bluuebunny/crossref_metadata_2025 huggingface dataset:
Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
Authors: Youngblut Nicholas D. , Reischer Georg H. , Walters William , Schuster Nathalie , Walzer Chris , Stalder Gabrielle , Ley Ruth E. , Farnleitner Andreas H.
Published: December 2018

Multiple factors modulate microbial community assembly in the gut, but the magnitude of each can vary substantially across studies. This may be in part due to a heavy reliance on captive animals, which can have very different gut microbiomes versus their wild counterparts. In order to better resolve the influence of evolution and diet on gut microbiome diversity, we generated a large and highly diverse animal distal gut 16S rRNA microbiome dataset, which comprises 80 % wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decoupled the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor explains different aspects of diversity. Moreover, we resolved particular microbial taxa associated with host phylogeny or diet, and we show that Mammalia have a stronger signal of cophylogeny versus non-mammalian hosts. Additionally, our results from ecophylogenetics and co-occurrence analyses suggest that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard
Authors: Migicovsky Zoë , Harris Zachary N. , Klein Laura L. , Li Mao , McDermaid Adam , Chitwood Daniel H. , Fennell Anne , Kovacs Laszlo G. , Kwasniewski Misha , Londo Jason P. , Ma Qin , Miller Allison J.
Published: December 2018

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we use the French-American hybrid grapevine ‘Chambourcin’ (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in ‘Chambourcin’ grown own-rooted as well as grafted to three different rootstocks (‘SO4’, ‘1103P’ and ‘3309C’) across two years and three different irrigation treatments. Results described here demonstrate that 1) the largest source of variation in leaf shape stems from the interaction of rootstock by irrigation; 2) leaf position, but also rootstock and rootstock by irrigation interaction, are the primary sources of variation in leaf ion concentrations; and 3) gene expression in scion leaves exhibited significantly different patterns of gene expression from ungrafted vines, and these expression patterns were rootstock-specific. Our work provides an initial description of the subtle and complex effect of grafting on ‘Chambourcin’ leaf morphology, ionomics and gene expression in grapevine scions. Further work across multiple years, environments and additional phenotypes is required in order to determine how the relationship between the rootstock and the scion can best be leveraged for adapting grapevines to a changing climate.
Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin
Authors: Vertii Anastassiia , Ou Jianhong , Yu Jun , Yan Aimin , Pagès Hervé , Liu Haibo , Zhu Lihua Julie , Kaufman Paul D.
Published: December 2018

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus-Associated Domains (NADs) and Lamina–Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, due to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery and with the nuclear lamina, and generally display characteristics of constitutive heterochromatin, including late DNA replication, enrichment of H3K9me3 and little gene expression. In contrast, Type II NADs associate with nucleoli but do not overlap with LADs. Type II NADs tend to replicate earlier, display greater gene expression, and are more often enriched in H3K27me3 than Type I NADs. The nucleolar associations of both classes of NADs were confirmed via DNA-FISH, which also detected Type I but not Type II probes enriched at the nuclear lamina. Interestingly, Type II NADs are enriched in distinct gene classes, notably factors important for differentiation and development. In keeping with this, we observed that a Type II NAD is developmentally regulated, present in MEFs but not in undifferentiated embryonic stem (ES) cells.
A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae
Authors: Fiore Cara L. , Alexander Harriet , Kido Soule Melissa C. , Kujawinski Elizabeth B.
Published: December 2018

Phosphorus (P) limits primary production in regions of the surface ocean, and many plankton species exhibit specific physiological responses to P-deficiency. The metabolic response of Micromonas pusilla, an ecologically relevant marine photoautotroph, to P-deficiency was investigated using environmental metabolomics and comparative genomics. The concentrations of some intracellular metabolites were elevated in the P-deficient cells (e.g., xanthine, inosine) and genes involved in the associated metabolic pathways shared a predicted conserved amino acid motif in the non-coding regions of each gene. The presence of the conserved motif suggests that these genes may be co-regulated, and the motif may constitute a regulatory element for binding a transcription factor, specifically that of Psr1 (Phosphate starvation response,), first described in the alga, Chlamydomonas reinhardtii. A putative phosphate starvation response gene (psr1-like) was identified in M. pusilla with homology to well characterized psr1/phr1 genes in algae and plants, respectively. This gene appears to be present and expressed in other marine algal taxa (e.g., Emiliania huxleyi) in field sites that are chronically phosphorus-limited. Results from the present study have implications for understanding phytoplankton taxon-specific roles in mediating P cycling in the ocean.
PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution
Authors: Gordon Sean P. , Levy Joshua J. , Vogel John P.
Published: December 2018

Existing methods for assigning sequences to individual species from pooled DNA samples rely on differences in genome properties like GC content or sequences from related species. These approaches do not work for closely related species where gross features are indistinguishable and related genomes are lacking. We describe a method and associated software package that uses rapidly evolving repetitive DNA to circumvent these limitations. By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes without any prior knowledge. This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.
OCHROdb: a comprehensive, quality checked database of open chromatin regions from sequencing data
Authors: Shooshtari Parisa , Feng Samantha , Nelakuditi Viswateja , Foong Justin , Brudno Michael , Cotsapas Chris
Published: December 2018

International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.
Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to modulate chromatin structure and gene expression
Authors: Miyaji Mary , Furuta Ryohei , Hosoya Osamu , Sano Kuniaki , Hara Norikazu , Kuwano Ryozo , Kang Jiyoung , Tateno Masaru , Tsutsui Kimiko M. , Tsutsui Ken
Published: December 2018

Background

Type II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T-segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be placed far from each other on the same chromosome. However, no direct evidence for this to occur has been described so far due to lack of proper methodology.

Results

The beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. To elucidate the enzyme’s role in the process, here we devise a genome-wide mapping technique for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It became clear that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that the DSP sites are intertwined or knotted and topo IIβ is engaged in unknotting reaction that leads to chromatin decondensation and gene regulation.

Conclusions

When combined with categorized gene expression analysis, the model-based prediction of DSP sites reveals that DSP is one of the key factors for topo IIβ-dependency of neuronal gene regulation.
Experimental evolution of independent genetic pathways for resistance toPseudomonas aeruginosapathogenicity within the nematodeCaenorhabditis remanei
Authors: Archer Heather , Phillips Patrick C.
Published: December 2018

Pathogenic host-microbe interactions can result from continuous evolution of a host’s ability to resist infection and a pathogen’s ability to survive and replicate.Pseudomonas aeruginosais a versatile and opportunistic pathogen, ubiquitous in the environment, and capable of damaging plants, vertebrates, and invertebrates. Previous studies in nematodes suggest that the pathogenic effects ofP. aeruginosacan result from multiple distinct pathways: a toxin-based effect that kills within a few hours and a generalized virulence that kills over the course of multiple days. Using experimental evolution in the highly polymorphic nematodeCaenorhabditis remanei, we show that nematode resistance to the two modes of pathogenesis inP. aeruginosaevolves through genetically independent pathways. These results demonstrate that multiple virulence patterns in a pathogen can result in multiple responses in the host, and the genetic lines established here create resources for further exploration of the genetic basis for resistance toP. aeruginosa.
Ancient DNA from chewing gums connects material culture and genetics of Mesolithic hunter-gatherers in Scandinavia
Authors: Kashuba Natalia , Kirdök Emrah , Damlien Hege , Manninen Mikael A. , Nordqvist Bengt , Persson Per , Götherstörm Anders
Published: December 2018

The discussion of an early postglacial dual-route colonization of the Scandinavian Peninsula is largely based on associating genomic data to an early dispersal of lithic technology from the East European Plain. However, a direct link between the two has been lacking. We tackle this problem by analysing human DNA from birch bark pitch mastics, “chewing gums”, from Huseby Klev, a site in western Sweden with eastern lithic technology. We generate genome- wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers, or more precisely, to individuals from postglacial Sweden. Our samples date to 9880-9540 calBP, expanding the temporal range of this genetic group as well as its distribution. Human DNA from mastics provides a clear connection between material culture and genetic data. We also propose that DNA from different types of mastics can be used to study environment, ecology, and oral microbiome of prehistoric populations.
Implementation of the Perfect Plasticity Approximation with biogeochemical compartments in R
Authors: Erickson Adam , Strigul Nikolay
Published: December 2018

Modeling forest ecosystems is a landmark challenge in science, due to the complexity of the processes involved and their importance in predicting future planetary conditions. While there are a number of open-source forest biogeochemistry models, few papers exist detailing the software development approach used to develop these models. This has left many forest biogeochemistry models large, opaque, and/or difficult to use, typically implemented in compiled languages for speed. Here, we present a forest biogeochemistry model from the SORTIE-PPA class of models, PPA-SiBGC. Our model is based on the Perfect Plasticity Approximation with simple biogeochemistry compartments and uses empirical vegetation dynamics rather than detailed prognostic processes to drive the estimation of carbon and nitrogen fluxes. This allows our model to be used with traditional forest inventory data, making it widely applicable and simple to parameterize. We detail the conceptual design of the model as well as the software implementation in the R language for statistical computing. Our aim is to provide a useful tool for the biogeochemistry modeling community that demonstrates the importance of vegetation dynamics in biogeochemical models.
Single-cell Transcriptomics reveals multi-step adaptations to endocrine therapy
Authors: Hong Sung Pil , Chan Thalia E. , Lombardo Ylenia , Corleone Giacomo , Rotmensz Nicole , Pruneri Giancarlo , McEwen Kirsten R. , Coombes R. Charles , Barozzi Iros , Magnani Luca
Published: December 2018

Resistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. Partially, this is due to our limited understanding on the effect of ET at the single cell level. In the present study, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare sub-population of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. PA cells show reduced oestrogen receptor α activity but increased features of quiescence and migration. We find evidence for sub-clonal expression of this PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.
SMCR8 negatively regulates AKT and MTORC1 signaling to modulate lysosome biogenesis and tissue homeostasis
Authors: Lan Yungang , Sullivan Peter M. , Hu Fenghua
Published: December 2018

The intronic hexanucleotide expansion in the C9orf72 gene is one of the leading causes of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS), 2 devastating neurodegenerative diseases. C9orf72 forms a heterodimer with SMCR8 (Smith-Magenis syndrome chromosome region, candidate 8) protein. However, the physiological function of SMCR8 remains to be characterized. Here we report that ablation of SMCR8 in mice results in splenomegaly with autoimmune phenotypes similar to that of C9orf72 deficiency. Furthermore, SMCR8 loss leads to a drastic decrease of C9orf72 protein levels. Many proteins involved in the macroautophagy-lysosome pathways are downregulated upon SMCR8 loss due to elevated activation of MTORC1 and AKT, which also leads to increased spine density in the Smcr8 knockout neurons. In summary, our studies demonstrate a key role of SMCR8 in regulating MTORC1 and AKT signaling and tissue homeostasis.
Isolation of adipose tissue derived regenerative cells from human subcutaneous tissue with or without the use of an enzymatic reagent
Authors: Winnier Glenn E. , Valenzuela Nick , Alt Christopher , Peters-Hall Jennifer , Kellner Joshua , Alt Eckhard U.
Published: December 2018

Background

Freshly isolated, uncultured autologous adipose derived regenerative cells (ADRCs) have emerged as a promising tool for regenerative cell therapy. The Transpose RT system (InGeneron, Inc., Houston, TX, USA) is a system for isolating ADRCs from adipose tissue, commercially available in Europe as a CE-marked medical device and under clinical evaluation in the United States. This system makes use of the proprietary, enzymatic Matrase Reagent for isolating cells. The present study addressed the question whether the use of Matrase Reagent influences cell yield, cell viability, live cell yield, biological characteristics, physiological functions or structural properties of the ADRCs in final cell suspension.

Methods

Identical samples of subcutaneous adipose tissue from 12 subjects undergoing elective lipoplasty were processed either with or without the use of Matrase Reagent. Then, characteristics of the ADRCs in the respective final cell suspensions were evaluated.

Results

Compared to non-enzymatic isolation, enzymatic isolation resulted in approximately twelve times higher mean cell yield (i.e., numbers of viable cells/ml lipoaspirate) and approximately 16 times more colony forming units. Despite these differences, cells isolated from lipoaspirate both with and without the use of Matrase Reagent were independently able to differentiate into cells of all three germ layers.

Discussion

The data of this study indicate that biological characteristics, physiological functions or structural properties relevant for the intended use were not altered or induced using Matrase Reagent. A comprehensive literature review demonstrated that isolation of ADRCs from lipoaspirate using the Transpose RT system and the Matrase Reagent results in the highest viable cell yield among all published data regarding isolation of ADRCs from lipoaspirate.
Adaptations in the echolocation behavior of fruit-eating bats when orienting under challenging conditions
Authors: Beetz M. Jerome , Kössl Manfred , Hechavarria Julio C.
Published: December 2018

For orientation, echolocating bats emit biosonar calls and use echoes arising from call reflections. They often pattern their calls into groups which increases the rate of sensory feedback over time. Insectivorous bats emit call groups at a higher rate when orienting in cluttered compared to uncluttered environments. Frugivorous bats increase the rate of call group emission when they echolocate in noisy environments. Here, calls emitted by conspecifics potentially interfere with the bat's biosonar signals and complicate the echolocation behavior. To minimize the information loss followed by signal interference, bats may profit from a temporally increased sensory acquisition rate, as it is the case for the call groups. In frugivorous bats, it remains unclear if call group emission represents an exclusive adaptation to avoid interference by signals from other bats or if it represents an adaptation that allows to orient under demanding environmental conditions. Here, we compared the emission pattern of the frugivorous bat Carollia perspicillata when the bats were flying in noisy versus silent, narrow versus wide or cluttered versus non-cluttered corridors. According to our results, the bats emitted larger call groups and they increased the call rate within the call groups when navigating in narrow, cluttered, or noisy environments. Thus, call group emission represents an adaptive behavior when the bats orient in complex environments.
Genetic interactions among Ghd7, Ghd7.1, Ghd8 and Hd1 contribute to large variation in heading date in rice
Authors: Xing Yongzhong , Zhang Bo , Liu Haiyang , Qi Feixiang , Zhang Zhanyi , Li Qiuping , Han Zhongmin
Published: December 2018

Several major heading date genes are sensitive to photoperiod and jointly regulate heading date in rice. However, it is not clear how these genes coordinate rice heading. In this study, a near-isogenic F2 population with Ghd7, Ghd7.1, Ghd8 and Hd1 segregating in the Zhenshan 97 (ZS97) background was used to evaluate the genetic interactions among these four genes under natural long-day (NLD) and natural short-day (NSD) conditions, and a series of Ghd7.1-segregating populations in different backgrounds were developed to estimate the genetic effects of Ghd7.1 on heading date under both conditions. Tetragenic, trigenic and digenic interactions among these four genes were observed under both conditions. In the functional Hd1 backgrounds, the strongest digenic interaction was Ghd7 by Ghd8 under NLD conditions but was Ghd7 by Ghd7.1 under NSD conditions. Interestingly, Ghd7.1 acted as a flowering suppressor under NLD conditions, while it functioned alternatively as an activator or a suppressor under NSD conditions depending on the status of the other three genes. Based on the performances of 16 homozygous four-gene combinations, a positive correlation between heading date and yield was found under NSD conditions, but changed to a negative correlation when heading date was over 90 days under NLD conditions. These results demonstrate the importance of genetic interactions in the rice flowering regulatory network and will help breeders to select favorable combinations to maximize rice yield potential for different ecological areas.
Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades
Authors: huang linbin , Yan Xing-hong
Published: December 2018

Pyropia yezoensis is an important economic seaweed, to construct a genetic linkage map and analyze the quantitative trait loci (QTLs) of blades, a doubled haploid (DH) population containing 148 DH strains established from the intraspecific hybridization between two strains with different colors was used in the present study and genotyped using 79 pairs of polymorphic sequence-related amplified polymorphism (SRAP) markers labeled with 5'-HEX and capillary electrophoresis. A chi-square test for significance of deviations from the expected ratio (1:1) on the loci which were polymorphic between parents and segregated in mapping population identified 301 loci with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed segregation (0.001 ≤ P < 0.01). The map was constructed using JoinMap software after a total of 92 loci were assembled into three linkage groups. The map spanned 557.36 cM covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM. Kolmogorov-Smirnov test (α=5%) of the marker positions along each LG showed a uniform distribution. After that, 10 QTLs associated with five economic traits of blades were detected, among which one QTL was for length, one for width, two for fresh weight, two for specific growth rate of length and four for specific growth rate of fresh weight. These QTLs could explain 2.29-7.87% of the trait variations, indicating that their effects were all minor. The results will serve as a framework for future marker-assisted breeding in P. yezoensis.
Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia
Authors: Timofeev Vitalii , Bakhteeva Irina , Mironova Raisa , Titareva Galina , Lev Igor , Christiany David , Borzilov Alexander , Bogun Alexander , Vergnaud Gilles
Published: December 2018

This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, as the Yamal strains. Despite the remoteness of Yamal from Yakutia, whole genome sequence analysis showed that the B.Br.001/002 strains are very closely related. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in B. anthracis population. The geographic distribution of the strains belonging to this polytomy is suggesting that this polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
Changes choroidal area following trabeculectomy: long-term effect of intraocular pressure reduction
Authors: Kojima Kazuhiro , Hirooka Kazuyuki , Sonoda Shozo , Sakamoto Taiji , Kiuchi Yoshiaki
Published: December 2018

Purpose: To investigate the long-term effects of intraocular pressure (IOP) changes after trabeculectomy on the macular and peripapillary choroidal areas.
Methods: This prospective longitudinal study examined 30 eyes of 30 patients with glaucoma that was uncontrolled by medical therapy. At 1 day before and at 1 year after the trabeculectomy surgery, macular and peripapillary choroidal images were recorded by enhanced depth imaging optical coherence tomography (EDI-OCT). Luminal and interstitial areas were converted to binary images using the Niblack method. Factors influencing the macular choroidal and peripapillary area were examined by multivariate analysis.
Results: After trabeculectomy, the mean IOP was 10.8±3.2 mmHg compared to 17.8±7.2 mmHg at baseline (P < 0.001). The total macular choroidal area after the surgery increased from 317,735±77,380 to 338,120±90,700 μm2, while the interstitial area increased from 108,598±24,502 to 119,172±31,495 μm2 (all P < 0.05). The total peripapillary choroidal area after the surgery also increased from 1,557,487±431,798 to 1,650,253±466,672 μm2, while the interstitial area increased from 689,891±149,476 to 751,816±162,457 μm2 (all P < 0.05). However, there were no significant differences observed in the luminal area before and after the surgery. A decrease in the IOP was among the factors associated with the changes in the peripapillary choroidal area.
Conclusions: IOP reductions after trabeculectomy led to increases in the macular and peripapillary choroidal areas for at least 1 year postoperative. Increases in the interstitial areas were the primary reason for observed changes in the choroidal area after trabeculectomy.
Repairing the lungs one breath at a time: How dedicated or facultative are you?
Authors: Leach John P. , Morrisey Edward E.
Published: December 2018

Tissue regeneration involves various types of cellular and molecular responses depending on the type of tissue and the injury or disease that is inflicted. While many tissues contain dedicated stem/progenitor cell lineages, many others contain cells that, during homeostasis, are considered physiologically functional and fully differentiated but, after injury or in disease states, exhibit stem/progenitor-like activity. Recent identification of subsets of defined cell types as facultative stem/progenitor cells has led to a re-examination of how certain tissues respond to injury to mount a regenerative response. In this review, we focus on lung regeneration to explore the importance of facultative regeneration controlled by functional and differentiated cell lineages as well as how they are positioned and regulated by distinct tissue niches. Additionally, we discuss the molecular signals to which cells respond in their differentiated state during homeostasis and those signals that promote effective regeneration of damaged or lost cells and structures after injury.
Evolution of aneuploidy: overcoming the original CIN
Authors: Storchova Zuzana
Published: December 2018

Chromosomal instability (CIN) generates continuously novel aneuploid genomes—unbalanced chromosome combinations that differ from the haploid chromosome set and its multiples. On one hand, this causes problems for cells, as high CIN and aneuploidy impair cellular proliferation by inducing multiple cellular stresses. At the same time, some genomes might provide an advantage under suboptimal conditions. However, what happens to cells that carry a mutation generating extremely high CIN? Are they sentenced to death, or can their instability help them to avert that fate? The elegant work from Ravichandran and colleagues (pp. 1485–1498) in this issue of Genes & Development exploits budding yeast to shed new light on cellular adaptations to CIN. The study presents exciting findings elucidating forces that shape aneuploid genomes in eukaryotic cells and likely influence karyotypic evolution in cancer cells.
Ultraviolet (UV) Cross-Linking of Live Cells, Lysate Preparation, and RNase Titration for Cross-Linking Immunoprecipitation (CLIP)
Authors: Darnell Jennifer C. , Mele Aldo , Hung Ka Ying Sharon , Darnell Robert B.
Published: December 2018

One of the great advantages of RNA CLIP (cross-linking immunoprecipitation) is that RNA–protein complexes can be “frozen” in situ in live cells by ultraviolet (UV) irradiation. This protocol describes UV cross-linking of mammalian tissue culture cells or whole tissues. For the latter, the tissue is typically triturated to allow UV penetration. However, depending on the thickness of the chosen tissue, this may not be necessary. It is preferable to handle the tissue as little as possible, to keep it in ice-cold buffers, and to cross-link as soon after the time of collection as is feasible to preserve native interactions at the time of cross-linking. This protocol also describes cell lysis following cross-linking, as well as treatment with RNase to partially hydrolyze the bound RNA. The first time this protocol is performed, a pilot experiment should be performed to determine the optimal RNase concentration for the particular sample. Once the RNase conditions are optimized this section of CLIP protocol can be repeated on experimental samples before proceeding through the rest of the protocol.
3′-Linker Ligation and Size Selection by SDS-PAGE for Cross-Linking Immunoprecipitation (CLIP)
Authors: Darnell Jennifer C. , Mele Aldo , Hung Ka Ying Sharon , Darnell Robert B.
Published: December 2018

This protocol describes the purification by denaturing polyacrylamide gel electrophoresis of RNA linkers for cross-linking immunoprecipitation (CLIP). Purification is necessary because if the 3′ linker loses the puromycin blocking group, concatemerization of the 3′ linker will occur during the 3′ linker ligation reaction. In addition, truncated linkers make bioinformatic processing of the sequencing results more difficult than it need be. Additionally, this protocol describes the treatment of coimmunoprecipitated RNA tags for CLIP with alkaline phosphatase to remove the 3′ phosphate remaining after RNase digestion. Dephosphorylation prevents intramolecular circularization of RNA during subsequent ligation to the linker. The purified RNA linker, blocked with puromycin at its 3′ end to prevent linker–linker multimerization, is then ligated to the 3′ end of the RNA tag. Removal of free linker is accomplished by performing the ligation while the RNABP:RNA complex is associated, via antibody, to protein A Dynabeads, allowing thorough washing and linker removal. Additional purification is achieved by SDS-PAGE and transfer of the size-selected RNABP:RNA complexes to nitrocellulose.
Preparing Antigens Using a Baculovirus Expression System
Authors: Greenfield Edward A. , DeCaprio James , Brahmandam Mohan
Published: December 2018

Baculovirus-produced recombinant proteins circumvent many of the issues that limit bacterial protein production. Baculoviruses contain double-stranded, circular, supercoiled DNA in a rod-shaped capsid. The viral life cycle includes three major phases: (1) early (or virus synthesis) phase (0.5–6 h after infection), which includes viral attachment, uncoating early viral gene expression, and shutting off host gene expression; (2) late phase (6–12 h after infection), which includes viral replication and formation of budded virus containing host plasma membrane and glycoprotein (gp)64, which is required for virus entry; and (3) very late phase (24–96 h after infection), which includes formation of polyhedral inclusion bodies and cell lysis. Large proteins can thus be produced readily in abundant quantities. Furthermore, posttranslational modifications of the protein similar to those of mammals (such as phosphorylation, disulfide-bond formation, and even glycosylation) will occur; indeed, because typical baculovirus constructs produce secreted proteins, most products will be glycosylated. Baculovirus expression systems are safe, because baculoviruses are nonpathogenic to mammals and plants, and insect cells can be grown easily in suspension culture, which makes protein production easy to scale up. Counterbalancing this approach, however, is the need to perform a two-step process: first cloning the gene into the recombination donor vector and then generating the viral construct. At that point, the virus can be used as a mixture or plaque-purified. Insect cells are then infected with the virus, and the proteins are produced.
Bertelsmann China: Supply Chains for Books (A)
Authors: Wagner Stephan M. , Heldt Viviane , Lentschig Katrin , Meyer Jennifer
Published: December 2018

The case of Bertelsmann China: Supply Chain for Books (A) focuses on one the world's leading media companies to illustrate a widespread problem in the supply chain strategy in extremely fast growing markets. Students learn about the basic challenges of supply chain strategy in an international context. The case covers important fields of management theory. Supply chain designs well as cost and performance drivers are revised by the use of frameworks.
BlueStar Office Supply Company
Authors: Thomas Rodney , Rutner Stephen , Boone Christopher
Published: December 2018

This case study addresses a number of common transportation management issues. It provides an opportunity to analyse historical freight payment data in order to reduce transportation costs and improve customer service, allowing students to utilise real freight payment data and order shipment history data to make recommendations that have strategic implications for both cost and service performance.
The application of trigonometric grey prediction model to average per capita natural gas consumption of households in China
Authors: Wang Qiuping , Liu Subing , Yan Haixia
Published: December 2018

Purpose

Due to high efficiency and low carbon of natural gas, the consumption of natural gas is increasing rapidly, and the prediction of natural gas consumption has become the focus. The purpose of this paper is to employ a prediction technique by combining grey prediction model and trigonometric residual modification for predicting average per capita natural gas consumption of households in China.

Design/methodology/approach

The GM(1,1) model is utilised to obtain the tendency term, then the generalised trigonometric model is used to catch the periodic phenomenon from the residual data of GM(1,1) model for improving predicting accuracy.

Findings

The case verified the view of Xie and Liu: “When the value of a is less, DGM model and GM(1,1) model can substitute each other.” The combination of the GM(1,1) and the trigonometric residual modification technique can observably improve the predicting accuracy of average per capita natural gas consumption of households in China. The mean absolute percentage errors of GM(1,1) model, DGM(1,1), unbiased grey forecasting model, and TGM model in ex post testing stage (from 2013 to 2015) are 32.5510, 33.5985, 36.9980, and 5.2996 per cent, respectively. The TGM model is suitable for the prediction of average per capita natural gas consumption of households in China.

Practical implications

According to the historical data of average per capita natural gas consumption of households in China, the authors construct GM(1,1) model, DGM(1,1) model, unbiased grey forecasting model, and GM(1,1) model with trigonometric residual modification. The accuracy of TGM is the best. TGM helps to improve the accuracy of GM(1,1).

Originality/value

This paper gives a successful practical application of grey model GM(1,1) with the trigonometric residual modification, where the cyclic variations exist in the residual series. The case demonstrates the effectiveness of trigonometric grey prediction model, which is helpful to understand the modeling mechanism of trigonometric grey prediction model.
Real-time monocular 3D perception with ORB-Features
Authors: Ji Babing , Cao Qixin
Published: December 2018

Purpose

This paper aims to propose a new solution for real-time 3D perception with monocular camera. Most of the industrial robots’ solutions use active sensors to acquire 3D structure information, which limit their applications to indoor scenarios. By only using monocular camera, some state of art method provides up-to-scale 3D structure information, but scale information of corresponding objects is uncertain.

Design/methodology/approach

First, high-accuracy and scale-informed camera pose and sparse 3D map are provided by leveraging ORB-SLAM and marker. Second, for each frame captured by a camera, a specially designed depth estimation pipeline is used to compute corresponding 3D structure called depth map in real-time. Finally, depth map is integrated into volumetric scene model. A feedback module has been designed for users to visualize intermediate scene surface in real-time.

Findings

The system provides more robust tracking performance and compelling results. The implementation runs near 25 Hz on mainstream laptop based on parallel computation technique.

Originality/value

A new solution for 3D perception is using monocular camera by leveraging ORB-SLAM systems. Results in our system are visually comparable to active sensor systems such as elastic fusion in small scenes. The system is also both efficient and easy to implement, and algorithms and specific configurations involved are introduced in detail.
Identifying and ranking CSFs for KM implementation in urban water and sewage companies using ISM-DEMATEL technique
Authors: Mousavizade Faeze , Shakibazad Mohammad
Published: December 2018

Purpose

This paper aims to study the critical success factors (CSF) of knowledge management (KM) in Iranian urban water and sewage companies (IUWSC) using interpretive structural modeling (ISM)-decision-making trial and evaluation laboratory (DEMATEL) method.

Design/methodology/approach

Through the literature review among many key factors of KM success, nine factors were selected as the main factors. After confirming the related indices by industry experts, a questionnaire was distributed among them for determining the relationship between the relevant components. Using ISM-DEMATEL approach, a structural model was formed and then the causal relationship among factors was visualized through a cause-effect relationship diagram.

Findings

The analysis of the results showed that among the studied factors, strategies and goals would have the greatest impact on success of KM implementation and senior management support, and teamwork and organizational culture are other CSFs of KM in IUWSC. In the end, the author’s proposed model for implementation of KM was presented based on the results for the status quo of the studied community.

Practical implications

The set of CSFs can act as a guideline for organizations to ensure that basic factors and issues are covered during implementation KM. Moreover, it provides a clue for effective development of KM in a stepwise approach.

Originality/value

This survey is probably the first to provide an integrated view of CSFs for implementation KM in IUWSC. It is hoped to give valuable information to help this business sector to accomplish KM effectively.
Organizational knowledge retention and knowledge loss
Authors: Levallet Nadège , Chan Yolande E.
Published: December 2018

Purpose

This paper aims to examine the effectiveness of organizational information technology (IT)-based and non-IT-based knowledge transfer mechanisms (KTMs) for the retention of different types of knowledge from mobile experts. It differentiates among four types of knowledge loss (KL), namely, conscious knowledge (i.e. individual explicit knowledge that can be codified); codified knowledge (i.e. explicit knowledge captured at the social level); automatic knowledge (i.e. implicit individual knowledge); and collective knowledge (i.e. implicit knowledge embedded in the organization).

Design/methodology/approach

A research framework connecting the organizational knowledge retention (KR) cycle to KL is developed and an exploratory analysis is conducted using data from two case studies in the Canadian federal public service. Findings are confirmed using a third government agency.

Findings

Without the right processes in place for organizational knowledge retrieval and reuse, the KR cycle is not complete, leading to KL. The lack of available social KTMs for the conversion of individual to social objectified knowledge leads to KL. KTMs shortcomings increase the risk of automatic and objectified KL.

Research limitations/implications

Exploratory results demonstrate that KL does not always equate to lack of KR. Implementing knowledge-specific organizational KTMs is important to encourage the retention of individual knowledge at the social level. Propositions and a framework are developed for future research.

Practical implications

Mobile experts hold valuable knowledge at high risk of being lost by organizations. This paper provides managers with a set of guidelines to develop a knowledge-specific strategy focused on KTMs that increase KR and mitigate KL.

Originality/value

This paper challenges the assumption that KL only results from poor retention and studies both retention and loss to identify additional types of unintentional loss that occur when individual knowledge is not converted to social knowledge.
Validity and accuracy of the Whooley questions to identify maternal distress in Dutch pregnant women
Authors: Fontein-Kuipers Yvonne , Jomeen Julie
Published: December 2018

Purpose

The purpose of this paper is to investigate the validity and accuracy of the Whooley questions for routine screening of maternal distress in Dutch antenatal care.

Design/methodology/approach

In this cohort design, the authors evaluated self-reported responses to the Whooley questions against the Edinburgh Depression Scale screening for antenatal depression, State-Trait Anxiety Inventory for general anxiety and the pregnancy-related anxiety questionnaire-revised screening for pregnancy-related anxiety, among Dutch pregnant women during the first and third trimester of pregnancy. The authors used standard diagnostic performance measures for the two case-finding items.

Findings

The Whooley items in this study showed a higher specificity than sensitivity. The Whooley results showed good evidence to identify women who are depressed or (trait)anxious in both trimesters of pregnancy, but the results showed weak to moderate evidence to identify pregnancy-related anxiety. The Whooley items had a low to moderate predictive ability for depression, trait-anxiety and pregnancy-related anxiety and a good ability for negative case-finding. The Whooley items proved to be more able to report how effective the case-finding questions are in identifying women without depression, trait-anxiety and pregnancy-related anxiety (ruling out) rather than how effective these are in identifying women with depression, trait-anxiety and pregnancy-related anxiety (ruling in). The Whooley items were accurate in identifying depression and trait-anxiety in both trimesters but were not very accurate to identify pregnancy-related anxiety.

Research limitations/implications

Assessment of pregnancy-related anxiety using a case-finding tool requires further attention.

Practical implications

The two-item Whooley case-finding tool has shown good utility as a screening instrument for maternal distress. The continuous assessment of maternal emotional health during the childbearing period or, at least, revisiting the topic, would both support the woman and the midwife in regarding perinatal emotional wellbeing as an important remit of midwifery care.

Originality/value

A novel aspect of this paper is the proposition of applying the Whooley questions at later stages of pregnancy or presenting the Whooley questions in a written or digital form.