bluuebunny/crossref_metadata_2025 huggingface dataset:
Significance of trends in gait dynamics
Authors: Kozlowska Klaudia , Latka Miroslaw , West Bruce J.
Published: June 2019

Trends in time series generated by physiological control systems are ubiquitous. Determining whether trends arise from intrinsic system dynamics or originate outside of the system is a fundamental problem of fractal series analysis. In the latter case, it is necessary to filter out the trends before attempting to quantify correlations in the noise (residuals). For over two decades, detrended fluctuation analysis (DFA) has been used to calculate scaling exponents of stride time (ST), stride length (SL), and stride speed (SS) of human gait. Herein, rather than relying on the very specific form of detrending characteristic of DFA, we adopt Multivariate Adaptive Regression Splines (MARS) to explicitly determine trends in spatio-temporal gait parameters during treadmill walking. Then, we use the madogram estimator to calculate the scaling exponent of the corresponding MARS residuals. The durations of ST and SL trends are determined to be independent of treadmill speed and have distributions with exponential tails. At all speeds considered, the trends of ST and SL are strongly correlated and are statistically independent of their corresponding residuals. The group-averaged values of scaling exponents of ST and ST MARS residuals are slightly smaller than 0.5, indicating weak anti-persistence. Thus, contrary to the interpretation prevalent in the literature, the statistical properties of ST and SL time series originate from the superposition of large scale trends and small scale fluctuations. We show that trends serve as the control manifolds about which ST and SL fluctuate. Moreover, the trend speed, defined as the ratio of instantaneous values of SL and ST trends, is tightly controlled about the treadmill speed. The strong coupling between the ST and SL trends ensures that the concomitant changes of their values correspond to movement along the constant speed goal equivalent manifold as postulated by Dingwell et al. doi:10.1371/journal.pcbi.1000856.

Author summary

During treadmill walking, the subject’s stride time (ST) and stride length (SL) must yield a stride speed which can fluctuate over a narrow range centered on the treadmill belt’s speed. The fact that both ST and SL are persistent is an intriguing property of human gait. For persistent fluctuations any deviation from the mean value is likely to be followed by a deviation in the same direction. To trace the origin of such persistence, we used a novel approach to determine trends in spatio-temporal gait parameters. We find that the trends of ST and SL of a subject are strongly correlated and are statistically independent of their corresponding residuals. Moreover, the trend speed, defined as the ratio of instantaneous values of SL and ST trends, is tightly controlled about the treadmill speed. The persistence of gait parameters stems from superposition of large scale trends and small scale fluctuations.
Disease driven extinction in the wild of the Kihansi spray toad (Nectophrynoides asperginis)
Authors: Weldon C. , Channing A. , Misinzo G. , Cunningham A.A.
Published: June 2019

The Kihansi spray toad, Nectophrynoides asperginis, became extinct in the wild despite population monitoring and conservation management of its habitat in the Kihansi gorge, Tanzania. Anecdotal evidence has indicated human induced habitat modification, predators, pesticides and disease as possible causes of a rapid population decline and the species extirpation. Here, we systematically investigate the role of disease in the extinction event of the wild toad population. The amphibian chytrid fungus, Batrachochytrium dendrobatidis, was detected in spray toads that died during the extinction event and subsequently in other amphibian species in Kihansi Gorge and the adjacent Udagaji Gorge, but not in any toads collected prior to this. Following the population decline, the remnant spray toad population gradually disappeared over a nine-month period. We demonstrate how demographic and behavioral attributes predisposed the spray toads to chytridiomycosis, due to B. dendrobatidis infection, and how epidemic disease could have been exacerbated by altered environmental conditions in the spray wetlands. Our results show that chytridiomycosis was the proximate cause of extinction in the wild of N. asperginis. This represents the first known case of extinction by disease of an amphibian species in Africa. A captive breeding program in the US and Tanzania ensures the survival of the species and a reintroduction program is underway. However, we caution that chytridiomycosis remains an existing threat that requires a comprehensive mitigation strategy before the desired conservation outcome of an established population of repatriated toads can be achieved.
Impact of white spotting alleles, includingW20, on phenotype in the American Paint Horse
Authors: Brooks Samantha A. , Palermo Katelyn M. , Kahn Alisha , Hein Jessica
Published: June 2019

The American Paint Horse Association (APHA) records pedigree and performance information for their breed, a stock-type horse valued as a working farm or ranch horse and as pleasure horses. As the name implies, the breed is also valued for attractive white spotting patterns on the coat. The APHA utilizes visual inspections of photographs to determine if coat spotting exceeds threshold anatomical landmarks considered characteristic of desirable patterns. Horses with sufficient white patterning enter the “Regular” registry, rather than the “Solid Paint-bred” division, providing a threshold modeled phenotype. Genetic studies previously defined sequence variants corresponding to 35 alleles for white spotting in the horse. Here, we calculate the allele frequency for nine common white spotting alleles in the American Paint horse using a sample of 1,054 registered animals. The APHA spotting phenotype is altered by additive interactions among spotting loci, and epistatically by theMC1RandASIPgenes controlling pigment production. TheW20allele within theKITgene, independent of other known spotting alleles, was strongly associated with the APHA-defined white spotting phenotype (p = 1.86 x10−18), refuting reports thatW20acts only as a modifier of other underlying white spotting patterns. The parentage of an individual horse, either American Paint or American Quarter Horse, did not alter the likelihood of entering the APHA Regular registry. An empirical definition of the action of these genetic loci on the APHA-defined white spotting phenotype will allow more accurate application of genome-assisted selection for improving color production and marketability of APHA horses.
Habitat specificity is not universal proxy for sensitivity to habitat conversion among rodents on the Canadian Prairies
Authors: Heisler Leanne M. , Simpson Gavin L. , Poulin Ray G. , Wellicome Troy I. , Hall Britt D.
Published: June 2019

Converting habitat for agricultural production threatens biodiversity loss worldwide and has significant implications for human well-being. Debates on how to conserve biodiversity as the demand for agriculture products rises is being informed by studies using habitat specificity as a proxy for sensitivity to land modification, assuming all species respond to habitat loss and fragmentation relative to their affinity towards the habitat type being converted. Here, we test this assumption among rodent assemblages on the Canadian Prairies, hypothesizing negative responses among grassland obligates and neutral or positive responses among habitat generalists to landscape change along a gradient of increasing agricultural intensity. We found complex, sometimes contradictory responses among rodent species, which depended on the magnitude of habitat loss that had occurred and did not always reflect each species’ relative affinity for grassland habitat. Our results suggest future studies should avoid assuming a single habitat type appropriately characterizes resource limitation among all species, and instead carefully consider which dimension of the ecological niche defines specificity for each species. Our results indicate habitat specificity is not always a reliable proxy for sensitivity to land modification, with significant implications for biodiversity conservation when used to inform agriculture and land use policies.
The evolution of realized niches within freshwater Synechococcus
Authors: Tromas Nicolas , Taranu Zofia E. , Castelli Mathieu , Pimentel Juliana S. M. , Pereira Daniel A. , Marcoz Romane , Shapiro B. Jesse , Giani Alessandra
Published: June 2019

Understanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.

Originality-Significance Statement

We address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.
Empirical characterization factors assessing the effects of hydroelectricity on fish richness across three large biomes
Authors: Turgeon Katrine , Trottier Gabrielle , Turpin Christian , Bulle Cécile , Margni Manuele
Published: June 2019

Hydroelectricity is often presented as a clean, reliable, and renewable energy source, but is also recognized for its potential impacts on aquatic ecosystem biodiversity. We used empirical data on change in fish species richness following impoundment to develop Characterisation Factors (CF) and Impact Scores (IS) for hydroelectricity production for use in Life Cycle Assessment (LCA). We used data collected on 89 sampling stations (63 upstream and 26 downstream of a dam) belonging to 27 reservoirs from three biomes (boreal, temperate and tropical). Overall, the impact of hydroelectricity production on fish species richness was significant in the tropics, of smaller amplitude in temperate and minimal in boreal biome, stressing for the need of regionalisation. The impact of hydroelectricity production was also quite consistent across scales (i.e., same directionality and statistical significance across sampling stations, reservoirs and biomes) but was sensitive to the duration of the study (i.e., the period over which data have been collected after impoundment), highlighting the need for a clear understanding of transient situations before reaching steady states. Our CFs and ISs contribute to fill a gap to assist decision makers using LCA to evaluate alternative technologies, such as hydropower, to decarbonize the worldwide economy.

Highlights

This paper is the first to develop global and empirically based characterization factors of the impact of hydroelectricity production on aquatic ecosystems biodiversity, to be used in LCA;

The impact of hydroelectricity production on fish species richness was significant in the tropics, of smaller amplitude in temperate and minimal in boreal biome;

The impact of hydroelectricity production on fish richness was consistent across scales - same directionality and statistical significance across sampling stations, reservoirs and biomes;

The impact of hydroelectricity production on fish richness was sensitive to the duration of the study, highlighting the need for a clear understanding of transient situations before reaching steady states in LCA.
A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation
Authors: Pei Wuhong , Xu Lisha , Chen Zelin , Slevin Claire C , Pettie Kade P , Wincovitch Stephen ,   NISC Comparative Sequencing Program, Burgess Shawn M
Published: June 2019

Spinal Muscular Atrophy (SMA) is the most common genetic disease in childhood. SMA is generally caused by mutations inSMN1. The Survival of Motor Neurons (SMN) complex consists of SMN1, Gemins (2–8) and Strap/Unrip. We previously demonstratedsmn1andgemin5inhibited tissue regeneration in zebrafish. Here we investigated each individual SMN complex member and identifiedgemin3as another regeneration-essential gene. These three genes are likely pan-regenerative since they affect the regeneration of hair cells, liver and caudal fin. RNA-Seq and miRNA-Seq analyses reveal thatsmn1, gemin3, andgemin5are linked to a common set of genetic pathways, including the tp53 and ErbB pathways. Additional studies indicated all three genes facilitate regeneration by inhibiting the ErbB pathway, thereby allowing cell proliferation in the injured neuromasts. This study provides a new understanding of the SMN complex and a potential etiology for SMA and potentially other rare unidentified genetic diseases with similar symptoms.
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria
Authors: Botelho João , Mourão Joana , Roberts Adam P. , Peixe Luísa
Published: June 2019

Carbapenemases inactivate most β-lactam antibiotics, including carbapenems and have been frequently reported amongEnterobacteriaceae,Acinetobacterspp. andPseudomonasspp. Traditionally, the horizontal gene transfer of carbapenemase encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted anin-silicoanalysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182,663). We detected 17,520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically-relevant bacteria asPseudomonas aeruginosa,Klebsiella pneumoniaeandEscherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFTand MPFFclasses and often encode resistance to other antibiotics (e.g., aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.

Author Notes

All supporting data has been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article.

Impact Statement

Carbapenems are commonly used to treat severe infections in humans. Resistance is often mediated by carbapenemases. These enzymes degrade carbapenems and are frequently present in plasmids. Here, we demonstrate that common carbapenemase-encoding genes (CEGs) found in clinical isolates (e.g.blaKPC,blaGES,blaIMP,blaNDM,blaVIM) can also be located within integrative and conjugative elements (ICEs). CEG-bearing ICEs belong to three mating-pair formation families. These mobile elements may be particularly important in bacteria where plasmids do not seem to play a significant role in the spread of antibiotic resistance genes, asPseudomonasspp. This study considerably expands the knowledge of the repertoire of CEGs-bearing ICEs among clinically-relevant bacterial pathogens, such asPseudomonas aeruginosa,Klebsiella pneumoniaeandEscherichia coli.

Data Summary

All the bacterial genomes scanned in this study have been deposited previously in the National Center for Biotechnology Information genome database and are listed on the supplementary tables. The extracted 66 ICEs in fasta format and the outputs for the profile HMMs scanned on the 386 putative MGEs identified in this study are deposited on figshare athttps://figshare.com/projects/_Comprehensive_genome_data_analysis_establishes_a_triple_whammy_of_carbapenemases_ICEs_and_multiple_clinically-relevant_bacteria/78369.
An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics
Authors: Wang Shaobo , Zhang Qiong , Hui Hui , Agrawal Kriti , Karris Maile Ann Young , Rana Tariq
Published: June 2019

Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from two healthy subjects (15,121 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters according to their unique gene expression programs; three of these (exhausted CD4+ and CD8+ T cells and interferon-responsive CD8+ T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in the exhausted T cell populations and further characterized in HIV infected individuals. We identified a novel HIV-1 specific exhausted CD8+ T cell population expressing KLRG1, TIGIT, and T-betdimEomeshi markers. Ex-vivo antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8+ T cells demonstrating the contribution of KLRG1+ population to T cell exhaustion and providing a novel target for developing immunotherapy to treat HIV chronic infection. Analysis of gene signatures also revealed impairment of B cell and NK cell function in HIV-infected donors. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
Natural selection towards wild-type in composite cross populations of winter wheat
Authors: Knapp Samuel , Döring Thomas F. , Jones Hannah E. , Snape John , Wingen Luzie U. , Wolfe Martin S. , Leverington-Waite Michelle , Griffiths Simon
Published: June 2019

Most of our crops are grown in monoculture with single genotypes grown over wide acreage. An alternative approach, where segregating populations are used as crops is an exciting possibility, but outcomes of natural selection upon this type of crop are not well understood. We tracked allelic frequency changes in evolving composite cross populations (CCPs) of wheat grown over ten generations under organic and conventional farming. At three generations, each population was genotyped with 19 SSR and 8 SNP markers. The latter were diagnostic for major functional genes. Gene diversity was constant at SSR markers but decreased over time for genic markers. Population differentiation between the four locations could not be detected, suggesting that organic vs. non-organic crop management did not drive allele frequency changes. However, we did see changes for genes controlling plant height and phenology in all populations independently and consistently. We interpret these changes as the result of a consistent natural selection towards wild-type. Independent selection for alleles that are associated with plant height suggests that competition for light was central, resulting in the predominance of stronger intraspecific competitors, and highlighting a potential trade-off between individual and population performance.
Transcriptional Activation of Arabidopsis Zygotes Is Required for Their Initial Division
Authors: Kao Ping , Nodine Michael
Published: June 2019

Commonly referred to as the maternal-to-zygotic transition, the shift of developmental control from maternal-to-zygotic genomes is a key event during animal and plant embryogenesis. Together with the degradation of parental gene products, the increased transcriptional activities of the zygotic genome remodels the early embryonic transcriptome during this transition. Although evidence from multiple flowering plants suggests that zygotes become transcriptionally active soon after fertilization, the timing and developmental requirements of zygotic genome activation inArabidopsis thaliana(Arabidopsis) remained a matter of debate until recently. In this report, we optimized an expansion microscopy technique for robust immunostaining of Arabidopsis ovules and seeds. This enabled the detection of marks indicative of active transcription in zygotes before the first cell division. Moreover, we employed a live-imaging culture system together with transcriptional inhibitors to demonstrate that such active transcription is required in zygotes. Our results indicate that zygotic genome activation occurs soon after fertilization and is physiologically required prior to the initial zygotic division in Arabidopsis.
Interplay of ERα binding and DNA methylation in the intron-2 determines the expression and estrogen regulation of Cystatin A in breast cancer cells
Authors: John Mary Dixcy Jaba Sheeba , Sikarwar Girija , Kumar Ajay , Limaye Anil Mukund
Published: June 2019

Despite advances in early detection and treatment, invasion and metastasis of breast tumors remains a major hurdle. Cystatin A (CSTA, also called stefin A), an estrogen-regulated gene in breast cancer cells, is an inhibitor of cysteine cathepsins, and a purported tumor suppressor. Loss of CSTA expression in breast tumors evidently shifts the balance in favor of cysteine cathepsins, thereby promoting extracellular matrix remodeling, tumor invasion and metastasis. However, the underlying mechanism behind the loss of CSTA expression in breast tumors is not known. Here, we have analyzed CSTA expression, and methylation of upstream and intron-2 CpG sites within the CSTA locus in human breast cancer cell lines and breast tumors of the TCGA cohort. Results showed an inverse relationship between expression and methylation. Sequence analysis revealed a potential estrogen response element (ERE) in the intron-2. Analysis of ChIP-seq data (ERP000380) and our own ChIP experiments showed that 17β-estradiol (E2) enhanced ERα binding to this ERE in MCF-7 cells. This ERE was located amidst the differentially methylated intron-2 CpG sites, which provoked us to examine the possible conflict between estrogen-regulation of CSTA and DNA methylation in the intron-2. We analyzed the expression of CSTA and its regulation by estrogen in MDA-MB-231 and T47D cells subjected to global demethylation by 5-azacytidine (5-aza). 5-aza, not only enhanced CSTA expression in these cell lines but also restored estrogen-regulation of CSTA in these cells. Taken together, our results indicate that DNA methylation-dependent silencing could play a significant role in the loss of CSTA expression in breast tumors. The potential of DNA methylation as an indicator of CSTA expression or as a marker of tumor progression can be explored in future investigations. Furthermore, our results indicate the convergence of ERα-mediated estrogen regulation and DNA methylation in the intron-2, thereby offering a novel context to understand the role of estrogen-ERα signaling axis in breast tumor invasion and metastasis.
Inference based decisions in a hidden state foraging task: differential contributions of prefrontal cortical areas
Authors: Vertechi Pietro , Lottem Eran , Sarra Dario , Godinho Beatriz , Treves Isaac , Quendera Tiago , Oude Lohuis Matthijs Nicolai , Mainen Zachary F.
Published: June 2019

Essential features of the world are often hidden and must be inferred by constructing internal models based on indirect evidence. Here, to study the mechanisms of inference we established a foraging task that is naturalistic and easily learned, yet can distinguish inference from simpler strategies such as the direct integration of sensory data. We show that both mice and humans learn a strategy consistent with optimal inference of a hidden state. However, humans acquire this strategy more than an order of magnitude faster than mice. Using optogenetics in mice we show that orbitofrontal and anterior cingulate cortex inactivation impact task performance, but only orbitofrontal inactivation reverts mice from an inference-based to a stimulus-bound decision strategy. These results establish a cross-species paradigm for studying the problem of inference-based decision-making and begin to dissect the network of brain regions crucial for its performance.
Transposable elements strongly contribute to cell-specific and species-specific looping diversity in mammalian genomes
Authors: Diehl Adam G , Ouyang Ningxin , Boyle Alan P
Published: June 2019

Background

Chromatin looping is exceedingly important to gene regulation and a host of other nuclear processes. Many recent insights into 3D chromatin structure across species and cell types have contributed to our understanding of the principles governing chromatin looping. However, 3D genome evolution and how it relates to Mendelian selection remain largely unexplored. CTCF, an insulator protein found at most loop anchors, has been described as the “master weaver” of mammalian genomes, and variations in CTCF occupancy are known to influence looping divergence. A large fraction of mammalian CTCF binding sites fall within transposable elements (TEs) but their contributions to looping variation are unknown. Here we investigated the effect of TE-driven CTCF binding site expansions on chromatin looping in human and mouse.

Results

TEs have broadly contributed to CTCF binding and loop boundary specification, primarily forming variable loops across species and cell types and contributing nearly 1/3 of species-specific and cell-specific loops.

Conclusions

Our results demonstrate that TE activity is a major source of looping variability across species and cell types. Thus, TE-mediated CTCF expansions explain a large fraction of population-level looping variation and may play a role in adaptive evolution.
RIPK3 upregulation confers robust proliferation and collateral cystine-dependence on breast cancer recurrence
Authors: Lin Chao-Chieh , Mabe Nathaniel , Lin Yi-Tzu , Yang Wen-Hsuan , Tang Xiaohu , Hong Lisa , Sun Tianai , Yao Tso-Pang , Alvarez James , Chi Jen-Tsan
Published: June 2019

The molecular and genetic basis of tumor recurrence is complex and poorly understood. RIPK3 is a key effector in programmed necrotic cell death and, therefore, its expression is frequently suppressed in primary tumors. In a transcriptome profiling between primary and recurrent breast tumor cells from a murine model of breast cancer recurrence, we found that RIPK3, while absent in primary tumor cells, is dramatically re-expressed in recurrent breast tumor cells by an epigenetic mechanism. Unexpectedly, we found that RIPK3 knockdown in recurrent tumor cells reduced clonogenic growth, causing cytokinesis failure, p53 stabilization, and repressed the activities of YAP/TAZ. These data uncover a surprising role of the pro-necroptotic RIPK3 kinase in enabling productive cell cycle during tumor recurrence. Remarkably, high RIPK3 expression also rendered recurrent tumor cells exquisitely dependent on extracellular cystine and undergo programmed necrosis upon cystine deprivation. The induction of RIPK3 in recurrent tumors unravels an unexpected mechanism that paradoxically confers on tumors both growth advantage and necrotic vulnerability, providing potential strategies to eradicate recurrent tumors.
Cantilever Sensors for Rapid Optical Antimicrobial Sensitivity Testing
Authors: Bennett Isabel , Pyne Alice , McKendry Rachel
Published: June 2019

Growing antimicrobial resistance (AMR) is a serious global threat to human health. Current methods to detect resistance include phenotypic antibiotic sensitivity testing (AST) which measures bacterial growth and is therefore hampered by slow time to result (~12-24 hours). Therefore new rapid phenotypic methods for AST are urgently needed. Nanomechanical cantilever sensors have recently shown promise for rapid AST but challenges of bacterial immobilization can lead to variable results. Herein a novel cantilever-based method is described for detecting phenotypic antibiotic resistance within ~45 minutes, capable of detecting single bacteria. This method does not require complex, variable bacterial immobilization, and instead uses the laser and detector system to detect single bacterial cells in media as they pass through the laser focus. This provides a simple read out of bacterial antibiotic resistance by detecting growth (resistant) or death (sensitive), much faster than current methods. The potential of this technique demonstrated by determining resistance in both lab and clinical strains of E. coli, a key species for clinically burdensome urinary tract infections. This work provides the basis for a simple and fast diagnostic tool to detect antibiotic resistance in bacteria, reducing the health and economic burdens of AMR.
Integrative omics analysis ofPseudomonas aeruginosavirus PA5oct highlights the molecular complexity of jumbo phages
Authors: Lood Cédric , Danis-Wlodarczyk Katarzyna , Blasdel Bob G. , Jang Ho Bin , Vandenheuvel Dieter , Briers Yves , Noben Jean-Paul , van Noort Vera , Drulis-Kawa Zuzanna , Lavigne Rob
Published: June 2019

Pseudomonasvirus vB_PaeM_PA5oct is a compelling model phage to investigate phage-bacteria interactions and is a potent candidate for phage therapy. Combining hybrid genome sequencing, RNA-Seq, and mass spectrometry of virion-associated proteins allowed us to accurately assemble and annotate PA5oct’s 286,783 bp genome. It encodes 461 coding regions, of which 93 were identified as virion-associated proteins using ESI-MS/MS. RNA-seq revealed twelve tRNA genes, four ncRNA regions, and a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. Although PA5oct is not organized into strictly contiguous regions of temporal transcription, defined genomic regions are expressed in early, middle, and late phases of infection. Interestingly, we observed distinct regions showing limited transcription activity throughout the infection cycle. The infection ofPseudomonas aeruginosaby PA5oct triggers the upregulation of bacterial operons related to NAD biosynthesis, Psl exopolysaccharide, and periplasmic nitrate reductase production and downregulates Type IV pili gene products, suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position this isolate amongst other phages using a protein-sharing network. This study expands our understanding of the molecular diversity of jumbo viruses and opens new questions towards cellular regulation and phage-encoded hijacking mechanisms.
The large GTPase, mGBP-2, regulates Rho family GTPases to inhibit migration and invadosome formation in Triple-Negative Breast Cancer cells
Authors: Nyabuto Geoffrey O. , Wilson John P. , Heilman Samantha A. , Kalb Ryan C. , Abnave Ankita V. , Vestal Deborah J.
Published: June 2019

Breast cancer is the most common cancer in women. Despite advances in early detection and treatment, it is predicted that over 40,000 women will die of breast cancer in 2019. This number of women is still too high. To lower this number, more information about the molecular players in breast cancer are needed. Several members of the Guanylate-Binding Proteins (GBPs) have been correlated with better prognosis in breast cancer. In this study, we asked if the expression of GBP-2 in breast cancer merely provided a biomarker for improved prognosis or whether it actually contributed to improving outcome. Specifically, we asked whether murine GBP-2 exhibited cell autonomous behavior that altered breast cancer cells in a manner predicted to improve prognosis. To answer this, the 4T1 model of murine Triple-Negative Breast Cancer was used. 4T1 cells themselves are highly aggressive and highly metastatic, while 67NR cells, isolated from the same tumor, do not leave the primary site. mGBP-2 did not alter cell proliferation in these two cell lines, but mGBP-2 expression inversely correlated with migration. More specifically, mGBP-2 inhibits cell migration and invadopodia formation by inhibiting the activation of Rac1, while promoting the activation of CDC42 and RhoA. Together these data demonstrate that mGBP-2 is responsible for cell autonomous activities that make breast cancer cells less aggressive.
Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes
Authors: Dialynas George , Delabaere Laetitia , Chiolo Irene
Published: June 2019

Repairing DNA double-strand breaks (DSBs) is particularly challenging in pericentromeric heterochromatin, where the abundance of repeated sequences exacerbates the risk of ectopic recombination. InDrosophilaKc cells, accurate homologous recombination (HR) repair of heterochromatic DSBs relies on the relocalization of repair sites to the nuclear periphery before Rad51 recruitment and strand invasion. This movement is driven by Arp2/3-dependent nuclear actin filaments and myosins’ ability to walk along them. Conserved mechanisms enable the relocalization of heterochromatic DSBs in mouse cells, and their defects lead to massive ectopic recombination in heterochromatin and chromosome rearrangements. InDrosophilapolytene chromosomes, extensive DNA movement is blocked by a stiff structure of chromosome bundles. Repair pathways in this context are poorly characterized, and whether heterochromatic DSBs relocalize in these cells is unknown. Here, we show that damage in heterochromatin results in relaxation of the heterochromatic chromocenter, consistent with a dynamic response in this structure. Arp2/3, the Arp2/3 activator Scar, and the myosin activator Unc45, are required for heterochromatin stability in polytene cells, suggesting that relocalization enables heterochromatin repair in this tissue. Together, these studies reveal critical roles for actin polymerization and myosin motors in heterochromatin repair and genome stability across different organisms and tissue types.

Impact Statement

Heterochromatin relies on dedicated pathways for ‘safe’ recombinational repair. In mouse and fly cultured cells, DNA repair requires the movement of repair sites away from the heterochromatin ‘domain’vianuclear actin filaments and myosins. Here, we explore the importance of these pathways inDrosophilasalivary gland cells, which feature a stiff bundle of endoreduplicated polytene chromosomes. Repair pathways in polytene chromosomes are largely obscure and how nuclear dynamics operate in this context is unknown. We show that heterochromatin relaxes in response to damage, and relocalization pathways are necessary for repair and stability of heterochromatic sequences. This deepens our understanding of repair mechanisms in polytenes, revealing unexpected dynamics. It also provides a first understanding of nuclear dynamics responding to replication damage or rDNA breaks, providing a new understanding of the importance of the nucleoskeleton in genome stability. We expect these discoveries to shed light on tumorigenic processes, including therapy-induced cancer relapses.
POL30 alleles in Saccharomyces cerevisiae reveal complexities of the cell cycle and ploidy on heterochromatin assembly
Authors: Brothers Molly , Rine Jasper
Published: June 2019

In Saccharomyces cerevisiae, transcriptional silencing at HML and HMR maintains mating-type identity. The repressive chromatin structure at these loci is replicated every cell cycle and must be re-established quickly to prevent transcription of the genes at these loci. Mutations in a component of the replisome, the Proliferating Cell Nuclear Antigen (PCNA), encoded by POL30, cause a loss of transcriptional silencing at HMR. We used an assay that captures transient losses of silencing at HML and HMR to perform extended genetic analyses of the pol30-6, pol30-8, and pol30-79 alleles. All three alleles destabilized silencing only transiently and only in cycling cells. Whereas pol30-8 caused loss of silencing by disrupting the function of Chromatin Assembly Factor 1 (CAF-I), pol30-6 and pol30-79 acted through a separate genetic pathway but one still dependent on histone chaperones. Surprisingly, the silencing-loss phenotypes depended on ploidy but not on POL30 dosage or mating-type identity. Separately from silencing loss, the pol30-6 and pol30-79 alleles also displayed high levels of mitotic recombination in diploids. These results established that histone trafficking involving PCNA at replication forks is crucial to the maintenance of chromatin state and genome stability during DNA replication. They also raised the possibility that increased ploidy may protect chromatin states when the replisome is perturbed.
Haploid selection drives new gene male germline expression
Authors: Raices Julia B. , Otto Paulo A. , Vibranovski Maria D.
Published: June 2019

New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization.
Robust adaptive super twisting controller: methodology and application of a human-driven knee joint orthosis
Authors: Bkekri Rihab , Benamor Anouar , Alouane Mohamed Amine , Fried Georges , Messaoud Hassani
Published: June 2019

Purpose

The application of the sliding mode control has two obstacle phenomena: chattering and high activity of control action. The purpose of this paper concerns a novel super-twisting adaptive sliding mode control law of a human-driven knee joint orthosis. The proposed control approach consists of using dynamically adapted control gains that ensure the establishment, in a finite time, of a real second-order sliding mode. The efficiency of the controller is evaluated using an experimental set-up.

Design/methodology/approach

This study presents the synthesis of a robust super-twisting adaptive controller for the control of a lower limb–orthosis system. The developed control strategy will take into consideration the nonlinearities as well as the uncertainties resulting from the dynamics of the lower limb–orthosis system. It must also guarantee a good follow-up of the reference trajectory.

Findings

The authors first evaluated on a valid subject, the performances of this controller which were studied and compared to several criteria. The obtained results show that the controller using the Adaptive Super-Twisting algorithm is the one that guarantees the best performance. Validation tests involved a subject and included robustness tests against external disturbances and co-contractions of antagonistic muscles.

Originality/value

The main contribution of this paper is in developing the adaptation super-twisting methodology for finding the control gain resulting in the minimization of the chattering effect.
Instances for the problem of pre-positioning emergency supplies
Authors: Turkeš Renata , Sörensen Kenneth
Published: June 2019

Purpose

Despite a growing body of research on the problem of increasing disaster preparedness by pre-positioning relief supplies at strategic locations, there is a lack of a benchmark set of problem instances that hinders thorough hypotheses testing, sensitivity analysis, model validation or solution procedure evaluation. The purpose of this paper is to address this issue by constructing a public library of diverse pre-positioning problem instances.

Design/methodology/approach

By carefully manipulating some of the instance parameters, the authors generated 30 case studies that were inspired by four instances collected from the literature that focus on disasters of different type and scale that occurred in different parts of the world. In addition, the authors developed a tool to algorithmically generate arbitrarily many diverse random instances of any size.

Findings

For many purposes, the problem library can eliminate or reduce the time-consuming process of data collection, conversion, digitization, calibration and validation, while simultaneously increasing the statistical significance of research results and allowing comparison with different works in the literature.

Research limitations/implications

The case studies are inspired by only four disasters, and some of the instance parameters are defined in a reasonable, albeit arbitrary way. The instances are also limited by the underlying problem assumptions.

Practical implications

The instances provide a more comprehensive and balanced experimental setting (compared to a single case study) that can be used to study the pre-positioning and related problems, or derive managerial implications that can directly benefit the practitioners.

Social implications

The instances can be used to derive practical guidelines that humanitarian workers can use on the ground to better plan their pre-positioning strategies and therefore minimize human suffering.

Originality/value

The case studies and the random instance generator are made publicly available to foster further research on the problem of pre-positioning relief supplies and humanitarian logistics in general.
Model of phosphorus diffusion in silicon for highly doped solar cell emitter layer
Authors: Filipowski Wojciech
Published: June 2019

Purpose

The purpose of this paper was the development of a model enabling precise determination of phosphorus concentration profile in the emitter layer of a silicon solar cell on the basis of diffusion doping process duration and temperature. Fick’s second law, which is fundamental for describing the diffusion process, was assumed as the basis for the model.

Design/methodology/approach

To establish a theoretical model of the process of phosphorus diffusion in silicon, real concentration profiles measured using the secondary ion mass spectrometry (SIMS) method were used. Samples with the phosphorus dopant source applied onto monocrystalline silicon surface were placed in the heat zone of the open quartz tube furnace, where the diffusion process took place in the temperature of 880°C-940°C. The measured real concentration profiles of these samples became template profiles for the model in development.

Findings

The model was developed based on phenomena described in the literature, such as the influence of the electric field of dopant ionized atoms and the influence of dopant atom concentration nearing the maximum concentration on the value of diffusion coefficient. It was proposed to divide the diffusion area into low and high dopant concentration region.

Originality/value

A model has been established which enabled obtaining a high level of consistency between the phosphorus concentration profile developed theoretically and the real profile measured using the SIMS method. A coefficient of diffusion of phosphorus in silicon dependent on dopant concentration was calculated. Additionally, a function describing the boundary between the low and high dopant concentration regions was determined.