bluuebunny/crossref_metadata_2025 huggingface dataset:
Biodiversity on Indigenous lands equals that in protected areas
Authors: Schuster Richard , Germain Ryan R. , Bennett Joseph R. , Reo Nicholas J. , Secord Dave L. , Arcese Peter
Published: May 2018

Declines in global biodiversity due to land conversion and habitat loss are driving a “Sixth Mass Extinction” and many countries currently fall short of meeting even nominal land protection targets to mitigate this crisis. Here, we quantify the potential contribution of Indigenous lands to biodiversity conservation using case studies of Australia, Brazil and Canada. Indigenous lands in each country are slightly more species rich than existing protected areas and, in Brazil and Canada, support more threatened species than existing protected areas or random sites. These results indicate that Indigenous lands and existing protected areas are similar in biodiversity. Enhanced partnerships between Indigenous communities and federal or state governments could help ameliorate current shortfalls in global biodiversity protection by facilitating protection for native species, helping to stem global biodiversity loss.
Epididymal glucocorticoid receptors promote intergenerational transmission of paternal stress
Authors: Chan Jennifer C , Nugent Bridget M , Morrison Kathleen E , Jašarević Eldin , Bhanu Natarajan V , Garcia Benjamin A , Bale Tracy L
Published: May 2018

Paternal preconception exposures and insults, including stress, dietary challenge and drugs of abuse, can shape offspring health and disease risk outcomes, as evidenced from retrospective human studies and more recent animal models1–16. Mechanistic examination has implicated small noncoding RNA populations in sperm, including microRNA (miRs), as carriers of paternal environmental information that consequently influence offspring development15,17–21. However, the cellular mechanisms by which these paternal signals are relayed to sperm and how they may persist remain unknown. Here, using our previously established paternal stress mouse model we identify caput epididymal epithelial glucocorticoid receptors as crucial upstream mediators of long-lasting germ cell programming. We show that glucocorticoid treatment of caput epididymal epithelial cells results in increased glucocorticoid receptor levels and enduring changes to the miR content of secreted extracellular vesicles (EVs), or epididymosomes, known to interact with sperm and alter their RNA content22,23. Further, significant changes were detected in the caput epididymal histone code long after stress ended, bothin vitroandin vivo, as a potential mechanism whereby stress programmed enduring changes to EV miRs. Genetic targeting to reduce caput epididymal epithelial-specific glucocorticoid receptors reversed stress-induced chromatin remodeling and promoted cellular resilience to paternal stress, ultimately rescuing transmission of a stress dysregulated offspring phenotype. Taken together, these studies identify glucocorticoid receptor regulation of EV miRs in the caput epididymis as a key contributor in the intergenerational transmission of paternal environmental stress experiences.
Tissue-specifictransregulation of the mouse epigenome
Authors: Baker Christopher L. , Walker Michael , Arat Seda , Ananda Guruprasad , Petkova Pavlina , Powers Natalie , Tian Hui , Spruce Catrina , Ji Bo , Rausch Dylan , Choi Kwangbom , Petkov Petko M. , Carter Gregory W. , Paigen Kenneth
Published: May 2018

Although a variety of writers, readers, and erasers of epigenetic modifications are known, we have little information about the underlying regulatory systems controlling the establishment and maintenance of the epigenetic landscape, which varies greatly among cell types. Here, we have explored how natural genetic variation impacts the epigenome in mice. Studying levels of H3K4me3, a histone modification at sites such as promoters, enhancers, and recombination hotspots, we found tissue-specifictrans-regulation of H3K4me3 levels in four highly diverse cell types: male germ cells, embryonic stem (ES) cells, hepatocytes and cardiomyocytes. To identify the genetic loci involved, we measured H3K4me3 levels in male germ cells in a mapping population of 60 BXD recombinant inbred lines, identifying extensivetrans-regulation primarily controlled by six major histone quantitative trait loci (hQTL). These chromatin regulatory loci act dominantly to suppress H3K4me3, which at hotspots reduces the likelihood of subsequent DNA double-strand breaks. QTL locations do not correspond with enzyme known to metabolize chromatin features. Instead their locations match clusters of zinc finger genes, making these possible candidates that explain the dominant suppression of H3K4me3. Collectively, these data describe an extensive, tissue-specific set of chromatin regulatory loci that control functionally related chromatin sites.
Underestimation of carbohydrates by sugar alcohols in classical anthrone-based colorimetric techniques compromises insect metabolic and energetic studies
Authors: Body Mélanie J.A. , Casas Jérôme , Christidès Jean-Philippe , Giron David
Published: May 2018

Physiologically based metabolic studies usually search for easy, sensitive, and cheap techniques to rapidly estimate biological parameters such as nutrient content. Colorimetric methods to estimate carbohydrates have been extensively used (over 120,000 references). However, sugar alcohols are underestimated under conventionally used analytical conditions, in particular if using the popular van Handel method. This may lead to misinterpretations of sugar implications in biological systems. We determined the anthrone reaction with various sugar alcohols and non-alcohols individually under standard conditions (Van Handel 1985). We then manipulated the proportion of either sugar alcohols or non-alcohols in three different sugar mixtures in order to estimate the impact on the total sugar estimation. In the case of a mixture with over 50% of sugar alcohols, total sugars are underestimated by 50% when using glucose as standard.
Mouse dLGN receives input from a diverse population of retinal ganglion cells with limited convergence
Authors: Rosón Miroslav Román , Bauer Yannik , Berens Philipp , Euler Thomas , Busse Laura
Published: May 2018

In the mouse, the parallel output of more than 30 functional types of retinal ganglion cells (RGCs) serves as the basis for all further visual processing. Little is known about how the representation of visual information changes between the retina and the dorsolateral geniculate nucleus (dLGN) of the thalamus, the main relay station between the retina and cortex. Here, we functionally characterized responses of retrogradely labeled dLGN-projecting RGCs and dLGN neurons to the same set of visual stimuli. We found that many of the previously identified functional RGC types innervate the dLGN, which maintained a high degree of functional diversity. Using a linear model to assess functional connectivity between RGC types and dLGN neurons, we found that the responses of dLGN neurons could be predicted as a linear combination of inputs from on average five RGC types, but only two of those had the strongest functional impact. Thus, mouse dLGN receives input from a diverse population of RGCs with limited functional convergence.
A low-cost hyperspectral scanner for natural imaging above and under water
Authors: Nevala N. E. , Baden T.
Published: May 2018

Hyperspectral imaging is a widely used technology for industrial and scientific purposes, but the high cost and large size of commercial setups have made them impractical for most basic research. Here, we designed and implemented a fully open source and low-cost hyperspectral scanner based on a commercial spectrometer coupled to custom optical, mechanical and electronic components. We demonstrate our scanner’s utility for natural imaging in both terrestrial and underwater environments. Our design provides sub-nm spectral resolution between 350–1000 nm, including the UV part of the light spectrum which has been mostly absent from commercial solutions and previous natural imaging studies. By comparing the full light spectra from natural scenes to the spectral sensitivity of animals, we show how our system can be used to identify subtle variations in chromatic details detectable by different species. In addition, we have created an open access database for hyperspectral datasets collected from natural scenes in the UK and India. Together with comprehensive online build- and use-instructions, our setup provides an inexpensive and customisable solution to gather and share hyperspectral imaging data.
Automatic Localization of the Subthalamic Nucleus on Patient-Specific Clinical MRI by Incorporating 7T MRI and Machine Learning: Application in Deep Brain Stimulation
Authors: Kim Jinyoung , Duchin Yuval , Shamir Reuben R. , Patriat Remi , Vitek Jerrold , Harel Noam , Sapiro Guillermo
Published: May 2018

Deep Brain Stimulation (DBS) of the subthalamic nucleus (STN) has shown clinical potential for relieving the motor symptoms of advanced Parkinson’s disease. While accurate localization of the STN is critical for consistent across-patients effective DBS, clear visualization of the STN under standard clinical MR protocols is still challenging. Therefore, intraoperative microelectrode recordings (MER) are incorporated to accurately localize the STN. However, MER require significant neurosurgical expertise and lengthen the surgery time. Recent advances in 7T MR technology facilitate the ability to clearly visualize the STN. The vast majority of centers, however, still do not have 7T MRI systems, and fewer have the ability to collect and analyze the data. This work introduces an automatic STN localization framework based on standard clinical MRIs without additional cost in the current DBS planning protocol. Our approach benefits from a large database of 7T MRI and its clinical MRI pairs. We first model in the 7T database, using efficient machine learning algorithms, the spatial and geometric dependency between the STN and its adjacent structures (predictors). Given a standard clinical MRI, our method automatically computes the predictors and uses the learned information to predict the patient-specific STN. We validate our proposed method on clinical T2W MRI of 80 subjects, comparing with experts-segmented STNs from the corresponding 7T MRI pairs. The experimental results show that our framework provides more accurate and robust patient-specific STN localization than using state-of-the-art atlases. We also demonstrate the clinical feasibility of the proposed technique assessing the post-operative electrode active contact locations.
Optimization of Golden Gate assembly through application of ligation sequence-dependent fidelity and bias profiling
Authors: Vladimir Potapov , Ong Jennifer L. , Kucera Rebecca B. , Langhorst Bradley W. , Bilotti Katharina , Pryor John M. , Cantor Eric J. , Canton Barry , Knight Thomas F. , Evans Thomas C. , Lohman Gregory J. S.
Published: May 2018

Modern synthetic biology depends on the manufacture of large DNA constructs from libraries of genes, regulatory elements or other genetic parts. Type IIS restriction enzyme-dependent DNA assembly methods (e.g., Golden Gate) enable rapid one-pot, ordered, multi-fragment DNA assembly, facilitating the generation of high-complexity constructs. The order of assembly of genetic parts is determined by the ligation of flanking Watson-Crick base-paired overhangs. The ligation of mismatched overhangs leads to erroneous assembly, and the need to avoid such pairings has typically been accomplished by using small sets of empirically vetted junction pairs, limiting the number of parts that can be joined in a single reaction. Here, we report the use of a comprehensive method for profiling end-joining ligation fidelity and bias to predict highly accurate sets of connections for ligation-based DNA assembly methods. This data set allows quantification of sequence-dependent ligation efficiency and identification of mismatch-prone pairings. The ligation profile accurately predicted junction fidelity in ten-fragment Golden Gate assembly reactions, and enabled efficient assembly of a lac cassette from up to 24-fragments in a single reaction. Application of the ligation fidelity profile to inform choice of junctions thus enables highly flexible assembly design, with >20 fragments in a single reaction.
Physiomarkers in Real-Time Physiological Data Streams Predict Adult Sepsis Onset Earlier Than Clinical Practice
Authors: van Wyk Franco , Khojandi Anahita , Davis Robert L. , Kamaleswaran Rishikesan
Published: May 2018

Rationale:Sepsis is a life-threatening condition with high mortality rates and expensive treatment costs. To improve short- and long-term outcomes, it is critical to detect at-risk sepsis patients at an early stage.

Objective:Our primary goal was to develop machine learning models capable of predicting sepsis using streaming physiological data in real-time.

Methods:A dataset consisting of high-frequency physiological data from 1,161 critically ill patients admitted to the intensive care unit (ICU) was analyzed in this IRB-approved retrospective observational cohort study. Of that total, 634 patients were identified to have developed sepsis. In this paper, we define sepsis as meeting the Systemic Inflammatory Response Syndrome (SIRS) criteria in the presence of the suspicion of infection. In addition to the physiological data, we include white blood cell count (WBC) to develop a model that can signal the future occurrence of sepsis. A random forest classifier was trained to discriminate between sepsis and non-sepsis patients using a total of 108 features extracted from 2-hour moving time-windows. The models were trained on 80% of the patients and were tested on the remaining 20% of the patients, for two observational periods of lengths 3 and 6 hours.

Results:The models, respectively, resulted in F1 scores of 75% and 69% half-hour before sepsis onset and 79% and 76% ten minutes before sepsis onset. On average, the models were able to predict sepsis 210 minutes (3.5 hours) before the onset.

Conclusions:The use of robust machine learning algorithms, continuous streams of physiological data, and WBC, allows for early identification of at-risk patients in real-time with high accuracy.
Understanding the impact of crosslinked PCL/PEG/GelMA electrospun nanofibers on bactericidal activity
Authors: De-Paula Mirian Michelle Machado , Ghannadian Paria , Afewerki Samson , Marciano Fernanda Roberta , Viana Bartolomeu Cruz , Harb Samarah Vargas , Bassous Nicole Joy , Webster Thomas Jay , Lobo Anderson Oliveira
Published: May 2018

Herein, we report the design of electrospun ultrathin fibers based on polycaprolactone (PCL), polyethylene glycol (PEG), and gelatin methacryloyl (GelMA), and their potential bactericidal activity against three different bacteriaStaphylococcus aureus, Pseudomonas aeruginosa, andMethicillin-resistant Staphylococcus aureus(MRSA). We evaluated the morphology, chemical structure and wettability before and after UV photocrosslinking of the produced scaffolds. Results showed that the developed scaffolds presented hydrophilic properties after PEG and GelMA incorporation. Our developed scaffolds were thus able to significantly reduce gram-positive, negative, and MRSA bacteria. Furthermore, we performed a series of study for better mechanistic understanding of the scaffolds bactericidal activity through protein adsorption study and analysis of the reactive oxygen species (ROS) levels. In summary, we have demonstrated the design and generation of electrospun fibers with improved hydrophilicity and efficient bactericidal activity without the association of any antibiotics.
Connectivity-Informed Adaptive Regularization for Generalized Outcomes
Authors: Brzyski Damian , Karas Marta , Ances Beau , Dzemidzic Mario , Goni Joaquin , Randolph Timothy W , Harezlak Jaroslaw
Published: May 2018

One of the challenging problems in the brain imaging research is a principled incorporation of information from different imaging modalities in association studies. Frequently, data from each modality is analyzed separately using, for instance, dimensionality reduction techniques, which result in a loss of mutual information. We propose a novel regularization method, griPEER (generalized ridgified Partially Empirical Eigenvectors for Regression) to estimate the association between the brain structure features and a scalar outcome within the generalized linear regression framework. griPEER provides a principled approach to use external information from the structural brain connectivity to improve the regression coefficient estimation. Our proposal incorporates a penalty term, derived from the structural connectivity Laplacian matrix, in the penalized generalized linear regression. We address both theoretical and computational issues and show that our method is robust to the incomplete information about the structural brain connectivity. We also provide a significance testing procedure for performing inference on the estimated coefficients in this model. griPEER is evaluated in extensive simulation studies and it is applied in classification of the HIV+ and HIV- individuals.
C. elegans germ cells divide and differentiate along a folded epithelium
Authors: Seidel Hannah S. , Smith Tilmira A. , Evans Jessica K. , Stamper Jarred Q. , Mast Thomas G. , Kimble Judith
Published: May 2018

Knowing how stem cells and their progeny are positioned within their tissues is essential for understanding their regulation. One paradigm for stem cell regulation is the C. elegans germline, which is maintained by a pool of germline stem cells in the distal gonad, in a region known as the ‘progenitor zone’. The C. elegans germline is widely used as a stem cell model, but the cellular architecture of the progenitor zone has been unclear. Here we characterize this architecture by creating virtual 3D models of the progenitor zone in both sexes. We show that the progenitor zone in adult hermaphrodites is essentially a folded epithelium. The progenitor zone in males is not folded. Analysis of germ cell division shows that daughter cells are born side-by-side along the surface of the epithelium. Analysis of a key regulator driving differentiation, GLD-1, shows that germ cells in hermaphrodites differentiate along the path of the folded epithelium, with previously described “steps” in GLD-1 expression corresponding to germline folds. Our study provides a three-dimensional view of how C. elegans germ cells progress from stem cell to overt differentiation, with critical implications for regulators driving this transition.
Viral Taxonomy Derived From Evolutionary Genome Relationships
Authors: Dougan Tyler J. , Quake Stephen R.
Published: May 2018

We describe a new genome alignment-based model for classification of viruses based on evolutionary genetic relationships. This approach uses information theory and a physical model to determine the information shared by the genes in two genomes. Pairwise comparisons of genes from the viruses are created from alignments using NCBI BLAST, and their match scores are combined to produce a metric between genomes, which is in turn used to determine a global classification using the 5,817 viruses on RefSeq. In cases where there is no measurable alignment between any genes, the method falls back to a coarser measure of genome relationship: the mutual information of k-mer frequency. This results in a principled model which depends only on the genome sequence, which captures many interesting relationships between viral families, and which creates clusters which correlate well with both the Baltimore and ICTV classifications. The incremental computational cost of classifying a novel virus is low and therefore newly discovered viruses can be quickly identified and classified.
The iron-dependent repressor YtgR regulates the tryptophan salvage pathway through a bipartite mechanism of transcriptional control inChlamydia trachomatis
Authors: Pokorzynski Nick D. , Brinkworth Amanda J. , Carabeo Rey A.
Published: May 2018

During infection, pathogens are starved of essential nutrients such as iron and tryptophan by host immune effectors. Without conserved global stress response regulators, how the obligate intracellular bacteriumChlamydia trachomatisarrives at a physiologically similar “persistent” state in response to starvation of either nutrient remains unclear. Here, we report on the iron-dependent regulation of thetrpRBAtryptophan salvage pathway inC. trachomatis. Iron starvation specifically inducestrpBAexpression from a novel promoter element within an intergenic region flanked bytrpRandtrpB.YtgR, the only known iron-dependent regulator inChlamydia,can bind to thetrpRBAintergenic region upstream of the alternativetrpBApromoter to repress transcription. Simultaneously, YtgR binding promotes the termination of transcripts from the primary promoter upstream oftrpR.This is the first description of an iron-dependent mechanism regulating prokaryotic tryptophan biosynthesis that may indicate the existence of novel approaches to gene regulation and stress response inChlamydia.
Protein mismatches caused by reassortment influence functions of the reovirus capsid
Authors: Thete Deepti , Danthi Pranav
Published: May 2018

Following attachment to host receptors via σ1, reovirus particles are endocytosed and disassembled to generate infectious subvirion particles (ISVPs). ISVPs undergo conformational changes to form ISVP*, releasing σ1 and membrane-targeting peptides from the viral μ1 protein. ISVP* formation is required for delivery of the viral core into the cytoplasm for replication. We characterized the properties of T3DF/T3DCS1, a S1 gene monoreassortant between two laboratory isolates of prototype reovirus strain T3D: T3DFand T3DC. T3DF/T3DCS1 is poorly infectious. This deficiency is a consequence of inefficient encapsidation of S1-encoded σ1 on T3DF/T3DCS1 virions. Additionally, in comparison to T3DF, T3DF/T3DCS1 undergoes ISVP-to-ISVP* conversion more readily, revealing an unexpected role for σ1 in regulating ISVP* formation. The σ1 protein is held within turrets formed by the λ2 protein. To test if the altered properties of T3DF/T3DCS1 are due to a mismatch between σ1 and λ2 proteins from T3DFand T3DC, properties of T3DF/T3DCL2 and T3DF/T3DCS1L2, which express a T3DC-derived λ2, were compared. The presence of T3DCλ2 allowed more efficient σ1 incorporation, producing particles that exhibit T3DF-like infectivity. In comparison to T3DF, T3DF/T3DCL2 prematurely converts to ISVP* uncovering a role for λ2 in regulating ISVP* formation. Importantly, a virus with matching σ1 and λ2 displayed a more regulated conversion to ISVP* than either T3DF/T3DCS1 or T3DF/T3DCL2. In addition to identifying new regulators of ISVP* formation, our results highlight that protein mismatches produced by reassortment can alter virus assembly and thereby influence subsequent functions of the virus capsid.
Bacterial plasma membrane is the main cellular target of silver nanoparticles inEscherichia coliandPseudomonas aeruginosa
Authors: Bondarenko Olesja M , Sihtmäe Mariliis , Kuzmičiova Julia , Ragelienė Lina , Kahru Anne , Daugelavičius Rimantas
Published: May 2018

Silver nanoparticles (AgNP) are widely used in consumer products, mostly due to their excellent antimicrobial properties. One of the well-established antibacterial mechanisms of AgNP is their efficient contact with bacteria and dissolution on cell membranes. To our knowledge, the primary mechanism of cell wall damage and the event(s) initiating bactericidal action of AgNP are not yet elucidated.

In this study we used a combination of different assays to reveal the effect of AgNP on i) bacterial envelope in general, ii) outer membrane (OM) and iii) on plasma membrane (PM). We showed that bacterial PM was the main target of AgNP in Gram-negative bacteriaEscherichia coliandPseudomonas aeruginosa. AgNP depolarized bacterial PM, induced the leakage of the intracellular K+, inhibited respiration and caused the depletion of the intracellular ATP. In contrast, AgNP had no significant effect on the bacterial OM. Most of the adverse effects on bacterial envelope and PM occurred within the seconds and in the concentration range of 7-160 μM AgNP, depending on the bacteria and assay used, while irreversible inhibition of bacterial growth (minimal bactericidal concentration after 1-h exposure of bacteria to AgNP) occurred at 40 μM AgNP forP. aeruginosaand at 320 μM AgNP forE. coli.

Flow cytometry analysis showed that AgNP were binding toP. aeruginosabut not toE. colicells and were found inside theP. aeruginosacells. Taking into account that AgNP did not damage OM, we speculate that AgNP enteredP. aeruginosa viaspecific mechanism, e.g., transport through porins.
The multidrug resistance efflux pump MexCD-OprJ is a switcher of thePseudomonas aeruginosaquorum sensing response
Authors: Alcalde-Rico Manuel , Olivares-Pacheco Jorge , Alvarez-Ortega Carolina , Cámara Miguel , Martínez José Luis
Published: May 2018

Most antibiotic resistance genes acquired by human pathogens originate from environmental microorganisms. Therefore, understanding the additional functions of these genes, other than conferring antibiotic resistance, is relevant from an ecological point of view. We examined the effect that overexpression of the MexCD-OprJ multidrug efflux pump has in the physiology of the environmental opportunistic pathogenPseudomonas aeruginosa. Overexpression of this intrinsic resistance determinant shuts down theP. aeruginosaquorum sensing (QS) response. Impaired QS response is due to the extrusion of 4-hydroxy-2-heptylquinoline (HHQ), the precursor of thePseudomonasQuinolone Signal (PQS), leading to low PQS intracellular levels and reduced production of QS signal molecules. TheP. aeruginosaQS response induces the expression of hundreds of genes, which can be costly unless such activation becomes beneficial for the bacterial population. While it is known that the QS response is modulated by population density, information on additional signals/cues that may alert the cells about the benefits of mounting the response is still scarce. It is possible that MexCD-OprJ plays a role in this particular aspect; our results indicate that, upon overexpression, MexCD-OprJ can act as a switcher in the QS population response. If MexCD-OprJ alleviate the cost associated to trigger the QS response when un-needed, it could be possible that MexCD-OprJ overproducer strains might be eventually selected even in the absence of antibiotic selective pressure, acting as antibiotic resistant cheaters in heterogeneousP. aeruginosapopulations. This possibility may have potential implications for the treatment ofP. aeruginosachronic infections.
Ascitic bacterial composition is associated with clinical outcomes in cirrhotic patients with culture-negative and nonneutrocytic ascites
Authors: Chen Yanfei , Guo Jing , Shi Ding , Fang Daiqiong , Chen Chunlei , Li Lanjuan
Published: May 2018

Background: Ascites bacterial burden is associated with poor clinical outcomes in patients with end-stage liver disease. However, the impact of ascitic microbial composition on clinical course was still not clear. In this study, the ascitic microbiota composition of 100 cirrhotic patients with culture-negative and nonneutrocytic ascites were researched. Results: By characterizing the ascitic microbial composition, two distinct microbial clusters were observed, Cluster 1 (86 patients) and Cluster 2 (14 patients). Cluster 1 showed lower microbial richness than Cluster 2. At the phylum level, Cluster 1 had greater abundance of Bacteroidetes and Firmicutes, but less abundance of Proteobacteria and Actinobacteria than Cluster 2. At the family level, family Bacteroidales S24-7 group, Prevotellaceae, Lachnospiraceae, Lactobacillaceae, Rikenellaceae, and Vibrionaceae were found over-represented in Cluster 1. And family Acetobacteraceae, Erysipelotrichaceae, Rickettsiaceae, and Streptococcaceae were found enriched in Cluster 2. The levels of plasma cytokine IL-17A, IL-7, and PDGF-BB were found significantly higher in Cluster 1 than in Cluster 2. There were four OTUs closely correlated with plasma cytokines, which were OTU 140 and OTU 271 (both from Bacteroidales S24-7 group), OTU 68 (Veillonellaceae), and OTU 53 (Helicobacteraceae). Patients from Cluster 1 showed significant higher short-term mortality than patients from Cluster 2. Conclusion: Our study demonstrated that the microbial composition of culture-negative and nonneutrocytic ascites in cirrhotic patients is associated with short-term clinical outcomes. The results here offer a rational for the identification of patients with high risk, and provide references for selective use of prophylactic methods.
The RZZ complex facilitates Mad1 binding to Bub1 ensuring efficient checkpoint signaling
Authors: Zhang Gang , Kruse Thomas , Nilsson Jakob
Published: May 2018

Introductory paragraph

The recruitment of Mad1 to unattached kinetochores is essential for generating a “wait anaphase” signal during mitosis yet Mad1 localization is poorly understood in mammalian cells. In yeast the Bub1 checkpoint protein is the sole Mad1 receptor but in mammalian cells the Rod-ZW10-Zwilch (RZZ) complex is also required for Mad1 kinetochore localization. The exact function of the two mammalian Mad1 receptors and whether there is any interplay between them is unclear. Here we use CRISPR genome editing to generate RNAi sensitized human cell lines revealing a strong requirement for both Rod and Bub1 in checkpoint signaling. We show that the RZZ complex facilitates Mad1 binding to Bub1 and that a region of Bub1 overlapping the Mad1 binding site stimulates RZZ kinetochore recruitment. The requirement for RZZ in the checkpoint, but not Bub1, can be bypassed by tethering Mad1 to kinetochores or by increasing the strength of the Bub1-Mad1 interaction. Our data support a model in which the primary role of RZZ is to localize Mad1 at kinetochores allowing for the efficient checkpoint generating Mad1-Bub1 interaction. As such, the core checkpoint principle is conserved from yeast to man.
Improving the consistency of functional genomics screens using molecular features - a multi-omics, pan-cancer study
Authors: Wang Wenyu , Malyutina Alina , Pessia Alberto , Heckman Caroline A. , Tang Jing
Published: May 2018

Probing the genetic dependencies of cancer cells helps understand the tumor biology and identify potential drug targets. RNAi-based shRNA and CRISPR/Cas9-based sgRNA have been commonly utilized in functional genetic screens to identify essential genes affecting growth rates in cancer cell lines. However, questions remain whether the gene essentiality profiles determined using these two technologies are comparable. In the present study, we collected 42 cell lines representing a variety of 10 tissue types, which had been screened both by shRNA and CRISPR techniques. We observed poor consistency of the essentiality scores between the two screens for the majority of the cell lines. The consistency did not improve after correcting the off-target effects in the shRNA screening, suggesting a minimal impact of off-target effects. We considered a linear regression model where the shRNA essentiality score is the predictor and the CRISPR essentiality score is the response variable. We showed that by including molecular features such as mutation, gene expression and copy number variation as covariates, the predictability of the regression model greatly improved, suggesting that molecular features may provide critical information in explaining the discrepancy between the shRNA and CRISPR-based essentiality scores. We provided a Combined Essentiality Score (CES) based on the model prediction and showed that the CES greatly improved the consensus of common essential genes. Furthermore, the CES also identified novel essential genes that are specific to individual cell types. Taken together, we provided a systematic approach to define a more accurate gene essentiality profile by integrating functional screen data and molecular profiles.
How will it look like? Human posterior parietal and dorsal premotor cortex encode the visual properties of an upcoming action
Authors: Pilacinski Artur , Wallscheid Melanie , Lindner Axel
Published: May 2018

Behavioral studies show that motor actions are planned by adapting motor programs to produce desired visual consequences. Does this mean that the brain plans these visual consequences independent of the motor actions required to obtain them? Here we addressed this question by investigating planning-related fMRI activity in human posterior parietal (PPC) and dorsal premotor (PMd) cortex. By manipulating visual movement of a virtual end-effector controlled via button presses we could dissociate motor actions from their sensory outcome. A clear representation of the visual consequences was visible in both PPC and PMd activity during early planning stages. Our findings suggest that in both PPC and PMd action plans are initially represented on the basis of the desired sensory outcomes while later activity shifts towards representing motor programs.
Molecular epidemiology and drug resistance patterns ofMycobacterium tuberculosiscomplex isolates from university students and the local community in Eastern Ethiopia
Authors: Mekonnen Abiyu , Merker Matthias , Collins Jeffrey M , Addise Desalegn , Aseffa Abraham , Petros Beyene , Ameni Gobena , Niemann Stefan
Published: May 2018

Background

Previous studies suggest the burden of pulmonary tuberculosis (PTB) in Ethiopia may be greater in university students relative to the overall population. However, little is known about the transmission dynamics of PTB among students and members of the communities surrounding university campuses in Eastern Ethiopia.

Methods

A cross sectional study was conducted in Eastern Ethiopia among culture-confirmed PTB cases from university students (n=36) and community members diagnosed at one of four hospitals (n=152) serving the surrounding area. Drug susceptibility testing (DST) was performed on Mycobacterium Tuberculosis Complex (MTBC) isolates using BD Bactec MGIT 960 and molecular genotyping was performed using spoligotyping and 24-loci MIRU-VNTR. MTBC strains with Identical genotyping patterns were assigned to molecular clusters as surrogate marker for recent transmission and further contact tracing was initiated among clustered patients.

Results

Among all study participants, four MTBC lineages and 11 sub-lineages were identified, with Ethiopia_3 being most common sub-lineage (29.4%) and associated with strain clustering (P= 0.016). We identified 13 (8.1%) strains phylogenetically related to the known Ethiopian sub-lineages with a distinct Spoligotyping patterns and designated as Ethiopia_4. The clustering rate of MTB strains was 52.9% for university students and 66.7% for community members with a Recent Transmission Index (RTI) of 17.6% and 48.4%, respectively. Female gender, urban residence, and new TB cases were significantly associated with strain clustering (p<0.05). Forty-eight (30%) of the study participants were resistant to one or more first line anti TB drugs, three patients were classified as multidrug resistant (MDR), defined by isoniazid and rifampicin resistance.

Conclusion

We found evidence of significant PTB cases clustering and recent transmission among Ethiopian university students and the local community in eastern Ethiopia; with Ethiopia_3 being the predominant circulating sub-lineage. A country wide comprehensive molecular surveillance and drug resistance profiling of MTBC strains and Implementation of TB control programs within universities and the surrounding community should be considered to decrease TB transmission.
Regulation of Harvester Ant Foraging as a Closed-Loop Excitable System
Authors: Pagliara Renato , Gordon Deborah M. , Leonard Naomi Ehrich
Published: May 2018

Ant colonies regulate activity in response to changing conditions without using centralized control. Harvester ant colonies forage in the desert for seeds, and their regulation of foraging manages a tradeoff between spending and obtaining water. Foragers lose water while outside in the dry air, but the colony obtains water by metabolizing the fats in the seeds they eat. Previous work shows that the rate at which an outgoing forager leaves the nest depends on its recent experience of brief antennal contact with returning foragers that carry a seed. We examine how this process can yield foraging rates that are robust to uncertainty and responsive to temperature and humidity across minutes to hour-long timescales. To explore possible mechanisms, we develop a low-dimensional analytical model with a small number of parameters that captures observed foraging behavior. The model uses excitability dynamics to represent response to interactions inside the nest and a random delay distribution to represent foraging time outside the nest. We show how feedback of outgoing foragers returning to the nest stabilizes the incoming and outgoing foraging rates to a common value determined by the “volatility” of available foragers. The model exhibits a critical volatility above which there is sustained foraging at a constant rate and below which there is cessation of foraging. To explain how the foraging rates of colonies adjust to temperature and humidity, we propose a mechanism that relies on foragers modifying their volatility after they leave the nest and get exposed to the environment. Our study highlights the importance of feedback in the regulation of foraging activity and points to modulation of volatility as a key to explaining differences in foraging activity in response to conditions and across colonies. Our results present opportunities for generalization to other contexts and systems with excitability and feedback across multiple timescales.

Author Summary

We investigate the collective behavior that allows colonies of desert harvester ants to regulate foraging activity in response to environmental conditions. We develop an analytical model connecting three processes: 1) the interactions between foragers returning to the nest and available foragers waiting inside the nest, 2) the effect of these interactions on the likelihood of available foragers to leave the nest to forage, and 3) the return of foragers to the nest after finding seeds. We propose a mechanism in which available foragers modify their response to interactions after their first exposure to the environment. We show how this leads to colony foraging rates that adjust to environmental conditions over time scales from minutes to hours. Our model may prove useful for studying resilience in other classes of systems with excitatory dynamics.
A proteome-wide screen reveals widespread roles for the phosphatase Cdc14 in theCandida albicanscell cycle
Authors: Kaneva Iliyana , Sudbery Ian , Dickman Mark J. , Sudbery Peter E.
Published: May 2018

The chromosome complement of the human fungal pathogenCandida albicansis unusually unstable, suggesting that process of nuclear division is error prone. The Cdc14 phosphatase plays a key role in organising the intricate choreography of mitosis and cell division. In order to understand the role of Cdc14 inC. albicanswe used quantitative proteomics to identify proteins that physically interact withCaCdc14. To distinguish genuine Cdc14-interactors from proteins that bound non-specifically bound to the affinity matrix we used an orthogonal approach of a substrate trapping mutant combined with mass spectrometry analysis using stable isotope labelling in cell culture (SILAC). The results identified 126 proteins that interact with Cdc14 of which 80% are novel. In this set, 53 proteins play known roles in the cell regulating the attachment of the mitotic spindle to kinetochores, mitotic exit, cytokinesis, licensing of DNA replication by re-activating pre-replication complexes, and DNA repair. Five Cdc14-interacting proteins with previously unknown functions localized to the Spindle Pole Bodies (SPBs). Intriguingly, 83 proteins that only interacted with Cdc14 in yeast were significantly enriched in components of the ergosterol biosynthesis pathway targeted by azole anti-fungal drugs. Thus we have greatly expanded the set of known substrates of this key cell cycle regulator inC. albicans.

Author summary

Candida albicansis an important fungal pathogen causing life-threatening bloodstream infections in humans, as well as debilitating mucosal infections. Here we used Mass Spectroscopy to identify proteins that physically interacted with an enzyme called Cdc14. By removing phosphate groups from proteins, and thus regulating their function, this enzyme orchestrates the intricate molecular mechanisms of nuclear division to ensure that each daughter cell receives a full complement of chromosomes.C. albicansis unusual in the way that changes in chromosome number and composition are much more common than in other organisms. This suggests that the process of nuclear division may be more error prone inC. albicans. Our work identified 126 proteins that physically associate with Cdc14 and are thus potential substrates, including 53 proteins that we know are involved in many cell cycle processes that are necessary for nuclear and cell division. Thus, we have laid the ground work to study how changes in chromosomal composition may arise due to errors in nuclear division in this important pathogen. Unexpectedly, we found that Cdc14 may also act on proteins involved in the synthesis of ergosterol, a key lipid in the cell membrane. Azoles, a major class of antifungal drugs, inhibit the synthesis of ergosterol, so Cdc14 may also be involved in the action of azoles and thus one possible way in which drug resistance arises.
Par3 regulates Rac1 signaling and microtubule organization during planar polarization of auditory hair cells
Authors: Malt Andre Landin , Dailey Zachary , Holbrook-rasmussen Julia , Zheng Yuqiong , Du Quansheng , Lu Xiaowei
Published: May 2018

In the inner ear sensory epithelia, hair bundles atop sensory hair cells are mechanosensory apparati with planar polarized structure and orientation. This is established during development by the concerted action of tissue-level planar cell polarity (PCP) signaling and a hair cell-intrinsic, microtubule-mediated machinery. However, how various polarity signals are integrated during hair bundle morphogenesis is poorly understood. Here, we show that the conserved cell polarity protein Par3 plays a key role in planar polarization of hair cells. Par3 deletion in the inner ear resulted in defects in cochlear length, hair bundle orientation and kinocilium positioning. During PCP establishment, Par3 promotes localized Rac-Pak signaling through an interaction with Tiam1. Par3 regulates microtubule dynamics and organization, which is crucial for basal body positioning. Moreover, there is reciprocal regulation of Par3 and the core PCP molecule Vangl2. Thus, we conclude that Par3 is an effector and integrator of cell-intrinsic and tissue-level PCP signaling.

One sentence summary

Par3 regulates planar polarity of auditory hair cells
Bit-parallel sequence-to-graph alignment
Authors: Rautiainen Mikko , Mäkinen Veli , Marschall Tobias
Published: May 2018

Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction, and variant calling with respect to a variation graph. Here, we generalize two linear sequence-to-sequence algorithms to graphs: the Shift-And algorithm for exact matching and Myers’ bitvector algorithm for semi-global alignment. These linear algorithms are both based on processing w sequence characters with a constant number of operations, where w is the word size of the machine (commonly 64), and achieve a speedup of w over naive algorithms. Our bitvector-based graph alignment algorithm reaches a worst case runtime of for acyclic graphs and O(V + mE log w) for arbitrary cyclic graphs. We apply it to four different types of graphs and observe a speedup between 3.1-fold and 10.1-fold compared to previous algorithms.
Development and decline of the hippocampal long-axis specialization and differentiation during encoding and retrieval of episodic memories
Authors: Langnes Espen , Vidal-Piñeiro Didac , Sneve Markus H. , Amlien Inge K. , Walhovd Kristine B , Fjell Anders M
Published: May 2018

Change in hippocampal function is a major factor in lifespan development and decline of episodic memory. Evidence indicates a long-axis specialization where anterior hippocampus is more engaged during encoding and posterior during retrieval. We tested the lifespan trajectory of hippocampal long-axis episodic memory-related activity and functional connectivity (FC). 496 participants (6.8-80.8 years) were scanned with functional MRI while encoding and retrieving associative memories. We found clear evidence for a long-axis encoding-retrieval specialization. These long-axis effects declined linearly during development and aging, eventually vanishing in the older adults. This was mainly driven by age effects on retrieval. Retrieval was associated with gradually lower activity from childhood to adulthood, followed by positive age-relationships until 70 years. Interestingly, this pattern characterized task engagement regardless of memory success or failure. Children engaged posterior hippocampus more than anterior, while anterior hippocampus was more activated relative to posterior already in teenagers. Intra-hippocampal connectivity increased during task, and this increase declined with age. In sum, the results suggest that hippocampal long-axis differentiation and communication during episodic memory tasks develop rapidly during childhood and adolescence, are markedly different in older compared to younger adults, and are related to task engagement, not the successful completion of the task.
Highly efficient homology-directed repair using Cas9 protein in Ceratitis capitata
Authors: Aumann Roswitha A. , Schetelig Marc F. , Häecker Irina
Published: May 2018

Background

The Mediterranean fruit fly Ceratitis capitata is a highly polyphagous and invasive insect pest, causing vast economical damage in horticultural systems. A currently used control strategy is the sterile insect technique (SIT) that reduces pest populations through infertile matings with mass-released, sterilized insects. Transgenic approaches hold great promise to improve key aspects of a successful SIT program. However, there is strict or even prohibitive legislation regarding the release of genetically modified organisms (GMO), while novel CRISPR-Cas technologies might allow to develop genetically enhanced strains for SIT programs classified as non-transgenic.

Results

Here we describe highly efficient homology-directed repair genome editing in C. capitata by injecting pre-assembled CRISPR-Cas9 ribonucleoprotein complexes using different guide RNAs and a short single-stranded oligodeoxynucleotide donor to convert an enhanced green fluorescent protein in C. capitata into a blue fluorescent protein. Six out of seven fertile and individually backcrossed G0 individuals generated 57-90% knock-in rate within their total offspring and 70-96% knock-in rate within their phenotypically mutant offspring.

Conclusion

Considering the possibility that CRISPR-induced alterations in organisms could be classified as a non-GMO in the US and Europe, our approach to homology-directed repair genome editing can be used to genetically improve strains for pest control systems like SIT without the need to struggle with GMO directives. Furthermore, it can be used to recreate and use mutations, found in classical mutagenesis screens, for pest control systems.