bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of parental genome balance in the generation of novel yet heritable epigenetic and transcriptional states during doubled haploid breeding
Authors: Price Jonathan , Antunez-Sanchez Javier , Hussain Nosheen , Wibowo Anjar , Papareddy Ranjith , Becker Claude , Teakle Graham , Barker Guy , Weigel Detlef , Gutierrez-Marcos Jose 
Published: October 2019

AbstractBackgroundDoubling the genome contribution of haploid plants has accelerated breeding in most cultivated crop species. Although plant doubled haploids are isogenic in nature, they frequently display unpredictable phenotypes, thus limiting the potential of this technology. Therefore, being able to predict the factors implicated in this phenotypic variability could accelerate the generation of desirable genomic combinations and ultimately plant breeding.ResultsWe use computational analysis to assess the transcriptional and epigenetic dynamics taking place during doubled haploids generation in the genome ofBrassica oleracea. We observe that doubled haploid lines display unexpected levels of transcriptional and epigenetic variation, and that this variation is largely due to imbalanced contribution of parental genomes. We reveal that epigenetic modification of transposon-related sequences during DH breeding contributes to the generation of unpredictable yet heritable transcriptional states. Targeted epigenetic manipulation of these elements using dCas9-hsTET3 confirms their role in transcriptional regulation. We have uncovered a hitherto unknown role for parental genome balance in the transcriptional and epigenetic stability of doubled haploids.ConclusionsThis is the first study that demonstrates the importance of parental genome balance in the transcriptional and epigenetic stability of doubled haploids, thus enabling predictive models to improve doubled haploid-assisted plant breeding.
Optimal Design of Single-Cell Experiments within Temporally Fluctuating Environments
Authors: Fox Zachary R , Neuert Gregor , Munsky Brian 
Published: October 2019

AbstractModern biological experiments are becoming increasingly complex, and designing these experiments to yield the greatest possible quantitative insight is an open challenge. Increasingly, computational models of complex stochastic biological systems are being used to understand and predict biological behaviors or to infer biological parameters. Such quantitative analyses can also help to improve experiment designs for particular goals, such as to learn more about specific model mechanisms or to reduce prediction errors in certain situations. A classic approach to experiment design is to use the Fisher information matrix (FIM), which quantifies the expected information a particular experiment will reveal about model parameters. The Finite State Projection based FIM (FSP-FIM) was recently developed to compute the FIM for discrete stochastic gene regulatory systems, whose complex response distributions do not satisfy standard assumptions of Gaussian variations. In this work, we develop the FSP-FIM analysis for a stochastic model of stress response genes in S. cerevisae under time-varying MAPK induction. We verify this FSP-FIM analysis and use it to optimize the number of cells that should be quantified at particular times to learn as much as possible about the model parameters. We then extend the FSP-FIM approach to explore how different measurement times or genetic modifications help to minimize uncertainty in the sensing of extracellular environments, and we experimentally validate the FSP-FIM to rank single-cell experiments for their abilities to minimize estimation uncertainty of NaCl concentrations during yeast osmotic shock. This work demonstrates the potential of quantitative models to not only make sense of modern biological data sets, but to close the loop between quantitative modeling and experimental data collection.
TetrahymenaPoc5 is a transient basal body component that is important for basal body maturation
Authors: Heydeck Westley , Bayless Brian A. , Stemm-Wolf Alexander J. , O’Toole Eileen T. , Ozzello Courtney , Nguyen Marina , Winey Mark 
Published: October 2019

ABSTRACTBasal bodies (BBs) are microtubule-based organelles that template and stabilize cilia at the cell surface. Centrins ubiquitously associate with BBs and function in BB assembly, maturation, and stability. Human POC5 (hPOC5) is a highly conserved centrin-binding protein that binds centrins through Sfi1p-like repeats and is required for building full-length, mature centrioles. Here, we use the BB-rich cytoskeleton ofTetrahymena thermophilato characterize Poc5 BB functions.TetrahymenaPoc5 (TtPoc5) uniquely incorporates into assembling BBs and is then removed from mature BBs prior to ciliogenesis. Complete genomic knockout ofTtPOC5leads to a significantly increased production of BBs yet a markedly reduced ciliary density, both of which are rescued by reintroduction of TtPoc5. A secondTetrahymena POC5-like gene,SFR1, is similarly implicated in modulating BB production. WhenTtPOC5andSFR1are co-deleted, cell viability is compromised, and levels of BB overproduction are exacerbated. Overproduced BBs display defective transition zone formation and a diminished capacity for ciliogenesis. This study uncovers a requirement for Poc5 in building mature BBs, providing a possible functional link betweenhPOC5mutations and impaired cilia.SUMMARY STATEMENTLoss ofTetrahymena thermophilaPoc5 reveals an important role for this centrin-binding protein in basal body maturation, which also impacts basal body production and ciliogenesis.
Opposing transcriptomic gradients explain orthogonal maps in human visual areas
Authors: Zhen Zonglei , Gomez Jesse , Weiner Kevin S. 
Published: October 2019

AbstractOpposing transcriptomic gradients explain the large-scale organization of cortex. Here, we show that opposing transcriptomic gradients also explain the fine-scale organization of orthogonal maps in human visual areas. We propose a model relating transcriptomics, cell density, and function, which predicts that specific cortical locations within these visual maps are microanatomically distinct and differentially susceptible to genetic mutations. We conclude with histological and translational data that support both predictions.
Characterisation of Quorum Sensing System and Its Role in Global Regulation in Hafnia alvei
Authors: Tan Jia Yi , See-Too Wah-Seng , Convey Peter , Chan Kok-Gan 
Published: October 2019

AbstractQuorum sensing (QS) is a regulatory process achieved via cell-to-cell communication that involves release and detection of autoinducers (AIs), and which occurs in a wide range of bacteria. To date, QS has been associated to events of pathogenesis, biofilm formation, and antibiotic resistance in clinical, industrial, and agricultural contexts. The main objective of this study was to characterise the role of N-Acyl homoserine lactone (AHL) type QS in Hafnia alvei FB1, a bacterial strain isolated from frozen vacuum-packed fish paste meatballs, via identification of QS core genes using a genomic approach, followed by comparative transcriptomic profiling between QS-deficient mutants and wild-type strains. H. alvei FB1 is known to produce two types of AHLs, namely, N-(3-oxohexanoyl) homoserine lactone (3OC6-HSL) and N-(3-oxooctanoyl) homoserine lactone (3OC8-HSL). The complete genome sequence of strain FB1 was obtained and a single gene for AHL synthase (halI) and its cognate receptor (halR) were identified. QS-deficient mutants of FB1 were constructed via the λ-Red recombineering method. Removal of the QS genes in strain FB1 affected mainly mechanisms in cell division and nutrient uptake, as well as resistance to a number of antibiotics, which are crucial for survival, adaptation and colonisation of both food and the host gut environment.Impact statementThe Hafnia genus is known as opportunistic pathogen in both nosocomial and community-acquired infections, however, involvement and mechanism of pathogenesis of Hafnia in infection diseases is uncertain. We investigate the role of the signalling molecule, N-acyl homoserine lactones (AHLs), in a Hafnia alvei strain, since AHLs play important roles in pathogenicity, survival or adaptation in other pathogen. This comparative transciptomic study has revealed that AHLs are involved in mechanisms in cell division and nutrient uptake, as well as resistance to a number of antibiotics, which are crucial for survival, adaptation and colonisation of both food and the host gut environment. This finding provides insight and possible strategy to combat this opportunistic pathogen.Data summaryGenome sequence is deposited in NCBI GenBank under accession number CP009706. The transcriptomic data, have been deposited in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds) under accession number GSE93000.
Music predictability and liking enhance pupil dilation and promote motor learning in non-musicians
Authors: Bianco R. , Gold B.P. , Johnson A.P. , Penhune V.B. 
Published: October 2019

AbstractHumans can anticipate music and derive pleasure from it. Expectations facilitate movements associated with anticipated events, and they are linked with reward, which may also facilitate learning of the anticipated rewarding events. The present study investigates the synergistic effects of predictability and hedonic responses to music on arousal and motor-learning in a naïve population. Novel melodies were manipulated in their overall predictability (predictable/unpredictable) as objectively defined by a model of music expectation, and ranked as high/medium/low liked based on participants’ self-reports collected during an initial listening session. During this session, we also recorded ocular pupil size as an implicit measure of listeners’ arousal. During the following motor task, participants learned to play target notes of the melodies on a keyboard (notes were of similar motor and musical complexity across melodies). Pupil dilation was greater for liked melodies, particularly when predictable. Motor performance was facilitated in predictable more than unpredictable melodies, but liked melodies were learned even in the unpredictable condition. Low-liked melodies also showed learning but mostly in participants with higher scores of task perceived competence. Taken together, these results suggest that effects of predictability on learning can be overshadowed by effects of stimulus liking or task-related intrinsic motivation.
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome
Authors: Wang Zhong , Ho Harrison , Egan Rob , Yao Shijie , Kang Dongwan , Froula Jeff , Sevim Volkan , Schulz Frederik , Shay Jackie E. , Macklin Derek , McCue Kayla , Orsini Rachel , Barich Daniel J. , Sedlacek Christopher J. , Li Wei , Morgan-Kiss Rachael M. , Woyke Tanja , Slonczewski Joan L. 
Published: October 2019

ABSTRACTCurrent supervised phylogeny-based methods fall short on recognizing species assembled from metagenomic datasets from under-investigated habitats, as they are often incomplete or lack closely known relatives. Here, we report an efficient software suite, “Genome Constellation”, that estimates similarities between genomes based on their k-mer matches, and subsequently uses these similarities for classification, clustering, and visualization. The clusters of reference genomes formed by Genome Constellation closely resemble known phylogenetic relationships while simultaneously revealing unexpected connections. In a dataset containing 1,693 draft genomes assembled from the Antarctic lake communities where only 40% could be placed in a phylogenetic tree, Genome Constellation improves taxa assignment to 61%. It revealed six clusters derived from new bacterial phyla and 63 new giant viruses, 3 of which missed by the traditional marker-based approach. In summary, we demonstrate that Genome Constellation can tackle the computational and algorithmic challenges in large-scale taxonomy analyses in metagenomics.
Metaxin 3 is a Highly Conserved Vertebrate Protein Homologous to Mitochondrial Import Proteins and GSTs
Authors: Adolph Kenneth W. 
Published: October 2019

ABSTRACTMetaxin 3 genes are shown to be widely conserved in vertebrates, including mammals, birds, fish, amphibians, and reptiles. Metaxin 3 genes, however, are not found in invertebrates, plants, and bacteria. The predicted metaxin 3 proteins were identified by their homology to the metaxin 3 proteins encoded by zebrafish and Xenopus cDNAs. Further evidence that they are metaxin proteins was provided by the presence of GST_N_Metaxin, GST_C_Metaxin, and Tom37 protein domains, and the absence of other major domains. Alignment of human metaxin 3 and human metaxin 1 predicted amino acid sequences showed 45% identities, while human metaxin 2 had 23% identities. These results indicate that metaxin 3 is a distinct metaxin. A wide variety of vertebrate species—including human, zebrafish, Xenopus, dog, shark, elephant, panda, and platypus—had the same genes adjacent to the metaxin 3 gene. In particular, the thrombospondin 4 gene (THBS4) is next to the metaxin 3 gene (MTX3). By comparison, the thrombospondin 3 gene (THBS3) is next to the metaxin 1 gene (MTX1). Phylogenetic analysis showed that metaxin 3, metaxin 1, and metaxin 2 protein sequences formed separate clusters, but with all three metaxins being derived from a common ancestor. Alpha-helices dominate the predicted secondary structures of metaxin 3 proteins. Little beta-strand is present. The pattern of 9 helical segments is also found for metaxins 1 and 2.
Effect of recombinant phycocyanin on photosynthetic system in Chlamydomonas reinhardtii
Authors: Zhang Feng , Cong Xiaomei , Wang Zhendong , Guo Yalin , Hou Lulu , Li Rui , Shang Menghui , Wei Xuehong , Yangzong Zhaxi , Xu Xiaoting , Zang Xiaonan 
Published: October 2019

AbstractThe phycobilisome is an important photosynthetic antenna in the photosynthetic cyanobacteria, and phycocyanin is one of the main components of phycobilisomes. It helps cells absorb green light that green-lineage photo-synthetic organisms cannot. In this work, phycocyanin, heme oxidase and ferredoxin oxidoreductase from Arthrospira platensis FACHB 314 were successfully expressed in the green algae Chlamydomonas reinhardtii. Then the effects of this expression on the photosynthesis and growth of C. reinhardtii were detected. Transcriptional level analysis showed that the phycocyanin gene was successfully expressed stably in the transgenic strains. The results of low-temperature fluorescence emission spectra and chlorophyll fluorescence showed that recombinant phycocyanin has considerable optical activity. The expression of phycocyanin, heme oxidase and ferredoxin oxidoreductase in low-light conditions is particularly evident in the promotion of photosynthesis in C. reinhardtii. The growth of transgenic strains was significantly promoted in the early growth phase under low-light conditions. However, the final growth and biomass accumulation of transgenic C. reinhardti were inhibited by this expression. In this paper, the possibility of photoenergy transfer between phycocyanin and heterologous host thylakoid membrane was researched, which provided a useful attempt for the construction of a new photosynthetic system using phycobiliprotein from cyanobacteria.One-sentence summaryPhycocyanin from Arthrospira platensis FACHB 314 expressed in Chlamydomonas reinhardtii can effect the photosynthetic system of C. reinhardtii.
PhyB induces intron retention and uORF-mediated translational inhibition of PIF3
Authors: Dong Jie , Chen Haodong , Deng Xing Wang , Irish Vivian F. , Wei Ning 
Published: October 2019

AbstractThe phytochrome B (phyB) photoreceptor stimulates light responses in plants in part by inactivating repressors of light responses such as phytochrome-interacting factor 3 (PIF3). It has been established that activated phyB inhibits PIF3 by rapid protein degradation and decreased transcription. PIF3 protein degradation has been shown to be mediated by EIN3-BINDING F-BOX PROTEIN (EBF) and LIGHT-RESPONSE BTB (LRB) E3 ligases, the latter simultaneously targeting phyB for degradation. In this study, we show that PIF3 level is additionally regulated by alternative splicing and protein translation. Overaccumulation of photo-activated phyB, which occur in the mutant defective for LRB genes under continuous red light (Rc), induces a specific alternative splicing of PIF3 that results in retention of an intron in the 5’UTR of PIF3 mRNA. In turn, the upstream opening reading frames (uORF) contained within this intron inhibit PIF3 protein synthesis. The phyB-dependent alternative splicing of PIF3 is diurnally regulated under the short-day light cycle. We hypothesize that this reversible regulatory mechanism may be utilized to fine-tune the level of PIF3 protein in light-grown plants, and may contribute to the oscillation of PIF3 protein abundance under the short-day environment.One Sentence SummaryLight down-regulates PIF3 by multiple mechanisms. We show that phyB induces an alternative splicing event that inhibits PIF3 protein translation, and that is regulated by short-day diurnal cycle.
A case to ruminate on: vomiting and weight loss in intellectual disability and autism
Authors: Mufti Shaista 
Published: October 2019

Purpose
The purpose of this paper is to review a case of a man with intellectual disability, autism and challenging behaviour who presented with vomiting, regurgitations and significant weight loss.

Design/methodology/approach
The paper examines the case history and identifies challenges contributing to symptom classification and management of a patient with intractable vomiting, regurgitations and significant weight loss.

Findings
This case illustrates the importance of the multidisciplinary team working required to reduce morbidity and risk of mortality, as well as highlighting some of the challenges associated with coordinating different approaches from different agencies. Pharmacological management did not result in lasting symptom resolution in this case. Difficulties in establishing diagnostic certainty and consideration of whether symptoms could be consistent with rumination syndrome are also discussed. The value of consistent implementation of positive behavioural support is also demonstrated.

Originality/value
The rapid and dangerous weight loss described in this case is associated with adverse physical health outcomes and has generated significant anxiety resulting in extensive liaison between primary and secondary mental and physical health services. Additionally, it considers whether the symptoms could be attributed to the relatively rare diagnosis of rumination syndrome which is historically underdiagnosed.
Social business process management
Authors: Bazan Patricia , Estevez Elsa 
Published: October 2019

Purpose
The purpose of this paper is to assess the state of the art of social business process management (Social BPM), explaining applied approaches, existing tools and challenges and to propose a research agenda for encouraging further development of the area.

Design/methodology/approach
The methodology comprises a qualitative analysis using secondary data. The approach relies on searches of scientific papers conducted in well-known databases, identifying research work related to Social BPM solutions and those contributing with social characteristics to BPM. Based on the identified papers, the authors selected the most relevant and the latest publications, and categorized their contributions and findings based on open and selective coding. In total, the analysis is based on 51 papers that were selected and analyzed in depth.

Findings
Main results show that there are several studies investigating modeling approaches for socializing process activities and for capturing implicit knowledge possessed and used by process actors, enabling to add some kind of flexibility to business processes. However, despite the proven interest in the area, there are not yet adequate tools providing effective solutions for Social BPM. Based on our findings, the authors propose a research agenda comprising three main lines: contributions of social software (SS) to Social BPM, Social BPM as a mechanism for adding flexibility to and for discovering new business processes and Social BPM for enhancing business processes with the use of new technologies. The authors also identify relevant problems for each line.

Practical implications
Some SS tools, like wikis, enable managing social aspects in executing business processes and can be used to coordinate simple business processes. Despite they are commonly used, they are not yet mature tools supporting Social BPM and more efficient tools are yet to appear. The lack of tools preclude organizations from benefitting from implicit knowledge owned by and shared among business process actors, which could contribute to better-informed decisions related to organizational processes. In addition, more research is needed for considering Social BPM as an approach for organizations to benefit from the adoption of new technologies in their business processes.

Originality/value
The paper assesses the state of the art in Social BPM, an incipient area in research and practice. The area can be defined as the intersection of two bigger areas highly relevant for organizations; on the one hand, the management and execution of business processes; and on the other hand, the use of social software, including social media tools, for leveraging on implicit knowledge shared by business process actors to improving efficiency of business processes.
Determining the odds of employment in Pakistan
Authors: Aftab Izza , Mazher Umair 
Published: October 2019

Purpose
The paper aims to identify the determinants of employment in Pakistan. In light of the jobless growth Pakistan has experienced starting from 2000, this is a valid concern. The paper discusses the structural relationship between employment and growth in Pakistan and analyzes it empirically within an economic geography framework.

Design/methodology/approach
The paper applies a Logit regression analysis to data from Pakistan Social and Living Standard Measurement Survey for the years 2010, 2012 and 2014. While this survey is published annually, the paper uses data at the district level, which is available only every alternate year. Data are collected at the individual level and can be mapped back to the household level. Each wave of data covers at least 70,000 households. The survey provides data on employment status, health, education, sanitation, economic situation and asset ownership. The analysis is conducted using Stata. The paper uses computer vision to present and trace changing employment patterns in Pakistan over time. To do so, the paper uses MATLAB. The data are transformed to KMV format and the plotting is done using Google Earth.

Findings
The paper shows how household characteristics affect the odds of employment in Pakistan, finding evidence of provincial disparities. Moreover, the paper shows that non-wage income from assets reduces the odds of being employed. The paper identifies the various income thresholds for the five income sources examined to have an impact on the odds of employment.

Originality/value
The novelty of this research is the identification of the determinants of employment in Pakistan and their analysis from the perspective of economic geography. This paper should be useful for policymakers and international financial organizations concerned with structural change in Pakistan.