bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering
Authors: Golub Maksym , Guillon Virginia , Gotthard Guillaume , Zeller Dominik , Martinez Nicolas , Seydel Tilo , Koza Michael M. , Lafaye Céline , Clavel Damien , von Stetten David , Royant Antoine , Peters Judith
Published: March 2019

Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.
Activation of cell migration via morphological changes in focal adhesions depends on shear stress in MYCN-amplified neuroblastoma cells
Authors: Hiraiwa Takumi , Yamada Takahiro G. , Miki Norihisa , Funahashi Akira , Hiroi Noriko
Published: March 2019

Neuroblastoma is the most common solid tumour of childhood, and it metastasizes to distant organs. However, the mechanism of metastasis, which generally depends on the cell motility of the neuroblastoma, remains unclear. In many solid tumours, it has been reported that shear stress promotes metastasis. Here, we investigated the relationship between shear stress and cell motility in the MYCN-amplified human neuroblastoma cell line IMR32, using a microfluidic device. We confirmed that most of the cells migrated downstream, and cell motility increased dramatically when the cells were exposed to a shear stress of 0.4 Pa, equivalent to that expected
in vivo
. We observed that the morphological features of focal adhesion were changed under a shear stress of 0.4 Pa. We also investigated the relationship between malignancy and the motility of IMR32 cells under shear stress. Decreasing the expression of MYCN in IMR32 cells via siRNA transfection inhibited cell motility by a shear stress of 0.4 Pa. These results suggest that MYCN-amplified neuroblastoma cells under high shear stress migrate to distant organs due to high cell motility, allowing cell migration to lymphatic vessels and venules.
Phase transitions of antiferromagnetic Ising spins on the zigzag surface of an asymmetrical Husimi lattice
Authors: Huang Ran , Gujrati Purushottam D.
Published: March 2019

An asymmetrical two-dimensional Ising model with a zigzag surface, created by diagonally cutting a regular square lattice, has been developed to investigate the thermodynamics and phase transitions on surface by the methodology of recursive lattice, which we have previously applied to study polymers near a surface. The model retains the advantages of simple formulation and exact calculation of the conventional Bethe-like lattices. An antiferromagnetic Ising model is solved on the surface of this lattice to evaluate thermal properties such as free energy, energy density and entropy, from which we have successfully identified a first-order order–disorder transition other than the spontaneous magnetization, and a secondary transition on the supercooled state indicated by the Kauzmann paradox.
Rapid migrations and dynamics of citizen response
Authors: Sahasranaman Anand , Jeldtoft Jensen Henrik
Published: March 2019

One of the pressing social concerns of our time is the need for meaningful responses to migrants and refugees fleeing conflict and environmental catastrophe. We develop a computational model to model the influx of migrants into a city, varying the rates of entry, and find a nonlinear inverse relationship between the fraction of resident population whose tolerance levels are breached due to migrant entry and the average time to such tolerance breach. Essentially, beyond a certain rate of migrant entry, there is a rapid rise in the fraction of residents whose tolerances are breached, even as the average time to breach decreases. We also model an analytical approximation of the computational model and find qualitative correspondence in the observed phenomenology, with caveats. The sharp increase in the fraction of residents with tolerance breach could potentially underpin the intensity of resident responses to bursts of migrant entry into their cities. Given this nonlinear relationship, it is perhaps essential that responses to refugee situations are multi-country or global efforts so that sharp spikes of refugee migrations are equitably distributed among nations, potentially enabling all participating countries to avoid impacting resident tolerances beyond limits that are socially sustainable.
Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs
Authors: Gutarra Susana , Moon Benjamin C. , Rahman Imran A. , Palmer Colin , Lautenschlager Stephan , Brimacombe Alison J. , Benton Michael J.
Published: March 2019

Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160 Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing the first quantitative evaluation of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep ‘torpedo-shaped’ bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics, and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence.
The possible role of ant larvae in the defence against social parasites
Authors: Pulliainen Unni , Helanterä Heikki , Sundström Liselotte , Schultner Eva
Published: March 2019

Temporary social parasite ant queens initiate new colonies by entering colonies of host species, where they begin laying eggs. As the resident queen can be killed during this process, host colonies may lose their entire future reproductive output. Selection thus favours the evolution of defence mechanisms, before and after parasite intrusion. Most studies on social parasites focus on host worker discrimination of parasite queens and their offspring. However, ant larvae can also influence brood composition by consuming eggs. This raises the question whether host larvae can aid in preventing colony takeover by consuming eggs laid by parasite queens. To test whether larvae could play a role in anti-parasite defence, we compared the rates at which larvae of a common host species,Formica fusca, consumed eggs laid by social parasite, non-parasite, nest-mate, or conspecific non-nest-mate queens. Larvae consumed social parasite eggs more than eggs laid by a heterospecific non-parasite queen, irrespective of the chemical distance between the egg cuticular profiles. Also, larvae consumed eggs laid by conspecific non-nest-mate queens more than those laid by nest-mate queens. Our study suggests that larvae may act as players in colony defence against social parasitism, and that social parasitism is a key factor shaping discrimination behaviour in ants.
Non-Invasive Assays of Cochlear Synaptopathy -- Candidates and Considerations
Authors: Bharadwaj Hari M. , Mai Alexandra R. , Simpson Jennifer M. , Choi Inyong , Heinz Michael G. , Shinn-Cunningham Barbara G.
Published: March 2019

Studies in multiple species, including in post-mortem human tissue, have shown that normal aging and/or acoustic overexposure can lead to a significant loss of afferent synapses innervating the cochlea. Hypothetically, this cochlear synaptopathy can lead to perceptual deficits in challenging environments and can contribute to central neural effects such as tinnitus. However, because cochlear synaptopathy can occur without any measurable changes in audiometric thresholds, synaptopathy can remain hidden from standard clinical diagnostics. To understand the perceptual sequelae of synaptopathy and to evaluate the efficacy of emerging therapies, sensitive and specific non-invasive measures at the individual patient level need to be established. Pioneering experiments in specific mice strains have helped identify many candidate assays. These include auditory brainstem responses, the middle-ear muscle reflex, envelope-following responses, and extended high-frequency audiograms. Unfortunately, because these non-invasive measures can be also affected by extraneous factors other than synaptopathy, their application and interpretation in humans is not straightforward. Here, we systematically examine six extraneous factors through a series of interrelated human experiments aimed at understanding their effects. Using strategies that may help mitigate the effects of such extraneous factors, we then show that these suprathreshold physiological assays exhibit across-individual correlations with each other indicative of contributions from a common physiological source consistent with cochlear synaptopathy. Finally, we discuss the application of these assays to two key outstanding questions, and discuss some barriers that still remain.
A reformulation of the selection ratio shed light on resource selection functions and leads to a unified framework for habitat selection studies
Authors: Chamaillé-Jammes Simon
Published: March 2019

The selection ratio (SR), i.e. the ratio of proportional use of a habitat over proportional availability of this habitat, has for long been the standard metric of habitat selection analyses. It is easy to compute and directly estimates disproportionate use. Its apparent restriction to habitat selection analyses using categorical predictors led to the development of the resource selection functions (RSF) approach, which has now become the norm.

The RSF approach has however led to debates and confusion. For instance, what functional form can be used remains debated, and the concept of relative probability of selection is often misunderstood.

I propose a reformulation of the SR demonstrating that it can be estimated in a regression context, and thus even with continuous predictors. This reformulation suggests that RSF can be seen as an intermediate step in the calculation of SR. This reformulation also clarifies some longstanding debates about RSF and data-selection/fitting practices.

I further suggest that SR estimates the strength of habitat selection, but that the contribution of selection in determining use, which should be more directly linked to fitness than selection per se, should be estimated by another metric, the selection effect on use (SE). SE could be estimated simply as thedifferencebetween proportional use and proportional availability, and can be computed from SR and a density estimation of availability.

I conduct a habitat selection analysis of plains zebras to demonstrate the added-value of going beyond RSF scores and using SR estimated in a regression context, and of combining SR and SE.

Overall, I highlight the inter-relation between various metrics used to study habitat selection (i.e., SR, other selection indices, RSF scores, marginality). I conclude by proposing that SR and SE can be the unifying metrics of habitat selection, as together they offer a comprehensive view on the strength of habitat selection and its effect on habitat use.
The Tangent copy-number inference pipeline for cancer genome analyses
Authors: Tabak Barbara , Saksena Gordon , Oh Coyin , Gao Galen F. , Meyers Barbara Hill , Reich Michael , Schumacher Steven E. , Westlake Lindsay C. , Berger Ashton C. , Carter Scott L.b , Cherniack Andrew D. , Meyerson Matthew , Beroukhim Rameen , Getz Gad
Published: March 2019

Motivation

Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas (TCGA), the Broad Institute Genome Characterization Center developed the Tangent copy-number inference pipeline to generate copy-number profiles using single-nucleotide polymorphism (SNP) array and whole-exome sequencing (WES) data from over 10,000 pairs of tumors and matched normal samples. Here, we describe the Tangent pipeline, which begins with DNA sequencing data in the form of .bam files or raw SNP array probe-level intensity data, and ends with segmented copy-number calls to facilitate the identification of novel genes potentially targeted by SCNAs. We also describe a modification of Tangent, Pseudo-Tangent, which enables denoising through comparisons between tumor profiles when few normal samples are available.

Results

Tangent Normalization offers substantial signal-to-noise ratio (SNR) improvements compared to conventional normalization methods in both SNP array and WES analyses. The improvement in SNRs is achieved primarily through noise reduction with minimal effect on signal. Pseudo-Tangent also reduces noise when few normal samples are available. Tangent and Pseudo-Tangent are broadly applicable and enable more accurate inference of SCNAs from DNA sequencing and array data.

Availability and Implementation

Tangent is available at https://github.com/coyin/tangent and as a Docker image (https://hub.docker.com/r/coyin/tangent). Tangent is also the normalization method for the Copy Number pipeline in Genome Analysis Toolkit 4 (GATK4).

Contact

matthew_meyerson@dfci.harvard.edu, rameen@broadinstitute.org, gadgetz@broadinstitute.org
Proteomic profiling of the oncogenic septin 9 reveals isoform-specific interactions in breast cancer cells
Authors: Devlin Louis , Perkins George , Bowen Jonathan R. , Montagna Cristina , Spiliotis Elias T.
Published: March 2019

Septins are a family of multimeric GTP-binding proteins, which are abnormally expressed in cancer. Septin 9(SEPT9)is an essential and ubiquitously expressed septin with multiple isoforms, which have differential expression patterns and effects in breast cancer cells. It is unknown, however, if SEPT9 isoforms associate with different molecular networks and functions. Here, we performed a proteomic screen in MCF-7 breast cancer cells to identify the interactome of GFP-SEPT9 isoforms 1, 4 and 5, which vary significantly in their N-terminal extensions. While all three isoforms associated with SEPT2 and SEPT7, the truncated SEPT9_i4 and SEPT9_i5 interacted with septins of the SEPT6 group more promiscuously than SEPT9_i1, which bound predominately SEPT8. Spatial mapping and functional clustering of non-septin partners showed isoform-specific differences in interactions with proteins of distinct subcellular organelles (e.g., nuclei, centrosomes, cilia) and functions such as cell signaling and ubiquitination. Notably, the interactome of the full length SEPT9_i1 was more enriched in cytoskeletal regulators, while the truncated SEPT9_i4 and SEPT9_i5 exhibited preferential and isoform-specific interactions with nuclear, signaling and ubiquitinating proteins. These data provide evidence for isoform-specific interactions, which arise from truncations in the N-terminal extensions of SEPT9, and point to novel roles in the pathogenesis of breast cancer.
Sex and age don’t matter but breed type does - Factors influencing eye wrinkle expression in horses
Authors: Schanz Lisa , Krueger Konstanze , Hintze Sara
Published: March 2019

Identifying valid indicators to assess animals’ emotional states is a critical objective of animal welfare science. In horses, eye wrinkles caused by the contraction of the inner eyebrow raiser have been shown to be affected by pain and other emotional states. Whether individual characteristics of a horse systematically affect eye wrinkle expression has not yet been studied. Therefore, the aim of this study was to assess how age, sex, breed type, body condition and coat colour affect the expression and/or the assessment of eye wrinkles in horses. To this end, we adapted the eye wrinkle assessment scale from Hintze et al. (2016) and assessed eye wrinkle expression on pictures taken from the left and the right eye of 181 horses in a presumably neutral situation, using five outcome measures: a qualitative first impression reflecting how worried the horse looks, the extent to which the eyebrow is raised, the number of wrinkles, their markedness and the angle between a line through the eyeball and the topmost wrinkle. All measures could be assessed highly reliable with respect to intra- and inter-observer agreement. Breed type affected the width of the angle (F2, 114= 8.20, p < 0.001), with thoroughbreds having the narrowest angle (M= 23.80,SD= 1.60), followed by warmbloods (M= 28.00,SD= 0.60), and coldbloods (M= 31.00,SD= 0.90). None of the other factors affected any of the outcome measures, and eye wrinkle expression did not differ between the left and the right eye area (all p-values > 0.05). Consequently, horses’ characteristics age, sex and coat colour did not systematically affect eye wrinkle expression, whereas ‘breed type’ explained some variation in ‘angle’; how much eye wrinkle expression is affected by emotion or perhaps mood needs further investigation and validation.
Looking forward does not mean forgetting about the past: ERP evidence for the interplay of predictive coding and interference during language processing
Authors: Schoknecht Pia , Roehm Dietmar , Schlesewsky Matthias , Bornkessel-Schlesewsky Ina
Published: March 2019

Interference and prediction have independently been identified as crucial influencing factors during language processing. However, their interaction remains severely underinvestigated. Furthermore, the neurobiological basis of cue-based retrieval and retrieval interference during language processing remains insufficiently understood. Here, we present an ERP experiment that systematically examined the interaction of interference and prediction during language processing. We used the neurobiologically well-established predictive coding framework and insights regarding the neuronal mechanisms of memory for the theoretical framing of our study. German sentence pairs were presented word-by-word, with an article in the second sentence constituting the critical word. We analyzed mean single trial EEG activity in the N400 time window and found an interaction between interference and prediction (measured by cloze probability). Under high predictability, no interference effects were observable. Under the predictive coding account, highly predictable input is totally explained by top-down activity. Therefore the input induces no retrieval operations which could be influenced by interference. In contrast, under low predictability, conditions with high interference or with a close, low-interference distractor showed a broadly distributed negativity compared to conditions with a distant, low-interference distractor. We interpret this result as showing that when unpredicted input induces model updating, this may elicit memory retrieval including the evaluation of distractor items, thus leading to interference effects. We conclude that interference should be included in predictive coding-based accounts of language because prediction errors can trigger retrieval operations and, therefore, induce interference.
Stalk Lodging: A Portable Device for Phenotyping Stalk Bending Strength of Maize and Sorghum
Authors: Cook Douglas D. , de la Chapelle Witold , Lin Ting-Che , Lee Shien Yang , Sun Wenhuan , Robertson Daniel J
Published: March 2019

Background

Stalk lodging (breakage of plant stems prior to harvest) is a major problem for both farmers and plant breeders. A limiting factor in addressing this problem is the lack of a reliable method for phenotyping stalk strength. Previous methods of phenotyping stalk strength induce failure patterns different from those observed in natural lodging events. This paper describes a new device for field-based phenotyping of stalk strength called “DARLING” (Device for Assessing Resistance to Lodging IN Grains). The DARLING apparatus consists of a vertical arm which is connected to a horizontal footplate by a hinge. The operator places the device next to a stalk, aligns the stalk with a force sensor, steps on the footplate, and then pushes the vertical arm forward until the stalk breaks. Force and rotation are continuously recorded during the test and these quantities are used to calculate two quantities: stalk flexural stiffness and stalk bending strength.

Results

Field testing of DARLING was performed at multiple sites. Validation was based upon three factors. First, the device induces the characteristic “crease” or Brazier buckling failure patterns observed in naturally lodged stalks. Second, in agreement with prior research, flexural stiffness values attained using the DARLING apparatus are strongly correlated with bending strength measurements. Finally, a paired specimen experimental design was used to determine that the flexural data obtained with DARLING is in agreement with laboratory-based flexural testing results of the same specimens. DARLING was also deployed in the field to assess phenotyping throughput (# of stalks phenotyped per hour). Over approximately 5000 tests, the average testing rate was found to be 210 stalks/hour.

Conclusions

The DARLING apparatus provides a quantitative assessment of stalk strength in a field setting. It induces the same failure patterns observed in natural lodging events. DARLING can also be used to perform non-destructive flexural tests. This new technology has many applications, including breeding, genetic studies on stalk strength, longitudinal studies of stalk flexural stiffness, and risk assessment of lodging propensity.
Field trial of a probiotic bacteria and a chemical, chitosan, to protect bats from white-nose syndrome
Authors: Hoyt Joseph R. , Langwig Kate E. , White J. Paul , Kaarakka Heather M. , Redell Jennifer A. , Parise Katy L. , Frick Winifred F. , Foster Jeffrey T. , Kilpatrick A. Marm
Published: March 2019

Tools for reducing wildlife disease impacts are needed to conserve biodiversity. White-nose syndrome (WNS), caused by the fungusPseudogymnoascus destructans, has caused widespread declines in North American bat populations and threatens several species with extinction. Few tools exist for managers to reduce WNS impacts. We tested the efficacy of two treatments, a probiotic bacterium,Pseudomonas fluorescens, and a chemical, chitosan, to reduce impacts of WNS in two simultaneous experiments conducted with caged and free-flyingMyotis lucifugusbats at a mine in Wisconsin, USA. In the free-flying experiment, treatment withP. fluorescensincreased apparent overwinter survival five-fold compared to the control group (from 8.4% to 46.2%) by delaying emergence of bats from the site by 30 days. Apparent overwinter survival for free-flying chitosan-treated bats was 18.0%, which did not differ significantly from control bats. In the cage experiment, chitosan-treated bats had significantly higher survival until release on March 8 (53%) than control andP. fluorescens-treated bats (both 27%). However, these differences were likely due to within-cage disturbance and not reduced WNS impacts, because chitosan-treated bats actually had significantly higher UV-fluorescence (a measure of disease severity), and body mass, not infection intensity, predicted mortality. Further, few of the bats released from the cage experiment were detected emerging from the mine, indicating that the survival estimates at the time of release did not carryover to overwinter survival. These results suggest that treatment of bats may reduce WNS mortality, but additional measures are needed to prevent declines.
Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains
Authors: Dong Pengfei , Tu Xiaoyu , Li Haoxuan , Zhang Jianhua , Grierson Donald , Li Pinghua , Zhong Silin
Published: March 2019

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation. Usingin situHi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We have also profiled their DNA methylation, open chromatin, histone modification and gene expression to investigate whether chromatin structural dynamics are associated with epigenome features changes. We found that plant global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic that is associated with differential gene expression. Plant domains are largely stable across tissues, while rare domain border changes are often associated with gene activation. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian cells. When comparing synteny gene pairs, we found those maize genes involved in gene island chromatin loops have shorter genomic distances in smaller genomes without gene island loops such as rice and foxtail millet, suggesting that they have conserved functions. Our study revealed that the 3D configuration of the plant chromatin is also complex and dynamic with unique features that need to be further examined.
Solving High-Resolution Forward Problems for Extra- and Intracranial Neurophysiological Recordings Using Boundary Element Fast Multipole Method
Authors: Makarov Sergey N , Hämäläinen Matti , Okada Yoshio , Noetscher Gregory M , Ahveninen Jyrki , Nummenmaa Aapo
Published: March 2019

We present a general numerical approach for solving the forward problem in high-resolution. This approach can be employed in the analysis of noninvasive electroencephalography (EEG) and magnetoencephalography (MEG) as well as invasive electrocorticography (ECoG), stereoencephalography (sEEG), and local field potential (LFP) recordings. The underlying algorithm is our recently developed boundary element fast multipole method (BEM-FMM) that simulates anatomically realistic head models with unprecedented numerical accuracy and speed. This is achieved by utilizing the adjoint double layer formulation and zeroth-order basis functions in conjunction with the FMM acceleration. We present the mathematical formalism in detail and validate the method by applying it to the canonical multilayer sphere problem. The numerical error of BEM-FMM is 2-10 times lower while the computational speed is 1.5–20 times faster than those of the standard first-order FEM. We present four practical case studies: (i) evaluation of the effect of a detailed head model on the accuracy of EEG/MEG forward solution; (ii) demonstration of the ability to accurately calculate the electric potential and the magnetic field in the immediate vicinity of the sources and conductivity boundaries; (iii) computation of the field of a spatially extended cortical equivalent dipole layer; and (iv) taking into account the effect a fontanel for infant EEG source modeling and comparison of the results with a commercially available FEM. In all cases, BEM-FMM provided versatile, fast, and accurate high-resolution modeling of the electromagnetic field and has the potential of becoming a standard tool for modeling both extracranial and intracranial electrophysiological signals.
Identification of novel glycosylation events on human serum-derived Factor IX
Authors: Pegg Cassandra L. , Zacchi Lucia F. , Recinos Dinora Roche , Howard Christopher B. , Schulz Benjamin L.
Published: March 2019

Human Factor IX is a highly post-translationally modified protein that is an important clotting factor in the blood coagulation cascade. Functional deficiencies in Factor IX result in the bleeding disorder haemophilia B, which is treated with plasma-derived or recombinant Factor IX concentrates. Here, we investigated the post-translational modifications of human serum-derived Factor IX and report previously undescribedO-linked monosaccharide compositions at serine 141 and a novel site of glycosylation. At serine 141 we observed two monosaccharide compositions, with HexNAc1Hex1NeuAc2dominant and a low level of HexNAc1Hex1NeuAc1. ThisO-linked site lies N-terminal to the first cleavage site for the activation peptide, an important region of the protein that is removed to activate Factor IX. The novel site is anN-linked site in the serine protease domain with low occupancy in a non-canonical consensus motif at asparagine 258, observed with a HexNAc4Hex5NeuAc2monosaccharide composition attached. This is the first reported instance of a site of modification in the serine protease domain. The description of these glycosylation events provides a basis for future functional studies and contributes to structural characterisation of native Factor IX for the production of effective therapeutic biosimilars and biobetters.
Thiostrepton hijacks pyoverdine receptors to inhibit growth ofPseudomonas aeruginosa
Authors: Ranieri Michael R. , Chan Derek C. K. , Yaeger Luke , Rudolph Madeleine , Karabelas-Pittman Sawyer , Abdo Hamdi , Chee Jessica , Harvey Hanjeong , Nguyen Uyen , Burrows Lori L.
Published: March 2019

Pseudomonas aeruginosais a biofilm-forming opportunistic pathogen and intrinsically resistant to many antibiotics. In a high-throughput screen for molecules that modulate biofilm formation, we discovered that the thiopeptide antibiotic, thiostrepton (TS) - considered inactive against Gram-negative bacteria - stimulatedP. aeruginosabiofilm formation in a dose-dependent manner. This phenotype is characteristic of exposure to antimicrobial compounds at sub-inhibitory concentrations, suggesting that TS was active againstP. aeruginosa. Supporting this observation, TS inhibited growth of a panel of 96 multidrug-resistant (MDR)P. aeruginosaclinical isolates at low micromolar concentrations. TS also had activity againstAcinetobacter baumanniiclinical isolates. Expression of Tsr - a 23S rRNA-modifying methyltransferase - in trans conferred TS resistance, confirming that the drug acted via its canonical mode of action, inhibition of ribosome function. Deletion of oligopeptide permease systems used by other peptide antibiotics for uptake failed confer TS resistance. TS susceptibility was inversely proportional to iron availability, suggesting that TS exploits uptake pathways whose expression is increased under iron starvation. Consistent with this finding, TS activity againstP. aeruginosaandA. baumanniiwas potentiated by FDA-approved iron chelators deferiprone and deferasirox. Screening ofP. aeruginosamutants for TS resistance revealed that it exploits pyoverdine receptors FpvA and FpvB to cross the outer membrane. Our data show that the biofilm stimulation phenotype can reveal cryptic sub-inhibitory antibiotic activity, and that TS has activity against select multidrug resistant Gram-negative pathogens under iron-limited growth conditions, similar to those encountered at sites of infection.
Early changes in the urine proteome in a rat liver tumor model
Authors: Zhang Yameng , Gao Yufei , Gao Youhe
Published: March 2019

Urine, as a potential biomarker source among the body fluids, can accumulate many changes in the body due to the lack of a mechanism to maintain a homeostatic state. Previous studies have demonstrated that proteomic technology can find many potential biomarkers to reflect different diseases in the urine. This study aims to detect early changes in the urinary proteome in a rat liver tumor model. The tumor model was established with the Walker-256 carcinosarcoma cell line (W256). Compared to before the injection, ninety-five differential proteins were significantly changed in the experimental rats. At day 3, twelve proteins were identified in the absence of pathological changes, and four of them were altered at all four time-points (B2MG, VCAM1, HA11, and LG3BP). Seven had previously been associated with liver cancer. At day 5, fifty-two differential proteins were identified. At day 7 and day 11, there was a significant decrease in the body weight of the rats, and tumor tissue was observed in the liver. Fifty-two and forty differential proteins were changed significantly at day 7 and day 11, respectively. Of the proteins that were identified at these three time-points, and twenty-four were reported to be associated with liver cancer. Comparing the differential urinary proteins and biological processes of liver tumor model with those in different models of W256 grown in other organs, specific differential protein patterns were found among the four models, which indicates that the differential urinary proteins can reflect the differences when the same tumor cell grown in different organs.

Significance

This study demonstrated that (1) the rat liver tumor model caused early changes in urinary proteins may give new insight into the early diagnosis of liver cancer; (2) the same tumor cell grown in different organs can be reflected in differential urinary proteins.
Pacing behaviour in laboratory macaques is an unreliable indicator of acute stress
Authors: Poirier Colline , Oliver Caitlin J. , Bueno Janire Castellano , Flecknell Paul , Bateson Melissa
Published: March 2019

Pacing behaviour, the most frequent stereotypic behaviour displayed by laboratory rhesus macaques (Macaca mulatta) is often used as an indicator of stress. In this study, we investigated how reliable this welfare indicator is at detecting acute stress by testing the reaction of macaques to the stressful event of being exposed to an agonistic interaction between conspecifics housed in the same room but in a different cage. Pacing, agitated locomotion, and stress-related displacement behaviours were quantified before, during and after agonistic interaction exposure, based on video recordings of 13 socially-housed macaques in their home cage. Displacement behaviours increased after agonistic interaction exposure, confirming that the events were experienced as stressful by the focal individuals. The occurrence of pacing did not increase during or after the agonistic interactions. Instead, agitated locomotion increased during the agonistic interactions. These results suggest either, that pacing as an indicator of acute stress is prone to false negative results, increasing in some stressful situations but not others, or that agitated locomotion has been mistaken for pacing in previous studies and that pacing is in fact unrelated to current acute stress. Both interpretations lead to the conclusion that pacing is unreliable as an indicator of acute stress in laboratory rhesus macaques.
Future ocean warming may prove beneficial for the northern population of European seabass, but ocean acidification does not
Authors: Howald Sarah , Cominassi Louise , Le Bayon Nicolas , Claireaux Guy , Mark Felix Christopher
Published: March 2019

The world's oceans are acidifying and warming due to increasing amounts of atmospheric CO2. Thermal tolerance of fish much depends on the cardiovascular ability to supply the tissues with oxygen. The heart itself is highly dependent on oxygen and heart mitochondria thus might play a key role in shaping an organism's tolerance to temperature. The present study aimed to investigate the effects of acute and chronic warming on respiratory capacities of European sea bass (Dicentrarchus labrax L.) heart mitochondria. We hypothesized that acute warming would impair mitochondrial respiratory capacities, but be compensated after long-term. Increasing PCO2 may cause intracellular changes, likely further constricting cellular energy metabolism. We found increased leak respiration rates in acutely warmed heart mitochondria of cold-conditioned fish in comparison to measurements at their rearing temperature, suggesting a lower aerobic capacity to synthesize ATP. However, thermal acclimation led to increased mitochondrial functionality, e.g. higher RCRo in heart mitochondria of warm-conditioned compared to cold-conditioned fish. Exposure to high PCO2 synergistically amplified the effects of acute and long-term warming, but did not result in changes by itself. We explained the high ability to maintain mitochondrial function under OA with the fact that seabass are moving between various environmental conditions. Improved mitochondrial capacities after warm conditioning could be due to the origin of this species in the warm waters of the Mediterranean. Our results also indicate that seabass are not yet fully adapted to the colder temperatures in their northern distribution range and might benefit from warmer temperatures.
DNA sequence differences are determinants of meiotic recombination outcome
Authors: Brown Simon D. , Mpaulo Samantha J. , Asogwa Mimi N. , Jézéquel Marie , Whitby Matthew C. , Lorenz Alexander
Published: March 2019

Meiotic recombination is essential for producing healthy gametes, and also generates genetic diversity. DNA double-strand break (DSB) formation is the initiating step of meiotic recombination, producing, among other outcomes, crossovers between homologous chromosomes (homologs), which provide physical links to guide accurate chromosome segregation. The parameters influencing DSB position and repair are thus crucial determinants of reproductive success and genetic diversity. UsingSchizosaccharomyces pombe, we show that the distance between sequence polymorphisms across homologs has a strong impact on meiotic recombination rate. The closer the sequence polymorphisms are to each other across the homologs the fewer recombination events were observed. In the immediate vicinity of DSBs, sequence polymorphisms affect the frequency of intragenic recombination events (gene conversions). Additionally, and unexpectedly, the crossover rate of flanking markers tens of kilobases away from the sequence polymorphisms was affected by their relative position to each other amongst the progeny having undergone intragenic recombination. A major regulator of this distance-dependent effect is the MutSα-MutLα complex consisting of Msh2, Msh6, Mlh1, and Pms1. Additionally, the DNA helicases Rqh1 and Fml1 shape recombination frequency, although the effects seen here are largely independent of the relative position of the sequence polymorphisms.

Preamble

Due to a mistake during analysis of a batch of Sanger sequencing reactions for Supplementary Figure S1, we erroneously stated that we found evidence for intragenic crossovers. We now show that intragenic crossovers are less likely than we initially thought. We sincerely apologize for our mishap and any inconvenience it might have caused. However, this does not affect the main conclusions of our paper, just how some of our results are interpreted. This new manuscript version has been amended accordingly.
Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer
Authors: Kim Yoo-Ah , Wojtowicz Damian , Basso Rebecca Sarto , Sason Itay , Robinson Welles , Hochbaum Dorit S. , Leiserson Mark D.M. , Sharan Roded , Vandin Fabio , Przytycka Teresa M.
Published: March 2019

Studies of cancer mutations typically focus on identifying cancer driving mutations. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of passenger somatic mutations resulting from normal DNA damage and repair processes as well as mutations triggered by carcinogenic exposures or cancer related aberrations of DNA maintenance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. Understanding the etiology of the mutational signatures shaping a cancer genome is an important step towards understanding tumorigenesis. Considering mutational signatures as phenotypes, we asked two complementary questions (i) what are functional pathways whose geneexpressionprofiles are associated with mutational signatures, and (ii) what aremutated pathways(if any) that might underlie specific mutational signatures? We have been able to identify pathways associated with mutational signatures on both expression and mutation levels. In particular, our analysis provides novel insights into mutagenic processes in breast cancer by capturing important differences in the etiology of different APOBEC related signatures and the two clock-like signatures. These results are important for understanding mutagenic processes in cancer and for developing personalized drug therapies.
Analysis of single nucleotide variants in CRISPR-Cas9 edited zebrafish embryos shows no evidence of off-target inflation
Authors: Mooney Marie R , Davis Erica E , Katsanis Nicholas
Published: March 2019

Therapeutic applications of CRISPR-Cas9 gene editing have spurred innovation in Cas9 enzyme engineering and single guide RNA (sgRNA) design algorithms to minimize potential off-target events. While recent work in rodents outlines favorable conditions for specific editing and uses a trio design to control for the contribution of natural genome variation, the potential for CRISPR-Cas9 to induce de novo mutations in vivo remains a topic of interest. In zebrafish, we performed whole exome sequencing (WES) on two generations of offspring derived from the same founding pair: 54 exomes from control and CRISPR-Cas9 edited embryos in the first generation (F0), and 16 exomes from the progeny of inbred F0 pairs in the second generation (F1). We did not observe an increase in the number of transmissible variants in edited individuals in F1, nor in F0 edited mosaic individuals, arguing that in vivo editing does not precipitate an inflation of deleterious point mutations.
Gut feelings begin in childhood: how the gut metagenome links to early environment, caregiving, and behavior
Authors: Flannery Jessica E , Stagaman Keaton , Burns Adam R , Hickey Roxana J , Roos Leslie E , Giuliano Ryan J , Fisher Philip A , Sharpton Thomas J
Published: March 2019

Psychosocial environments impact normative behavioral development in children, increasing the risk of problem behaviors and psychiatric disorders across the lifespan. Converging evidence demonstrates early normative development is affected by the gut microbiome, which itself can be altered by early psychosocial environments. Nevertheless, these relationships are poorly understood in childhood, particularly beyond peri- and postnatal microbial colonization. To determine the gut microbiome’s role in the associations between childhood adversity and behavioral development, we conducted a metagenomic investigation among cross-sectional sample of early school-aged children with a range of adverse experiences and caregiver stressors and relationships. Our results indicate that the taxonomic and functional composition of the gut microbiome links to behavioral dysregulation during a critical period of child development. Furthermore, our analysis reveals that both socioeconomic risk exposure and child behaviors associate with the relative abundances of specific taxa (e.g.,BacteroidesandBifidobacteriumspecies) as well as functional modules encoded in their genomes (e.g., monoamine metabolism) that have been linked to cognition and health. We also identified heretofore novel linkages between gut microbiota, their functions, and behavior. These findings hold important translational implications for developmental psychology and microbiome sciences alike, as they suggest that caregiver behavior might mitigate the impact of socioeconomic risk on the microbiome and modify the relationship between subclinical symptoms of behavioral dysregulation and the gut microbiome in early school-aged children.
Neural Correlates of Cognition in Primary Visual versus Neighboring Posterior Cortices during Visual Evidence-Accumulation-based Navigation
Authors: Koay Sue Ann , Thiberge Stephan Y. , Brody Carlos D. , Tank David W.
Published: March 2019

Studies of perceptual decision-making have often assumed that the main role of sensory cortices is to provide sensory input to downstream processes that accumulate and drive behavioral decisions. We performed a systematic comparison of neural activity in primary visual (V1) to secondary visual and retrosplenial cortices, as mice performed a task where they should accumulate pulsatile visual cues through time to inform a navigational decision. Even in V1, only a small fraction of neurons had sensory-like responses to cues. Instead, in all areas neurons were sequentially active, and contained information ranging from sensory to cognitive, including cue timings, evidence, place/time, decision and reward outcome. Per-cue sensory responses were amplitude-modulated by various cognitive quantities, notably accumulated evidence. This inspired a multiplicative feedback-loop circuit hypothesis that proposes a more intricate role of sensory areas in the accumulation process, and furthermore explains a surprising observation that perceptual discrimination deviates from Weber-Fechner Law.

Highlights / eTOC Blurb

Mice made navigational decisions based on accumulating pulsatile visual cues

The bulk of neural activity in visual cortices was sequential and beyond-sensory

Accumulated pulse-counts modulated sensory (cue) responses, suggesting feedback

A feedback-loop neural circuit explains behavioral deviations from Weber’s Law

In a task where navigation was informed by accumulated pulsatile visual evidence, neural activity in visual cortices predominantly coded for cognitive variables across multiple timescales, including outside of a visual processing context. Even sensory responses to visual pulses were amplitude-modulated by accumulated pulse counts and other variables, inspiring a multiplicative feedback-loop circuit hypothesis that in turn explained behavioral deviations from Weber-Fechner Law.