bluuebunny/crossref_metadata_2025 huggingface dataset:
Touch DNA on objects can be analysed at low cost using simplified direct amplification methods
Authors: Gammon Katherine , Murray-Jones Kirk , Shenton Daniel , Wood Zoe , Mayers Carl
Published: February 2019

Previous studies reported in the literature demonstrate that a range of sampling vehicles can be used effectively for forensic analysis of human DNA in direct amplification reactions. In this study we compared Copan microFLOQ®swabs with a range of alternative sampling vehicles, using touch DNA samples donated by 15 different volunteers. MicroFLOQ swabs performed well, as did 3 mm diameter discs punched from analytical filter paper. The 3 mm discs could be used in a 5 µl PCR volume, increasing sensitivity, and reducing costs when compared with other methods that require a larger PCR volume. Other inert sampling vehicles, such as interdental toothbrushes and toothpicks also gave good results in direct amplification. The study found a large variation in results between the 15 touch DNA donors, demonstrating the importance of validating touch DNA recovery techniques with a large pool of donors.
Segment 2 from influenza A(H1N1)pdm09 viruses confers temperature sensitive HA yield on candidate vaccine virus growth in eggs that is complemented by PB2 701D
Authors: Hussain Saira , Turnbull Matthew L. , Pinto Rute M. , McCauley John W. , Engelhardt Othmar G. , Digard Paul
Published: February 2019

Candidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with a high-yielding egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 H1N1 pandemic (pdm09) high-growth reassortants (HGRs) selected by this process contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6:2 or 5:3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5:3 viruses replicated better in MDCK-SIAT1 cells than the 6:2 viruses, but the 6:2 CVVs gave higher HA antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as HA yields from eggs for the 5:3 viruses improved substantially when viruses were grown at 35°C compared with 37.5°C, whereas 6:2 virus yield did not. Authentic 5:3 pdm09 HGRs, X-179A and X-181, were not markedly temperature-sensitive however, despite their PB1 sequences being identical to that of Cal7, suggestive of compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified single changes in PB2 and NP, 5 in NS1, and 1 in NS2. PB2 N701D but not NP T130A affected the temperature dependency of viral transcription. Furthermore, introducing the PB2 701D change into a 5:3 CVV mimic improved and drastically reduced the temperature sensitivity of HA yield. We conclude that RG PR8 backbones used for vaccine manufacture in eggs should contain PB2 701D to maximise virus yield.
The impact of the “World’s 25 Most Endangered Primates” list on scientific publications and media
Authors: Kerhoas Daphneé , Acerbi Alberto , Webber Amanda D. , McCabe Gráinne , Mittermeier Russell A. , Schwitzer Christoph
Published: February 2019

Assessing the impact of conservation campaigns is of high importance for optimizing the use of limited resources. Lists of threatened species are often used as media outreach tools, but their usefulness is rarely tested. We investigated whether the inclusion of a species in the list “World’s 25 Most Endangered Primates”, published biannually by the International Primatological Society, the International Union for Conservation of Nature’s Species Survival Commission Primate Specialist Group, and Conservation International from 2000, had an effect both on scientific publications and on the general public. We analyzed a database of 40 million articles from major scientific publishers (Elsevier, Springer, Nature, Plos, Pubmed, Biomed Central) finding an increase in the number of papers mentioning a species after its inclusion in the list. We also analyzed media penetration (data from Google News), and online interest (data from Google Blogs, Twitter, and Google Trends), collecting daily data for one month before and one after the official launch of the 2014-2016 list (24th November 2015). The results show a short spike of interest on Google News and Twitter but no long term effect, indicating a limited effect on the general public. Our results are important for the understanding of the impact of current conservation campaigns and to provide strategies for future campaigns.
Differential side-effects ofBacillus thuringiensisbioinsecticide on non-targetDrosophilaflies
Authors: Babin Aurélie , Nawrot-Esposito Marie-Paule , Gallet Armel , Gatti Jean-Luc , Poirié Marylène
Published: February 2019

Biopesticides based onBacillus thuringiensis(Bt) spores and toxins are alternate pest management solutions widely used to control insect pests. Their increasing use could lead to accumulation in the environment, hence leading to chronic exposure of non-target organisms. Here, we tested for potential non-intentional side-effects of chronic exposure toBtbiopesticide on larvae of non-targetDrosophilaspecies present inBt-treated areas. Doses up to those recommended for field application (106CFU/g of fly medium) had no effect on the fly development, whereas doses 10 to 100-fold higher (107-108CFU/g) increased developmental time and decreased adult emergence rates in a dose-dependent manner and with varying effect amplitudes for all the species and strains tested. For all them, all larvae died before pupation at the highest dose tested (109CFU/g). Focusing onD. melanogaster, delayed development and reduced emergence resulted from stage-dependent larval mortality, and fitness-related traits of adult flies emerging from survivingBtbiopesticide exposure were moderately increased. The effects ofBtbiopesticide seemed to result from the spores/cleaved toxins synergy, and possibly additives. While recommended doses had no effect on non-targetDrosophilaspecies, misuse or local accumulation ofBtbioinsecticides in the environment could have non-intentional side-effects on fly populations with potential implications for their associated communities.
Descriptive epidemiology of energy expenditure in the UK: Findings from the National Diet and Nutrition Survey 2008 – 2015
Authors: Brage Soren , Lindsay Tim , Venables Michelle , Wijndaele Katrien , Westgate Kate , Collins David , Bluck Les , Wareham Nick , Page Polly
Published: February 2019

Background

Little is known about population levels of energy expenditure as national surveillance systems typically employ only crude measures. The National Diet and Nutrition Survey (NDNS) in the UK measures energy expenditure in a 10% subsample by gold-standard doubly-labelled water (DLW).

Methods

DLW-subsample participants from the NDNS (383 males, 387 females) aged 4-91yrs were recruited between 2008 and 2015. Height and weight were measured, and bodyfat percentage was estimated by deuterium dilution.

Results

Absolute Total Energy Expenditure (TEE) increases steadily throughout childhood, ranging from 6.3 and 7.2 MJ/day in 4-7yr-old to 9.9 and 11.8 MJ/day for 14-16yr-old girls and boys, respectively. TEE peaked in 17-27yr-old women (10.9 MJ/day) and 28-43yr-old men (14.4 MJ/day), before decreasing gradually in old age. Physical Acitivty Energy Expenditure (PAEE) declines steadily with age from childhood (87.7 kJ/day/kg in 4-7yr olds) through to old age (38.9 kJ/day/kg in 71-91yr olds). Bodyfat percentage was strongly inversely associated with PAEE throughout life, irrespective of expressing PAEE relative to bodymass or fat-free mass. Compared to females with <30% bodyfat, females >40% recorded 28 kJ/day/kg and 17 kJ/day/kg fat-free mass less PAEE in analyses adjusted for age, geographical region, and time of assessment. Similarly, compared to males with <25% bodyfat, males >35% recorded 26 kJ/day/kg and 10 kJ/day/kg fat-free mass less PAEE.

Conclusions

This first nationally representative study reports levels of human energy expenditure as measured by gold-standard methodology; values may serve as reference for other population studies. Age, sex and body composition are main biological determinants of energy expenditure.

Key messages

First nationally representative study of human energy expenditure, covering the UK in the period 2008-2015

Total Energy Expenditure (MJ/day) increases steadily with age thoughout childhood and adolescence, peaks in the 3rd decade of life in women and 4th decade of life in men, before decreasing gradually in old age

Physical Acitivty Energy Expenditure (kJ/day/kg or kJ/day/kg fat-free mass) declines steadily with age from childhood to old age, more steeply so in males

Bodyfat percentage is strongly inversely associated with physical activity energy expenditure
Using extreme gradient boosting (XGBoost) to evaluate the importance of a suite of environmental variables and to predict recruitment of young-of-the-year spotted seatrout in Florida
Authors: Herdter Smith Elizabeth
Published: February 2019

Environmental factors strongly influence the success of juvenile fish recruitment and productivity, but species-specific environment-recruitment relationships have eluded researchers for decades. Most likely, this is because the environment-recruitment relationship is nonlinear, there are multi-level interactions between factors, and environmental variability may differentially affect recruitment among populations due to spatial heterogeneity. Identifying the most influential environmental variables may result in more accurate predictions of future recruitment and productivity of managed species. Here, gradient tree boosting was implemented using XGBoost to identify the most important predictors of recruitment for six estuary populations of spotted seatrout (Cynoscion nebulosus), an economically valuable marine resource in Florida. XGBoost, a machine learning method for regression and classification, was employed because it inherently models variable interactions and seamlessly deals with multi-collinearity, both of which are common features of ecological datasets. Additionally, XGBoost operates at a speed faster than many other gradient boosting algorithms due to a regularization factor and parallel computing functionality. In this application of XGBoost, the results indicate that the abundance of pre-recruit, juvenile spotted seatrout in spatially distinct estuaries is influenced by nearly the same set of environmental predictors. But perhaps of greater importance is that the results of this study show that this algorithm is highly effective at predicting species abundance and identifying important environmental factors (i.e. predictors of recruitment). It is strongly encouraged that future research explore the applicability of the XGBoost algorithm to other topics in marine and fisheries science and compare its performance to that of other statistical methods.
Single-cell profiling of tumor-reactive CD4+T-cells reveals unexpected transcriptomic diversity
Authors: Magen Assaf , Nie Jia , Ciucci Thomas , Tamoutounour Samira , Zhao Yongmei , Mehta Monika , Tran Bao , McGavern Dorian B. , Hannenhalli Sridhar , Bosselut Rémy
Published: February 2019

Most current tumor immunotherapy strategies leverage cytotoxic CD8+T cells. Despite evidence for clinical potential of CD4+tumor-infiltrating lymphocytes (TILs), their functional diversity has limited our ability to harness their activity. To address this issue, we have used single-cell mRNA sequencing to analyze the response of CD4+T cells specific for a defined recombinant tumor antigen, both in the tumor microenvironment and draining lymph nodes (dLN). Designing new computational approaches to characterize subpopulations, we identify TIL transcriptomic patterns strikingly distinct from those elicited by responses to infection, and dominated by diversity among T-bet-expressing T helper type 1 (Th1)-like cells. In contrast, the dLN response includes follicular helper (Tfh)-like cells but lacks Th1 cells. We identify a type I interferon-driven signature in Th1-like TILs, and show that it is found in human liver cancer and melanoma, in which it is negatively associated with response to checkpoint therapy. Our study unveils unsuspected differences between tumor and virus CD4+T cell responses, and provides a proof-of-concept methodology to characterize tumor specific CD4+T cell effector programs. Targeting these programs should help improve immunotherapy strategies.

One Sentence Summary

Single-cell RNA sequencing reveals novel and highly diverse transcriptomic patterns characteristic of CD4+T cell responses to tumors.
Attention updates the perceived position of moving objects
Authors: Nakayama Ryohei , Holcombe Alex O.
Published: February 2019

The information used by conscious perception may be somewhat different from that which drives certain actions. In support of this notion, recent studies reported that although internal grating motion can accumulate over seconds into a large illusory position shift, this position shift is not reflected in saccade targeting (action). Another possibility however is that rather than saccades and other actions having privileged access to the correct position, the attention shift thought to precede saccades resets the accumulated position shift to zero. Here we found that the accumulation of illusory position shift can be reset by transients near the moving object and also by the observer pressing a button at the time the object is perceived to reach a particular position. This creates a striking impression of the object jumping back to near its actual position. These results suggest that both stimulus-driven attention and attention associated with control of action may update the perceived position of moving objects and mediate the previously reported dissociation between conscious perception and saccades.
RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Authors: Li Leyuan , Ning Zhibin , Zhang Xu , Mayne Janice , Cheng Kai , Stintzi Alain , Figeys Daniel
Published: February 2019

The gut microbiome has been associated with a growing list of diseases. Drugs and other compounds can affect the microbiome, but our understanding of drug-induced changes in individual microbiomes is limited due to a lack of rapid and effective high-throughput assay methods. We developed an approach named Rapid Assay of Individual Microbiome (RapidAIM) to screen xenobiotics against individual microbiomes. RapidAIM was evaluated by testing 43 compounds against five individual microbiomes using a metaproteomic approach. We show that our workflow enables quantitative profiling of the microbiome. The tested compounds significantly affected overall microbiome abundance, microbiome composition and functional pathways at multiple taxonomic levels. The microbiome responses to berberine, metformin, diclofenac, fructooligosaccharide and most antibiotics were consistent among most individuals. Interestingly, most of our tested NSAIDs, statins, and histamine-2 blockers induced strong and individually distinct responses. Our workflow offers an effective solution to systematically study the effects of many different compounds on individual microbiomes.
Optimal biochemical information processing at criticality
Authors: Stanoev Angel , Nandan Akhilesh P. , Koseska Aneta
Published: February 2019

How cells utilize surface receptors for chemoreception is a recurrent question spanning between physics and biology over the past few decades. However, the dynamical mechanism for processing time-varying signals is still unclear. Using dynamical systems formalism to describe criticality in non-equilibrium systems, we propose generic principle for temporal information processing through phase-space trajectories using dynamic transient memory. In contrast to short-term memory, dynamic memory generated via ghost attractor enables signal integration depending on stimulus history, and thus balance between stability and plasticity in receptor responses. We propose that self-organization at criticality can arise through fluctuation-sensing mechanism, illustrated for the experimentally established epidermal growth factor sensing system. This framework applies irrespective of the intrinsic node dynamics or network size, as we show using also a basic neuronal model. Processing of non-stationary signals, a feature previously attributed only to neuronal networks, thus uniquely emerges for biochemical networks organized at criticality.
hicap:in silicoserotyping of theHaemophilus influenzaecapsule locus
Authors: Watts Stephen C. , Holt Kathryn E.
Published: February 2019

Haemophilus influenzaeexclusively colonises the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases including meningitis and sepsis. A key virulence determinant ofH. influenzaeis the polysaccharide capsule of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a tocap-f).H. influenzaetype b (Hib) was historically responsible for the majority of invasiveH. influenzaedisease and prevalence has been markedly reduced in countries that have implemented vaccination programs targeting this serotype. In the postvaccine era, non-typeableH. influenzaeemerged as the most dominant group causing disease but in recent years a resurgence of encapsulatedH. influenzaestrains has also been observed, most notably serotype a. Given the increasing incidence of encapsulated strains and the high frequency of Hib in countries without vaccination programs, there is growing interest in genomic epidemiology ofH. influenzae. Here we present hicap, a software tool for rapid in silico serotype prediction fromH. influenzaegenome sequences. hicap is written using Python3 and is freely available at github.com/scwatts/hicap under a GPLv3 license. To demonstrate the utility of hicap, we used it to investigate the cap locus diversity and distribution in 691 high-qualityH. influenzaegenomes from GenBank. These analyses identifiedcaploci in 95 genomes and confirmed the general association of each serotype with a unique clonal lineage and also identified occasional recombination between lineages giving rise to hybridcaploci (2% of encapsulated strains).
Long-term vegetation change in species-rich Nardus grasslands of central Germany caused by eutrophication, recovery from acidification and management change
Authors: Peppler-Lisbach Cord , Stanik Nils , Könitz Natali , Rosenthal Gert
Published: February 2019

Questions

The impact of environmental changes on species-rich Nardus grasslands has been documented from the Atlantic biogeographic region but not from Central Europe. Which patterns and trends of community change in species-rich Nardus grassland of the Continental biogeographic region occurred in past decades? Are patterns and trends similar across areas within the Continental biographic region of Germany? Do they correspond to identified changes in the Atlantic biogeographic region of Europe?

Location

East Hesse Highlands, Germany

Methods

In 2012/15, we re-surveyed vegetation relevés on quasi-permanent plots originally surveyed between 1971 and 1986/87 and re-measured soil parameters. We tested for differences in species frequency and abundance, mean Ellenberg indicator values, diversity measures and soil variables. Nitrogen and sulphur deposition data were analysed to evaluate effects of atmospheric pollutants. We used regression analyses to identify the contribution of environmental drivers to changes in species composition.

Results

We found significant increases in soil pH, Ellenberg R and N values, species of agricultural grasslands and grassland fallows. C:N ratio, Nardus grassland specialists and low-nutrient indicators declined, while changes in species composition relate to changes in pH and management. There was a strong decrease in sulphur and a moderate increase in nitrogen deposition. Local patterns in atmospheric depositions did not correlate with local changes in species composition and soil parameters.

Conclusion

The findings indicate significant overall eutrophication, a trend towards less acidic conditions, and insufficient management and abandonment. This is widely consistent across study areas and correspond to recent reports on vegetation changes and recovery from acidification in the Atlantic biogeographic region. We strongly assume reduction in sulphur deposition during recent decades to be a major driver of these changes combined with increased nitrogen deposition and reduced management intensity. This suggests a large-scale validity of processes triggering changes in Nardus grasslands across Western and Central Europe.

Nomenclature

The nomenclature follows the German taxonomic reference list (GermanSL version 1.3) of Jansen & Dengler (2008).
Temporal switching of species roles in a plant–pollinator network
Authors: Miele Vincent , Ramos-Jiliberto Rodrigo , Vázquez Diego P.
Published: February 2019

Mutualistic networks are highly dynamic, characterized by high temporal turnover of species and interactions. Yet, we have a limited understanding of how the internal structure of these networks and the roles species play in them vary through time. We used six years of observation data and a novel statistical method (dynamic stochastic block models) to assess how network structure and species roles change across time in a quantitative plant–pollinator network from a dryland ecosystem in Argentina. Our analyses revealed a core–periphery structure persistent through seasons and years. Yet, species roles as core or peripheral were highly dynamic: virtually all species that played a core role in some seasons were also peripheral in other seasons, while many other species remained always peripheral. Our results illuminate our understanding of the dynamics of ecological networks and have important implications for ecosystem management and conservation.
The FACTS model of speech motor control: fusing state estimation and task-based control
Authors: Parrell Benjamin , Ramanarayanan Vikram , Nagarajan Srikantan , Houde John
Published: February 2019

We present a new computational model of speech motor control: the Feedback-Aware Control of Tasks in Speech orFACTSmodel. This model is based on a state feedback control architecture, which is widely accepted in non-speech motor domains. The FACTS model employs a hierarchical observer-based architecture, with a distinct higher-level controller of speech tasks and a lower-level controller of speech articulators. The task controller is modeled as a dynamical system governing the creation of desired constrictions in the vocal tract, based on the Task Dynamics model. Critically, both the task and articulatory controllers rely on an internal estimate of the current state of the vocal tract to generate motor commands. This internal state estimate is derived from initial predictions based on efference copy of applied controls. The resulting state estimate is then used to generate predictions of expected auditory and somatosensory feedback, and a comparison between predicted feedback and actual feedback is used to update the internal state prediction. We show that the FACTS model is able to qualitatively replicate many characteristics of the human speech system: the model is robust to noise in both the sensory and motor pathways, is relatively unaffected by a loss of auditory feedback but is more significantly impacted by the loss of somatosensory feedback, and responds appropriately to externally-imposed alterations of auditory and somatosensory feedback. The model also replicates previously hypothesized trade-offs between reliance on auditory and somatosensory feedback in speech motor control and shows for the first time how this relationship may be mediated by acuity in each sensory domain. These results have important implications for our understanding of the speech motor control system in humans.
Respiratory gas levels interact to control ventilatory motor patterns in isolated locust ganglia
Authors: Talal Stav , Ayali Amir , Gefen Eran
Published: February 2019

Large insects actively ventilate their tracheal system even at rest, using abdominal pumping movements, which are controlled by a central pattern generator (CPG) in the thoracic ganglia. We studied the effects of respiratory gases on the ventilatory rhythm by isolating the thoracic ganglia and perfusing its main tracheae with various respiratory gas mixtures. Fictive ventilation activity was recorded from motor nerves controlling spiracular and abdominal ventilatory muscles. Both hypoxia and hypercapnia increased the ventilation rate, with the latter being much more potent. Sub-threshold hypoxic and hypercapnic levels were still able to modulate the rhythm as a result of interactions between the effects of the two respiratory gases. Additionally, changing the oxygen levels in the bathing saline affected ventilation rate, suggesting a modulatory role for haemolymph oxygen. Central sensing of both respiratory gases as well as interactions of their effects on the motor output of the ventilatory CPG reported here indicate convergent evolution of respiratory control among terrestrial animals of distant taxa.

Summary statement

Tight control over respiratory gas supply to the isolated locust CNS reveals interactions of oxygen and carbon dioxide effects on central ventilatory output.
Identifying Drug Sensitivity Subnetworks with NETPHLIX
Authors: Kim Yoo-Ah , Basso Rebecca Sarto , Wojtowicz Damian , Hochbaum Dorit S. , Vandin Fabio , Prztycka Teresa M.
Published: February 2019

Phenotypic heterogeneity in cancer is often caused by different patterns of genetic alterations. Understanding such phenotype-genotype relationships is fundamental for the advance of personalized medicine. One of the important challenges in the area is to predict drug response on a personalized level. The pathway-centric view of cancer significantly advanced the understanding of genotype-phenotype relationships. However, most of network identification methods in cancer focus on identifying subnetworks that include general cancer drivers or are associated with discrete features such as cancer subtypes, hence cannot be applied directly for the analysis of continuous features like drug response. On the other hand, existing genome wide association approaches do not fully utilize the complex proprieties of cancer mutational landscape. To address these challenges, we propose a computational method, named NETPHLIX (NETwork-to-PHenotpe mapping LeveragIng eXlusivity), which aims to identify mutated subnetworks that are associated with drug response (or any continuous cancer phenotype). Utilizing properties such as mutual exclusivity and interactions among genes, we formulate the problem as an integer linear program and solve it optimally to obtain a set of genes satisfying the constraints. NETPHLIX identified gene modules significantly associated with many drugs, including interesting response modules to MEK1/2 inhibitors in both directions (increased and decreased sensitivity to the drug) that the previous method, which does not utilize network information, failed to identify. The genes in the modules belong to MAPK/ERK signaling pathway, which is the targeted pathway of the drug.
The role of mutational spectrum in the selection against mutator alleles
Authors: Couce Alejandro , Tenaillon Olivier
Published: February 2019

Rapidly adapting microbe and cancer cell populations often evolve high mutation rates. Yet, once adaptive opportunity declines, antimutator alleles are expected to take over as a result of indirect selection against deleterious mutations. Theory indicates that the most important determinant of antimutator invasions is the extent of mutation rate reduction. However, inconsistent results from evolution experiments suggest that additional factors may also play a major role in antimutator dynamics. Here we show that the idiosyncratic mutation bias exhibited by different mutators – a previously unrecognized factor – can greatly alter mutator susceptibility to antimutator invasions. Using a simulation model calibrated to mimic a well-known long-term evolution experiment with bacteria, we show that differences in average deleterious load can account for order-of-magnitude changes in antimutator fitness for a realistic range of parameters. Since these parameters are known to vary with the environment, our results reveal an unanticipated source of variability in antimutator dynamics. Finally, we estimated the genome-wide average disruptive effect on proteins of mutations caused by different mutators, and found marked and systematic differences emerging across mutators and species with different genomic GC compositions. Taken together, our results suggest that antimutator dynamics may be highly dependent on the specific genetic, ecological and evolutionary history of a given population. Such dependence reveals a more complex picture than anticipated, being relevant for understanding mutators in clinical settings, as well as how hypermutability shapes the evolution of bacterial genome size and composition.
Asymmetric Tug-of-War leads to Cooperative Transport of a Cargo by Multiple Kinesins
Authors: Tjioe Marco , Shukla Saurabh , Vaidya Rohit , Troitskaia Alice , Bookwalter Carol , Trybus Kathleen M. , Chemla Yann R. , Selvin Paul R.
Published: February 2019

How cargoes move within a crowded cell—over long distances and at speeds that are nearly the same as when moving on an unimpeded pathway—has long been mysterious. Through an in vitro gliding assay, which involves measuring nanometer displacement and piconewtons of force, we have evidence that when kinesins, a cytoplasmic molecular motor, operate in small groups, from 2-10, they can communicate among themselves through an asymmetric tug-of-war by inducing tension (up to 4 pN) on the cargo. Surprisingly, the primary role of approximately one-third of kinesins is to develop tension, which instantaneously slows forward motion but helps increase cargo run length. These hindering kinesins fall off rapidly when experiencing a forward tug. Occasionally, they may be ripped off from their anchors by other driving kinesins working in tandem. Furthermore, with roadblocks on the microtubule, multiple kinesins cooperate to overcome impediments. Hence, kinesin may employ an asymmetric tug-of-war and a cooperative motion to navigate through cellular environment.
Induction of microbial oxidative stress as a new strategy to enhance the enzymatic degradation of organic micropollutants in wastewater
Authors: Bains Amrita , Perez-Garcia Octavio , Lear Gavin , Greenwood David , Swift Simon , Middleditch Martin , Kolodziej Edward , Singhal Naresh
Published: February 2019

Organic micropollutants (OMPs) are pervasive anthropogenic contaminants of fresh and marine waters with known potential to adversely affect aquatic life (e.g. endocrine disruption). Their ubiquitous environmental occurrence is primarily attributed to wastewater treatment plant discharges following their incomplete removal by common biological treatment processes. This study assesses a new strategy for promoting the degradation of six model OMPs (i.e. sulfamethoxazole, carbamazepine, tylosin, atrazine, naproxen and ibuprofen) by stimulating microbial oxidoreductase production to counter the effects of oxidative stress caused by oxygen perturbation. Microbial cultures from dairy farm wastewater were exposed to a cyclical ON-OFF perturbations of oxygen supply, ranging from 0.16 to 2 cycles per hour (i.e. 2, 1, 0.5, 0.25 and 0.16 cycles/hour), in laboratory bioreactors. The activity and relative abundances of microbial oxidoreductases (such as peroxidases, cytochromes P450) were upregulated by oxygen perturbation. In comparison to controls subjected to constant oxygen levels, OMP concentrations in perturbed cultures decreased by 70±9% (mean ± SD). A distance-based linear model confirmed strong positive correlations between the relative abundance of the bacterial families, Rhodocyclaceae, Syntrophaceae and Syntrophobacteraceae, and oxygen perturbations. Our results confirm that intentional perturbation of oxygen supply to induce microbial oxidative stress can improve OMP removal efficiencies in wastewater treatment bioreactors.
Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae)
Authors: Kretzschmar A.L. , Verma A. , Kohli G.S. , Murray S.A.
Published: February 2019

Ciguatera fish poisoning is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, in triplicate to determine the presence and patchiness of these species across samples from Chnoospora sp., Padina sp. and Sargassum macroalgal hosts.

Author’s summary

Ciguatera fish poisoning is a human disease contracted by ingesting seafood contaminated with a group of neurotoxins. The group of neurotoxins, named ciguatoxins, are synthesised by species of single celled marine algae from the genus Gambierdiscus.

Ciguatera fish poisoning occurs worldwide, particularly in tropical nations. Pacific Island nations are disproportionately impacted, and this impact is predicted to increase as the effects of climate change unfold. Few effective monitoring and mitigation strategies exist for ciguatera fish poisoning, and reporting rates of the disease are estimated to be approximately 20% at best. A global ciguatera strategy was developed by a group of researchers coordinated by UNESCO’s Intergovernmental Oceanographic Commission to characterise the cause and mode of action of ciguatera fish poisoning, as a matter of urgency.

In this study, we designed a qPCR assay to detect a species of microalgae, Gambierdiscus lapillus. Gambierdiscus lapillus produces compounds with ciguatoxin-like properties, which may lead to ciguatoxin uptake in fish in the Australian region. This assay was sensitive and able to detect the presence of Gambierdiscus lapillus in a range of environmental samples from the Great Barrier Reef region, Australia.
Influence of Mismarking Fiducial Locations on EEG Source Estimation
Authors: Shirazi Seyed Yahya , Huang Helen J.
Published: February 2019

Mismarking locations of the fiducials can have a significant influence on the digitized electrode locations and cortical source estimation using high-density EEG. Under-standing and quantifying how uncertainties in the fiducial locations affect the locations of cortical sources is important for interpreting EEG analyses. We systematically shifted fiducial locations to investigate the relationship between variations of fiducial locations and the corresponding estimations of the source locations. We quantified the uncertainty of the dipole locations using the enclosing volume of the dipole locations and the maximum width of the dipole cluster. Shifting fiducial locations 1.5 cm increased the uncertainty of the dipole locations to span a volume >1 cm3 and about 2.5 cm wide. Results suggest that the fiducials need to be digitized accurately within at least 0.5 cm of the absolute actual fiducial location to limit the uncertainty of a dipole location to <1 cm. Additionally, we used random fiducial shift combinations to estimate the effects of combinations of the fiducial shifts on dipole location estimation. This analysis showed that dipole locations were within the bounds of our dipole estimation uncertainty volumes. Based on the outcomes, we suggest marking fiducials carefully before placement of the cap and to use a digitization method with an accuracy of <0.5 cm.
The mycobacterial cell wall partitions the plasma membrane to organize its own synthesis
Authors: García-Heredia Alam , Kado Takehiro , Sein Caralyn E. , Puffal Julia , Osman Sarah H. , Judd Julius , Gray Todd A. , Morita Yasu S. , Siegrist M. Sloan
Published: February 2019

Many antibiotics target the assembly of cell wall peptidoglycan, an essential, heteropolymeric mesh that encases most bacteria. Different species have characteristic subcellular sites of peptidoglycan synthesis that they must carefully maintain for surface integrity and, ultimately, viability. In rod-shaped bacteria, cell wall elongation is spatially precise yet relies on a limited pool of lipid-linked precursors that generate and are attracted to membrane disorder. By tracking enzymes, substrates and products of peptidoglycan biosynthesis inMycobacterium smegmatis, we show that precursors are made in plasma membrane domains that are laterally and biochemically distinct from sites of cell wall assembly. Membrane partitioning is required for robust, orderly peptidoglycan synthesis, indicating that these domains help template peptidoglycan synthesis. The cell wall-organizing protein DivIVA and the cell wall itself are essential for domain homeostasis. Thus, the peptidoglycan polymer feeds back on its membrane template to maintain an environment conducive to directional synthesis. We further show that our findings are applicable to rod-shaped bacteria that are phylogenetically distant fromM. smegmatis, demonstrating that horizontal compartmentalization of precursors is a general feature of bacillary cell wall biogenesis.
netNMF-sc: Leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis
Authors: Elyanow Rebecca , Dumitrascu Bianca , Engelhardt Barbara E. , Raphael Benjamin J.
Published: February 2019

Motivation

Single-cell RNA-sequencing (scRNA-seq) enables high throughput measurement of RNA expression in individual cells. Due to technical limitations, scRNA-seq data often contain zero counts for many transcripts in individual cells. These zero counts, ordropout events, complicate the analysis of scRNA-seq data using standard analysis methods developed for bulk RNA-seq data. Current scRNA-seq analysis methods typically overcome dropout by combining information across cells, leveraging the observation that cells generally occupy a small number of RNA expression states.

Results

We introduce netNMF-sc, an algorithm for scRNA-seq analysis that leverages information acrossbothcells and genes. netNMF-sc combines network-regularized non-negative matrix factorization with a procedure for handling zero inflation in transcript count matrices. The matrix factorization results in a low-dimensional representation of the transcript count matrix, which imputes gene abundance for both zero and non-zero entries and can be used to cluster cells. The network regularization leverages prior knowledge of gene-gene interactions, encouraging pairs of genes with known interactions to be close in the low-dimensional representation. We show that netNMF-sc outperforms existing methods on simulated and real scRNA-seq data, with increasing advantage at higher dropout rates (e.g. above 60%). Furthermore, we show that the results from netNMF-sc – including estimation of gene-gene covariance – are robust to choice of network, with more representative networks leading to greater performance gains.

Availability

netNMF-sc is available atgithub.com/raphael-group/netNMF-sc.

Contact

braphael@princeton.edu
Multivariate genome-wide association analysis of a cytokine network reveals variants with widespread immune, haematological and cardiometabolic pleiotropy
Authors: Nath Artika P. , Ritchie Scott C. , Grinberg Nastasiya F. , Tang Howard Ho-Fung , Huang Qin Qin , Teo Shu Mei , Ahola-Olli Ari V. , Würtz Peter , Havulinna Aki S. , Aalto Kristiina , Pitkänen Niina , Lehtimäki Terho , Kähönen Mika , Lyytikäinen Leo-Pekka , Raitoharju Emma , Seppälä Ilkka , Sarin Antti-Pekka , Ripatti Samuli , Palotie Aarno , Perola Markus , Viikari Jorma S , Jalkanen Sirpa , Maksimow Mikael , Salmi Marko , Wallace Chris , Raitakari Olli T. , Salomaa Veikko , Abraham Gad , Kettunen Johannes , Inouye Michael
Published: February 2019

Cytokines are essential regulatory components of the immune system and their aberrant levels have been linked to many disease states. Despite increasing evidence that cytokines operate in concert, many of the physiological interactions between cytokines, and the shared genetic architecture that underlie them, remain unknown. Here we aimed to identify and characterise genetic variants with pleiotropic effects on cytokines – to do this we performed a multivariate genome-wide association study on a correlation network of 11 circulating cytokines measured in 9,263 individuals. Meta-analysis identified a total of 8 loci significantly associated with the cytokine network, of which two (PDGFRB and ABO) had not been detected previously. Bayesian colocalisation analysis revealed shared causal variants between the eight cytokine loci and other traits; in particular, cytokine network variants at the ABO, SERPINE2, and ZFPM2 loci showed pleiotropic effects on the production of immune-related proteins; on metabolic traits such as lipoprotein and lipid levels; on blood-cell related traits such as platelet count; and on disease traits such as coronary artery disease and type 2 diabetes.
Non-canonical Features of Pentatricopeptide Repeat Protein-Facilitated RNA Editing in Arabidopsis Chloroplasts
Authors: Kelly Sun Yueming , Gutmann Bernard , Small Ian
Published: February 2019

Cytosine (C) to uracil (U) RNA editing in plant mitochondria and chloroplasts is facilitated by site-specific pentatricopeptide repeat (PPR) editing factors. PPR editing factors contain multiple types of PPR motifs, and PPR motifs of the same type also show sequence variations. Therefore, no PPR motifs are invariant within a PPR protein or between different PPR proteins. This work evaluates the functional diversity of PPR motifs in CHLOROPLAST RNA EDITING FACTOR 3 (CREF3). The results indicate that previously overlooked features of PPR editing factors could also contribute to RNA editing activity. In particular, the N-terminal degenerated PPR motifs and the two L1-type PPR motifs in CREF3 are functionally indispensable. Furthermore, PPR motifs of the same type in CREF3 are not interchangeable. These non-canonical features of CREF3 have important implications on the understanding of PPR-facilitated RNA editing in plant organelles.
Characterization of Peripheral Blood Mononuclear Cells Gene Expression Profiles of PediatricStaphylococcus aureusPersistent and Non-Carriers Using a Targeted Assay
Authors: Israelsson Elisabeth , Chaussabel Damien , Fischer Rebecca S.B. , Moore Heather C. , Robinson D. Ashley , Essigmann Heather T. , Brown Eric L.
Published: February 2019

Defects in innate immunity affect many different physiologic systems and several studies of patients with primary immunodeficiency disorders demonstrated the importance of innate immune system components in disease prevention or colonization of bacterial pathogens. To assess the role of the innate immune system on nasal colonization withStaphylococcus aureus, innate immune responses in pediatricS. aureusnasal persistent carriers (n=15) and non-carriers (n=15) were profiled by analyzing co-clustered gene sets (modules) identified through large-scale transcriptome data analysis as the basis for the development of a targeted assay. We stimulated previously frozen peripheral blood mononuclear cells (PBMCs) from these subjects with i) a panel of TLR ligands, ii) liveS. aureus(either a mixture of strains or stimulation with respective carriage isolates), or iii) heat-killedS. aureus. We found no difference in responses between carriers and non-carriers when PBMCs were stimulated with a panel of TLR ligands. However, PBMCs stimulated with liveS. aureuselicited a significantly different response that also differed from the response elicited following stimulation with deadS. aureus. Furthermore, we observed a distinct stimulation profile for PBMCs isolated from persistent carriers stimulated with their respective live or dead carriage strains compared to responses observed for PBMCs isolated from non-carriers that were similar regardless of whether or not the bacteria were alive or not. These data suggested that innate pathway signaling is different between persistent and non-carriers ofS. aureus.
Electrophysiological correlates of state transition prediction errors
Authors: Shahnazian Danesh , Ribas-Fernandes José J.F , Holroyd Clay B.
Published: February 2019

Planning behavior depends crucially on the ability to distinguish between the likely and unlikely consequences of an action. Formal computational models of planning postulate the existence of a neural mechanism that tracks the transition model of the environment, i.e., a model that explicitly represents the probabilities of action consequences. However, empirical findings relating to such a mechanism are scarce. Here we report the results of two electroencephalographic experiments examining the neural correlates of transition model learning. The results implicate fronto-midline theta and delta oscillations in this process and suggest a role of the anterior midcingulate cortex in planning behavior.
A genetically-encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling
Authors: Prole David L. , Taylor Colin W.
Published: February 2019

Background

Intrabodies enable targeting of proteins in live cells, but it remains a huge task to generate specific intrabodies against the thousands of proteins in a proteome. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags.

Results

We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerizing or heterodimerizing modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria, and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane.

Conclusions

This toolkit greatly expands the utility of intrabodies for studying cell signalling in live cells.