bluuebunny/crossref_metadata_2025 huggingface dataset:
CryoGAN: A New Reconstruction Paradigm for Single-Particle Cryo-EMviaDeep Adversarial Learning
Authors: Gupta Harshit , McCann Michael T. , Donati Laurène , Unser Michael
Published: March 2020

We present CryoGAN, a new paradigm for single-particle cryo-EM reconstruction based on unsupervised deep adversarial learning. The major challenge in single-particle cryo-EM is that the imaged particles have unknown poses. Current reconstruction techniques are based on a marginalized maximum-likelihood formulation that requires calculations over the set of all possible poses for each projection image, a computationally demanding procedure. CryoGAN sidesteps this problem by using a generative adversarial network (GAN) to learn the 3D structure that has simulated projections that most closely match the real data in a distributional sense. The architecture of CryoGAN resembles that of standard GAN, with the twist that the generator network is replaced by a model of the cryo-EM image acquisition process. CryoGAN is an unsupervised algorithm that only demands projection images and an estimate of the contrast transfer function parameters. No initial volume estimate or prior training is needed. Moreover, CryoGAN requires minimal user interaction and can provide reconstructions in a matter of hours on a high-end GPU. In addition, we provide sound mathematical guarantees on the recovery of the correct structure. CryoGAN currently achieves a 8.6 Å resolution on a realistic synthetic dataset. Preliminary results on realβ-galactosidase data demonstrate CryoGAN’s ability to exploit data statistics under standard experimental imaging conditions. We believe that this paradigm opens the door to a family of novel likelihood-free algorithms for cryo-EM reconstruction.
Conductance mechanisms of rapidly desensitizing cation channelrhodopsins from cryptophyte algae
Authors: Sineshchekov Oleg A. , Govorunova Elena G. , Li Hai , Wang Yumei , Melkonian Michael , Wong Gane K.-S. , Brown Leonid S. , Spudich John L.
Published: March 2020

Channelrhodopsins guide algal phototaxis and are widely used as optogenetic probes for control of membrane potential with light. “Bacteriorhodopsin-like” cation channelrhodopsins (BCCRs) from cryptophytes differ in primary structure from other CCRs, lacking usual residues important for their cation conductance. Instead, BCCR sequences match more closely those of rhodopsin proton pumps, containing residues responsible for critical proton transfer reactions. We report 19 new BCCRs, which, together with the earlier 6 known members of this family, form three branches (subfamilies) of a phylogenetic tree. Here we show that the conductance mechanisms in two subfamilies differ with respect to involvement of the homolog of the proton donor in rhodopsin pumps. Two BCCRs from the genusRhodomonasgenerate photocurrents that rapidly desensitize under continuous illumination. Using a combination of patch clamp electrophysiology, absorption and Raman spectroscopy, and flash photolysis, we found that the desensitization is due to rapid accumulation of a long-lived nonconducting intermediate of the photocycle with unusually blue-shifted absorption with a maximum at 330 nm. These observations reveal diversity within the BCCR family and contribute to deeper understanding of their independently evolved cation channel function.

IMPORTANCE

Cation channelrhodopsins, light-gated channels from flagellate green algae, are extensively used as optogenetic photoactivators of neurons in research and recently have progressed to clinical trials for vision restoration. However, the molecular mechanisms of their photoactivation remain poorly understood. We recently identified cryptophyte cation channelrhodopsins, structurally different from those of green algae, which have separately evolved to converge on light-gated cation conductance. This study reveals diversity within this new protein family and describes a subclade with unusually rapid desensitization that results in short transient photocurrents in continuous light. Such transient currents have not been observed in the green algae channelrhodopsins and are potentially useful in optogenetic protocols. Kinetic UV-vis spectroscopy and photoelectrophysiology reveal the desensitization is caused by rapid accumulation of a non-conductive photointermediate in the photochemical reaction cycle. The absorption maximum of the intermediate is 330 nm, the shortest wavelength reported in any rhodopsin, indicating a novel chromophore structure.
The pathognomonic FOXL2 C134W mutation alters DNA binding specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Rachelle , Grace Cheng S.-W. , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: March 2020

The somatic missense point mutation c.402C>G (p.C134W) in the FOXL2 transcription factor is pathognomonic for adult-type granulosa cell tumours (AGCT) and a diagnostic marker for this tumour type. However, the molecular consequences of this mutation and its contribution to the mechanisms of AGCT pathogenesis remain unclear. To explore the mechanisms driving FOXL2C134W pathogenicity we engineered V5-FOXL2WT and V5-FOXL2C134W inducible isogenic cell lines and performed ChIP-seq and transcriptome profiling. We found that FOXL2C134W associates with the majority of the FOXL2 WT DNA elements as well as a large collection of unique elements genome-wide. We confirmed an altered DNA binding specificity for FOXL2C134Win vitro and identified unique targets of FOXL2C134W including SLC35F2 whose expression increased sensitivity to YM155 in our model.

Statement of Significance

Mechanistic understanding of FOXL2C134W induced regulatory state alterations drives discovery of a rationally designed therapeutic strategy.
Combining mass spectrometric platforms for lipidome investigation - Application to the characterisation of disruptions in the lipid profile of pig serum upon β-agonist treatment
Authors: Marchand Jérémy , Guitton Yann , Martineau Estelle , Royer Anne-Lise , Balgoma David , Le Bizec Bruno , Giraudeau Patrick , Dervilly Gaud
Published: March 2020

In the last decade, many mass spectrometric fingerprinting methods dedicated to lipidomics have been proposed: either non-targeted approaches, coupled with annotation methods, or targeted strategies, aiming at specifically monitoring a limited number of substances.

In a general public health perspective and through a strategy combining non-targeted and targeted lipidomics MS-based approaches, this study aims at identifying disrupted patterns in serum lipidome upon growth promoter treatment in pig and evaluating the relative contributions of the three platforms involved.

Pig serum samples collected during an animal experiment involving control and treated animals, whose food had been supplemented with ractopamine, were extracted and characterised using three MS strategies: Non-targeted RP LC-HRMS; the targeted Lipidyzer™ platform (differential ion mobility associated with shotgun lipidomics) and a homemade LC-HRMS triglyceride platform.

The three different platforms showed complementarity insight into lipid characterisation, which, applied to a selected set of samples, enabled highlighting specific lipid profile patterns involving various lipid classes, mainly in relation with cholesterol esters, sphingomyelins, lactosylceramide, phosphatidylcholines and triglycerides.

Thanks to the combination of both non-targeted and targeted MS approaches, the exploration of various compartments of the pig serum lipidome could be performed, including commonly characterised lipids (Lipidyzer™), triglyceride isomers (Triglyceride platform) -whose accurate analysis was considered an analytical challenge, and unique lipid features (non-targeted LC-HRMS). Thanks to their respective characteristics, the complementarity of the three tools could be demonstrated for public health purposes, with enhanced lipidome coverage, level of characterisation and applicability.
Analysis ofPlasmodium vivaxschizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions
Authors: Siegel Sasha V. , Chappell Lia , Hostetler Jessica B. , Amaratunga Chanaki , Suon Seila , Böhme Ulrike , Berriman Matthew , Fairhurst Rick M. , Rayner Julian C.
Published: March 2020

Plasmodium vivaxgene regulation remains difficult to study due to the lack of a robustin vitroculture method, low parasite densities in peripheral circulation and asynchronous parasite development. We adapted an RNA-seq protocol “DAFT-seq” to sequence the transcriptome of fourP. vivaxfield isolates that were cultured for a short periodex vivobefore using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5’ and 3’ untranslated regions (UTRs), some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity betweenP. vivaxschizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lackPlasmodium falciparumhomologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity withinP. vivaxtranscriptomes will be essential for the prioritisation of novel vaccine targets.
Sulfopin, a selective covalent inhibitor of Pin1, blocks Myc-driven tumor initiation and growthin vivo
Authors: Dubiella Christian , Pinch Benika J. , Zaidman Daniel , Manz Theresa D. , Poon Evon , He Shuning , Resnick Efrat , Langer Ellen M. , Daniel Colin J. , Seo Hyuk-Soo , Chen Ying , Ficarro Scott B. , Jamin Yann , Lian Xiaolan , Kibe Shin , Kozono Shingo , Koikawa Kazuhiro , Doctor Zainab M. , Nabet Behnam , Browne Christopher M. , Yang Annan , Stoler-Barak Liat , Shah Richa B. , Vangos Nick E. , Geffken Ezekiel A. , Oren Roni , Sidi Samuel , Shulman Ziv , Wang Chu , Marto Jarrod A. , Dhe-Paganon Sirano , Look Thomas , Zhou Xiao Zhen , Lu Kun Ping , Sears Rosalie C. , Chesler Louis , Gray Nathanael S. , London Nir
Published: March 2020

The peptidyl-prolyl cis-trans isomerase, Pin1, acts as a unified signaling hub that is exploited in cancer to activate oncogenes and inactivate tumor suppressors, in particular through up-regulation of c-Myc target genes. However, despite considerable efforts, Pin1 has remained an elusive drug target. Here, we screened an electrophilic fragment library to discover covalent inhibitors targeting Pin1’s active site nucleophile - Cys113, leading to the development of Sulfopin, a double-digit nanomolar Pin1 inhibitor. Sulfopin is highly selective for Pin1, as validated by two independent chemoproteomics methods, achieves potent cellular andin vivotarget engagement, and phenocopies genetic knockout of Pin1. Although Pin1 inhibition had a modest effect on viability in cancer cell cultures, Sulfopin induced downregulation of c-Myc target genes and reduced tumor initiation and tumor progression in murine and zebrafish models of MYCN-driven neuroblastoma. Our results suggest that Sulfopin is a suitable chemical probe for assessing Pin1-dependent pharmacology in cells andin vivo. Moreover, these studies indicate that Pin1 should be further investigated as a potential cancer target.
Development of Nanobodies as first-in-class inhibitors for the NEDP1 deNEDDylating enzyme
Authors: Abidi Naima , Trauchessec Helene , Hassanzadeh-Ghassabeh Gholamreza , Pugniere Martine , Muyldermans Serge , Xirodimas Dimitris P.
Published: March 2020

Protein NEDDylation emerges as an important post-translational modification and an attractive target for therapeutic intervention. Modification of NEDD8 onto substrates is finely balanced by the co-ordinated activity of conjugating and deconjugating enzymes. The NEDP1/DEN1/SENP8 protease is a NEDD8 specific processing and deconjugating enzyme that regulates the NEDDylation mainly of non-cullin substrates. Here, we report the development and characterisation of nanobodies as first-in-class inhibitors for NEDP1. The nanobodies display high-affinity (low nM) against NEDP1 and specifically inhibit NEDP1 processing activityin vitroand NEDP1 deconjugating activity in tissue-culture cells and in cell extracts. We also isolated nanobodies that bind to NEDP1 with high-affinity but do not affect NEDP1 activity. The developed nanobodies provide new tools to study the function of NEDP1 and to prevent deNEDDylation in cell extracts used in biochemical assays.
True S-cones are concentrated in the ventral mouse retina for color detection in the upper visual field
Authors: Nadal-Nicolás Francisco M. , Kunze Vincent P. , Ball John M. , Peng Brian , Krisnan Akshay , Zhou Gaohui , Dong Lijin , Li Wei
Published: March 2020

Color, an important visual cue for survival, is encoded by comparing signals from photoreceptors with different spectral sensitivities. The mouse retina expresses a short wavelength-sensitive and a middle/long wavelength-sensitive opsin (S- and M-opsin), forming opposing, overlapping gradients along the dorsal-ventral axis. Here, we analyzed the distribution of all cone types across the entire retina for two commonly used mouse strains. We found, unexpectedly, that ‘true’ S-cones (S-opsin only) are highly concentrated (up to 30% of cones) in ventral retina. Moreover, S-cone bipolar cells (SCBCs) are also skewed towards ventral retina, with wiring patterns matching the distribution of true S-cones. In addition, true S-cones in the ventral retina form clusters, which may augment synaptic input to SCBCs. Such a unique true S-cone pattern forms a basis for mouse color vision, likely reflecting evolutionary adaption to enhance color coding for the upper visual field suitable for mice’s habitat and behavior.
Detection and skeletonization of single neurons and tracer injections using topological methods
Authors: Wang Dingkang , Magee Lucas , Huo Bing-Xing , Banerjee Samik , Li Xu , Jayakumar Jaikishan , Lin Meng Kuan , Ram Keerthi , Wang Suyi , Wang Yusu , Mitra Partha P.
Published: March 2020

Neuroscientific data analysis has traditionally relied on linear algebra and stochastic process theory. However, the tree-like shapes of neurons cannot be described easily as points in a vector space (the subtraction of two neuronal shapes is not a meaningful operation), and methods from computational topology are better suited to their analysis. Here we introduce methods from Discrete Morse (DM) Theory to extract the tree-skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. Since individual neurons are topologically trees, it is sensible to summarize the collection of neurons using a consensus tree-shape that provides a richer information summary than the traditional regional ‘connectivity matrix’ approach. The conceptually elegant DM approach lacks hand-tuned parameters and captures global properties of the data as opposed to previous approaches which are inherently local. For individual skeletonization of sparsely labelled neurons we obtain substantial performance gains over state-of-the-art non-topological methods (over 10% improvements in precision and faster proofreading). The consensus-tree summary of tracer injections incorporates the regional connectivity matrix information, but in addition captures the collective collateral branching patterns of the set of neurons connected to the injection site, and provides a bridge between single-neuron morphology and tracer-injection data.
Iodine staining as a useful probe for distinguishing amyloid fibril polymorphs
Authors: Hiramatsu Takato , Yamamoto Naoki , Ha Seongmin , Masuda Yuki , Yasuda Mitsuru , Ishigaki Mika , Yuzu Keisuke , Ozaki Yukihiro , Chatani Eri
Published: March 2020

It is recently suggested that amyloid polymorphism, i.e., structural diversity of amyloid fibrils, has a deep relationship with pathology. However, its prompt recognition is almost halted due to insufficiency of analytical methods for detecting polymorphism of amyloid fibrils sensitively and quickly. Here, we propose that iodine staining, a historically known reaction that was firstly found by Virchow, can be used as a method for distinguishing amyloid polymorphs. When insulin fibrils were prepared and iodine-stained, they exhibited different colors depending on polymorphs. Each of the colors was inherited to daughter fibrils by seeding reactions. The colors were fundamentally represented as a sum of three absorption bands in visible region between 400-750 nm, and the bands showed different titration curves against iodine, suggesting that there are three specific iodine binding sites. The analysis of resonance Raman spectra and polarization microscope suggested that several polyiodide ions composed of I3−and/or I5−were formed on the grooves or the edges of β-sheets. It was concluded that the polyiodide species and conformations formed are sensitive to surface structure of amyloid fibrils, and the resultant differences in color will be useful for detecting polymorphism in a wide range of diagnostic samples.
In vivo validation of spray-dried mesoporous bioactive glass microspheres acting as prolonged local release systems for BMP-2 to induce bone regeneration
Authors: Berkmann Julia C. , Herrera Martin Aaron X. , Pontremoli Carlotta , Zheng Kai , Bucher Christian H. , Ellinghaus Agnes , Boccaccini Aldo R. , Fiorilli Sonia , Vitale-Brovarone Chiara , Duda Georg N. , Schmidt-Bleek Katharina
Published: March 2020

Despite years of diligent research in fracture healing, an unmet clinical need for safe and effective pharmacological treatments to improve bone regeneration persists with 10 – 20 % of fracture cases exhibiting impaired healing. Bone morphogenetic protein-2 (BMP-2) is a known key mediator of physiological bone regeneration and is clinically approved for selected musculoskeletal interventions. Yet, broad usage of this growth factor is impeded due to side effects that are majorly evoked by high dosages and burst release kinetics.

In this study, mesoporous bioactive glass microspheres (MBGs) produced by an aerosol assisted spray-drying, scalable process were found to be biocompatible and to induce a pro-osteogenic response on human MSCs in vitro. Loading of the MBGs with BMP-2 resulted in prolonged, low-dose BMP-2 release without affecting the material features. In a pre-clinical rodent model, BMP-2 loaded MBGs significantly enhanced bone formation and influenced the microarchitecture of newly formed bone. The MBG carriers alone performed equal to the untreated (empty) control in most parameters tested, while additionally exerting mild pro-angiogenic effects.

Using MBGs as a biocompatible, pro-regenerative carrier for local and sustained low dose BMP-2 release could limit side effects, thus enabling a safer usage of BMP-2 as a potent pro-osteogenic growth factor.
Mouse higher visual areas provide both distributed and discrete contributions to visually guided behaviors
Authors: Jin Miaomiao , Glickfeld Lindsey L.
Published: March 2020

Cortical parallel processing streams segregate many diverse features of a sensory scene. However, some features are distributed across streams, begging the question of whether and how such distributed representations contribute to perception. We determined the necessity of primary visual cortex (V1) and three key higher visual areas (LM, AL and PM) for perception of orientation and contrast, two features that are robustly encoded across all four areas. Suppressing V1, LM or AL decreased sensitivity for both orientation discrimination and contrast detection, consistent with a role for these areas in sensory perception. In comparison, suppressing PM selectively increased false alarm rates during contrast detection, without any effect on orientation discrimination. This effect was not retinotopically-specific, suggesting a distinct role for PM in the regulation of noise during decision-making. Thus, we find that distributed representations in the visual system can nonetheless support specialized perceptual roles for higher visual cortical areas.
Time-resolved, single-molecule, correlated chemical probing of RNA
Authors: Ehrhardt Jeffrey E. , Weeks Kevin M.
Published: March 2020

Methods for capturing the folding dynamics of functionally important RNAs, especially large RNAs, have relied primarily on global measurements of structure or on per-nucleotide chemical probing. These approaches infer, but do not directly measure, through-space tertiary interactions. Here we introduce trimethyloxonium (TMO) as a chemical probe for RNA. TMO enables time-resolved, single-molecule, through-space structure probing of RNA folding using a correlated chemical probing framework. TMO methylates RNA about 90 times faster than the widely used dimethyl sulfate probe, allowing structure interrogation on the second time scale. We used TMO to monitor folding of the RNase P RNA – a functional RNA with extensive long-range and noncanonical interactions – by direct measurement of through-space tertiary interactions in a time-resolved way. Time-dependent correlation changes directly revealed the central role of a long-range tertiary loop-loop interaction that guides native RNA folding. Single-molecule, time-resolved RNA structure probing with TMO is poised to reveal a wide range of dynamic RNA folding processes and principles of RNA folding.
Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis
Authors: Sardar Rahila , Satish Deepshikha , Birla Shweta , Gupta Dinesh
Published: March 2020

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein function and stability, using computational approach. To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa-miR-27b is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes
The single flagellum ofLeishmaniahas a fixed polarisation of its asymmetric beat
Authors: Wang Ziyin , Beneke Tom , Gluenz Eva , Wheeler Richard John
Published: March 2020

Eukaryotic flagella undergo different beat types necessary for their function. The single flagellum onLeishmaniaparasites, for example, undergoes a symmetric tip-to-base beat for forward swimming and an asymmetric base-to-tip beat to rotate the cell. Asymmetric beats are most commonly associated with multi-ciliated tissues or organisms where the asymmetry has a constant polarisation. We asked whether this also holds for the singleLeishmaniaflagellum. To do so, we used high frame rate dual colour fluorescence microscopy to visualise intracellular and intraflagellar structure in live swimming cells. This showed that the asymmetricLeishmaniabeat has a fixed polarisation. As inChlamydomonas, this asymmetry arose from an asymmetric static curvature combined with a symmetric dynamic curvature. Some axoneme protein deletion mutants give flagella which retain static curvature, but lack dynamic curvature. We saw that these retain a fixed polarisation. Similarly, deletion mutants which disrupt vital asymmetric extra-axonemal and rootlet-like flagellum-associated structures also retain a fixed polarisation. This indicated that beat asymmetry does not originate from rootlet-like and extra-axonemal structures and is likely intrinsic to either the nine-fold rotational symmetry of the axoneme structure or due to differences between the outer doublet decorations.
Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2
Authors: Munster Vincent J. , Feldmann Friederike , Williamson Brandi N. , van Doremalen Neeltje , Pérez-Pérez Lizzette , Schulz Jonathan , Meade-White Kimberly , Okumura Atsushi , Callison Julie , Brumbaugh Beniah , Avanzato Victoria A. , Rosenke Rebecca , Hanley Patrick W. , Saturday Greg , Scott Dana , Fischer Elizabeth R. , de Wit Emmie
Published: March 2020

An outbreak of a novel coronavirus, now named SARS-CoV-2, causing respiratory disease and a ∼2% case fatality rate started in Wuhan, China in December 2019. Following unprecedented rapid global spread, the World Health Organization declared COVID-19 a pandemic on March 11, 2020. Although data on disease in humans are emerging at a steady pace, certain aspects of the pathogenesis of SARS-CoV-2 can only be studied in detail in animal models, where repeated sampling and tissue collection is possible. Here, we show that SARS-CoV-2 causes respiratory disease in infected rhesus macaques, with disease lasting 8-16 days. Pulmonary infiltrates, a hallmark of human disease, were visible in lung radiographs of all animals. High viral loads were detected in swabs from the nose and throat of all animals as well as in bronchoalveolar lavages; in one animal we observed prolonged rectal shedding. Taken together, the rhesus macaque recapitulates moderate disease observed in the majority of human cases. The establishment of the rhesus macaque as a model of COVID-19 will increase our understanding of the pathogenesis of this disease and will aid development and testing of medical countermeasures.
Alternative Conformations and Motions Adopted by 30S Ribosomal Subunits Visualized by Cryo-Electron Microscopy
Authors: Jahagirdar Dushyant , Jha Vikash , Basu Kaustuv , Gomez-Blanco Josue , Vargas Javier , Ortega Joaquin
Published: March 2020

It is only after recent advances in cryo-electron microscopy that is now possible to describe at high resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between the “active” and “inactive” conformations. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6Å resolution and study its motions. In the inactive conformation, three nucleotides at the 3’ end of the 16S rRNA cause the region of helix 44 forming the decoding center to adopt an unlatched conformation and the 3’ end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42 °C reverts these structural changes. The position adopted by helix 44 dictates the most prominent motions of the 30S subunit. We found that extended exposures to low magnesium concentrations induces unfolding of large rRNA structural domains. The air-water interface to which ribosome subuints are exposed during sample preparation also peel off some ribosomal proteins. Overall this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution.
A molecular mechanism for LINC complex branching by structurally diverse SUN-KASH 6:6 assemblies
Authors: Gurusaran Manickam , Davies Owen R.
Published: March 2020

The LINC complex mechanically couples cytoskeletal and nuclear components across the nuclear envelope to fulfil a myriad of cellular functions, including nuclear shape and positioning, hearing and meiotic chromosome movements. The canonical model of the LINC complex is of individual linear nucleocytoskeletal linkages provided by 3:3 interactions between SUN and KASH proteins. Here, we provide crystallographic and biophysical evidence that SUN-KASH is a constitutive 6:6 complex in which two SUN trimers interact back-to-back. A common SUN-KASH topology is achieved through structurally diverse 6:6 interaction mechanisms by distinct KASH proteins, including zinc-coordination by Nesprin-4. The SUN-KASH 6:6 complex is incompatible with the current model of a linear LINC complex and instead suggests the formation of a branched LINC complex network. In this model, SUN-KASH 6:6 complexes act as nodes for force distribution and integration between adjacent SUN and KASH molecules, enabling the coordinated transduction of large forces across the nuclear envelope.
Japanese Clinical Practice Guidelines for Vascular Anomalies 2017
Authors: Mimura Hidefumi , Akita Sadanori , Fujino Akihiro , Jinnin Masatoshi , Ozaki Mine , Osuga Keigo , Nakaoka Hiroki , Morii Eiichi , Kuramochi Akira , Aoki Yoko , Arai Yasunori , Aramaki Noriko , Inoue Masanori , Iwashina Yuki , Iwanaka Tadashi , Ueno Shigeru , Umezawa Akihiro , Ozeki Michio , Ochi Junko , Kinoshita Yoshiaki , Kurita Masakazu , Seike Shien , Takakura Nobuyuki , Takahashi Masataka , Tachibana Takao , Chuman Kumiko , Nagata Shuji , Narushima Mitsunaga , Niimi Yasunari , Nosaka Shunsuke , Nozaki Taiki , Hashimoto Kazuki , Hayashi Ayato , Hirakawa Satoshi , Fujikawa Atsuko , Hori Yumiko , Matsuoka Kentaro , Mori Hideki , Yamamoto Yuki , Yuzuriha Shunsuke , Rikihisa Naoaki , Watanabe Shoji , Watanabe Shinichi , Kuroda Tatsuo , Sugawara Shunsuke , Ishikawa Kosuke , Sasaki Satoru
Published: March 2020

The objective was to prepare guidelines to perform the current optimum treatment by organizing effective and efficient treatments of hemangiomas and vascular malformations, confirming the safety and systematizing treatment, employing evidence‐based medicine techniques and aimed at improvement of the outcomes. Clinical questions (CQ) were decided based on the important clinical issues. For document retrieval, key words for published work searches were set for each CQ, and work published from 1980 to the end of September 2014 was searched in PubMed, Cochrane Library and Japana Centra Revuo Medicina databases. The strengths of evidence and recommendations acquired by systematic reviews were determined following the Medical Information Network Distribution System technique. A total of 33 CQ were used to compile recommendations and the subjects included efficacy of resection, sclerotherapy/embolization, drug therapy, laser therapy, radiotherapy and other conservative treatment, differences in appropriate treatment due to the location of lesions and among symptoms, appropriate timing of treatment and tests, and pathological diagnosis deciding the diagnosis. Thus, the Japanese Clinical Practice Guidelines for Vascular Anomalies 2017 have been prepared as the evidence‐based guidelines for the management of vascular anomalies.
Comparison of the effects of adding microbial transglutaminase to milk and ice cream mixture on the properties of ice cream
Authors: Al Merve , Ersöz Fatma , Özaktaş Tuğba , Türkanoğlu‐Özçelik Aysun , Küçükçetin Ahmet
Published: March 2020

In this study, the effect of recombinant microbial transglutaminase enzyme on the physicochemical properties of ice cream produced by two different methods was investigated. For this purpose, different enzyme units (2, 4 and 6 U/g milk protein) were applied to both ice cream mixture and milk. While with the first method, a 10% increase in the overrun value of ice cream samples was observed, a 7% increase was obtained by the second method. All ice cream samples exhibited pseudoplastic behaviour. This study indicated that  transglutaminase concentration is an important factor in terms of improving the physicochemical properties of ice cream.
Similarities and spatial variations of bacterial and fungal communities in field rice planthopper (Hemiptera: Delphacidae) populations
Authors: Bing Xiao‐Li , Zhao Dian‐Shu , Peng Chang‐Wu , Huang Hai‐Jian , Hong Xiao‐Yue
Published: March 2020

Rice planthoppers are notorious plant sap‐feeding pests which cause serious damage. While several microbes in rice planthoppers have been broadly characterized, the abundance and diversity of bacteria and fungi in field planthoppers are largely unknown. This study investigated the bacterial and fungal community compositions of Chinese wild rice planthoppers Laodelphax striatellus and Sogatella furcifera using parallel 16S rRNA gene amplicon and internal transcribed space region sequencing. The bacteria varied significantly between the species and were partitioned significantly by sex, tissues and host environments in each species. The majority of bacteria were affiliated with the genera Wolbachia, Cardinium, Rickettsia and Pantoea. The abundance of Wolbachia was negatively correlated with that of Cardinium in both planthopper species. Compared with bacteria, the abundance and diversity of fungi did not differ between sexes but both were enriched in the gut. The bacterial community as a whole showed no significant correlation with the fungal community. The majority of fungi were related to Sarocladium, Alternaria, Malassezia, Aspergillus and Curvularia. A phylogenetic analysis revealed that these fungi were closely related to botanic symbionts or pathogens. Our results provide novel insights into the bacteria and fungi of rice planthoppers.
Exceptional colloidal stability of acidified whey protein beverages stabilized by soybean soluble polysaccharide
Authors: Zamani Hediyeh , Zamani Somayeh , Zhang Zhong , Abbaspourrad Alireza
Published: March 2020

Protein‐rich beverages have gained significant attention in recent years. It is a challenge to produce whey protein beverages with high stability, good transparency, and a smooth mouthfeel. The polysaccharide (PS)–protein complex might help the food industry overcome these obstacles. In this study, soybean soluble polysaccharide (SSPS) and high methoxylated pectin (HMP, a traditional PS) are used, at different ratios to the protein, to improve the colloidal stability of the acidified whey protein solution. Both heated and unheated complexes were studied. SSPS–whey protein complexes have shown exceptional stabilities in all ratios while HMP–whey protein complexes revealed coacervation after 72 hr of storage. The prepared complexes exhibited comparable sizes and ζ‐potentials. The SSPS–whey protein complexes were less turbid than HMP–whey protein complexes at similar PS to protein ratios. Results also show that greater repulsive interactions occurred in SSPS–whey protein complexes when compared to HMP–whey protein complexes, as examined by free thiol content and intrinsic fluorescence intensity measurements.

Practical Application

It is a challenge to produce whey protein isolate (WPI) beverages with high stability, good transparency, and smooth mouthfeel. The polysaccharide (PS)–protein complex might help the food industry overcome these obstacles. We have demonstrated that soybean soluble polysaccharide (SSPS), at [SSPS]:[acWPI] ratios of 1:2 to 1:30, can significantly improve the colloidal stability of the acidified whey protein beverages. This SSPS–whey protein system could be used as a stable beverage base for a variety of beverages.
Modeling buffer capacity and pH in acid and acidified foods
Authors: Price Robert E. , Longtin Madyson , Conley‐Payton Summer , Osborne Jason A. , Johanningsmeier Suzanne D. , Bitzer Donald , Breidt Fred
Published: March 2020

Standard ionic equilibria equations may be used for calculating pH of weak acid and base solutions. These calculations are difficult or impossible to solve analytically for foods that include many unknown buffering components, making pH prediction in these systems impractical. We combined buffer capacity (BC) models with a pH prediction algorithm to allow pH prediction in complex food matrices from BC data. Numerical models were developed using Matlab software to estimate the pH and buffering components for mixtures of weak acid and base solutions. The pH model was validated with laboratory solutions of acetic or citric acids with ammonia, in combinations with varying salts using Latin hypercube designs. Linear regressions of observed versus predicted pH values based on the concentration and pK values of the solution components resulted in estimated slopes between 0.96 and 1.01 with and without added salts. BC models were generated from titration curves for 0.6 M acetic acid or 12.4 mM citric acid resulting in acid concentration and pK estimates. Predicted pH values from these estimates were within 0.11 pH units of the measured pH. Acetic acid concentration measurements based on the model were within 6% accuracy compared to high‐performance liquid chromatography measurements for concentrations less than 400 mM, although they were underestimated above that. The models may have application for use in determining the BC of food ingredients with unknown buffering components. Predicting pH changes for food ingredients using these models may be useful for regulatory purposes with acid or acidified foods and for product development.

Practical Application

Buffer capacity models may benefit regulatory agencies and manufacturers of acid and acidified foods to determine pH stability (below pH 4.6) and how low‐acid food ingredients may affect the safety of these foods. Predicting pH for solutions with known or unknown buffering components was based on titration data and models that use only monoprotic weak acids and bases. These models may be useful for product development and food safety by estimating pH and buffering capacity.
Chromosome‐level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune‐related genes in bivalves
Authors: Peng Jinxia , Li Qiongzhen , Xu Lian , Wei Pinyuan , He Pingping , Zhang Xingzhi , Zhang Li , Guan Junliang , Zhang Xiaojuan , Lin Yong , Gui Jianfang , Chen Xiaohan
Published: March 2020

Crassostrea hongkongensis is a popular and important native oyster species that is cultured mainly along the coast of the South China Sea. However, the absence of a reference genome has restricted genetic studies and the development of molecular breeding schemes for this species. Here, we combined PacBio and 10 × Genomics technologies to create a C. hongkongensis genome assembly, which has a size of 610 Mb, and is close to that estimated by flow cytometry (~650 Mb). Contig and scaffold N50 are 2.57 and 4.99 Mb, respectively, and BUSCO analysis indicates that 95.8% of metazoan conserved genes are completely represented. Using a high‐density linkage map of its closest related species, C. gigas, a total of 521 Mb (85.4%) was anchored to 10 haploid chromosomes. Comparative genomic analyses with other molluscs reveal that several immune‐ or stress response‐related genes extensively expanded in bivalves by tandem duplication, including C1q, Toll‐like receptors and Hsp70, which are associated with their adaptation to filter‐feeding and sessile lifestyles in shallow sea and/or deep‐sea ecosystems. Through transcriptome sequencing, potential genes and pathways related to sex determination and gonad development were identified. The genome and transcriptome of C. hongkongensis provide valuable resources for future molecular studies, genetic improvement and genome‐assisted breeding of oysters.
Surgical outcomes of segmental bronchial sleeve resection in central non‐small cell lung cancer
Authors: Qu Rirong , Ping Wei , Hao Zhipeng , Cai Yixin , Zhang Ni , Fu Xiangning
Published: March 2020

Background

The purpose of this study was to present the clinical and surgical results in patients who underwent segmental bronchial sleeve reconstruction.

Methods

The clinical and pathological data of 16 patients with central non‐small cell lung cancer (NSCLC) who underwent segmental bronchial sleeve resection from April 2015 to May 2019 were retrospectively analyzed.

Results

According to the type of segmental bronchial reconstruction, procedures were divided into four types: right upper S6 sleeve lobectomy in three cases (type A); left lower lingular sleeve lobectomy in 10 cases (type B); left upper S6 sleeve lobectomy in two cases (type C); and left lower propriolateral superior sleeve lobectomy in one case (type D). A total of three patients (18.75%) experienced anastomotic complications, including two with anastomotic stenosis and one with anastomotic fistula. All patients achieved R0 resection. Apart from one patient who died of acute lung infection after surgery, the rest were successfully discharged. The average follow‐up time was 28 months, and the overall survival rates of patients at one, two, and three years were 80.0%, 53.3%, and 40.0%, respectively.

Conclusions

Segmental bronchial sleeve resection is complex in technique and may have an increased risk of complications compared to a standard sleeve resection, but it is an effective and safe procedure, especially for selected patients with central lung cancer.
Comparison of safety of loop ileostomy and loop transverse colostomy for low‐lying rectal cancer patients undergoing anterior resection: A retrospective, single institution, propensity score‐matched study
Authors: Sun Xiyu , Han Huiqiao , Qiu Huizhong , Wu Bin , Lin Guole , Niu Beizhan , Zhou Jiaolin , Lu Junyang , Xu Lai , Zhang Guannan , Xiao Yi
Published: March 2020

Introduction

This study was to compare the prevalence of stoma‐related complications and stoma reversal perioperative complications of patients with low‐lying rectal cancer who received preventative loop ileostomy and those who underwent loop transverse colostomy.

Methods

This retrospective single‐center study analyzed the clinicopathologic and surgical data of 288 patients with pathologically proven primary rectal cancer who underwent anterior resection with either preventative loop ileostomy (n = 82) or loop transverse colostomy. To achieve comparability of a propensity score matching method was used to match patients from each group in a 1:2 ratio. Determinants of stoma‐related complications were analyzed by multivariate logistic regression analysis.

Results

Forty‐nine (74.3%) patients in the loop ileostomy group experienced stoma‐related complications versus 48.7% in the loop transverse colostomy group (P < 0.01). Irritant dermatitis was the most frequent complication in both groups. The loop ileostomy group had a significantly higher rate (24.24%) of stoma reversal perioperative complications than the loop transverse colostomy group. Multivariate logistic regression analysis showed that ileostomy versus loop transverse colostomy was a significant independent risk for stoma‐related complications and stoma reversal perioperative complications. Furthermore, by Clavien–Dindo classification, patients receiving loop ileostomy had an overall higher rate of complications and stoma reversal perioperative complications versus those undergoing loop transverse colostomy (P < 0.01). The rate of grade II complications was significantly higher in the loop ileostomy group (43.9%) than that of loop transverse colostomy group (13.5%, P < 0.01), whereas the rate of grade I, and grade IIIa and IIIb complications and stoma reversal perioperative complications was comparable between the two groups.

Conclusion

The study has demonstrated that loop transverse colostomy is associated with significantly lower rates of stoma‐related complications and stoma reversal perioperative complications compared to loop transverse colostomy.
Safety, pharmacokinetics and pharmacodynamics of branebrutinib (BMS‐986195), a covalent, irreversible inhibitor of Bruton's tyrosine kinase: Randomised phase I, placebo‐controlled trial in healthy participants
Authors: Catlett Ian M. , Nowak Miroslawa , Kundu Sudeep , Zheng Naiyu , Liu Ang , He Bing , Girgis Ihab G. , Grasela Dennis M.
Published: March 2020

Aims

Branebrutinib (BMS‐986195) is a potent, highly selective, oral, small‐molecule, covalent inhibitor of Bruton's tyrosine kinase (BTK). This study evaluated safety, pharmacokinetics and pharmacodynamics of branebrutinib in healthy participants.

Methods

This double‐blind, placebo‐controlled, single‐ and multiple‐ascending dose (SAD; MAD) Phase I study (NCT02705989) enrolled participants into 3 parts: SAD, MAD and JMAD (MAD in first‐generation Japanese participants). In each part, participants were randomised 3:1 to receive branebrutinib (SAD: 0.3–30 mg; [J]MAD: 0.3–10 mg) or placebo. Participants in the MAD parts received branebrutinib daily for 14 days and were followed for 14 days postdosing. Safety was assessed by monitoring, laboratory and physical examinations, vital signs, and recording adverse events (AEs). Pharmacodynamics were assessed with a mass spectrometry assay that measured drug‐occupied and free BTK.

Results

The SAD, MAD and JMAD parts of the study included 40, 32 and 24 participants. Branebrutinib was well tolerated and AEs were mild/moderate, except for 1 serious AE that led to discontinuation. Branebrutinib was rapidly absorbed, with maximum plasma concentration occurring within 1 hour and a half‐life of 1.2—1.7 hours, dropping to undetectable levels within 24 hours. BTK occupancy was rapid, with 100% occupancy reached after a single 10‐mg dose. BTK occupancy decayed predictably over time (mean half‐life in MAD panels: 115–154 hours), such that pharmacodynamic effects were maintained after branebrutinib plasma levels fell below the lower limit of quantification.

Conclusion

Rapid and high occupancy of BTK and the lack of notable safety findings support further clinical development of branebrutinib.
Helicobacter pylori CagA oncoprotein interacts with SHIP2 to increase its delivery into gastric epithelial cells
Authors: Fujii Yumiko , Murata-Kamiya Naoko , Hatakeyama Masanori
Published: March 2020

Chronic infection with Helicobacter pylori cagA‐positive strains is causally associated with the development of gastric diseases, most notably gastric cancer. The cagA‐encoded CagA protein, which is injected into gastric epithelial cells by bacterial type IV secretion, undergoes tyrosine phosphorylation at the Glu‐Pro‐Ile‐Tyr‐Ala (EPIYA) segments (EPIYA‐A, EPIYA‐B, EPIYA‐C, and EPIYA‐D), which are present in various numbers and combinations in its C‐terminal polymorphic region, thereby enabling CagA to promiscuously interact with SH2 domain‐containing host cell proteins, including the prooncogenic SH2 domain‐containing protein tyrosine phosphatase 2 (SHP2). Perturbation of host protein functions by aberrant complex formation with CagA has been considered to contribute to the development of gastric cancer. Here we show that SHIP2, an SH2 domain‐containing phosphatidylinositol 5′‐phosphatase, is a hitherto undiscovered CagA‐binding host protein. Similar to SHP2, SHIP2 binds to the Western CagA‐specific EPIYA‐C segment or East Asian CagA‐specific EPIYA‐D segment through the SH2 domain in a tyrosine phosphorylation‐dependent manner. In contrast to the case of SHP2, however, SHIP2 binds more strongly to EPIYA‐C than to EPIYA‐D. Interaction with CagA tethers SHIP2 to the plasma membrane, where it mediates production of phosphatidylinositol 3,4‐diphosphate [PI(3,4)P2]. The CagA‐SHIP2 interaction also potentiates the morphogenetic activity of CagA, which is caused by CagA‐deregulated SHP2. This study indicates that initially delivered CagA interacts with SHIP2 and thereby strengthens H. pylori‐host cell attachment by altering membrane phosphatidylinositol compositions, which potentiates subsequent delivery of CagA that binds to and thereby deregulates the prooncogenic phosphatase SHP2.