bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications
Authors: Baianu I.
Published: July 2019

Molecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for 'skeletal models', graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Structural and Dynamic Studies of Amino Acids, Proteins and Nucleic Acids By Chemical-Hyperspectral Imaging, FT-IR/NIR, Vibro-Rotational Spectroscopy, Plasma, Microwave and Neutron Spectroscopy
Authors: Baianu I.
Published: July 2019

A detailed review of structural and dynamic studies of amino acids, proteins and nucleic acids by spectroscopic techniques: microwaves, near infrared, UV, X-rays and neutrons, including also EXAFS, chemical-hyperspectral imaging and fluorescence correlation spectroscopy and FLIM, FRAP imaging with references, instrumentation diagrams and application examples for several related areas.
An insight into the kinships of the fungi
Authors: Datta Riddhi , Sarkar Joy , Acharya Krishnendu
Published: July 2019

The evolutionary origin of fungi is important in determining the phylogenetic relationships between fungi, animals and plants. However, determining the true relationship of fungi has been somewhat difficult owing to their simple morphology and presence of convergent characters. With the advent of newer molecular techniques, analysis of conserved protein sequences, cytochrome systems, mitochondrial and nuclear genetic material and rRNAs are being employed in elucidating phylogenetic kinships among the eukaryotes. These emerging evidences suggest that the derivation of the fungi from plants or algae would require more evolutionary changes than its derivation from protozoa, the unicellular ancestor of the animals. To gain an overview of the current state of the science, we have extensively reviewed the existing literatures and it appeared to us that fungi are more closely related to animals than to plants.
Human neuromaturation, juvenile extreme energy liability, and adult cognition/cooperation
Authors: Skoyles John
Published: July 2019

Human childhood and adolescence is the period in which adult cognitive competences (including those that create the unique cooperativeness of humans) are acquired. It is also a period when neural development puts a juvenile’s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses ≈50% of its total energy expenditure (TEE) (cf. adult ≈12%). This brain expensiveness is due to (1) the brain making up ≈6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is ≈100% greater in the gray matter of a child than in an adult (a result of the extra costs of synaptic neuromaturation). The high absolute number of neurons in the human brain requires as part of learning a prolonged neurodevelopment. This refines inter- and intraarea neural networks so they become structured with economical “small world” connectivity attributes (such as hub organization and high cross-brain differentiation/integration). Once acquired, this connectivity enables highly complex adult cognitive capacities. Humans evolved as hunter-gatherers. Contemporary hunter-gatherers (and it is also likely Middle Paleolithic ones) pool high energy foods in an egalitarian manner that reliably supported mothers and juveniles with high energy intake. This type of sharing unique to humans protects against energy shortage happening to the immature brain. This cooperation that protects neuromaturation arises from adults having the capacity to communicate and evaluate social reputation, cognitive skills that exist as a result of extended neuromaturation. Human biology is therefore characterized by a presently overlooked bioenergetic-cognition loop (called here the “HEBE ring”) by which extended neuromaturation creates the cooperative abilities in adults that support juveniles through the potentially vulnerable period of the neurodevelopment needed to become such adults.
Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Authors: Prisecaru V. , Baianu I
Published: July 2019

A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such 'dynamically inter-connected' biomolecules form numerous inter-related pathways referred to as 'molecular networks'. One such family of signaling pathways contains the cell cyclins. Cyclins are proteins that link several critical pro-apoptotic and other cell cycling/division components, including the tumor suppressor gene TP53 and its product, the Thomsen-Friedenreich antigen (T antigen), Rb, mdm2, c-Myc, p21, p27, Bax, Bad and Bcl-2, which play major roles in various neoplastic transformations of many tissues.The novel theoretical analysis presented here is based on recently published studies of arrested cell differentiation that normally leads to neural system formation during early developmental stages; the perturbed development may involve cyclin signaling and cell cycling responsible for rapidly induced cell proliferation without differentiation into neural cells in such experimental studies.
Generalized Theory of Life
Authors: Kalmykov Vyacheslav
Published: July 2019

The paper is mathematically, physically and biologically inspired - it is a deductive attempt of the biologist to find the most appropriate language for modelling of life. Applications of mathematical structures - groupoids, groups, categories, functors and monads, which are the most effective for the description of the complex objects, are discussed. Some new conceptions and interpretations were introduced: unified classification of complex systems; the generalized conception about stationary states of any autonomous agent ("Statology"); the total quantitative criterions of evolutionary direction; the generalized group of symmetry. The definitions of information, entropy, organization, behavior, evolution, creation, life, culture, cognition were formulated. An actually closed and potentially opened ecosystem was introduced as the elementary object of organization and evolution of life. Evolution considered as process of generating of a concrete group G of permutations of elements of ecosystems, which is based on activities of the intrinsic autonomous agents. Life was considered as the way of realization of extreme principles of physics through co-organizing of behavior of the ecosystem elements and through dilating borders of the ecosystem by an interiorization of an extrinsic environment.
Nonlinear Models of Neural and Genetic Network Dynamics
Authors: Baianu I.
Published: July 2019

A categorical and Łukasiewicz-Topos framework for Łukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks.
On Asymmetry in Biology and Nature
Authors: Baianu I.
Published: July 2019

Symmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by ‘perfect’ order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered ‘structure’ that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to anatomy- one often finds asymmetry to be present , although symmetries are also encountered whenever nature affords it. An important case is that of cell biomembranes that possess a marked structural and functional asymmetry which is essential to the survival of cells and microorganisms. Asymmetry both in time and selection ‘criteria’ plays a key role in the evolution of organisms and species.
Analysis of DTC nutrigenetic services in Italy: state of the art, agreement to the ESHG statement and future outlooks
Authors: Cocozza Sergio , Pinelli Michele , Cinque Vincenzo , Acquaviva Fabio , Vergara Paola , Cianflone Alessandra , Castaldo Imma , Monticelli Antonella
Published: July 2019

Background:

In both USA and Europe operate companies selling Direct-to-consumer genetic tests (DTC). These tests are offered to healthy people aiming to identify predispositions to complex diseases and to take preventive measures. Several DTC-nutrigenetic tests (DNTs) are available on the market. They propose the definition of a personalized diet, on the basis of the investigated genetic variants, which would reduce the risk of developing those diseases which have been associated to specific genetic markers. However, the risk/benefit balance of exposing unselected population to genetic testing without any medical surveillance is far from be established. Furthermore, it lacks an accepted procedure to select which genetic markers needs to be investigated, to evaluate their specific role and, as consequence, to define a personalized diet. Within this context, the European Society of Human Genetics (ESHG) released a statement regarding the DTC tests that has been ratified by several national societies including the Italian one.In the present study we analyzed the DNT offered in Italy, the state of the art and the abidance with the ESHG statement.

Methods:

We queried web search engine for the DNT offered to italian population, portraying a non-specialized customer. We examined the DNTs vendor websites and/or directly contacted the companies to collect information on: 1) genetic marker essayed, 2) diseases and phenotypes considered and 3) kind of dietary advices provided. Finally, we evaluated the abidance to the ESHG statement. The study was conducted between November, 2010 and May, 2011.

Results:

Six companies operate in Italy with a total of seven different DNTs offered. Both studied phenotypes and investigated genetic markers were very different among companies, with a relative higher level of agreement for phenotype than for genes. None of the companies described the methods used to select markers and to define diet advices. None of the companies showed a complete agreement to the statement of the ESHG.

Conclusion:

Although DNT companies' efforts are worthy, a standardization of methods and a more strictly agreement with ESHG statement should be encouraged.
Epigenetic reprogramming of primary pancreatic cancer cells counteracts their in vivo tumourigenicity
Authors: Khoshchehreh Reyhaneh , Totonchi Mehdi , Carlos Ramirez Juan , Torres Raul , Baharvand Hossein , Aicher Alexandra , Ebrahimi Marzieh , Heeschen Christopher
Published: July 2019

Pancreatic ductal adenocarcinoma (PDAC) arises through accumulation of multiple genetic alterations. However, cancer cells also acquire and depend on cancer-specific epigenetic changes. To conclusively demonstrate the crucial relevance of the epigenetic programme for the tumourigenicity of the cancer cells, we used cellular reprogramming technology to reverse these epigenetic changes. We reprogrammed human PDAC cultures using three different techniques – (1) lentivirally via induction of Yamanaka Factors (OSKM), (2) the pluripotency-associated gene OCT4 and the microRNA mir-302, or (3) using episomal vectors as a safer alternative without genomic integration. We found that induction with episomal vectors was the most efficient method to reprogram primary human PDAC cultures as well as primary human fibroblasts that served as positive controls. Successful reprogramming was evidenced by immunostaining, alkaline phosphatase staining, and real-time PCR. Intriguingly, reprogramming of primary human PDAC cultures drastically reduced their in vivo tumourigenicity, which appeared to be driven by the cells’ enhanced differentiation and loss of stemness upon transplantation. Our study demonstrates that reprogrammed primary PDAC cultures are functionally distinct from parental PDAC cells resulting in drastically reduced tumourigenicity in vitro and in vivo. Thus, epigenetic alterations account at least in part for the tumourigenicity and aggressiveness of pancreatic cancer, supporting the notion that epigenetic modulators could be a suitable approach to improve the dismal outcome of patients with pancreatic cancer.
Environmental conditions shape the nature of a minimal bacterial genome
Authors: Antczak Magdalena , Michaelis Martin , Wass Mark N.
Published: July 2019

Of the 473 genes in the genome of the bacterium with the smallest genome generated to date, 149 genes have unknown function, emphasising a universal problem; less than 1% of proteins have experimentally determined annotations. Here, we combine the results from state-of-the-art in silico methods for functional annotation and assign functions to 66 of the 149 proteins. Proteins that are still not annotated lack orthologues, lack protein domains, and/ or are membrane proteins. Twenty-four likely transporter proteins are identified indicating the importance of nutrient uptake into and waste disposal out of the minimal bacterial cell in a nutrient-rich environment after removal of metabolic enzymes. Hence, the environment shapes the nature of a minimal genome. Our findings also show that the combination of multiple different state-of-the-art in silico methods for annotating proteins is able to predict functions, even for difficult to characterise proteins and identify crucial gaps for further development.
Apoptotic signalling targets the post-endocytic sorting machinery of the death receptor Fas/CD95
Authors: Sharma Shruti , Carmona Antonio , Skowronek Agnieszka , Yu Fangyan , Collins Mark O. , Naik Sindhu , Murzeau Claire M. , Tseng Pei-Li , Erdmann Kai S.
Published: July 2019

Fas plays a major role in regulating ligand-induced apoptosis in many cell types. It is well known that several cancers demonstrate reduced cell surface levels of Fas and thus escape a potential control system via ligand-induced apoptosis, although underlying mechanisms are unclear. Here we report that the endosome associated trafficking regulator 1 (ENTR1), controls cell surface levels of Fas and Fas-mediated apoptotic signalling. ENTR1 regulates, via binding to the coiled coil domain protein Dysbindin, the delivery of Fas from endosomes to lysosomes thereby controlling termination of Fas signal transduction. We demonstrate that ENTR1 is cleaved during Fas-induced apoptosis in a caspase-dependent manner revealing an unexpected interplay of apoptotic signalling and regulation of endolysosomal trafficking resulting in a positive feedback signalling-loop. Our data provide insights into the molecular mechanism of Fas post-endocytic trafficking and signalling, opening possible explanations on how cancer cells regulate cell surface levels of death receptors.
Mutation bias and GC content shape antimutator invasions
Authors: Couce Alejandro , Tenaillon Olivier
Published: July 2019

Mutators represent a successful strategy in rapidly adapting asexual populations, but theory predicts their eventual extinction due to their unsustainably large deleterious load. While antimutator invasions have been documented experimentally, important discrepancies among studies remain currently unexplained. Here we show that a largely neglected factor, the mutational idiosyncrasy displayed by different mutators, can play a major role in this process. Analysing phylogenetically diverse bacteria, we find marked and systematic differences in the protein-disruptive effects of mutations caused by different mutators in species with different GC compositions. Computer simulations show that these differences can account for order-of-magnitude changes in antimutator fitness for a realistic range of parameters. Overall, our results suggest that antimutator dynamics may be highly dependent on the specific genetic, ecological and evolutionary history of a given population. This context-dependency further complicates our understanding of mutators in clinical settings, as well as their role in shaping bacterial genome size and composition.
The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data
Authors: Xia Enhua , Li Fangdong , Tong Wei , Yang Hua , Wang Songbo , Zhao Jian , Liu Chun , Gao Liping , Tai Yuling , She Guangbiao , Sun Jun , Cao Haisheng , Gao Qiang , Li Yeyun , Deng Weiwei , Jiang Xiaolan , Wang Wenzhao , Chen Qi , Zhang Shihua , Li Haijing , Wu Junlan , Wang Ping , Li Penghui , Shi Chengying , Zheng Fengya , Jian Jianbo , Huang Bei , Shan Dai , Shi Mingming , Fang Congbing , Yue Yi , Wu Qiong , Ge Ruoheng , Zhao Huijuan , Li Daxiang , Wei Shu , Han Bin , Jiang Changjun , Yin Ye , Xia Tao , Zhang Zhengzhu , Zhao Shancen , Bennetzen Jeffrey L. , Wei Chaoling , Wan Xiaochun
Published: July 2019

Tea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124 Gb short and 125 Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more comprehensive omics datasets with improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be utilized to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, thus help to breed new varieties with high yield and better quality in the future.
Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data
Authors: Bang Sohyun , Yoo DongAhn , Kim Soo-Jin , Jhang Soyun , Cho Seoae , Kim Heebal
Published: July 2019

Diseases prediction has been performed by machine learning approaches with various biological data. One of the representative data is the gut microbial community, which interacts with the host’s immune system. The abundance of a few microorganisms has been used as markers to predict diverse diseases. In this study, we hypothesized that multi-classification using machine learning approach could distinguish the gut microbiome from following six diseases: multiple sclerosis, juvenile idiopathic arthritis, myalgic encephalomyelitis/chronic fatigue syndrome, acquired immune deficiency syndrome, stroke and colorectal cancer. We used the abundance of microorganisms at five taxonomy levels as features in 696 samples collected from different studies to establish the best prediction model. We built classification models based on four multi-class classifiers and two feature selection methods including a forward selection and a backward elimination. As a result, we found that the performance of classification is improved as we use the lower taxonomy levels of features; the highest performance was observed at the genus level. Among four classifiers, LogitBoost–based prediction model outperformed other classifiers. Also, we suggested the optimal feature subsets at the genus-level obtained by backward elimination. We believe the selected feature subsets could be used as markers to distinguish various diseases simultaneously. The finding in this study suggests the potential use of selected features for the diagnosis of several diseases.
HLA class II-Restricted CD8+ T cells in HIV-1 Virus Controllers
Authors: Nyanhete Tinashe E. , Frisbee Alyse L. , Bradley Todd , Faison William J. , Robins Elizabeth , Payne Tamika , Freel Stephanie A. , Sawant Sheetal , Weinhold Kent J. , Wiehe Kevin , Haynes Barton F. , Ferrari Guido , Li Qi-Jing , Moody M. Anthony , Tomaras Georgia D.
Published: July 2019

A paradigm shifting study demonstrated that induction of MHC class E and II-restricted CD8+ T cells was associated with the clearance of SIV infection in rhesus macaques. Another recent study highlighted the presence of HIV-1-specific class II-restricted CD8+ T cells in HIV-1 patients who naturally control infection (virus controllers; VCs). However, questions regarding class II-restricted CD8+ T cells ontogeny, distribution across different HIV-1 disease states and their role in viral control remain unclear. In this study, we investigated the distribution and anti-viral properties of HLA-DRB1*0701 and DQB1*0501 class II-restricted CD8+ T cells in different HIV-1 patient cohorts; and whether class II-restricted CD8+ T cells represent a unique T cell subset. We show that memory class II-restricted CD8+ T cell responses were more often detectable in VCs than in chronically infected patients, but not in healthy seronegative donors. We also demonstrate that VC CD8+ T cells inhibit virus replication in both a class I- and class II-dependent manner, and that in two VC patients the class II-restricted CD8+ T cells with an anti-viral gene signature expressed both CD4+ and CD8+ T cell lineage-specific genes. These data demonstrated that anti-viral memory class II-restricted CD8+ T cells with hybrid CD4+ and CD8+ features are present during natural HIV-1 infection.
Using weather radar to monitor the number, timing and directions of flying-foxes emerging from their roosts
Authors: Meade Jessica , van der Ree Rodney , Stepanian Phillip M. , Westcott David A. , Welbergen Justin A.
Published: July 2019

Knowledge of species’ population trends is crucial when planning for conservation and management; however, this information can be difficult to obtain for extremely mobile species such as flying-foxes (Pteropus spp.; Chiroptera, Pteropodidae). In mainland Australia, flying-foxes are of particular management concern due their involvement in human-wildlife conflict, and their role as vectors of zoonotic diseases; and two species, the grey-headed flying-fox (Pteropus poliocephalus) and the spectacled flying-fox (P. conspicillatus), are currently threatened with extinction. Here we demonstrate that archival weather radar data over a period of ten years can be used to monitor a large colony of grey-headed flying-foxes near Melbourne. We show that radar estimates of colony size closely match those derived from traditional counting methods. Moreover, we show that radar data can be used to determine the timing and departure direction of flying-foxes emerging from the roost. Finally, we show that radar observations of flying-foxes can be used to identify signals of important ecological events, such as mass flowering and extreme heat events, and can inform human activities, e.g. the safe operation of airports and windfarms. As such, radar represents an extremely promising tool for the conservation and management of vulnerable flying-fox populations and for managing human interactions with these ecologically-important mammals.
Early evaluation of corneal collagen crosslinking in ex-vivo human corneas using two-photon imaging
Authors: Batista Ana , Breunig Hans Georg , Hager Tobias , Seitz Berthold , König Karsten
Published: July 2019

The clinical outcome of corneal collagen crosslinking (CXL) is typically evaluated several weeks after treatment. An earlier assessment of its outcome could lead to an optimization of the treatment, including an immediate re-intervention in case of failure, thereby, avoiding additional discomfort and pain to the patient. In this study, we propose two-photon imaging (TPI) as an earlier evaluation method. CXL was performed in human corneas by application of riboflavin followed by UVA irradiation. Autofluorescence (AF) intensity and lifetime images were acquired using a commercial clinically certified multiphoton tomograph prior to CXL and after 2h, 24h, 72h, and 144h storage in culture medium. The first monitoring point was determined as the minimum time required for riboflavin clearance from the cornea. As control, untreated samples and samples treated only with riboflavin (without UVA irradiation) were monitored at the same time points. Significant increases in the stroma AF intensity and lifetime were observed as soon as 2h after treatment. A depth-dependent TPI analysis showed higher AF lifetimes anteriorly corresponding to areas were CXL was most effective. No alterations were observed in the control groups. Using TPI, the outcome of CXL can be assessed non-invasively and label-free much sooner than with conventional clinical devices.
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality
Authors: Carballo J. , Santos B. A. C. M. , Zappacosta D. , Garbus I. , Selva J. P. , Gallo C. A. , Díaz A. , Albertini E. , Caccamo M. , Echenique V.
Published: July 2019

The Poaceae constitute a taxon of flowering plants (grasses) that cover almost all Earth’s inhabitable range and comprises some of the genera most commonly used for human and animal nutrition. Many of these crops have been sequenced, like rice, Brachypodium, maize and, more recently, wheat. Some important members are still considered orphan crops, lacking a sequenced genome, but having important traits that make them attractive for sequencing. Among these traits is apomixis, clonal reproduction by seeds, present in some members of the Poaceae like Eragrostis curvula. A de novo, high-quality genome assembly and annotation for E. curvula have been obtained by sequencing 602 Mb of a diploid genotype using a strategy that combined long-read length sequencing with chromosome conformation capture. The scaffold N50 for this assembly was 43.41 Mb and the annotation yielded 56,469 genes. The availability of this genome assembly has allowed us to identify regions associated with forage quality and to develop strategies to sequence and assemble the complex tetraploid genotypes which harbor the apomixis control region(s). Understanding and subsequently manipulating the genetic drivers underlying apomixis could revolutionize agriculture.
Fingerprinting Proterozoic Bedrock in Interior Wilkes Land, East Antarctica
Authors: Maritati Alessandro , Halpin Jacqueline A. , Whittaker Joanne M. , Daczko Nathan R.
Published: July 2019

Wilkes Land in East Antarctica remains one of the last geological exploration frontiers on Earth. Hidden beneath kilometres of ice, its bedrock preserves a poorly-understood tectonic history that mirrors that of southern Australia and holds critical insights into past supercontinent cycles. Here, we use new and recently published Australian and Antarctic geological and geophysical data to present a novel interpretation of the age and character of crystalline basement and sedimentary cover of interior Wilkes Land. We combine new zircon U–Pb and Hf isotopic data from remote Antarctic outcrops with aeromagnetic data observations from the conjugate Australian-Antarctic margins to identify two new Antarctic Mesoproterozoic basement provinces corresponding to the continuation of the Coompana and Madura provinces of southern Australia into Wilkes Land. Using both detrital zircon U–Pb–Hf and authigenic monazite U–Th–Pb isotopic data from glacial erratic sandstone samples, we identify the presence of Neoproterozoic sedimentary rocks covering Mesoproterozoic basement. Together, these new geological insights into the ice-covered bedrock of Wilkes Land substantially improve correlations of Antarctic and Australian geological elements and provide key constraints on the tectonic architecture of this sector of the East Antarctic Shield and its role in supercontinent reconstructions.
Structural visualization of key steps in nucleosome reorganization by human FACT
Authors: Mayanagi Kouta , Saikusa Kazumi , Miyazaki Naoyuki , Akashi Satoko , Iwasaki Kenji , Nishimura Yoshifumi , Morikawa Kosuke , Tsunaka Yasuo
Published: July 2019

Facilitates chromatin transcription (FACT) is a histone chaperone, which accomplishes both nucleosome assembly and disassembly. Our combined cryo-electron microscopy (EM) and native mass spectrometry (MS) studies revealed novel key steps of nucleosome reorganization conducted by a Mid domain and its adjacent acidic AID segment of human FACT. We determined three cryo-EM structures of respective octasomes complexed with the Mid-AID and AID regions, and a hexasome alone. We discovered extensive contacts between a FACT region and histones H2A, H2B, and H3, suggesting that FACT is competent to direct functional replacement of a nucleosomal DNA end by its phosphorylated AID segment (pAID). Mutational assays revealed that the aromatic and phosphorylated residues within pAID are essential for octasome binding. The EM structure of the hexasome, generated by the addition of Mid-pAID or pAID, indicated that the dissociation of H2A-H2B dimer causes significant alteration from the canonical path of the nucleosomal DNA.
Increase in weighting of vision vs. proprioception associated with force field adaptation
Authors: Sexton Brandon M. , Liu Yang , Block Hannah J.
Published: July 2019

Hand position can be estimated by vision and proprioception (position sense). The brain is thought to weight and integrate these percepts to form a multisensory estimate of hand position with which to guide movement. Force field adaptation, a type of cerebellum-dependent motor learning, is associated with both motor and proprioceptive changes. The cerebellum has connections with multisensory parietal regions; however, it is unknown if force adaptation is associated with changes in multisensory perception. If force adaptation affects all relevant sensory modalities similarly, the brain’s weighting of vision vs. proprioception should be maintained. Alternatively, if force perturbation is interpreted as somatosensory unreliability, vision may be up-weighted relative to proprioception. We assessed visuo-proprioceptive weighting with a perceptual estimation task before and after subjects performed straight-ahead reaches grasping a robotic manipulandum. Each subject performed one session with a clockwise or counter-clockwise velocity-dependent force field, and one session in a null field. Subjects increased their weight of vision vs. proprioception in the force field session relative to the null session, regardless of force field direction, in the straight-ahead dimension (F1,44 = 5.13, p = 0.029). This suggests that force field adaptation is associated with an increase in the brain’s weighting of vision vs. proprioception.
Strain-stress study of AlxGa1−xN/AlN heterostructures on c-plane sapphire and related optical properties
Authors: Feng Yining , Saravade Vishal , Chung Ting-Fung , Dong Yongqi , Zhou Hua , Kucukgok Bahadir , Ferguson Ian T. , Lu Na
Published: July 2019

This work presents a systematic study of stress and strain of AlxGa1−xN/AlN with composition ranging from GaN to AlN, grown on a c-plane sapphire by metal-organic chemical vapor deposition, using synchrotron radiation high-resolution X-ray diffraction and reciprocal space mapping. The c-plane of the AlxGa1−xN epitaxial layers exhibits compressive strain, while the a-plane exhibits tensile strain. The biaxial stress and strain are found to increase with increasing Al composition, although the lattice mismatch between the AlxGa1−xN and the buffer layer AlN gets smaller. A reduction in the lateral coherence lengths and an increase in the edge and screw dislocations are seen as the AlxGa1−xN composition is varied from GaN to AlN, exhibiting a clear dependence of the crystal properties of AlxGa1−xN on the Al content. The bandgap of the epitaxial layers is slightly lower than predicted value due to a larger tensile strain effect on the a-axis compared to the compressive strain on the c-axis. Raman characteristics of the AlxGa1−xN samples exhibit a shift in the phonon peaks with the Al composition. The effect of strain on the optical phonon energies of the epitaxial layers is also discussed.
Stable, predictable and training-free operation of superconducting Bi-2212 Rutherford cable racetrack coils at the wire current density of 1000 A/mm2
Authors: Shen Tengming , Bosque Ernesto , Davis Daniel , Jiang Jianyi , White Marvis , Zhang Kai , Higley Hugh , Turqueti Marcos , Huang Yibing , Miao Hanping , Trociewitz Ulf , Hellstrom Eric , Parrell Jeffrey , Hunt Andrew , Gourlay Stephen , Prestemon Soren , Larbalestier David
Published: July 2019

High-temperature superconductors (HTS) could enable high-field magnets stronger than is possible with Nb-Ti and Nb3Sn, but two challenges have so far been the low engineering critical current density JE, especially in high-current cables, and the danger of quenches. Most HTS magnets made so far have been made out of REBCO coated conductor. Here we demonstrate stable, reliable and training-quench-free performance of Bi-2212 racetrack coils wound with a Rutherford cable fabricated from wires made with a new precursor powder. These round multifilamentary wires exhibited a record JE up to 950 A/mm2 at 30 T at 4.2 K. These coils carried up to 8.6 kA while generating 3.5 T at 4.2 K at a JE of 1020 A/mm2. Different from the unpredictable training performance of Nb-Ti and Nb3Sn magnets, these Bi-2212 magnets showed no training quenches and entered the flux flow state in a stable manner before thermal runaway and quench occurred. Also different from Nb-Ti, Nb3Sn, and REBCO magnets for which localized thermal runaways occur at unpredictable locations, the quenches of Bi-2212 magnets consistently occurred in the high field regions over a long conductor length. These characteristics make quench detection simple, enabling safe protection, and suggest a new paradigm of constructing quench-predictable superconducting magnets from Bi-2212.
Integrated targeted metabolomic and lipidomic analysis: A novel approach to classifying early cystic precursors to invasive pancreatic cancer
Authors: Gaiser Rogier Aäron , Pessia Alberto , Ateeb Zeeshan , Davanian Haleh , Fernández Moro Carlos , Alkharaan Hassan , Healy Katie , Ghazi Sam , Arnelo Urban , Valente Roberto , Velagapudi Vidya , Sällberg Chen Margaret , Del Chiaro Marco
Published: July 2019

Pancreatic cystic neoplasms (PCNs) are a highly prevalent disease of the pancreas. Among PCNs, Intraductal Papillary Mucinous Neoplasms (IPMNs) are common lesions that may progress from low-grade dysplasia (LGD) through high-grade dysplasia (HGD) to invasive cancer. Accurate discrimination of IPMN-associated neoplastic grade is an unmet clinical need. Targeted (semi)quantitative analysis of 100 metabolites and >1000 lipid species were performed on peri-operative pancreatic cyst fluid and pre-operative plasma from IPMN and serous cystic neoplasm (SCN) patients in a pancreas resection cohort (n = 35). Profiles were correlated against histological diagnosis and clinical parameters after correction for confounding factors. Integrated data modeling was used for group classification and selection of the best explanatory molecules. Over 1000 different compounds were identified in plasma and cyst fluid. IPMN profiles showed significant lipid pathway alterations compared to SCN. Integrated data modeling discriminated between IPMN and SCN with 100% accuracy and distinguished IPMN LGD or IPMN HGD and invasive cancer with up to 90.06% accuracy. Free fatty acids, ceramides, and triacylglycerol classes in plasma correlated with circulating levels of CA19-9, albumin and bilirubin. Integrated metabolomic and lipidomic analysis of plasma or cyst fluid can improve discrimination of IPMN from SCN and within PMNs predict the grade of dysplasia.
TNFAIP3 genetic polymorphisms reduce ankylosing spondylitis risk in Eastern Chinese Han population
Authors: Yang Jiajia , Hu Xingxing , Wu Meng , Ma Yubo , Zhang Xu , Chen Mengya , Yuan Yaping , Han Renfang , Liu Rui , Guan Shiyang , Deng Jixiang , Xu Shanshan , Gao Xing , Xu Shengqian , Shuai Zongwen , Jiang Shanqun , Guan Shihe , Chen Liwen , Pan Faming
Published: July 2019

This study was conducted to clarify the associations of tumor necrosis factor-α induced protein 3 (TNFAIP3) and TNFAIP3-interacting protein 1 (TNIP1) genetic polymorphisms with ankylosing spondylitis (AS) susceptibility. Five single nucleotide polymorphisms (SNPs) in TNFAIP3 gene and four in TNIP1 gene were genotyped in 667 AS patients and 667 matched healthy controls. Genotypes and haplotype analysis were conducted by using SPSS 23.0 and Haploview 4.2 software. The T allele and CT genotype in TNFAIP3 rs10499194 were significantly associated with a reduced AS risk (T allele vs. C allele, OR = 0.619, 95% CI = 0.430–0.889, P = 0.009; CT vs. CC, OR = 0.603, 95% CI = 0.416–0.875, P = 0.007). However, no association remained significant after Bonferroni correction. The rs13207033A- rs10499194T haplotype of TNFAIP3 conferred a protective effect on AS susceptibility. Stratification analyses suggested that rs10499194 polymorphism decreased the risk of AS in the male subgroup, subgroup aged ≥ 29, HLA-B27 positive subgroup as well as the subgroups of BASFI < 4 and BASDAI < 4 (all P < 0.05). Furthermore, the functional annotation suggested a potential function of rs10499194 mutation. Our results demonstrated that TNFAIP3 rs10499194 polymorphism may be associated with a reduced risk of AS.
REV-ERBα and REV-ERBβ function as key factors regulating Mammalian Circadian Output
Authors: Ikeda Ryosuke , Tsuchiya Yoshiki , Koike Nobuya , Umemura Yasuhiro , Inokawa Hitoshi , Ono Ryutaro , Inoue Maho , Sasawaki Yuh , Grieten Tess , Okubo Naoki , Ikoma Kazuya , Fujiwara Hiroyoshi , Kubo Toshikazu , Yagita Kazuhiro
Published: July 2019

The circadian clock regulates behavioural and physiological processes in a 24-h cycle. The nuclear receptors REV-ERBα and REV-ERBβ are involved in the cell-autonomous circadian transcriptional/translational feedback loops as transcriptional repressors. A number of studies have also demonstrated a pivotal role of REV-ERBs in regulation of metabolic, neuronal, and inflammatory functions including bile acid metabolism, lipid metabolism, and production of inflammatory cytokines. Given the multifunctional role of REV-ERBs, it is important to elucidate the mechanism through which REV-ERBs exert their functions. To this end, we established a Rev-erbα/Rev-erbβ double-knockout mouse embryonic stem (ES) cell model and analyzed the circadian clock and clock-controlled output gene expressions. A comprehensive mRNA-seq analysis revealed that the double knockout of both Rev-erbα and Rev-erbβ does not abrogate expression rhythms of E-box-regulated core clock genes but drastically changes a diverse set of other rhythmically-expressed output genes. Of note, REV-ERBα/β deficiency does not compromise circadian expression rhythms of PER2, while REV-ERB target genes, Bmal1 and Npas2, are significantly upregulated. This study highlight the relevance of REV-ERBs as pivotal output mediators of the mammalian circadian clock.
The transcriptome of potato tuber phellogen reveals cellular functions of cork cambium and genes involved in periderm formation and maturation
Authors: Vulavala Vijaya K. R. , Fogelman Edna , Faigenboim Adi , Shoseyov Oded , Ginzberg Idit
Published: July 2019

The periderm is a protective corky tissue that is formed through the cambial activity of phellogen cells, when the outer epidermis is damaged. Timely periderm formation is critical to prevent pathogen invasion and water loss. The outer layers of the potato periderm, the tuber skin, serves as a model to study cork development. Early in tuber development the phellogen becomes active and produces the skin. During tuber maturation it becomes inactive and the skin adheres to the tuber flesh. The characterization of potato phellogen may contribute to the management of costly agricultural problems related to incomplete skin-set and the resulting skinning injuries, and provide us with new knowledge regarding cork development in planta. A transcriptome of potato tuber phellogen isolated by laser capture microdissection indicated similarity to vascular cambium and the cork from trees. Highly expressed genes and transcription factors indicated that phellogen activation involves cytokinesis and gene reprograming for the establishment of a dedifferentiation state; whereas inactivation is characterized by activity of genes that direct organ identity in meristem and cell-wall modifications. The expression of selected genes was analyzed using qPCR in native and wound periderm at distinct developmental stages. This allowed the identification of genes involved in periderm formation and maturation.
Establishing next-generation pest control services in rice fields: eco-agriculture
Authors: Ali M. P. , Bari M. N. , Haque S. S. , Kabir M. M. M. , Afrin S. , Nowrin F. , Islam M. S. , Landis D. A.
Published: July 2019

Pesticides are commonly used in food crop production systems to control crop pests and diseases and ensure maximum yield with high market value. However, the accumulation of these chemical inputs in crop fields increases risks to biodiversity and human health. In addition, people are increasingly seeking foods in which pesticide residues are low or absent and that have been produced in a sustainable fashion. More than half of the world’s human population is dependent on rice as a staple food and chemical pesticides to control pests is the dominant paradigm in rice production. In contrast, the use of natural enemies to suppress crop pests has the potential to reduce chemical pesticide inputs in rice production systems. Currently, predators and parasitoids often do not persist in rice production landscapes due to the absence of shelter or nutritional sources. In this study, we modified the existing rice landscape through an eco-engineering technique that aims to increase natural biocontrol agents for crop protection. In this system, planting nectar-rich flowering plants on rice bunds provides food and shelter to enhance biocontrol agent activity and reduce pest numbers, while maintaining grain yield. The abundance of predators and parasitoids and parasitism rates increased significantly in the eco-engineering plots compared to the insecticide-treated and control plots. Moreover, a significantly lower number of principal insect pests and damage symptoms were found in treatments where flowering plants were grown on bunds than in plots where such plants were not grown. This study indicates that manipulating habitat for natural enemies in rice landscapes enhances pest suppression and maintains equal yields while reducing the need for insecticide use in crop fields.
Dual resistance of transgenic plants against Cymbidium mosaic virus and Odontoglossum ringspot virus
Authors: Chen Ting-Yu , Pai Hsuan , Hou Liang-Yu , Lee Shu-Chuan , Lin Tzu-Tung , Chang Chih-Hao , Hsu Fu-Chen , Hsu Yau-Heiu , Lin Na-Sheng
Published: July 2019

Taxonomically distinctCymbidium mosaic potexvirus(CymMV) andOdontoglossum ringspot tobamovirus(ORSV) are two of the most prevalent viruses worldwide; when co-infecting orchids, they cause synergistic symptoms. Because of the huge economic loss in quality and quantity in the orchid industry with virus-infected orchids, virus-resistant orchids are urgently needed. To date, no transgenic resistant lines against these two viruses have been reported. In this study, we generated transgenicNicotiana benthamianaexpressing various constructs of partial CymMV and ORSV genomes. Several transgenic lines grew normally and remained symptomless after mixed inoculation with CymMV and ORSV. The replication of CymMV and ORSV was approximately 70–90% lower in protoplasts of transgenic lines than wild-type (WT) plants. Of note, we detected extremely low or no viral RNA or capsid protein of CymMV and ORSV in systemic leaves of transgenic lines after co-infection. Grafting experiments further revealed that CymMV and ORSV trafficked extremely inefficiently from co-infected WT stocks to transgenic scions, presumably due to RNA-mediated interference. This study reports the first successful creation of dual resistant transgenic lines against CymMV and ORSV. Our studies shed light on the commercial development of transgenic orchid production to combat the global viral threat.
Hemodynamic Performance of Multilayer Stents in the Treatment of Aneurysms with a Branch Attached
Authors: Li Zhongyou , Hu Lijuan , Chen Chong , Wang Zhenze , Zhou Zhihong , Chen Yu
Published: July 2019

Although multilayer stents (MSs) can be used to treat aneurysm effectively, for some aneurysms with branches attached, the hemodynamic mechanisms are still unclear. In this work, we modeled five cases that involve 1–4-layer stents implanted in aneurysms with side branches, and the numerical approach was used. Case 1 corresponds to an aneurysm without a stent, and cases 2–5 represent 1–4-layer stents being employed within aneurysms, respectively. The results showed that the velocity within the sac declined dramatically and the eddies’ intensity weakened with increased number of stent layers, time-averaged wall shear stress (TAWSS), and nitric oxide production rate (TARNO) dropped linearly with increase in stent porosity, and oscillatory shear index (OSI) and relative residence time (RRT) increased evidently with MS intervention. Moreover, the MSs had a slight effect on the patency of the side branch; its flow rate was still above the normal case than without aneurysm. It can be concluded that MSs are helpful in promoting the growth of thrombus within the aneurysm through an isolated hemodynamic environment and keeping the branch unobstructed, but more clinical evidences are required.
Enhancement of trapping efficiency by utilizing a hollow sinh-Gaussian beam
Authors: Liu Zhirong , Wang Xun , Hang Kelin
Published: July 2019

Propagation properties and optical forces upon a Rayleigh dielectric sphere for a newly proposed hollow sinh-Gaussian beam (HsGB) are intensively investigated. In view of the targeted laser beam’s unique tight focusing properties that a significantly sharp, peak-centered, and adjustable intensity distribution would be produced in the focal vicinity, the tightly focused HsGB could be exploited to trap and manipulate nano-sized dielectric spheres with high-refractive index in the focal region. The interesting and meaningful features for the novel HsGB mainly include that, compared with the conventional fundamental Gaussian beams under the same optical power, the tightly focused HsGB has much higher intensity gradient and deeper potential well through optimizing targeted laser beam’s parameters. Theretofore, the novel HsGB optical tweezers could drastically enhance its trapping efficiency. Finally, the trapping stability conditions are discussed in detail. The analytical and numerical results obtained here could provide a directive suggestion for researchers in optimizing experimental parameters in constructing a novel HsGB tweezers and making use of a HsGB.