bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct shoot regeneration from cotyledon, leaf and root ofCitrus jambhiriLush
Authors: Sharma Priyanka , Roy Bidhan 
Published: October 2020

ABSTRACTCitrus jambhiri(Rough lemon) is popularly preferred for rootstock for cultivated species ofCitrus. Tissue culture is an appreciable technique for mass-multiplication of plant propagules. In this communication direct regeneration of plantlets ofCitrus jambhiriLush. were obtained from cotyledons, roots and leaves. Most of the cotyledon (96%) enlarged on medium supplemented with 50 mg/L of casein hydrolysate. Few of those enlarged cotyledons responded to direct regeneration of shoots. Maximum shoot per responded cotyledon was 32. Conversely, the health of the plantlets were poor with semi-cylindrical leaves. Most of them dried on maintenance medium or on rooting medium ad died. Plantlets regenerated on medium supplemented with IAA in combination with IBA were healthy and they established on maintenance medium and rooted on rooting medium. Direct regeneration was also obtained from leaf on MS medium supplemented with 0.50 mg/L of dicamba. Our finding concluded that tissue culture tools may be used for direct regeneration of plantlets from different explants ofC. jambhirito obtained true-to-type plant propagules.
Use of non-invasive intracranial pressure pulse waveform to monitor patients with End-Stage Renal Disease (ESRD) Intracranial pressure in patients with ESRD
Authors: Rickli Cristiane , Cosmoski Lais Daiene , dos Santos Fábio André , Frigieri Gustavo Henrique , Rabelo Nicollas Nunes , Schuinski Adriana Menegat , Mascarenhas Sérgio , Vellosa José Carlos Rebuglio 
Published: October 2020

AbstractEnd-stage renal disease (ESRD) is treated mainly by hemodialysis, however, hemodialysis is associated with frequent complications, some of them involve the increased intracranial pressure. In this context, monitoring the intracranial pressure of these patients may lead to a better understanding of how intracranial pressure morphology varies with hemodialysis. This study aimed to follow-up patients with ESRD by monitoring intracranial pressure before and after hemodialysis sessions using a noninvasive method. We followed-up 42 patients with ESRD in hemodialysis, for six months. Noninvasive intracranial pressure monitoring data were obtained through analysis of intracranial pressure waveform morphology, this information was uploaded to Brain4care®cloud algorithm for analysis. The cloud automatically sends a report containing intracranial pressure parameters. In total, 4881 data points were collected during the six months of follow-up. The intracranial pressure parameters (time to peak and P2/P1 ratio) were significantly higher in predialysis when compared to postdialysis for the three weekly sessions and throughout the follow-up period (p<0.01) data showed general improvement in brain compliance after the hemodialysis session. Furthermore, intracranial pressure parameters were significantly higher in the first weekly hemodialysis session (p<0.05). In conclusion, there were significant differences between pre and postdialysis intracranial pressure in patients with ESRD on hemodialysis. Additionally, the pattern of the intracranial pressure alterations was consistent over time suggesting that hemodialysis can improve time to peak and P2/P1 ratio which may reflect in brain compliance.
Genetic interactions among ADAMTS metalloproteases and basement membrane molecules in cell migration inCaenorhabditis elegans
Authors: Imanishi Ayaka , Aoki Yuma , Kakehi Masaki , Mori Shunsuke , Takano Tomomi , Kubota Yukihiko , Kim Hon-Song , Shibata Yukimasa , Nishiwaki Kiyoji 
Published: October 2020

AbstractDuring development of theCaenorhabditis elegansgonad, the gonadal leader cells, called distal tip cells (DTCs), migrate in a U-shaped pattern to form the U-shaped gonad arms. The ADAMTS (adisintegrinandmetalloprotease withthrombospondin motifs) family metalloproteases MIG-17 and GON-1 are required for correct DTC migration. Mutations inmig-17result in misshapen gonads due to the misdirected DTC migration, and mutations ingon-1result in shortened and swollen gonads due to the premature termination of DTC migration. Although the phenotypes shown bymig-17andgon-1mutants are very different from one another, mutations that result in amino acid substitutions in the same basement membrane protein genes,emb-9/collagen IV a1, let-2/collagen IV a2andfbl-1/fibulin-1, were identified as genetic suppressors ofmig-17andgon-1mutants. To understand the roles shared by these two proteases, we examined the effects of themig-17suppressors ongon-1and the effects of thegon-1suppressors and enhancers onmig-17gonadal defects. Some of theemb-9, let-2andfbl-1mutations suppressed bothmig-17andgon-1, whereas others acted only onmig-17orgon-1. These results suggest thatmig-17andgon-1have their specific functions as well as functions commonly shared between them for gonad formation. The levels of collagen IV accumulation in the DTC basement membrane were significantly higher in thegon-1mutants as compared with wild type and were reduced to the wild-type levels when combined with suppressor mutations, but not with enhancer mutations, suggesting that the ability to reduce collagen IV levels is important forgon-1suppression.
Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars
Authors: Pincot Dominique D.A. , Ledda Mirko , Feldmann Mitchell J. , Hardigan Michael A. , Poorten Thomas J. , Runcie Daniel E. , Heffelfinger Christopher , Dellaporta Stephen L. , Cole Glenn S. , Knapp Steven J. 
Published: October 2020

ABSTRACTThe widely recounted story of the origin of cultivated strawberry (Fragaria×ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three century long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying exclusion analysis to array-genotyped single nucleotide polymorphisms. We identified 187 wild octoploid and 1,171F.×ananassafounders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent-offspring edges in the global pedigree network, we found that selection cycle lengths over the last 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation) but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations and shed light on forces that have shaped phenotypic diversity inF.×ananassa.
Effects of sheared chromatin length on ChIP-seq quality and sensitivity
Authors: Keller Cheryl A. , Heuston Elisabeth F. , Giardine Belinda , Long Maria R. , Miller Amber , Wixom Alexander Q. , Anderson Stacie M. , Bodine David M. , Hardison Ross C. 
Published: October 2020

AbstractChromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for identifying, on a genome-wide scale, the segments of DNA bound by specific transcription factors (TFs) or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets vary over a wide range, with a substantial fraction being of intermediate to poor quality. Such experimental variability can lead to many false positives or false negatives, impairing the ability to interpret the data. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focus on the sonication step to produce sheared chromatin, a variable controllable by the user and applicable to all ChIP-seq protocols. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measured the distribution of resultant fragment lengths using the Agilent Bioanalzyer 2100, and then immunoprecipitated these batches of chromatin using highly specific antibodies against either TAL1 or CTCF. We found that the level of sonication, which was affected by both the number of sonication cycles, as well as the starting cell number, had a pronounced impact on the quality of resulting ChIP-seq signals. Specifically, over-sonication led to degradation of quality (e.g. increased background and reduction in signal), while the impact of under-sonication of chromatin differed between the two transcription factors, leading to the loss of sites occupied by TAL1 but not those bound by CTCF. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in primary hematopoietic progenitor cells, including several rare cell types. Together, these results suggest that the amount of sonication is a key variable in success of ChIP-seq experiments, and that carefully monitoring the level of chromatin sonication is one way to improve ChIP-seq quality and reproducibility, which in turn facilitates low input ChIP-seq in rare cell types.
Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms
Authors: Top Oguz , Milferstaedt Stella W. L. , van Gessel Nico , Hoernstein Sebastian N. W. , Özdemir Bugra , Decker Eva L. , Reski Ralf 
Published: October 2020

ABSTRACTProduction of biopharmaceuticals relies on the expression of mammalian cDNAs in host organisms. Here we show that the expression of a human cDNA in the mossPhyscomitrella patensgenerates the expected full-length and four additional transcripts due to unexpected splicing. This mRNA splicing results in non-functional protein isoforms, cellular misallocation of the proteins and low product yields. We integrated these results together with the results of our analysis of all 32,926 protein-encodingP. patensgenes and their 87,533 annotated transcripts in a web application, physCO, for automatized codon-optimization. A thus optimized cDNA results in about eleven times more protein, which correctly localizes to the ER. An analysis of codon preferences of different production hosts suggests that similar effects also occur in non-plant hosts. We anticipate that the use of our methodology will prevent so far undetected mRNA heterosplicing resulting in maximized functional protein amounts for basic biology and biotechnology.
The genotype-phenotype landscape of an allosteric protein
Authors: Tack Drew S. , Tonner Peter D. , Pressman Abe , Olson Nathanael D. , Levy Sasha F. , Romantseva Eugenia F. , Alperovich Nina , Vasilyeva Olga , Ross David 
Published: October 2020

AbstractAllostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: thelacrepressor fromEscherichia coli, LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 105variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.
Harmonicity aids hearing in noise
Authors: McPherson Malinda J. , Grace River C. , McDermott Josh H. 
Published: October 2020

AbstractHearing in noise is a core problem in audition, and a challenge for hearing-impaired listeners, yet the underlying mechanisms are poorly understood. We explored whether harmonic frequency relations, a signature property of many communication sounds, aid hearing in noise for normal hearing listeners. We measured detection thresholds in noise for tones and speech synthesized to have harmonic or inharmonic spectra. Harmonic signals were consistently easier to detect than otherwise identical inharmonic signals. Harmonicity also improved discrimination of sounds in noise. The largest benefits were observed for two-note up-down “pitch” discrimination and melodic contour discrimination, both of which could be performed equally well with harmonic and inharmonic tones in quiet, but which showed large harmonic advantages in noise. The results show that harmonicity facilitates hearing in noise, plausibly by providing a noise-robust pitch cue that aids detection and discrimination.Significance statementNoise is ubiquitous, and being able to hear in noise is critical to real-world behavior. We report that hearing in noise is aided by sensitivity to the harmonic frequency relations that occur in vocal communication signals and music: harmonic sounds are easier to hear in noise than inharmonic sounds. This effect was present in both musicians and non-musicians and for synthetic as well as natural sounds, suggesting a role in everyday hearing.
Growth-dependent signals drive an increase in early G1 cyclin concentration to link cell cycle entry with cell growth
Authors: Sommer Robert A. , DeWitt Jerry T. , Tan Raymond , Kellogg Douglas R. 
Published: October 2020

AbstractEntry into the cell cycle occurs only when sufficient growth has occurred. In budding yeast, the cyclin Cln3 initiates cell cycle entry by inactivating a transcriptional repressor called Whi5. Growth-dependent changes in the concentrations of Cln3 or Whi5 have been proposed to link cell cycle entry to cell growth. However, there are conflicting reports regarding the behavior and roles of Cln3 and Whi5. Here, we found no evidence that changes in the concentration of Whi5 play a major role in controlling cell cycle entry. Rather, the data suggest that cell growth triggers cell cycle entry by driving an increase in the concentration of Cln3. We further found that accumulation of Cln3 is dependent upon homologs of mammalian SGK kinases that play roles in control of cell growth and size. Together, the data are consistent with models in which Cln3 serves as the crucial link between the cell cycle and signals that control cell growth and size.
Early growth response 2 (EGR2) is a novel regulator of the senescence program
Authors: Tyler Eleanor J. , del Arroyo Ana Gutierrez , Wallis Ryan , Hughes Bethany , Garbe James C. , Stampfer Martha R. , Koh Jim , Lowe Robert , Philpott Michael P , Bishop Cleo L. 
Published: October 2020

SummarySenescence, a state of stable growth arrest, plays an important role in ageing and age-related diseasesin vivo. Although the INK4/ARF locus is known to be essential for senescence programs, the key regulators drivingp16andARFtranscription remain largely underexplored. Using siRNA screening for modulators of the p16/pRB and ARF/p53/p21 pathways in deeply senescent human mammary epithelial cells (DS HMECs) and fibroblasts (DS HMFs), we identified EGR2 as a novel regulator of senescence. EGR2 expression is up-regulated during senescence and its ablation by siRNA in DS HMECs and HMFs transiently reverses the senescent phenotype. We demonstrate that EGR2 activates theARFandp16promoters and directly binds to theARFpromoter. Loss of EGR2 downregulates p16 levels and increases the pool of p16- p21- ‘reversed’ cells in the population. Moreover, EGR2 overexpression is sufficient to induce senescence. Our data suggest that EGR2 is a regulator of the p16/pRB and direct transcriptional activator of the ARF/p53/p21 pathways in senescence and a novel marker of senescence.
Gut Microbiota-Targeted Diets Modulate Human Immune Status
Authors: Wastyk Hannah C. , Fragiadakis Gabriela K , Perelman Dalia , Dahan Dylan , Merrill Bryan D , Yu Feiqiao B. , Topf Madeline , Gonzalez Carlos G. , Robinson Jennifer L. , Elias Joshua E. , Sonnenburg Erica D. , Gardner Christopher D. , Sonnenburg Justin L. 
Published: October 2020

AbstractDiet modulates the gut microbiome, and gut microbes, in turn, can impact the immune system. Here, we used two gut microbiota-targeted dietary interventions, plant-based fiber or fermented foods, to determine how each influences the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study design combined with -omics measurements of microbiome and host, including extensive immune profiling, we found distinct effects of each diet. High-fiber consumers showed increased gut microbiome-encoded glycan-degrading CAZymes despite stable community diversity. Three distinct immunological trajectories in high fiber-consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Our results indicate that fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in the industrialized society.
Effect of earthworms in removal and fate of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARG) during clinical laboratory wastewater treatment by vermifiltration
Authors: Arora Sudipti , Saraswat Sakshi , Rajpal Ankur , Shringi Harshita , Mishra Rinki , Sethi Jasmine , Rajvanshi Jayana , Nag Aditi , Saxena Sonika , Kazmi A.A. 
Published: October 2020

AbstractThe wastewater treatment plants effluent has been implicated in the spread of antibiotic resistant bacteria (ARB) as these environment contains multiple selective pressures that may increase mutation rates, pathogen survivability, and induce gene transfer between bacteria. In lieu of this, the present study explored the dynamics of earthworm-microorganisms interactions on the treatment efficacy of clinical laboratory wastewater treatment by vermifiltration and the effect of earthworms in the fate of removal of pathogens and ARB. The results of the study showed that earthworms and VF associated microbial community had a significant effect on BOD and COD reduction (78-85%), pathogen removal (>99.9 %) and caused a significant shift in the prevalence pattern of ARB. Additionally, molecular profiling of ESBL (blaSHV, blaTEMand blaCTX-M), MRSA (mec-A)and Colistin (mcr-1) gene confirmed the probable mechanisms behind the resistance pattern. The microbial community diversity assists in the formation of biofilm, which helps in the removal of pathogens and results in a paradigm shift in the resistance profile of ARB and ARG, specifically most effective against drugs, targeting cell wall and protein synthesis inhibition like Ampicillin, Ticarcillin, Gentamicin and Chloramphenicol. These findings prove vermifiltration technology as a sustainable and natural treatment technology for clinical laboratory wastewater.
LncRNAs interacting with the translation machinery contribute to human neuronal differentiation
Authors: Douka Katerina , Birds Isabel , Wang Dapeng , Clayton Sophie , Byford Abigail , Vasconcelos Elton J. R. , O’Connell Mary J. , Deuchars Jim , Whitehouse Adrian , Aspden Julie L. 
Published: October 2020

AbstractLncRNAs are less conserved, yet more tissue and developmental-stage specific than mRNAs and are particularly enriched in the nervous system ofDrosophila melanogaster, mouse and human. The function of cytoplasmic lncRNAs and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of SH-SH5Y cells. We discovered 237 cytoplasmic lncRNAs upregulated during early neuronal differentiation, most of which are associated with polysome complexes. The majority are cytoplasmically enriched and are intergenic or anti-sense. In addition, we find 45 small ORFs in lncRNAs to be actively translated, 17 specifically upon differentiation. 11 of these smORFs exhibit high sequence conservation acrossHominidaesuggesting they are under strong selective constraint with putative function in this clade. We discover LINC01116 is induced upon differentiation and contains an 87 codon smORF, which we detect as translated, with increased ribosome profiling signal upon differentiation. The LINC01116 peptide exhibits a cytoplasmic distribution and is detected in neurites. Knockdown of LINC01116 results in significant reduction of neurite length in differentiated cells indicating it contributes to neuronal differentiation. Our findings indicate lncRNAs are a source of non-canonical peptides and contribute to neuronal function.
Robust metabolic transcriptional components in 34,494 patient-derived samples and cell lines
Authors: Leeuwenburgh V.C. , Urzúa-Traslaviña C.G. , Bhattacharya A. , Walvoort M.T.C. , Jalving M. , de Jong S. , Fehrmann R.S.N. 
Published: October 2020

ABSTRACTPatient-derived expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Therefore, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. We, therefore, performed consensus Independent Component Analyses (c-ICA) with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. c-ICA enabled us to create a transcriptional metabolic landscape in which many robust metabolic transcriptional components and their activation score in individual samples were defined. Here we demonstrate how this landscape can be used to explore associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. The metabolic landscape can be explored athttp://www.themetaboliclandscapeofcancer.com.