bluuebunny/crossref_metadata_2025 huggingface dataset:
Long non-coding RNA Gm15441 attenuates hepatic inflammasome activation in response to metabolic stress
Authors: Brocker Chad N. , Kim Donghwan , Melia Tisha , Karri Kritika , Velenosi Thomas J. , Takahashi Shogo , Bonzo Jessica A. , Waxman David J. , Gonzalez Frank J.
Published: June 2019

Fasting paradigms elicit a wide-range of health benefits including suppressing inflammation. Exploring the molecular mechanisms that prevent inflammation during caloric restriction may yield promising new therapeutic targets. During fasting, activation of the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARA) promotes the utilization of lipids as an energy source. Herein, we show that ligand activation of PPARA directly upregulates the long non-coding RNA geneGm15441through binding sites within its promoter.Gm15441expression suppresses its antisense transcript, encoding thioredoxin interacting protein (TXNIP). This, in turn, decreases TXNIP-stimulated NLRP3 inflammasome activation, caspase-1 (CASP1) cleavage, and proinflammatory interleukin 1 beta (IL1B) maturation.Gm15441-null mice were developed and shown to be more susceptible to NLRP3 inflammasome activation and to exhibit elevated CASP1 and IL1B cleavage in response to metabolic and inflammatory stimuli. These findings provide evidence for a novel mechanism by which PPARA attenuates hepatic inflammasome activation in response to metabolic stress through lncRNAGm15441induction.

Graphical abstract
A new family of Type VI secretion system-delivered effector proteins displays ion-selective pore-forming activity
Authors: Mariano Giuseppina , Trunk Katharina , Williams David J. , Monlezun Laura , Strahl Henrik , Pitt Samantha J. , Coulthurst Sarah J.
Published: June 2019

Type VI secretion systems (T6SSs) are nanomachines widely used by bacteria to compete with rivals. T6SSs deliver multiple toxic effector proteins directly into neighbouring cells and play key roles in shaping diverse polymicrobial communities. A number of families of T6SS-dependent anti-bacterial effectors have been characterised, however the mode of action of others remains unknown. Here we report that Ssp6, an anti-bacterial effector delivered by theSerratia marcescensT6SS, is an ion-selective pore-forming toxin.In vivo, Ssp6 inhibits growth by causing depolarisation of the inner membrane of intoxicated cells and also leads to increased outer membrane permeability, whilst reconstruction of Ssp6 activityin vitrodemonstrated that it forms cation-selective pores. A survey of bacterial genomes revealed that Ssp6-like effectors are widespread in Enterobacteriaceae and often linked with T6SS genes. We conclude that Ssp6 represents a new family of T6SS-delivered anti-bacterial effectors, further diversifying the portfolio of weapons available for deployment during inter-bacterial conflict.
Intragenic recruitment of NF-κB drives alternative splicing modifications upon activation by the viral oncogene TAX of HTLV-1
Authors: Ameur Lamya Ben , Thenoz Morgan , Giraud Guillaume , Combe Emmanuel , Claude Jean-Baptiste , Lemaire Sebastien , Fontrodona Nicolas , Polveche Hélène , Bastien Marine , Gessain Antoine , Wattel Eric , Bourgeois Cyril F. , Auboeuf Didier , Mortreux Franck
Published: June 2019

The chronic NF-κB activation in inflammation and cancer has long been linked to persistent activation of NF-κB responsive gene promoters. However, NF-κB factors such as RELA also massively bind to gene bodies. Here, we demonstrate that the recruitment of RELA to intragenic regions regulates alternative splicing upon activation of NF-κB by the viral oncogene TAX of HTLV-1. Integrative analysis of RNA splicing and chromatin occupancy, combined with chromatin tethering assays, demonstrate that DNA-bound RELA interacts with and recruits the splicing regulator DDX17 in a NF-kB activation-dependent manner, leading to alternative splicing of target exons thanks to DDX17 RNA helicase activity. This NF-kB/DDX17 axis accounts for a major part of the TAX-induced alternative splicing landscape that mainly affects genes involved in oncogenic pathways. Collectively, our results demonstrate a physical and direct involvement of NF-κB in alternative splicing regulation, which significantly revisits our knowledge of HTLV-1 pathogenesis and other NF-κB-related diseases.
Ramified rolling circle amplification for efficient and flexible synthesis of nucleosomal DNA sequences
Authors: van Emmerik Clara L. , Gachulincova Ivana , Lobbia Vincenzo R. , Daniëls Mark A. , Heus Hans A. , Soufi Abdenour , Nelissen Frank H.T. , van Ingen Hugo
Published: June 2019

Nucleosomes are a crucial platform for the recruitment and assembly of protein complexes that process the DNA. Mechanistic and structuralin vitrostudies typically rely on recombinant nucleosomes that are reconstituted using artificial, strong-positioning DNA sequences. To facilitate such studies on native, genomic nucleosomes, there is a need for methods to produce any desired DNA sequence in an efficient manner. The current methods either do not offer much flexibility in choice of sequence or are less efficient in yield and labor. Here, we show that using ramified rolling circle amplification (RCA) milligram amounts of a genomic nucleosomal DNA fragment can be produced in a scalable, one-pot reaction overnight. The ramified RCA reaction is more efficient than the existing methods, is flexible in DNA sequence and shows a 10-fold increase in yield compared to PCR, rivalling the production using plasmids. We demonstrate the method by producing the genomic DNA from the human LIN28B locus and show that it forms functional nucleosomes capable of binding pioneer transcription factor Oct4.
Characterization of consensus operator site for Streptococcus pneumoniae copper repressor, CopY
Authors: O’Brien Henrik , Alvin Joseph W. , Menghani Sanjay V. , Van Doorslaer Koenraad , Johnson Michael D. L.
Published: June 2019

Copper is broadly toxic to bacteria. As such, bacteria have evolved specialized copper export systems (cop operons) often consisting of a DNA-binding/copper-responsive regulator (which can be a repressor or activator), a copper chaperone, and a copper exporter. For those bacteria using DNA-binding copper repressors, few studies have examined the regulation of this operon regarding the operator DNA sequence needed for repression. In Streptococcus pneumoniae (the pneumococcus), CopY is the copper repressor for the cop operon. Previously, these homologs have been characterized to bind a 10-base consensus sequence T/GACAnnTGTA. Here, we bioinformatically and empirically characterize these operator sites across species using S. pneumoniae CopY as a guide for binding. By examining the 21-base repeat operators for the pneumococcal cop operon and comparing binding of recombinant CopY to this, and the operator sites found in Enterococcus hirae, we show using biolayer interferometry that the T/GACAnnTGTA sequence is essential to binding, but it is not sufficient. We determine a more comprehensive S. pneumoniae CopY operator sequence to be RnYKACAAATGTARnY (where “R” is purine, “Y” is pyrimidine, and “K” is either G or T) binding with an affinity of 28 nM. We further propose that the cop operon operator consensus site of pneumococcal homologs be RnYKACAnnYGTARnY. This study illustrates the necessity to explore bacterial operator sites further to better understand bacterial gene regulation.
Sampling strategies to assess microbial diversity of Antarctic cryptoendolithic communities
Authors: Coleine Claudia , Stajich Jason E. , Pombubpa Nuttapon , Zucconi Laura , Onofri Silvano , Selbmann Laura
Published: June 2019

Describing the total biodiversity of an environmental metacommunity is challenging due to the presence of cryptic and rare species and incompletely described taxonomy. How many samples to collect is a common issue faces ecologists when designing fieldwork sampling: collecting many samples may indeed capture the whole metacommunity structure, but can be prohibitively costly and lead to an enormous amount of data to analyse. Conversely, too few samples may yield inadequate and incomplete data which can prohibit complete assessment of community diversity. High-throughput sequencing allows examination of large numbers of samples enabling comprehensive biodiversity assessments. In this study, we sought to estimate how the scale of sampling affects accuracy of community diversity description in order to develop strategies to exhaustively describe the microbial diversity of cryptoendolithic communities in the McMurdo Dry Valleys in Antarctica accounted as the closest Martian analogue on Earth, exhibiting extreme conditions such as low temperatures, wide thermal fluctuations, low nutrient availability and high UV radiation. We found that sampling effort, based on accumulation curves analysis, had a considerable impact on assessing species richness and composition in these ecosystems, confirming that a sampling as large as nine rock specimens was necessary to detect almost all fungal species present, but was not sufficient to capture whole bacterial assemblage.
Emergence timing and voltinism of phantom midges, Chaoborus spp., in the UK
Authors: Cockroft R. , Jenkins W.R. , Irwin A. , Norman S. , Brown K.C.
Published: June 2019

After introduction of overwintered fourth instar larvae (2027 in total), emergence timing of adult Chaoborus spp. (Diptera: Chaoboridae) was investigated in four outdoor freshwater microcosms in the UK in 2017. Adults started emerging on 13 April and emergence reached a peak on 2 May. The majority of emergence was completed by 3 June. Emergence rates for each microcosm ranged from 51.4% to 66.2% with a mean of 60.9%. The great majority of emerged adults were C. obscuripes (99.68%). Males appeared to emerge slightly earlier than females. The results indicated that for overwintered C. obscuripes larvae, the adults emerged en masse in spring (rather than emerging gradually over the course of spring and summer). In a separate experiment at the same location, the number of Chaoborus spp. life-cycles occurring per year was determined using six replicate groups of microcosms, each group containing four microcosms. Each microcosm contained 200 L of water and was enclosed within a ‘pop-up’ frame covered with ‘insect-proof’ mesh (1 mm2 aperture). The first microcosm in each group was ‘seeded’ with egg rafts (first generation) of Chaoborus spp. Following adult emergence, as soon as the first egg rafts were laid in each microcosm these were removed and transferred to the second microcosm in that group, and so on. The larvae sampled from the second and subsequent generations in the microcosms were all C. crystallinus. C. crystallinus produced up to four discrete generations within the experimental period, and life-cycle times from egg-to-egg ranged from 14 days (replicate group 5, first generation) to 56 days (replicate 3, second generation). These two experiments, indicated that i) adult C. obscuripes arising from overwintered larvae emerged en masse in the spring, and ii) up to four generations of C. crystallinus occurred; i.e. C. crystallinus exhibited a multi-voltine life history under the temperate conditions of this UK study.
Down-regulatedGDF9andBMP15mRNAs are the important determining factors for the unexplained female infertility cases advised for assisted reproductive technology
Authors: Gupta Sumita Dutta , Kundu Sharbadeb , Dhar Bishal , Das Nabarun , Choudhury Arun Paul , Deb Monica , Das Abhijit , Das Amrita , Das Nayanika , Choudhury Biswadeep , Varghese Alex C , Kar Kushal Kumar , Choudhury Yashmin , Ghosh Sankar Kumar
Published: June 2019

DISCLAIMER

The authors have withdrawn this manuscript because they intend to revise this version of pre-print substantially in response to comments received from the reviewers and other peers on some analytical parts along with the interpretation of corresponding results, in order to make a fresh submission to an impacted reputed journal. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Intracellular cyclic AMP levels modulate differential adaptive responses on epimastigotes and cell culture trypomastigotes of Trypanosoma cruzi
Authors: Sternlieb Tamara , Schoijet Alejandra C. , Alonso Guillermo D.
Published: June 2019

Among the many environmental challenges the parasite Trypanosoma cruzi has to overcome to complete its life cycle through different hosts, oxidative stress plays a central role. Different stages of this parasite encounter distinct sources of oxidative stress, such as the oxidative burst of the immune system, or the Heme released from hemoglobin degradation in the triatomine’s midgut. Also, the redox status of the surroundings functions as a signal to the parasite, triggering processes coupled to differentiation or proliferation. Intracellular second messengers, like cAMP, are responsible for the transduction of environmental queues and initiating cellular processes accordingly. In trypanosomatids cAMP is involved in a variety of processes, including proliferation, differentiation, osmoregulation and quorum sensing. Trypanosomatid phosphodiesterases (PDE) show atypical pharmacological properties and some have been involved in key processes for the survival of the parasites, which validates them as attractive therapeutic targets. Our work here shows that cAMP modulates different processes according to parasite stage. Epimastigotes become more resistant to oxidative stress when pre-treated with cAMP analogs, while trypomastigotes do not alter their response to oxidative stress under the same treatment. However, cAMP analogs do increase trypomastigotes infectivity in vitro. Also, we show that TcrPDEA1, a functionally enigmatic phosphodiesterase with very high Km, is involved in the epimastigotes response to oxidative stress.
Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum
Authors: dos Santos Jhonathan P. R. , Fernandes Samuel B. , Lozano Roberto , Brown Patrick J. , Buckler Edward S. , Garcia Antonio A. F. , Gore Michael A.
Published: June 2019

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor(L.) Moench] lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In 5-fold cross-validation, prediction accuracies ranged from 0.48 (PBN) to 0.51 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.74 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits.
Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity
Authors: Zhang Zhe , Xiong Peng , Zhang Tongchuan , Wang Junfeng , Zhan Jian , Zhou Yaoqi
Published: June 2019

Despite the transcription of noncoding RNAs in 75% of the human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained only from costly and inefficient 3D structure determination. Here, we performed deep mutational scanning of self-cleaving CPEB3 ribozyme by error-prone PCR and showed that a library of <5×104 single-to-triple mutants is sufficient to infer all 26 including nonhelical and noncanonical base pairs at the precision of a single false positive. The accurate inference, further confirmed by a twister ribozyme, is resulted from covariation analysis by utilizing both functional and nonfunctional variants for unsupervised learning, followed by restrained optimization. The result highlights the usefulness of deep mutational scanning for high-accuracy structural inference.
DeepTetrad: high-throughput analysis of meiotic tetrads by deep learning in plants
Authors: Lim Eun-Cheon , Kim Jaeil , Park Jihye , Kim Eun-Jung , Kim Juhyun , Cho Hyun Seob , Byun Dohwan , Henderson Ian R , Copenhaver Gregory P , Hwang Ildoo , Choi Kyuha
Published: June 2019

Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be measured by observing the inheritance of linked transgenes expressing different colors of fluorescent protein in Arabidopsis pollen tetrads. Here we establish DeepTetrad, a deep learning-based image recognition package for pollen tetrad analysis that enables high-throughput measurements of crossover frequency and interference in individual plants. DeepTetrad will accelerate genetic dissection of mechanisms that control meiotic recombination.
Genetic diversity of Collaborative Cross mice controls viral replication, clinical severity and brain pathology induced by Zika virus infection, independently of Oas1b
Authors: Manet Caroline , Simon-Lorière Etienne , Jouvion Grégory , Hardy David , Prot Matthieu , Flamand Marie , Panthier Jean-Jacques , Sakuntabhai Anavaj , Montagutelli Xavier
Published: June 2019

The explosive spread of Zika virus (ZIKV) has been associated with major variations in severe disease and congenital afflictions among infected populations, suggesting an influence of host genes. We investigated how genome-wide variants could impact susceptibility to ZIKV infection in mice. We first describe that the susceptibility of Ifnar1 knockout mice is largely influenced by their genetic background. We then show that the broad genetic diversity of Collaborative Cross mice, which receptor to type I interferon (IFNAR) was blocked by anti-IFNAR antibody, expressed phenotypes ranging from complete resistance to severe symptoms and death with large variations in the peak and rate of decrease of plasma viral load, in brain viral load, in brain histopathology and in viral replication rate in infected cells. Differences of susceptibility between CC strains were correlated between Zika, Dengue and West Nile viruses. We identified highly susceptible and resistant mouse strains as new models to investigate the mechanisms of human ZIKV disease and other flavivirus infections. Genetic analyses revealed that phenotypic variations are driven by multiple genes with small effects, reflecting the complexity of ZIKV disease susceptibility in human population. Notably, our results rule out a role of the Oas1b gene in the susceptibility to ZIKV. Altogether, this study emphasizes the role of host genes in the pathogeny of ZIKV infection and lays the foundation for further genetic and mechanistic studies.

IMPORTANCE

In recent outbreaks, ZIKV has infected millions of people and induced rare but potentially severe complications, including Guillain-Barré syndrome and encephalitis in adults. While several viral sequence variants were proposed to enhance the pathogenicity of ZIKV, the influence of host genetic variants in the clinical heterogeneity remains mostly unexplored. We have addressed this question using a mouse panel which models the genetic diversity of human population and a ZIKV strain from a recent clinical isolate. Through a combination of in vitro and in vivo approaches, we demonstrate that multiple host genetic variants determine viral replication in infected cells, and clinical severity, kinetics of blood viral load and brain pathology in mice. We describe new mouse models expressing high susceptibility or resistance to ZIKV and to other flaviviruses. These models will facilitate the identification and mechanistic characterization of host genes that influence ZIKV pathogenesis.
Adaptive evolution targets a piRNA precursor transcription network
Authors: Parhad Swapnil S. , Yu Tianxiong , Zhang Gen , Rice Nicholas P. , Weng Zhiping , Theurkauf William E.
Published: June 2019

InDrosophila, transposon-silencing piRNAs are derived from heterochromatic clusters and a subset of euchromatic transposon insertions, which are transcribed from internal non-canonical initiation sites and flanking canonical promoters. Rhino binds to Deadlock, which recruits TRF2 to promote non-canonical transcription of these loci. Cuff co-localizes with Rhino and Del. The role of Cuff is less well understood, but thecuffgene shows hallmarks of adaptive evolution, which frequently targets functional interactions within host defense systems. We show thatDrosophila simulans cuffis a dominant negative allele when expressed inDrosophila melanogaster, where it traps Deadlock, TRF2 and the transcriptional co-repressor CtBP in stable nuclear complexes. Cuff promotes Rhino and Deadlock localization, driving non-canonical transcription. CtBP, by contrast, suppresses canonical cluster and transposon transcription, which interferes with downstream non-canonical transcription and piRNA production. Cuff, TRF2 and CtBP thus form a network that balances canonical and non-canonical piRNA precursor transcription.
The Goldilocks effect of lake size on within-population diversity in stickleback
Authors: Bolnick Daniel I. , Ballare Kimberly
Published: June 2019

Many generalist species consist of disparate specialized individuals, a phenomenon known as ‘individual specialization’. This within-population niche variation can stabilize population dynamics, reduce extinction risk, and alter community composition. But, we still only vaguely understand the ecological contexts that promote niche variation and its stabilizing effects. Adaptive dynamics models predict that intraspecific variation should be greater in environments with two or more equally-profitable resources, but reduced in environments dominated by one resource. Here, we confirm this prediction using a comparison of threespine stickleback in 33 lakes in on Vancouver Island, Canada. Stickleback consume a combination of benthic and limnetic invertebrates, focusing on the former in small lakes, the latter in large lakes. Intermediate-sized lakes support generalist populations, which arise via greater among-individual diet variation, not by greater individual diet breadth. These intermediate lakes exhibit correspondingly greater morphological diversity, while genomic diversity increases linearly with lake size. These results support the theoretical expectation that habitats with an intermediate ratio of resources are “just right” for promoting ecologically relevant intraspecific diversification.
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase
Authors: Abramo Kristin , Valton Anne-Laure , Venev Sergey V. , Ozadam Hakan , Fox A. Nicole , Dekker Job
Published: June 2019

Chromosome folding is extensively modulated as cells progress through the cell cycle. During mitosis, condensin complexes fold chromosomes in helically arranged nested loop arrays. In interphase, the cohesin complex generates loops that can be stalled at CTCF sites leading to positioned loops and topologically associating domains (TADs), while a separate process of compartmentalization drives the spatial segregation of active and inactive chromatin domains. We used synchronized cell cultures to determine how the mitotic chromosome conformation is transformed into the interphase state. Using Hi-C, chromatin binding assays, and immunofluorescence we show that by telophase condensin-mediated loops are lost and a transient folding intermediate devoid of most loops forms. By late telophase, cohesin-mediated CTCF-CTCF loops and positions of TADs start to emerge rapidly. Compartment boundaries are also established in telophase, but long-range compartmentalization is a slow process and proceeds for several hours after cells enter G1. Our results reveal the kinetics and order of events by which the interphase chromosome state is formed and identify telophase as a critical transition between condensin and cohesin driven chromosome folding.
The draft nuclear genome assembly ofEucalyptus pauciflora: new approaches to comparingde novoassemblies
Authors: Wang Weiwen , Das Ashutosh , Kainer David , Schalamun Miriam , Morales-Suarez Alejandro , Schwessinger Benjamin , Lanfear Robert
Published: June 2019

Background

Selecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plantEucalyptus pauciflora(snow gum) as a test case.Eucalyptus pauciflorais a long-lived tree with high economic and ecological importance. Currently, little genomic information forEucalyptus pauciflorais available.

Findings

We generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a singleEucalyptus paucifloraindividual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.

Conclusions

We report a draft genome ofEucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.
Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis
Authors: Akamatsu Matthew , Vasan Ritvik , Serwas Daniel , Ferrin Michael , Rangamani Padmini , Drubin David G.
Published: June 2019

Force generation due to actin assembly is a fundamental aspect of membrane sculpting for many essential processes. In this work, we use a multiscale computational model constrained by experimental measurements to show that a minimal branched actin network is sufficient to internalize endocytic pits against physiological membrane tension. A parameter sweep identified the number of Arp2/3 complexes as particularly important for robust internalization, which prompted the development of a molecule-counting method in live mammalian cells. Using this method, we found that ~200 Arp2/3 complexes assemble at sites of clathrin-mediated endocytosis in human cells. Our simulations also revealed that actin networks self-organize in a radial branched array with barbed filament ends oriented to grow toward the base of the pit, and that the distribution of linker proteins around the endocytic pit is critical for this organization. Surprisingly, our model predicted that long actin filaments bend from their attachment sites in the coat to the base of the pit and store elastic energy that can be harnessed to drive endocytosis. This prediction was validated using cryo-electron tomography on cells, which revealed the presence of bent actin filaments along the endocytic site. Furthermore, we predict that under elevated membrane tension, the self-organized actin network directs more growing filaments toward the base of the pit, increasing actin nucleation and bending for increased force production. Thus, our study reveals that spatially constrained actin filament assembly utilizes an adaptive mechanism that enables endocytosis under varying physical constraints.
Glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins from pathogenic bacteria
Authors: Turner Matthew L. , Owens Sian E. , Sheldon I. Martin
Published: June 2019

Pathogenic bacteria often damage tissues by secreting toxins that form pores in cell membranes, and the most common pore-forming toxins are cholesterol-dependent cytolysins. During bacterial infections, glutamine becomes a conditionally essential amino acid, and glutamine is an important nutrient for immune cells. However, the role of glutamine in protecting tissue cells against pore-forming toxins is unclear. Here we tested the hypothesis that glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins. Stromal and epithelial cells were sensitive to damage by cholesterol-dependent cytolysins, pyolysin and streptolysin O, as determined by leakage of potassium and lactate dehydrogenase from cells, and reduced cell viability. However, glutamine helped protect cells against cholesterol-dependent cytolysins because glutamine deprivation increased the leakage of lactate dehydrogenase and reduced the viability of cells challenged with cytolysins. Without glutamine, stromal cells challenged with pyolysin leaked lactate dehydrogenase (control vs. pyolysin, 2.6 ± 0.6 vs. 34.4 ± 4.5 AU, n = 12), which was more than three-fold the leakage from cells supplied with 2 mM glutamine (control vs. pyolysin, 2.2 ± 0.3 vs. 9.4 ± 1.0 AU). The cytoprotective effect of glutamine was not dependent on glutaminolysis, replenishing the Krebs cycle via succinate, changes in cellular cholesterol, or regulators of cell metabolism (AMPK and mTOR). In conclusion, although the mechanism remains elusive, we found that glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins from pathogenic bacteria.
Hepatitis E Virus infection and waste pickers: a case-control seroprevalence study
Authors: Alvarado-Esquivel Cosme , Gutierrez-Martinez Verónica Dayali , Ramírez-Valles Eda Guadalupe , Sifuentes-Alvarez Antonio
Published: June 2019

Whether waste pickers are a risk group for hepatitis E virus (HEV) infection is largely unknown. Therefore, this study aimed to determine the association between HEV exposure and: 1) the occupation of waste picker; and 2) the work characteristics of waste pickers. An age-and gender-matched case-control seroprevalence study of 86 waste pickers (mean age: 35.45 ± 17.15 years) and 86 control subjects of the general population was performed. We determined anti-HEV IgG antibodies in sera of cases and controls using a commercially available enzyme-linked immunoassay. The McNemar’s test was used to assess the association between HEV seropositivity and the occupation of waste picker. The association between HEV seropositivity and work characteristics of waste pickers was assessed by bivariate and regression analyses. Anti-HEV IgG antibodies were detected in 14 (16.3%) of the 86 waste pickers and in 8 (9.3%) of the 86 control subjects (McNemar’s pair test: OR = 13.0; 95% CI: 0.73-230.77; P=0.02). Ill waste pickers had a higher HEV seroprevalence than those who were apparently healthy (6/15: 40% vs 8/71: 11.3%, respectively: P=0.01). Waste pickers with reflexes impairment had a higher HEV seroprevalence than those without this impairment (5/10: 50% and 9/76: 11.8%, respectively; P=0.009). Logistic regression analysis of sociodemographic, work, and behavioral characteristics of waste pickers showed that HEV seropositivity was associated with increasing age (OR = 6.52; 95% CI: 1.95-21.78; P=0.002) and raising pigs (OR = 12.01; 95% CI: 1.48-97.26; P=0.02). This is the first age- and gender-matched case-control study on the association between HEV infection and the occupation of waste picker. Waste pickers represent a risk group for HEV infection. Factors associated with HEV seropositivity found in this study may help in the design of optimal planning to avoid HEV infection.
Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency
Authors: Friedrich Dhana , Friedel Laura , Herrmann Andreas , Preibisch Stephan , Loewer Alexander
Published: June 2019

ABSTRACT

Discontinuous transcription has been described for different mammalian cell lines and numerous promoters. However, our knowledge of how the activity of individual promoters is adjusted by dynamic signaling inputs from transcription factor is limited. To address this question, we characterized the activity of selected target genes that are regulated by pulsatile accumulation of the tumor suppressor p53 in response to ionizing radiation. We performed time resolved measurements of gene expression at the single cell level by smFISH and used the resulting data to inform a mathematical model of promoter activity. We found that p53 target promoters are regulated by frequency modulation of stochastic bursting and can be grouped along three archetypes of gene expression. The occurrence of these archetypes cannot solely be explained by nuclear p53 abundance or promoter binding of total p53. Instead, we provide evidence that the time-varying acetylation state of p53’s C-terminal lysine residues is critical for gene-specific regulation of stochastic bursting.
Radiation-damage investigation of a DNA 16-mer
Authors: Bugris Valéria , Harmat Veronika , Ferenc Györgyi , Brockhauser Sándor , Carmichael Ian , Garman Elspeth F.
Published: June 2019

In macromolecular crystallography, a great deal of effort has been invested in understanding radiation-damage progression. While the sensitivity of protein crystals has been well characterized, crystals of DNA and of DNA–protein complexes have not thus far been studied as thoroughly. Here, a systematic investigation of radiation damage to a crystal of a DNA 16-mer diffracting to 1.8 Å resolution and held at 100 K, up to an absorbed dose of 45 MGy, is reported. The RIDL (Radiation-Induced Density Loss) automated computational tool was used for electron-density analysis. Both the global and specific damage to the DNA crystal as a function of dose were monitored, following careful calibration of the X-ray flux and beam profile. The DNA crystal was found to be fairly radiation insensitive to both global and specific damage, with half of the initial diffraction intensity being lost at an absorbed average diffraction-weighted dose, D
1/2, of 19 MGy, compared with 9 MGy for chicken egg-white lysozyme crystals under the same beam conditions but at the higher resolution of 1.4 Å. The coefficient of sensitivity of the DNA crystal was 0.014 Å2 MGy−1, which is similar to that observed for proteins. These results imply that the significantly greater radiation hardness of DNA and RNA compared with protein observed in a DNA–protein complex and an RNA–protein complex could be due to scavenging action by the protein, thereby protecting the DNA and RNA in these studies. In terms of specific damage, the regions of DNA that were found to be sensitive were those associated with some of the bound calcium ions sequestered from the crystallization buffer. In contrast, moieties farther from these sites showed only small changes even at higher doses.
Determine the optimal capital structure of BOT projects using interval numbers with Tianjin Binhai New District Metro Z4 line in China as an example
Authors: Wang Yuning , Jin Xiaohua
Published: June 2019

Purpose

Various factors may influence project finance when a multi-sourced debt financing strategy is used for financing capital investments, in general, and public infrastructure investments, in particular. Traditional indicators lack comprehensive consideration of the influences of many internal and external factors, such as investment structure, financing mode and credit guarantee structure, which exist in the financing decision making of BOT projects. An effective approach is, thus, desired. The paper aims to discuss these issues.

Design/methodology/approach

This paper develops a financial model that uses an interval number to represent the uncertain factors and, subsequently, conducts a standardization of the interval number. Decision makers determine the weight of each objective through the analytic hierarchy process. Through the optimization procedure, project investors and sponsors are provided with a strategy regarding the optimal amount of debt to be raised and the insight on the risk level based on the net present value, as well as the probability of bankruptcy for each different period of debt service.

Findings

By using an example infrastructure project in China and based on the comprehensive evaluation, comparison and ranking of the capital structures of urban public infrastructure projects using the interval number method, the final ranking can help investors to choose the optimal capital structure for investment. The calculation using the interval number method shows that X2 is the optimal capital structure plan for the BOT project of the first stage of Tianjin Binhai Rail Transit Z4 line. Therefore, investors should give priority to selecting a capital contribution ratio of 45 per cent for this investment.

Research limitations/implications

In this paper, some parameters, such as depreciation life, construction period and concession period, are assumed to be deterministic parameters, although the interval number model has been introduced to analyze the uncertainty indicators, such as total investment and passenger flow, of BOT rail transport projects. Therefore, more of the above deterministic parameters can be taken as uncertainty parameters in future research so that calculation results fit actual projects more closely.

Originality/value

This model can be used to make the optimal investment decision for a project by determining the impact of uncertainty factors on the profitability of the project in its lifecycle during the project financial feasibility analysis. Project sponsors can determine the optimal capital structure of a project through an analysis of the irregular fluctuation of the unpredictable factors in project construction such as construction investment, operating cost and passenger flow. The model can also be used to examine the effects of different capital investment ratios on indicators so that appropriate measures can be taken to reduce risks and maximize profit.
Three configurations of corporate innovation programs and their interplay
Authors: Kötting Michael , Kuckertz Andreas
Published: June 2019

Purpose

The success of corporate innovation is based less upon the success of a single innovation program than on a holistic and overarching corporate innovation system integrating various activities. Taking this perspective, the purpose of this paper is to extend existing research on the design of innovation programs.

Design/methodology/approach

Utilizing an inductive theory-building case study approach, this study provides a detailed analysis of how one of the largest and most successful German technology companies structures its many innovation activities.

Findings

The analysis identifies key elements of innovation programs and suggests three configurations that illustrate how these generic elements can be structured so as to offer the best fit with the underlying logic of the respective innovation program. Furthermore, this study highlights how the identified configurations come together to deliver overarching strategic innovation goals.

Originality/value

Existing research too often focuses solely on single innovation programs. The current research is among the first to take a holistic and overarching perspective, considering different innovation programs within a single company and analyzing their configuration and their interplay.
Transformational leadership and innovative work behavior
Authors: Afsar Bilal , Umrani Waheed Ali
Published: June 2019

Purpose

The purpose of this paper is to investigate the effect of transformational leadership on employee’s innovative work behavior, and the mediating role of motivation to learn, and the moderating role of task complexity and innovation climate on the link between transformational leadership and innovative work behavior.

Design/methodology/approach

A questionnaire, designed as a self-reported survey, was distributed to full-time employees and their respective supervisors working in 35 firms (services and manufacturing sectors) in Pakistan. Data were collected from 338 employee–supervisor dyads. The hypotheses were tested using structural equation modeling.

Findings

Results showed that transformational leadership had a positive impact on employees’ innovative work behavior and motivation to learn mediated transformational leadership–innovative work behavior link. The study further showed that task complexity and innovation climate moderated the relationship between transformational leadership and employees’ innovative work behavior.

Research limitations/implications

Based on the premises of interactionist perspectives on individual innovation, this study integrated multi-level variables to investigate leaders’ influences on followers’ innovative work behavior. This study contributed to the existing literature by providing empirical evidence on influence of transformational leadership on employees’ innovative work behavior as well as the impact of both individual and organizational level variables.

Practical implications

The close connection among transformational leadership, motivation to learn and innovative work behavior suggests that transformational leadership traits among managers are important to enhance employees’ innovative work behavior. Organizations should pay attention to creating a climate that is supportive of innovation and encourage individuals to learn new knowledge and skills, and provide employees with opportunities to use their acquired knowledge and skills.

Originality/value

This paper contributed to leadership and innovation literatures and provided insights into how the practitioners could use an appropriate leadership style to enhance innovative work behavior among employees. The study adopted a distinct model comprising five variables to investigate innovative work behavior from a multi-level perspective, i.e., motivation to learn and innovative work behavior at the individual level, task complexity at the unit level and innovation climate and leadership at the organizational level. This integrated model of using predictors from multiple levels supported the theoretical assumptions that innovative work behavior resulted from the interaction of individual, group and organizational level factors.
Evolution of sub-floor moisture management requirements in UK, USA and New Zealand 1600s to 1969
Authors: Isaacs Nigel
Published: June 2019

Purpose

The purpose of this paper is to review the historic development of the requirements for sub-floor (also known as “basementless space” or “crawl space”) moisture management in the USA, UK and New Zealand (NZ) from 1600s to 1969.

Design/methodology/approach

The review of 171 documents, including legislation, research papers, books and magazines, identified three time periods where the focus differed: 1849, removal of impure air; 1850–1929, the use of ground cover and thorough ventilation; and 1930–1969, the development of standards.

Findings

Published moisture management guidance has been found from 1683, but until the 1920s, it was based on the provision of “adequate” ventilation and, in the UK, the use of impermeable ground cover. Specific ventilation area calculations have been available from 1898 in the UK, 1922 in the USA and 1924 in NZ. These are based on the area of ventilation per unit floor area, area of ventilation per unit length of perimeter wall, or a combination of both. However, it was not until 1937 in the USA, 1944 in NZ and after the period covered by this paper in the UK, that numerical values were enforced in codes. Vents requirements started at 1 in. of vent per square foot of floor area (0.7 per cent but first published in the USA with a misplaced decimal point as 7 per cent). The average vent area was 0.69 per cent in USA for 19 cases, 0.54 per cent in NZ for 7 cases and 0.13 per cent in UK for 3 cases. The lower UK vent area requirements were probably due to the use of ground covers such as asphalt or concrete in 1854, compared with in 1908 in NZ and in 1947 in USA. The use of roll ground cover (e.g. plastic film) was first promoted in 1949 in USA and 1960 in NZ.

Practical implications

Common themes found in the evolution of sub-floor moisture management include a lack of documented research until the 1940s, a lack of climate or site-based requirements and different paths to code requirements in the three countries. Unlike many building code requirements, a lack of sub-floor moisture management seldom leads to catastrophic failure and consequent political pressure for immediate change. From the first published use of performance-based “adequate” ventilation to the first numerical or “deemed to satisfy” solutions, it took 240 years. The lessons from this process may provide guidance on improving modern building codes.

Originality/value

This is the first time such an evaluation has been undertaken for the three countries.
Valuing firm’s financial flexibility under default risk and bankruptcy costs: a WACC based approach
Authors: Mari Carlo , Marra Marcella
Published: June 2019

Purpose

The purpose of this paper is to present a model to value leveraged firms in the presence of default risk and bankruptcy costs under a flexible firm’s debt structure.

Design/methodology/approach

The authors assume that the total debt of the ﬁrm is a combination of two debt components. The ﬁrst component is an active debt component which is assumed to be proportional to the ﬁrm’s value. The second one is a passive predetermined risk-free debt component. The combination of the two debt categories makes the ﬁrm’s capital structure more realistic and allows us to include ﬂexibility into the ﬁrm’s debt structure management. The ﬁrm’s valuation is performed using the discounted cash flow technique based on the weighted average cost of capital (WACC) method.

Findings

The model can be used to define active debt management strategies that can induce the firm to deviate from its capital structure target in order to preserve debt capacity for future funding needs. The firm’s valuation is performed by using the WACC method and a closed form valuation formula is provided. Such a formula can be used to value costs and benefits of financial flexibility.

Research limitations/implications

The proposed approach provides a good compromise between mathematical complexity and model capability of interpreting the various economic and financial aspects involved in the firm’s debt structure puzzle.

Practical implications

This model offers a realistic approach to practical applications where real financing decisions are characterized by a simultaneous use of these two debt categories. By comparing costs and benefits deriving from using unused debt capacity for future funding needs, the model provides a quantitative support to investigate if financial flexibility can add value to firms.

Originality/value

To the authors knowledge, the approach the authors propose is the first attempt to build a valuation scheme that accounts for firm’s financial flexibility under default risky debt and bankruptcy costs. Including financial flexibility, this model fills an important gap in the literature on this topic.