective approach to quantify global gene expression profiles from low input bacterial samples.
The Impact of the Siemens Trio to Prisma Upgrade and Volumetric Navigators on MRI Indices: A Reliability Study with Implications for Longitudinal Study Designs
Authors: Plitman Eric , Bussy Aurelie , Valiquette Vanessa , Salaciak Alyssa , Patel Raihaan , Béland Marie-Lise , Tullo Stephanie , Tardif Christine , Rajah M. Natasha , Near Jamie , Devenyi Gabriel A. , Chakravarty M. Mallar 
Published: June 2020

AbstractMany magnetic resonance imaging (MRI) indices are being studied longitudinally to explore topics such as biomarker detection and clinical staging. A pertinent concern to longitudinal work is MRI scanner upgrades. When upgrades occur during the course of a longitudinal MRI neuroimaging investigation, there may be an impact on the compatibility of pre- and post-upgrade measures. Similarly, subject motion is another issue that may be detrimental to longitudinal MRI work; however, embedding volumetric navigators (vNavs) within acquisition sequences has emerged as a technique that allows for prospective motion correction. Our research group recently implemented an upgrade from a Siemens MAGNETOM 3T Trio system to a Siemens MAGNETOM 3T Prisma Fit system. The goals of the current work were to: 1) investigate the impact of this upgrade on commonly used structural imaging measures and proton magnetic resonance spectroscopy indices (“Prisma Upgrade protocol”) and 2) examine structural imaging measures in a sequence with vNavs alongside a standard acquisition sequence (“vNav protocol”). In both protocols, while high reliability was observed for most of the investigated MRI outputs, suboptimal reliability was observed for certain indices. Across the scanner upgrade, increases in frontal, temporal, and cingulate cortical thickness (CT) and thalamus volume, along with decreases in parietal CT, amygdala, globus pallidus, hippocampus, and striatum volumes were observed across the Prisma upgrade, and were linked to increases in signal-to-noise ratios. No significant impact of the upgrade was found in 1H-MRS analyses. Further, CT estimates were found to be larger in MPRAGE acquisitions compared to vNav-MPRAGE acquisitions mainly within temporal areas, while the opposite was found mostly in parietal brain regions. The results from this work should be considered in longitudinal study designs and comparable prospective motion correction investigations are warranted in cases of marked head movement.
Everyone Can Meditate: Characterizing a Personalized Connectomic State Space among Meditation Groups and Non-meditators
Authors: van Doorn Jacob , Xing Mengqi , Cahn B. Rael , Delorme Arnaud , Ajilore Olusola , Leow Alex D. 
Published: June 2020

AbstractAlterations in brain connectivity has been shown for many disease states and groups of people from different levels of cognitive training. To study dynamic functional connectivity, we propose a method for a personalized connectomic state space called Thought Chart. Experienced meditators are an interesting group of healthy subjects for brain connectivity analyses due to their demonstrated differences in resting state dynamics, and altered brain connectivity has been implicated as a potential factor in several psychiatric disorders. Three distinct techniques of meditation are explored: Isha Yoga, Himalayan Yoga, and Vipassana, as well as a meditation-naïve group of individuals. All individuals participated in a breath awareness task, an autobiographical thinking task, and one of three different meditation practices according to their expertise, while being recorded by a 64-electrode electroencephalogram (EEG). The functional brain connectivity was estimated using weighted phase lag index (WPLI) and the connectivity dynamics were investigated using a within-individual formulation of Thought Chart, a previously proposed dimensionality reduction method which utilizes manifold learning to map out a state space of functional connectivity. Results showed that the two meditation tasks (breath awareness task and own form of meditation) in all groups were found to have consistently different functional connectivity patterns relative to those of the instructed mind-wandering (IMW) tasks in each individual, as measured using the Hausdorff distance in the state space. The specific meditation state was found to be most similar to the breath awareness state in all groups, as expected in these meditation traditions which all incorporate breath awareness training in their practice trajectory. The difference in connectivity was found to not be solely driven by specific frequency bands. These results demonstrate that the within-individual form of Thought Chart consistently and reliably separates similar tasks among healthy meditators and non-meditators during resting state-like EEG recordings. Unexpectedly, we found the dissimilarity between breath awareness/meditation and IMW, measured via Hausdorff distance, regardless of meditation experience or tradition, with no significant group differences.
Dengue virus clinical isolates sustain viability of infected hepatic cells by counteracting apoptosis-mediated DNA breakage
Authors: Nath Himadri , Ghosh Anisa , Basu Keya , De Abhishek , Biswas Subhajit 
Published: June 2020

AbstractNS1, a virotoxin, abundantly present in Dengue patients’ blood, is a major player behind disease patho-biogenesis including plasma leakage and damage to the liver. Despite the presence of NS1 in blood, Dengue is asymptomatic and self-limiting in ≥80% Dengue virus (DV) infected people. We investigated this observation and found that plasmid-mediated NS1 expression and secretion in liver cells (Huh7) are sufficient to cause programmed cell death (apoptosis) and associated cellular DNA breakage. However, liver or kidney cell lines infected with DV and secreting equivalent amounts of NS1 didn’t exhibit apoptotic DNA breakage. In fact, DV-infected cells showed better survival than cells in which only NS1 was transiently expressed by transfection. We also found that DV can even prevent chemical-induced apoptotic DNA damage in infected host cells. So, DV thwarts host antiviral defence i.e. apoptosis, by counteracting cellular DNA breakages and keeps the infected cells metabolically active to prolong virus replication.
Stress enhances hippocampal neuronal synchrony and prolongs sharp-wave ripples
Authors: Tomar Anupratap , Polygalov Denis , Chattarji Sumantra , McHugh Thomas 
Published: June 2020

AbstractChronic stress affects hippocampal function at multiple levels of neural organization. However, much of this understanding is derived from postmortem analyses of molecular, morphological, physiological and behavioral changes at fixed time points. Neural signatures of an ongoing stressful experience in the intact brain of awake animals and their links to later hippocampal dysfunction remain poorly understood. Here we usedin vivotetrode recordings to analyze the dynamic impact of 10 days of immobilization stress on neuronal activity in area CA1 of mice. Unexpectedly, there was a net decrease in pyramidal cell activity in stressed animals. Although these results suggest a lack of stress-induced hyperexcitability, more detailed analysis revealed that a greater fraction of spikes occurred specifically during sharp-wave ripples, resulting in an increase in neuronal synchrony. After repeated stress some of these alterations were visible during rest even in the absence of stress. These findings offer new insights into stress-induced alterations in ripple-spike interactions and mechanisms through which chronic stress may interfere with subsequent information processing.
Natural competence inChlorogloeopsis fritschiiPCC 6912 and other ramified cyanobacteria
Authors: Springstein Benjamin L. , Nies Fabian , Dagan Tal 
Published: June 2020

AbstractLateral DNA transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA acquisition via transformation involves the uptake of DNA from the environment. The ability of recipient cells to actively transport DNA into the cytoplasm – termed natural competence – depends on the presence of type IV pili and competence proteins. Natural competence has been described in cyanobacteria for several organisms including unicellular and filamentous species. However, the presence of natural competence in ramified cyanobacteria, which are considered the peak of cyanobacterial morphological complexity, remains unknown. Here we show that ramified cyanobacteria harbour the genes essential for natural competence and experimentally demonstrate natural competence in the ramified cyanobacteriumChlorogloeopsis fritschiiPCC 6912 (hereafterChlorogloeopsis). Searching for homologs to known natural competence genes in ramified cyanobacteria showed that these genes are conserved in the majority of tested isolates. Experimental validation of natural competence using several alternative protocols demonstrates thatChlorogloeopsiscould be naturally transformed with a replicative plasmid. Our results show that natural competence is a common trait in ramified cyanobacteria and that natural transformation is likely to play an important role in cyanobacteria evolution.ImportanceCyanobacteria are crucial players in the global biogeochemical cycles where they contribute to CO2- and N2-fixation. Their main ecological significance is the oxygen-producing photosynthetic apparatus that contributes to contemporary food chains. Ramified cyanobacteria form true-branching and multiseriate cell filament structures that represent a peak of prokaryotic multicellularity. Species in that group inhabit fresh and marine water habitats, thermal springs, arid environments, as well as endolithic and epiphytic habitats. Here we show that ramified cyanobacteria harbor the mechanisms required for DNA acquisition via natural transformation. The prevalence of mechanisms for natural uptake of DNA has implications for the role of DNA acquisition in the evolution of cyanobacteria. Furthermore, presence of mechanisms for natural transformation in ramified cyanobacteria opens up new possibilities for genetic modification of ramified cyanobacteria.
Comparative analysis reveals the modular functional build-up of megaplasmid pTTS12 ofPseudomonas putidaS12: a paradigm for transferable traits, plasmid stability and inheritance?
Authors: Kusumawardhani Hadiastri , Hosseini Rohola , de Winde Johannes H. 
Published: June 2020

AbstractThePseudomonas putidaS12 genome contains 583 kbp megaplasmid pTTS12 that carries over 600 genes enabling tolerance to various stress conditions, including the solvent extrusion pump SrpABC. We performed a comparative analysis of pTTS12 against 28915 plasmids from NCBI databases. We investigated putative roles of genes encoded on pTTS12 and further elaborated on its role in the establishment and maintenance of several stress conditions, specifically focusing on solvent tolerance inP. putidastrains. The backbone of pTTS12 was found to be closely related to that of the carbapenem-resistance plasmid pOZ176, member of the IncP-2 incompatibility group, although remarkably the carbapenem resistance cassette is absent from pTTS12. Megaplasmid pTTS12 contains multiple transposon-flanked cassettes mediating resistance to various heavy metals such as tellurite, chromate (Tn7), and mercury (Tn5053 and Tn5563). Additionally, pTTS12 also contains a P-type, Type IV secretion system (T4SS) supporting self-transfer to otherP. putidastrains. This study increases our understanding in the build-up of IncP-2 plasmids and several promising exchangeable gene clusters to construct robust microbial hosts for biotechnology applications.ImportanceOriginating from various environmental niches, large numbers of bacterial plasmids have been found carrying heavy metal and antibiotic resistance genes, degradation pathways and specific transporters for organic solvents or aromatic compounds. Such genes may constitute promising candidates for novel synthetic biology applications. Our systematic analysis of gene clusters encoded on megaplasmid pTTS12 underscores that a large portion of its genes is involved in stress response increasing survival under harsh conditions like heavy metal and organic solvent resistance. We show that pTTS12 belongs to the IncP-2 plasmid family. Comparative analysis of pTTS12 provides thorough insight into the structural and functional build-up of members of the IncP-2 plasmid family. pTTS12 is highly stable and carries a complex arrangement of transposable elements containing heavy metal resistance clusters as well as distinct aromatic degradation pathways and solvent-extrusion pump. This offers interesting insight into the evolution of solvent tolerance in theP. putidafamily.
Transmission Clusters of Hepatitis C Virus among Public Health and Correctional Settings in Wisconsin, 2016-2017
Authors: Hochstatter Karli R. , Tully Damien C. , Power Karen A. , Koepke Ruth , Akhtar Wajiha Z. , Prieve Audrey F. , Whyte Thomas , Bean David J. , Seal David W. , Allen Todd M. , Westergaard Ryan P. 
Published: June 2020

ABSTRACTEnding the hepatitis C virus (HCV) epidemic requires stopping transmission among networks of people who inject drugs (PWID). Identification of transmission networks through the application of genomic epidemiology may inform community response models that can quickly interrupt transmission. We retrospectively identified HCV RNA-positive specimens corresponding to 459 individuals tested in public health settings, including correctional facilities and syringe service programs, in Wisconsin from 2016-2017. Next-generation sequencing of HCV was conducted and analyzed for phylogenetic linkage using the CDC’s Global Hepatitis Outbreak Surveillance Technology platform. Transmission network analysis showed that 126 individuals were linked across 42 clusters (range: 2-11 individuals per cluster). Phylogenetic clustering was higher in rural communities and associated with female gender and younger age among rural residents. These data highlight that the increasing rurality of opioid injection use and HCV transmission among young PWID could be better supported by the expansion of molecular-based surveillance strategies to reduce transmission.Article Summary LineIntegrating existing public health surveillance and molecular analyses with Global Hepatitis Outbreak Surveillance Technology allows for the identification and characterization of growing HCV transmission clusters among key populations in Wisconsin.
LOCKDOWN AS A PANDEMIC MITIGATING POLICY INTERVENTION IN INDIA
Authors: Mandal Subhayan , Kumar Manoj , Sarkar Debasish 
Published: June 2020

AbstractWe use publicly available timeline data on the Covid-19 outbreak for nine indian states to calculate the important quantifier of the outbreak, the sought after Rt or the time varying reproduction number of the outbreak. This quantity can be measured in in several ways, e.g. by application of Stochastic compartmentalised SIR (DCM) model, Poissonian likelihood based (ML) model & the exponential growth rate (EGR) model. The third one is known as the effective reproduction number of an outbreak. Here we use, mostly, the second one. It is known as the instantaneous reproduction number for an outbreak. This number can faithfully tell us the success of lockdown measures inside indian states, as containment policy for the spread of Covid-19 viral disease. This can also, indirectly yield notional value of the generation time inteval in different states. In doing this work we employ, pan India serial interval of the outbreak estimated directly from data from January 30th to April 19th, 2020. Simultaneously, in conjunction with the serial interval data, our result is derived from incidences data between March 14th, 2020 to June 1st, 2020, for the said states. We find the lockdown had marked positive effect on the nature of time dependent reproduction number in most of the Indian states, barring a couple. The possible reason for such failures have been investigated.