bluuebunny/crossref_metadata_2025 huggingface dataset:
Trans-heteroclinic bifurcation: a novel type of catastrophic shift
Authors: Sardanyés Josep , Martínez Regina , Simó Carles
Published: January 2018

Global and local bifurcations are extremely important since they govern the transitions between different qualitative regimes in dynamical systems. These transitions or tipping points, which are ubiquitous in nature, can be smooth or catastrophic. Smooth transitions involve a continuous change in the steady state of the system until the bifurcation value is crossed, giving place to a second-order phase transition. Catastrophic transitions involve a discontinuity of the steady state at the bifurcation value, giving place to first-order phase transitions. Examples of catastrophic shifts can be found in ecosystems, climate, economic or social systems. Here we report a new type of global bifurcation responsible for a catastrophic shift. This bifurcation, identified in a family of quasi-species equations and named astrans-heteroclinic bifurcation, involves an exchange of stability between two distant and heteroclinically connected fixed points. Since the two fixed points interchange the stability without colliding, a catastrophic shift takes place. We provide an exhaustive description of this new bifurcation, also detailing the structure of the replication–mutation matrix of the quasi-species equation giving place to this bifurcation. A perturbation analysis is provided around the bifurcation value. At this value the heteroclinic connection is replaced by a line of fixed points in the quasi-species model. But it is shown that, if the replication–mutation matrix satisfies suitable conditions, then, under a small perturbation, the exchange of heteroclinic connections is preserved, except on a tiny range around the bifurcation value whose size is of the order of magnitude of the perturbation. The results presented here can help to understand better novel mechanisms behind catastrophic shifts and contribute to a finer identification of such transitions in theoretical models in evolutionary biology and other dynamical systems.
Enhanced light-harvesting by plasmonic hollow gold nanospheres for photovoltaic performance
Authors: Ding Hao , Lv Jindian , Wu Huaping , Chai Guozhong , Liu Aiping
Published: January 2018

A ‘sandwich'-structured TiO
2
NR/HGN/CdS photoanode was successfully fabricated by the electrophoretic deposition of hollow gold nanospheres (HGNs) on the surface of TiO
2
nanorods (NRs). The HGNs presented a wide surface plasmon resonance character in the visible region from 540 to 630 nm, and further acted as the scatter elements and light energy ‘antennas' to trap the local-field light near the TiO
2
NR/CdS layer, resulting in the increase of the light harvesting. An outstanding enhancement in the photochemical behaviour of TiO
2
NR/HGN/CdS photoanodes was attained by the contribution of HGNs in increasing the light absorption and the number of electron-hole pairs of photosensitive semiconductors. The optimized photochemical performance of TiO
2
NR/HGN/CdS photoanodes by using plasmonic HGNs demonstrated their potential application in energy conversion devices.
Study of mixed mode fracture toughness and fracture trajectories in gypsum interlayers in corrosive environment
Authors: Xiankai Bao , Meng Tao , Jinchang Zhao
Published: January 2018

Based on the engineering background of water dissolving mining for hydrocarbon storage in multi-laminated salt stratum, the mixed mode fracture toughness and fracture trajectory of gypsum interlayers soaked in half-saturated brine at various temperatures (20°C, 50°C and 80°C) were studied by using CSNBD (centrally straight-notched Brazilian disc) specimens with required inclination angles (0°, 7°, 15°, 22°, 30°, 45°, 60°, 75°, 90°) and SEM (scanning electron microscopy). The results showed: (i) The fracture load of gypsum specimens first decreased then increased with increasing inclination angle, due to the effect of friction coefficient. When soaked in brine, the fracture toughness of gypsum specimens gradually decreased with increasing brine temperature. (ii) When soaked in brine, the crystal boundaries of gypsum separated and became clearer, and the boundaries became more open between the crystals with increasing brine temperature. Besides, tensile micro-cracks appeared on the gypsum crystals when soaked in 50°C brine, and the intensity of tensile cracks became more severe when soaking in 80°C brine. (iii) The experimental fracture envelopes derived from the conventional fracture criteria and lay outside these conventional criteria. The experimental fracture envelopes were dependent on the brine temperature and gradually expanded outward as brine temperature increases. (iv) The size of FPZ (fracture process zone) was greatly dependent on the damage degree of materials and gradually increased with increase of brine temperature. The study has important implication for the control of shape and size of salt cavern.
A prediction model of compressor with variable-geometry diffuser based on elliptic equation and partial least squares
Authors: Li Xu , Yang Chuanlei , Wang Yinyan , Wang Hechun
Published: January 2018

To achieve a much more extensive intake air flow range of the diesel engine, a variable-geometry compressor (VGC) is introduced into a turbocharged diesel engine. However, due to the variable diffuser vane angle (DVA), the prediction for the performance of the VGC becomes more difficult than for a normal compressor. In the present study, a prediction model comprising an elliptical equation and a PLS (partial least-squares) model was proposed to predict the performance of the VGC. The speed lines of the pressure ratio map and the efficiency map were fitted with the elliptical equation, and the coefficients of the elliptical equation were introduced into the PLS model to build the polynomial relationship between the coefficients and the relative speed, the DVA. Further, the maximal order of the polynomial was investigated in detail to reduce the number of sub-coefficients and achieve acceptable fit accuracy simultaneously. The prediction model was validated with sample data and in order to present the superiority of compressor performance prediction, the prediction results of this model were compared with those of the look-up table and back-propagation neural networks (BPNNs). The validation and comparison results show that the prediction accuracy of the new developed model is acceptable, and this model is much more suitable than the look-up table and the BPNN methods under the same condition in VGC performance prediction. Moreover, the new developed prediction model provides a novel and effective prediction solution for the VGC and can be used to improve the accuracy of the thermodynamic model for turbocharged diesel engines in the future.
Metal and polymer-mediated synthesis of porous crystalline hydroxyapatite nanocomposites for environmental remediation
Authors: Manatunga Danushika C. , de Silva Rohini M. , Nalin de Silva K. M. , de Silva Nuwan , Premalal E. V. A.
Published: January 2018

This study was focused on the preparation of metal and polymer-mediated porous crystalline hydroxyapatite (HAp) nanocomposites for environmental applications. Four different nano HAp systems were synthesized, namely, microwave irradiated HAp (M1), Zn doped HAp (M2), Mg-doped HAp (M3) and sodium alginate incorporated HAp (M4), and characterized using X-ray diffraction (XRD), Fourier transform infra-red spectroscopy, scanning electron microscopy, transmission electron microscopy, atomic force microscopy, nuclear magnetic resonance (NMR), X-ray fluorescence, thermogravimetric analysis and Brunauer–Emmett–Teller (BET) analyses. Systems M1–M4 showed morphologies similar to coral shapes, polymer-like interconnected structures, sponges and feathery mycelium assemblies. Using XRD, selected area electron diffraction patterns and
1
H and
31
P CP/MAS solid-state NMR studies, crystallinity variation was observed from highest to lowest in the order of M4 > M1 > M3 > M2. Surface area estimates using BET isotherm reflected the highest surface area for M3, and M1 > M2 > M4. Four systems of M1–M4 were used as potential adsorbent materials for the removal of metal containing azo dye from aqueous system. Adsorption data were correlated to Freundlich and Langmuir isotherm models. According to the results, the highest capacity of 212.8 mg g
−1
was exhibited by M4 having mycelium like morphology with alginate groups. This study highlights the possibility of developing HAp nanocomposites for the effective removal of dye contaminants in the environment.
The evolution and anatomy of the horse manus with an emphasis on digit reduction
Authors: Solounias Nikos , Danowitz Melinda , Stachtiaris Elizabeth , Khurana Abhilasha , Araim Marwan , Sayegh Marc , Natale Jessica
Published: January 2018

We revisit digit reduction in the horse and propose that all five digits are partially present in the modern adult forelimb. Osteological descriptions of selected tetradactyl, tridactyl and monodactyl equids demonstrate the evolution of the forelimb. Histological, osteological and palaeontological evidence suggest that theEquusdistal forelimb is more complex than traditionally conceived. The current understanding is that the horse distal forelimb consists of one complete digit (III) and two reduced splint metacarpals (II and IV). Metacarpals II and IV each exhibit a ventral ridge, which we suggest represents the undifferentiated digits I and V. These ridges are present in the tridactylMesohippus, but are absent in the tetradactylHyracotherium.The carpal articulations of the five metacarpals match those of pentadactyl taxa. Distally, the frog, a V-shaped structure on the ventral hoof represents digits II and IV, and the wings and hoof cartilages of the distal phalanx are digits I and V. We relate this revised interpretation of theEquusforelimb to Laetoli footprints, and suggest theHipparionside impressions are created from the hooves of I and V, rather than from II and IV. We show shades of pentadactyly within theEquusmanus.
Experimental evidence of a pathogen invasion threshold
Authors: Dallas Tad A. , Krkošek Martin , Drake John M.
Published: January 2018

Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and disease-free states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean zooplankton (Daphnia dentifera) hosts across a range of host densities (20–640 hosts l−1) that were exposed to an environmentally transmitted fungal pathogen (Metschnikowia bicuspidata). Epidemiological model simulations, parametrized independently of the experiment, qualitatively predicted experimental pathogen invasion thresholds. Variability in parameter estimates did not strongly influence outcomes, though systematic changes to key parameters have the potential to shift pathogen invasion thresholds. In summary, we provide one of the first clear experimental demonstrations of pathogen invasion thresholds in a replicated experimental system, and provide evidence that such thresholds may be predictable using independently constructed epidemiological models.
Responses to auxin signals: an operating principle for dynamical sensitivity yet high resilience
Authors: Grigolon S. , Bravi B. , Martin O. C.
Published: January 2018

Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signalling network involves a negative feedback on Aux/IAA proteins which mediate the influence of auxin (the
signal
) on the auxin response factor (ARF) transcription factors (the
drivers
of the response). To probe the role of this feedback, we consider alternative
in silico
signalling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative feedback allows the system to have a far larger sensitivity in its dynamical response to auxin and that this sensitivity does
not
prevent the system from being highly resilient. Given this insight, we build a new biomolecular signalling model for quantitatively describing such Aux/IAA and ARF responses.
Skipping on uneven ground: trailing leg adjustments simplify control and enhance robustness
Authors: Müller Roy , Andrada Emanuel
Published: January 2018

It is known that humans intentionally choose skipping in special situations, e.g. when descending stairs or when moving in environments with lower gravity than on Earth. Although those situations involve uneven locomotion, the dynamics of human skipping on uneven ground have not yet been addressed. To find the reasons that may motivate this gait, we combined experimental data on humans with numerical simulations on a bipedal spring-loaded inverted pendulum model (BSLIP). To drive the model, the following parameters were estimated from nine subjects skipping across a single drop in ground level: leg lengths at touchdown, leg stiffness of both legs, aperture angle between legs, trailing leg angle at touchdown (leg landing first after flight phase), and trailing leg retraction speed. We found that leg adjustments in humans occur mostly in the trailing leg (low to moderate leg retraction during swing phase, reduced trailing leg stiffness, and flatter trailing leg angle at lowered touchdown). When transferring these leg adjustments to the BSLIP model, the capacity of the model to cope with sudden-drop perturbations increased.
Finite indentation of highly curved elastic shells
Authors: Pearce S. P. , King J. R. , Steinbrecher T. , Leubner-Metzger G. , Everitt N. M. , Holdsworth M. J.
Published: January 2018

Experimentally measuring the elastic properties of thin biological surfaces is non-trivial, particularly when they are curved. One technique that may be used is the indentation of a thin sheet of material by a rigid indenter, while measuring the applied force and displacement. This gives immediate information on the fracture strength of the material (from the force required to puncture), but it is also theoretically possible to determine the elastic properties by comparing the resulting force–displacement curves with a mathematical model. Existing mathematical studies generally assume that the elastic surface is initially flat, which is often not the case for biological membranes. We previously outlined a theory for the indentation of curved isotropic, incompressible, hyperelastic membranes (with no bending stiffness) which breaks down for highly curved surfaces, as the entire membrane becomes wrinkled. Here, we introduce the effect of bending stiffness, ensuring that energy is required to change the shell shape without stretching, and find that commonly neglected terms in the shell equilibrium equation must be included. The theory presented here allows for the estimation of shape- and size-independent elastic properties of highly curved surfaces via indentation experiments, and is particularly relevant for biological surfaces.
Masking of an auditory behaviour reveals how male mosquitoes use distortion to detect females
Authors: Simões P. M. V. , Ingham R. , Gibson G. , Russell I. J.
Published: January 2018

The mating behaviour of many mosquito species is mediated essentially by sound: males follow and mate with a female mid-flight by detecting and tracking the whine of her flight-tones. The stereotypical rapid frequency modulation (RFM) male behaviour, initiated in response to the detection of the female's flight-tones, has provided a means of investigating these auditory mechanisms while males are free-flying. Mosquitoes hear with their antennae, which vibrate to near-field acoustic excitation. The antennae generate nonlinear vibrations (distortion products, DPs) at frequencies that are equal to the difference between the two simultaneously presented tones, e.g. the male and female flight-tones, which are detected by mechanoreceptors in the auditory Johnston's organ (JO) at the base of the antenna. Recent studies indicated the male mosquito's JO is tuned not to the female flight-tone, but to the frequency difference between the male and female flight-tones. To test the hypothesis that mosquitoes detect this frequency difference,Culex quinquefasciatusmales were presented simultaneously with a female flight-tone and a masking tone, which should suppress the male's RFM response to sound. The free-flight behavioural andin vivoelectrophysiological experiments revealed that acoustic masking suppresses the RFM response to the female's flight-tones by attenuating the DPs generated in the nonlinear vibration of the antennae. These findings provide direct evidence in support of the hypothesis that male mosquitoes detect females when both are in flight through difference tones generated in the vibrations of their antennae owing to the interaction between their own flight-tones and those of a female.
Cooperative defence operates by social modulation of biogenic amine levels in the honey bee brain
Authors: Nouvian Morgane , Mandal Souvik , Jamme Charlène , Claudianos Charles , d'Ettorre Patrizia , Reinhard Judith , Barron Andrew B. , Giurfa Martin
Published: January 2018

The defence of a society often requires that some specialized members coordinate to repel a threat at personal risk. This is especially true for honey bee guards, which defend the hive and may sacrifice their lives upon stinging. Central to this cooperative defensive response is the sting alarm pheromone, which has isoamyl acetate (IAA) as its main component. Although this defensive behaviour has been well described, the neural mechanisms triggered by IAA to coordinate stinging have long remained unknown. Here we show that IAA upregulates brain levels of serotonin and dopamine, thereby increasing the likelihood of an individual bee to attack and sting. Pharmacological enhancement of the levels of both amines induces higher defensive responsiveness, while decreasing them via antagonists decreases stinging. Our results thus uncover the neural mechanism by which an alarm pheromone recruits individuals to attack and repel a threat, and suggest that the alarm pheromone of honey bees acts on their response threshold rather than as a direct trigger.
Harmonizing semantic annotations for computational models in biology
Authors: Neal ML , König M , Nickerson D , Mısırlı G , Kalbasi R , Dräger A , Atalag K , Chelliah V , Cooling M , Cook DL , Crook S , de Alba M , Friedman SH , Garny A , Gennari JH , Gleeson P , Golebiewski M , Hucka M , Juty N , Le Novère N , Myers C , Olivier BG , Sauro HM , Scharm M , Snoep JL , Touré V , Wipat A , Wolkenhauer O , Waltemath D
Published: January 2018

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition, and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current semantic annotation practices among the COmputational Modeling in BIology NEtwork (COMBINE) community and provide a set of recommendations for building a consensus approach to semantic annotation.
Atomic force microscopy of phase separation on ruptured, giant unilamellar vesicles
Authors: Jiang Yanfei , Genin Guy M. , Pryse Kenneth M. , Elson Elliot L.
Published: January 2018

Giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs) are synthetic model systems widely used in biophysical studies of lipid membranes. Phase separation behaviors of lipid species in these two model systems differ due to the lipid-substrate interactions that are present only for SLBs. Therefore, GUVs are believed to resemble natural cell membranes more closely, and a very large body of literature focuses on applying nano-characterization techniques to quantify phase separation on GUVs. However, one important technique, atomic force microscopy (AFM), has not yet been used successfully to study phase separation on GUVs. In the present study, we report that in binary systems, certain phase domains on GUVs retain their original shapes and patterns after the GUVs rupture on glass surfaces. This enabled AFM experiments on phase domains from binary GUVs containing 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and either 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC). These DLPC/DSPC and DLPC/DPPC GUVs both presented two different gel phases, one of which (bright phase) included a relatively high concentration of DiI-C20but excluded Bodipy-HPC, and the other of which (dark phase) excluded both probes. The bright phases are of interest because they seem to stabilize dark phases against coalescence. Results suggested that the gel phases labeled by DiI-C20in the DLPC/DSPC membrane, which surround the dark gel phase, is an extra layer of membrane, indicating a highly curved structure that might stabilize the interior dark domains. This phenomenon was not found in the DLPC/DPPC membrane. These results show the utility of AFM on collapsed GUVs, and suggest a possible mechanism for stabilization of lipid domains.
HDL-AuNPs-BMS nanoparticle conjugates as molecularly targeted therapy for leukemia
Authors: Shen Na , Yan Fei , Pang Jiuxia , Gao Zhe , Al-Kali Aref , Haynes Christy L. , Litzow Mark R. , Liu Shujun
Published: January 2018

In previous work, gold nanoparticles (AuNPs) with adsorbed high-density lipoprotein (HDL) nanoparticles have been utilized to deliver oligonucleotides, yet HDL-AuNPs functionalized with small molecule inhibitors have not been systematically explored. Here, we report an AuNP-based therapeutic system (HDL-AuNPs-BMS) for acute myeloid leukemia (AML) by delivering BMS309403 (BMS), a small molecule that selectively inhibits AML-promoting factor fatty acid binding protein 4 (FABP4). HDL-AuNPs-BMS are synthesized using a gold nanoparticle as template to control conjugate size and ensure a spherical shape to engineer HDL-like nanoparticle containing BMS. The zeta potential and size of the HDL-AuNPs obtained from transmission electron microscopy (TEM) show that the nanoparticles are electrostatically stable and 25 nm in diameter. Functionally, compared to free drug, HDL-AuNPs-BMS conjugates are more readily internalized by AML cells and have more pronounced effect on downregulation of DNA methyltransferase 1 (DNMT1), reduction of global DNA methylation, and restoration of epigenetically-silenced tumor suppressorp15INK4bcoupled with AML growth arrest. Importantly, systemic administration of HDL-AuNPs-BMS conjugates into AML-bearing mice inhibits DNMT1-dependent DNA methylation, induces AML cell differentiation and diminishes AML disease progression without obvious side effects. In summary, these data, for the first time, demonstrate HDL-AuNPs as an effective delivery platform with great potential to attach distinct inhibitors, and HDL-AuNPs-BMS conjugates as a promising therapeutic platform to treat leukemia.
Inference of CRISPR Edits from Sanger Trace Data
Authors: Hsiau Tim , Conant David , Rossi Nicholas , Maures Travis , Waite Kelsey , Yang Joyce , Joshi Sahil , Kelso Reed , Holden Kevin , Enzmann Brittany L , Stoner Rich
Published: January 2018

Efficient precision genome editing requires a quick, quantitative, and inexpensive assay of editing outcomes. Here we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs (gRNAs) and then determines which are supported by the data via regression. Additionally, we develop a score called ICE-D (Discordance) that can provide information on large or unexpected edits. We empirically confirm through over 1,800 edits that the ICE algorithm is robust, reproducible, and can analyze CRISPR experiments within days after transfection. We also confirm that ICE strongly correlates with next-generation sequencing of amplicons (Amp-Seq). The ICE tool is free to use and offers several improvements over current analysis tools. For instance, ICE can analyze individual experiments as well as multiple experiments simultaneously (batch analysis). ICE can also detect a wider variety of outcomes, including multi-guide edits (multiple gRNAs per target) and edits resulting from homology-directed repair (HDR), such as knock-ins and base edits. ICE is a reliable analysis tool that can significantly expedite CRISPR editing workflows. It is available online at ice.synthego.com, and the source code is at github.com/synthego-open/ice
Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution
Authors: Munro Catriona , Siebert Stefan , Zapata Felipe , Howison Mark , Damian Serrano Alejandro , Church Samuel H. , Goetz Freya E. , Pugh Philip R. , Haddock Steven H.D. , Dunn Casey W.
Published: January 2018

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at all depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. Siphonophores play an important role in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups, however there was little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 30 siphonophore species analyzed in combination with 13 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose twice.
Title: Basal constriction during midbrain-hindbrain boundary morphogenesis is mediated by Wnt5b and Focal Adhesion Kinase
Authors: Gutzman Jennifer H. , Graeden Ellie , Brachmann Isabel , Yamazoe Sayumi , Chen James K. , Sive Hazel
Published: January 2018

Basal constriction occurs at the zebrafish midbrain-hindbrain boundary constriction (MHBC) and is likely a widespread morphogenetic mechanism. 3D reconstruction demonstrates that MHBC cells are wedge-shaped, and initially constrict basally, with subsequent apical expansion.wnt5bis expressed in the MHB and is required for basal constriction. Consistent with a requirement for this pathway, expression of dominant negative Gsk3β overcomeswnt5bknockdown. Immunostaining identifies focal adhesion kinase (Fak) as active in the MHB region, and knockdown demonstrates Fak is a regulator of basal constriction. Tissue specific knockdown further indicates that Fak functions cell autonomously within the MHBC. Fak is epistatic townt5b, suggesting that Wnt5b signals locally as an early step in basal constriction and acts together with more widespread Fak activation. This study delineates signaling pathways that regulate basal constriction during brain morphogenesis.
Insights into the effect of the J-domain on the substrate binding domain (SBD) of the 70 kDa heat shock protein, Hsp70, from a chimeric human J-SBD polypeptide
Authors: Tiroli-Cepeda Ana O. , Seraphim Thiago V. , Borges Júlio C. , Ramos Carlos H. I.
Published: January 2018

DnaJ/Hsp40 chaperones deliver unfolded proteins and stimulate the ATPase activity of DnaK/Hsp70 via their J-domain, a crucial event for the function that this system has in assisting protein folding. The interaction between Hsp40 and Hsp70 is transient and thus difficult to study, since mixing the binding partners can lead to quick dissociation due to their low affinity, creating a challenge for detailed analysis. As a consequence, knowledge of many important aspects of the mechanism of interaction is still lacking, for instance, the effect that J-domain binding has on Hsp70. In this study, we investigated whether it would be possible to gain understanding of this interaction by engineering a chimeric polypeptide where the J-domain of Hsp40 was covalently attached to the substrate binding domain (SBD) of Hsp70 by a flexible linker. The rationale for this is that an increase in the proximity between the interacting partners in this engineered chimera will promote the natural interaction and facilitate the characterization of the protein– protein interaction, which is a requirement to gain further understanding of many biological processes. The resulting chimera, termed J-SBD, was properly folded and had properties not present in the SBD alone. J-SBD behaved primarily as a monomer in all conditions tested and exhibited chaperone activity, as shown by aggregation protection and substrate binding assays, which revealed decreased binding to bis-ANS, a probe for hydrophobic patches. Collectively, our results suggest that Hsp40 binding to Hsp70 via the J-domain shifts the Hsp70 equilibrium towards the monomer state to expose hydrophobic sites prone to substrate accommodation.

Abbreviations

Bis-ANS (4,4’-Dianilino-1,1’-Binaphthyl-5,5’-Disulfonic Acid; CD, circular dichroism; Hsp, heat shock protein; J-SBD, chimeric polypeptide in which the J-domain of Hsp40 (at the N-terminus) is covalently attached to the substrate binding domain of Hsp70 (at the C-terminus) by a flexible linker; SBD: substrate binding domain of Hsp70.
Enhancing resolution of natural methylome reprogramming behavior in plants
Authors: Sanchez Robersy , Yang Xiaodong , Barreras Jose R , Kundariya Hardik , Mackenzie Sally A.
Published: January 2018

Background

Natural methylome reprogramming within chromatin involves changes in local energy landscapes that are subject to thermodynamic principles. Signal detection permits the discrimination of methylation signal from dynamic background noise that is induced by thermal fluctuation. Current genome-wide methylation analysis methods do not incorporate biophysical properties of DNA, and focus largely on DNA methylation density changes, which limits resolution of natural, more subtle methylome behavior in relation to gene activity.

Results

We present here a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection step, and the method was designed to discriminate methylation regulatory signal from background variation. Comparisons with commonly used programs and two publicly available methylome datasets, involving stages of seed development and drought stress effects, were implemented. Information divergence between methylation levels from different groups, measured in terms of Hellinger divergence, provides discrimination power between control and treatment samples. Differentially informative methylation positions (DIMPs) achieved higher sensitivity and accuracy than standard differentially methylated positions (DMPs) identified by other methods. Differentially methylated genes (DMG) that are based on DIMPs were significantly enriched in biologically meaningful networks.

Conclusions

Methyl-IT analysis enhanced resolution of natural methylome reprogramming behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods.
Selection-free, high frequency genome editing by homologous recombination of human pluripotent stem cells using Cas9 RNP and AAV6
Authors: Martin Renata M. , Ikeda Kazuya , Uchida Nobuko , Cromer Kyle , Nishimura Toshi , Dever Daniel P. , Camarena Joab , Bak Rasmus , Laustsen Anders , Jakobsen Martin R. , Wiebking Volker , Sebastiano Vittorio , Nakauchi Hiromitsu , Porteus Matthew
Published: January 2018

Combination of genome editing and human pluripotent stem cells (hPSCs) offers a platform for in vitro disease modeling, drug discovery and personalized stem cell therapeutics. However, incorporation of large modifications using CRISPR/Cas9-based genome editing in hPSCs typically requires the use of selection markers due to low editing efficiencies. Here we report a novel editing technology in hPSCs using Cas9 protein complexed with chemically modified single guide RNA (sgRNA) and recombinant AAV6 (rAAV6) vectors for donor delivery without marker selection. With these components, we demonstrate targeted integration of a 2.2 kb DNA expression cassette in hPSCs at frequencies up to 94% and 67% at the HBB and MYD88 loci, respectively. We used this protocol to correct the homozygous sickle cell disease (SCD) mutation in an iPSC line derived from a SCD patient with a frequency of 63%. This Cas9/AAV6 system allows for both the integration of large gene cassettes and the creation of single nucleotide changes in hPSCs at high frequencies, eliminating the need for multiple editing steps and marker selection, thus increasing the potential of editing human pluripotent cells for both research and translational applications.
Spatiotemporal mosaic patterning of pluripotent stem cells using CRISPR interference
Authors: Libby Ashley R.G. , Joy David A. , So Po-Lin , Mandegar Mohammad A. , Muncie Jonathon M. , Weaver Valerie M. , Conklin Bruce R. , McDevitt Todd C.
Published: January 2018

Morphogenesis results from the interactions of asymmetric cell populations to form complex multicellular patterns and structures comprised of distinct cell types. However, current methods to model morphogenic events offer little control over parallel cell type co-emergence and do not offer the capability to selectively perturb gene expression in specific subpopulations of cells. We have developed anin vitrosystem that can spatiotemporally interrogate cell-cell interactions and multicellular organization within human induced pluripotent stem cell (hiPSC) colonies. We examined the effects of independently knocking down molecular regulators of cortical tension and cell-cell adhesion using inducible CRISPRi: Rho-associated kinase-1 (ROCK1) and E-cadherin (CDH1), respectively. Induced mosaic knockdown of ROCK1 or CDH1 in hiPSC populations resulted in differential patterning events within hiPSC colonies indicative of cell-driven population organization. Patterned colonies retained an epithelial phenotype and nuclear expression of pluripotency markers. Gene expression within each of the mixed populations displayed a transient wave of differential expression with induction of knockdown that stabilized in coordination with intrinsic pattern formation. Mosaic patterning of hiPSCs enables the genetic interrogation of emergent multicellular properties of pluripotent cells, leading to a greater mechanistic understanding of the specific molecular pathways regulating the dynamics of symmetry breaking events that transpire during developmental morphogenesis.

SIGNIFICANCE

Human embryonic development entails a series of multicellular morphogenic events that lead to primitive tissue formation. Attempts to study human morphogenic processes experimentally have been limited due to divergence from model organisms and the inability of current humanin vitromodels to accurately control the coincident emergence of heterogeneous cell populations in the spatially controlled manner necessary for proper tissue structure. We developed a human induced pluripotent stem cell (iPSC)in vitromodel that enables temporal control over the emergence of heterotypic subpopulations of cells. We examined mosaic knockdown of two target molecules to create predictable and robust cell-patterning events within hiPSC colonies. This method allows for dynamic interrogation of intrinsic cell mechanisms that initiate symmetry breaking events and provides direct insight(s) into tissue developmental principles.
High precision automated detection of labeled nuclei in Gigapixel resolution image data of Mouse Brain
Authors: Das Sukhendu , Jayakumar Jaikishan , Banerjee Samik , Ramaswamy Janani , Vangala Venu , Ram Keerthi , Mitra Partha
Published: January 2018

There is a need in modern neuroscience for accurate and automated image processing techniques for analyzing the large volume of neuroanatomical imaging data. Even at light microscopic levels, imaging mouse brains produces individual data volumes in the TerraByte range. A fundamental task involves the detection and quantification of objects of a given type, e.g. neuronal nuclei or somata, in brain scan dataset. Traditionally this quantification has been performed by human visual inspection with high accuracy, that is not scalable. When modern automated CNN and SVM-based methods are used to solve this classification problem, they achieve accuracy levels that range between 85 – 92%. However, higher rates of precision and recall that are close to that of human performance are necessary. In this paper, we describe an unsupervised, iterative algorithm, which provides a high performance for a specific problem of detecting Green Fluorescent Protein labeled nuclei in 2D scans of mouse brains. The algorithm judiciously combines classical computer vision techniques and is focused on the complex problem of decomposing strong overlapped objects of interest. Our proposed technique uses feature detection methods on ridge lines over distance transformation of the image and an arc based iterative spatial-filling method to solve the problem. We demonstrate our results on mouse brain dataset of Gigabyte resolution and compare it with manual annotation of the brains. Our results show that an aptly designed CV algorithm with classical feature extractors when tailored to this problem of interest achieves near-ideal human-like performance. Quantitative comparative analysis, using manually annotated ground truth, reveals that our approach performs better on mouse brain scans than general purpose machine learning (including deep CNN) methods.
Altered Developmental Trajectories in Intrinsic Function between Default, Salience, and Executive Networks in High-Functioning Autism
Authors: Yang Liu , Chen Xiao , Li Xue , Shen Yang-Qian , Wang Hui , Liu Jing-Ran , Mei Ting , Ji Zhao-Zheng , Guo Yan-Qing , Wang Fei-Fei , Xu Ling-Zi , Tang Xin-Zhou , Ma Zeng-Hui , Wang Li-Qi , Liu Jing , Cao Qing-Jiu , Yan Chao-Gan
Published: January 2018

Although many studies have focused on abnormal patterns of brain functional connectivity in Autism spectrum disorder (ASD), one important factor, the developmental effect of brain networks was largely overlooked. To clarify the abnormal developmental trajectory of brain functional connectivity in ASD, we focused on the age-related changes in three “core” neurocognitive networks: default mode network (DMN), salience network (SN) and central executive network (CEN, also divided into left and right CEN, i.e., lCEN and rCEN). The development of intrinsic functional connectivity (iFC) within and between these networks were analyzed in 107 Chinese participants, including children, adolescents, and adults (54 patients with ASD and 53 typically developed (TD) participants; ages 6-30 years). We found that diagnosis-related distinctions in age-related changes suggest three maturation patterns in networks’ or nodes’ iFC: delayed (iFC between SN and rCEN), ectopic (iFC between SN and DMN, and iFC between posterior cingulate cortex (PCC) and right anterior insula/dorsal anterior cingulate cortex (dACC)), and failure maturation (iFC between dACC and ventral medial prefrontal cortex). Compared with age-matched TD participants, ASD patients in children and adolescents exhibited hypo-connectivity, while that in adults showed hyper-connectivity. In addition, an independent verification based on Autism Brain Imaging Data Exchange (ABIDE) datasets confirmed our findings of developmental trajectories in ASD group, which also showed unchanged functional connectivity with age between DMN and SN and increasing iFC between rCEN and SN. The conspicuous differences in the development of three “core” networks in ASD were demonstrated, which may lead a nuanced understanding towards the abnormal brain network maturation trajectory of autism.
Brain network segregation and integration during an epoch-related working memory fMRI experiment
Authors: Fransson Peter , Schiffler Björn C. , Hedley Thompson William
Published: January 2018

The characterization of brain subnetwork segregation and integration has previously focused on changes that are detectable at the level of entire sessions or epochs of imaging data. In this study, we applied time-varying functional connectivity analysis together with temporal network theory to calculate point-by-point estimates in subnetwork segregation and integration during an epoch-based (2-back, 0-back, baseline) working memory fMRI experiment as well as during resting-state. This approach allowed us to follow task-related changes in subnetwork segregation and integration at a high temporal resolution. At a global level, the cognitively more taxing 2-back epochs elicited an overall stronger response of integration between subnetworks compared to the 0-back epochs. Moreover, the visual and fronto-parietal subnetworks displayed characteristic and distinct temporal profiles of segregation and integration during the 0- and 2-back epochs. During the interspersed epochs of baseline, many subnetworks, including the default mode, visual, fronto-parietal, cingulo-opercular and dorsal attention subnetworks showed pronounced increases in segregation. Using a drift diffusion model we show that the response time for the 2-back trials are correlated with integration for the fronto-parietal subnetwork and correlated with segregation for the visual subnetwork. Our results elucidate the fast-evolving events with regard to subnetwork integration and segregation that occur in an epoch-related task fMRI experiment. Our findings suggest that minute changes in subnetwork integration are of importance for task performance.
EssC is a specificity determinant for Staphylococcus aureus type VII secretion
Authors: Jäger Franziska , Kneuper Holger , Palmer Tracy
Published: January 2018

The Type VII protein secretion system (T7SS) is found in actinobacteria and firmicutes, and plays important roles in virulence and interbacterial competition. A membrane-bound ATPase protein, EssC in Staphylococcus aureus, lies at the heart of the secretion machinery. The EssC protein from S. aureus strains can be grouped into four variants (EssC1-EssC4) that display sequence variability in the C-terminal region. Here we show that the EssC2, EssC3 and EssC4 variants can be produced in a strain deleted for essC1 and that they are able to mediate secretion of EsxA, an essential component of the secretion apparatus. They are, however, unable to support secretion of the substrate protein EsxC, which is encoded only in essC1-specific strains. This finding indicates that EssC is a specificity determinant for T7 protein secretion. Our results support a model where the C-terminal domain of EssC interacts with substrate proteins whereas EsxA interacts elsewhere.
An NAD+–dependent sirtuin depropionylase and deacetylase (Sir2La) from the probiotic bacteriumLactobacillus acidophilusNCFM
Authors: Olesen Sita V. , Rajabi Nima , Svensson Birte , Olsen Christian A. , Madsen Andreas S.
Published: January 2018

Sirtuins—a group of NAD+-dependent deacylases—have emerged as key in the connection between NAD+metabolism and aging. This class of enzymes hydrolyze a range ofε-N-acyllysine PTMs and determining the repertoire of catalyzed deacylation reactions is of high importance to fully elucidate the roles of a given sirtuin. Here we have identified and produced two potential sirtuins from the probiotic bacteriumLactobacillus acidophilusNCFM and screening more than 80 different substrates, covering 26 acyl groups on five peptide scaffolds, showed that one of the investigated proteins—Sir2La—is abona fideNAD+-dependent sirtuin, catalyzing hydrolysis of acetyl‐, propionyl‐, and butyryllysine. Further substantiating the identity as a sirtuin, known sirtuin inhibitors nicotinamide and suramin as well as a thioacetyllysine compound inhibit the deacylase activity in a concentration-dependent manner. Based on steady-state kinetics Sir2La showed a slight preference for propionyllysine over acetyllysine and butyryllysine, driven both byKM(14 μMvs21 μM and 15 μM) andkcat(4.4·10−3s−1vs2.5·10−3s−1and 1.21·10−3s−1). Moreover, while NAD+is a prerequisite for Sir2La-mediated deacylation, Sir2La has very highKMfor NAD+compared to the expected levels of the dinucleotide inL. acidophilus. Sir2La is the first sirtuin from Lactobacillales and of the Gram-positive bacterial subclass of sirtuins to be functionally characterized. The ability to hydrolyze propionyl‐ and butyryllysine emphasizes the relevance of further exploring the role of other short-chain acyl moieties as PTMs.