bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling predicts that heat stress and not drought will limit wheat yield in Europe
Authors: Semenov Mikhail , Shewry Peter
Published: July 2019

Global warming is characterised by shifts in weather patterns and increases in extreme weather events. New crop cultivars with specific physiological traits will therefore be required if climate change is not to result in losses of yield and food shortages. However, the intrinsic uncertainty of climate change predictions poses a challenge to plant breeders and crop scientists who have limited time and resources and must select the most appropriate traits for improvement. Modelling is, therefore, a powerful tool to identify future threats to crop production and hence targets for improvement. Wheat is the most important crop in temperate zones, including Europe, and is the staple food crop for many millions of humans and their livestock. However, its production is highly sensitive to environmental conditions, with increased temperature and incidence of drought associated with global warming posing potential threats to yield in Europe. We have therefore predicted the future impacts of these environmental changes on wheat yields using a wheat simulation model combined with climate scenarios based on fifteen global climate models from the IPCC AR4 multi-model ensemble. Despite the lower summer precipitation predicted for Europe, the impact of drought on wheat yields is likely to be smaller than at present, because the warmer conditions will result in earlier maturation before drought becomes severe later in the summer. By contrast, the probability of heat stress around flowering is predicted to increase significantly which is likely to result in considerable yield losses for heat sensitive wheat cultivars commonly grown in north Europe. Breeding strategies should therefore focus on the development of wheat varieties which are tolerant to high temperature around flowering, rather than on developing varieties resistant to drought which may be required for other parts of the world.
Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils
Authors: Nova Andrea , Keten Sinan , Pugno Nicola , Redaelli Alberto , Buehler Markus
Published: July 2019

Spider silk is one of the strongest, most extensible and toughest biological materials known, exceeding the properties of many engineered materials including steel. Silks feature a hierarchical architecture where highly organized, densely H-bonded beta-sheet nanocrystals are arranged within a semi-amorphous protein matrix consisting of 31-helices and beta-turn protein structures. By using a bottom-up molecular-based mesoscale model that bridges the scales from Angstroms to hundreds of nanometers, here we show that the specific combination of a crystalline phase and a semi-amorphous matrix is crucial for the unique properties of silks. Specifically, our results reveal that the superior mechanical properties of spider silk can be explained solely by structural effects, where the geometric confinement of beta-sheet nanocrystals combined with highly extensible semi-amorphous domains with a large hidden length is the key to reach great strength and great toughness, despite the dominance of mechanically inferior chemical interactions such as H-bonding. Our model directly shows that semi-amorphous regions unravel first when silk is being stretched, leading to the large extensibility of silk. Conversely, the large-deformation mechanical properties and ultimate tensile strength of silk is controlled by the strength of beta-sheet nanocrystals, which is directly related to their size, where small beta-sheet nanocrystals are crucial to reach outstanding levels of strength and toughness. Our model agrees well with observations in recent experiments, where it was shown that a significant change in the strength and toughness can be achieved solely by tuning the size of beta-sheet nanocrystals. Our findings unveil the material design strategy that enables silks to achieve superior material performance despite simple and inferior constituents, resulting in a new paradigm in materials design where enhanced functionality is not achieved using complex building blocks, but rather through the utilization of simple repetitive constitutive elements arranged in hierarchical structures.
Biostratigraphy of the Danian/Selandian transition: A case study from Kamestan anticline section, northwest of Izeh city in Khuzestan province, Southern Iran
Authors: Hadavandkhani Nasrin , Sadeghi Abbas
Published: July 2019

The planktonic foraminifera turnover across the Danian-Selandian boundary (early to late Paleocene, ~60 Ma) has been studied in the Kamestan anticline section. The studied interval span planktonic foraminifera zones P2-P3. In this section Danian-Selandian boundary is located in Pabedeh – Gurpi Formations transition. Here, the boundary of Pabeh and Gurpi Formations is a transitional one and identified by with color change of from grey shale to purple shale of Gurpi Formation to Pabdeh Formation .
Co-detection: Ultra-reliable Nanoparticle-Based Electrical Detection of Biomolecules in the Presence of Large Background Interference
Authors: Liu Yang , Alocilja Evangelyn , Chakrabartty Shantanu
Published: July 2019

Contrary to popular belief, we report that background interference in conductimetric biochips can be exploited using a novel "co-detection" principle to significantly improve the reliability of detecting trace quantities of biomolecules. The technique called "co-detection" exploits the non-linear redundancy amongst synthetically patterned biomolecular logic circuits for deciphering the presence or absence of target biomolecules in a sample. In this paper, we demonstrate the "co-detection" principle on gold-nanoparticle based conductimetric soft-logic circuits which uses a silver-enhancement technique for signal amplification. Using co-detection, we have been able to measure a 1000 times improvement in the reliability of detecting mouse IgG at concentration levels that are 10^5^ lower than the concentration of rabbit IgG which serves as background interference.
Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton
Authors: Gilbert Jack , Somerfield Paul , Temperton Ben , Huse Susan , Joint Ian , Field Dawn
Published: July 2019

Marine bacterial diversity is vast, but seasonal variation in diversity is poorly understood. Here we present the longest bacterial diversity time series consisting of monthly (72) samples from the western English Channel over a 6 year period (2003-2008) using 747,494 16SrDNA-V6 amplicon-pyrosequences. Although there were characteristic cycles for each phylum, the overall community cycle was remarkably stable year after year. The majority of taxa were not abundant, although on occasion these rare bacteria could dominate the assemblage. Bacterial diversity peaked at the winter solstice and showed remarkable synchronicity with day-length, which had the best explanatory power compared to a combination of other variables (including temperature and nutrient concentrations). Day-length has not previously been recognised as a major force in structuring microbial communities.
Proliferating Cell Nuclear Antigen (PCNA) allows the automatic identification of follicles in microscopic images of human ovarian tissue
Authors: Kelsey Tom , Caserta Benedicta , Castillo Luis , Wallace Hamish , Cóppola Gonzálvez Francisco
Published: July 2019

Background:

Human ovarian reserve is defined by the population of non-growing follicles (NGFs) in the ovary. Direct estimation of ovarian reserve involves the identification of NGFs in prepared ovarian tissue. Previous studies involving human tissue have used hematoxylin and eosin (HE) stain, with NGF populations estimated by human examination either of tissue under a microscopic, or of images taken of this tissue. Methods: In this study we replace HE with Proliferating Cell Nuclear Antigen (PCNA), and automate the identification and enumeration of NGFs that appear in the resulting microscopic images. We compared the automated estimates to those obtained by human experts, with the gold standard taken to be the average of the conservative and liberal estimates by three human experts. Results: The automated estimates were within 10% of the gold standard, for images at both 100x and 200x magnifications. Automated analysis took longer than human analysis for several hundred images, not allowing for breaks from analysis needed by humans.

Conclusion:

Our results both replicate and improve on those of previous studies involving rodent ovaries, and demonstrate the viability of large-scale studies of human ovarian reserve using a combination of immunohistochemistry and computational image analysis techniques.
Report on trial of SatScan tray scanner system by SmartDrive Ltd.
Authors: Blagoderov Vladimir , Kitching Ian , Simonsen Thomas , Smith Vincent
Published: July 2019

Smartdrive Ltd. has developed a prototype imaging system, SatScan, that captures digitised images of large areas while keeping smaller objects in focus at very high resolution. The system was set up in the Sackler Biodiversity Imaging laboratory of Natural History Museum on March 8, 2010 for a one-month trial. A series of projects imaging parts of the entomological, botanical and palaeoentomological collection were conducted to assess the systems utility for museum collection management and biodiversity research. The technical and practical limitations of the system were investigated as part of this process.
Unlocking biomarker discovery: Large scale application of aptamer proteomic technology for early detection of lung cancer
Authors: Ostroff Rachel , Bigbee William , Franklin Wilbur , Gold Larry , Mehan Mike , Miller York , Pass Harvey , Rom William , Siegfried Jill , Stewart Alex , Walker Jeffrey , Weissfeld Joel , Williams Stephen , Zichi Dom , Brody Edward
Published: July 2019

Lung cancer is the leading cause of cancer deaths, because ~84% of cases are diagnosed at an advanced stage. Worldwide in 2008, ~1.5 million people were diagnosed and ~1.3 million died – a survival rate unchanged since 1960. However, patients diagnosed at an early stage and have surgery experience an 86% overall 5-year survival. New diagnostics are therefore needed to identify lung cancer at this stage. Here we present the first large scale clinical use of aptamers to discover blood protein biomarkers in disease with our breakthrough proteomic technology. This multi-center case-control study was conducted in archived samples from 1,326 subjects from four independent studies of non-small cell lung cancer (NSCLC) in long-term tobacco-exposed populations. We measured >800 proteins in 15uL of serum, identified 44 candidate biomarkers, and developed a 12-protein panel that distinguished NSCLC from controls with 91% sensitivity and 84% specificity in a training set and 89% sensitivity and 83% specificity in a blinded, independent verification set. Performance was similar for early and late stage NSCLC. This is a significant advance in proteomics in an area of high clinical need.
Aptamer-based multiplexed proteomic technology for biomarker discovery
Authors: Gold Larry , Ayers Deborah , Bertino Jennifer , Bock Christopher , Bock Ashley , Brody Edward , Carter Jeff , Cunningham Virginia , Dalby Andrew , Eaton Bruce , Fitzwater Tim , Flather Dylan , Forbes Ashley , Foreman Trudi , Fowler Cate , Gawande Bharat , Goss Meredith , Gunn Magda , Gupta Shashi , Halladay Dennis , Heil Jim , Heilig Joe , Hicke Brian , Husar Gregory , Janjic Nebojsa , Jarvis Thale , Jennings Susan , Katilius Evaldas , Keeney Tracy , Kim Nancy , Kaske Terese , Koch Tad , Kraemer Stephan , Kroiss Luke , Le Ngan , Levine Daniel , Lindsey Wes , Lollo Bridget , Mayfield Wes , Mehan Mike , Mehler Robert , Nelson Michele , Nelson Sally , Nieuwlandt Dan , Nikrad Malti , Ochsner Urs , Ostroff Rachel , Otis Matt , Parker Thomas , Pietrasiewicz Steve , Resnicow Dan , Rohloff John , Sanders Glenn , Sattin Sarah , Schneider Dan , Singer Britta , Stanton Martin , Sterkel Alana , Stewart Alex , Stratford Suzanne , Vaught Jonathan , Vrkljan Mike , Walker Jeffrey , Watrobka Mike , Waugh Sheela , Weiss Allison , Wilcox Sheri , Wolfson Alexey , Wolk Steve , Zhang Chi , Zichi Dom
Published: July 2019

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.
Protection from avian influenza H5N1 virus infection with antibody-impregnated filters
Authors: Kamiyama Yoichiro , Adachi Kazuhide , Handharyani Ekowati , Soejoedono Retno Damajanti , Kusano Takayuki , Inai Marie , Tsukamoto Masaya , Kashiwagi Seizaburo , Tsukamoto Yasuhiro
Published: July 2019

There is worldwide concern over the possibility of a new influenza pandemic originating from the highly pathogenic avian H5N1 influenza viruses. We herein demonstrate that functional air filters impregnated with ostrich antibodies against the hemagglutinin of the H5N1 virus protect chickens from death by H5N1 transmission. These results suggest that the use of ostrich antibody-impregnated filters might be a powerful way to prevent the transmission of H5N1.
Adversity and sex differences in social and emotional sensitivity in children; a possible mechanism for sex differences in psychiatric disorders
Authors: Hill Jonathan , Sharp Helen , Murray Lynne
Published: July 2019

Females are superior to males on a range of tasks indexing social sensitivity, the capacity to infer others' mental states and respond with appropriate behaviours and emotions(1-3). There are also sex differences in psychiatric disorders in children and adolescents. Boys have higher rates of psychiatric disorders before puberty, but disorders increase markedly in girls after puberty (4). The causes of the commonest forms of disorder, antisocial behaviour problems in boys, and depression in girls, entail altered brain function caused by genetic variations and psychosocial adversities mainly arising in the family, and the interaction between the two (5;6). This may be explained by sex differences in social and emotional sensitivity provided they can, first, account for male vulnerability to develop antisocial problems in the face of adversity before puberty, second, explain girls' resilience before puberty, and third, account for female vulnerability to depression in the face of adversity after puberty. Associations between reduced social sensitivity and antisocial problems in young children (7;8), and between increased social sensitivity and depressive symptoms in adolescents (9) have previously been demonstrated. However sex differences in the effects of adversity on social and emotional sensitivity have not previously been examined. Here we show that among five year olds, recent adversities (maternal depression and marital discord) are associated with elevated sensitivity in girls but with reduced sensitivity in boys.
Phyloinformatics in the age of Wikipedia
Authors: Page Roderic
Published: July 2019

This talk describes a mapping between the NCBI taxonomy database and Wikipedia. These two databases were chosen because the NCBI taxonomy contains all the taxa for which sequences are publicly available, and for many taxa Wikipedia is the first site returned in a Google search on that taxon's scientific name. The NCBI web pages for nearly 53,000 NCBI taxa now have a link to the corresponding page in Wikipedia.
On the Origin of Western Diet Pathologies
Authors: Schloss John
Published: July 2019

The ratio of the two sulfur-containing amino acids, methionine (Met) and cysteine (Cys), may be a determining factor for which foods contribute to longevity and health. It is shown here that substantially more Met than Cys is consistently found in foods, such as dairy and meat products, thought to contribute to pathologies associated with the Western Diet.
Human-triggered earthquakes and their impacts on human security
Authors: Klose Christian
Published: July 2019

A comprehensive understanding of earthquake risks in urbanized regions requires an accurate assessment of both urban vulnerabilities and earthquake hazards. Socioeconomic risks associated with human-triggered earthquakes are often misconstrued and receive little scientific, legal, and public attention. However, more than 200 damaging earthquakes, associated with industrialization and urbanization, were documented since the 20th century. This type of geohazard has impacts on human security on a regional and national level. For example, the 1989 Newcastle earthquake caused 13 deaths and US$3.5 billion damage (in 1989). The monetary loss was equivalent to 3.4 percent of Australia’s national income (GDI) or 80 percent of Australia’s GDI per capita growth of the same year. This article provides an overview of global statistics of human-triggered earthquakes. It describes how geomechanical pollution due to large-scale geoengineering activities can advance the clock of earthquakes or trigger new seismic events. Lastly, defense-oriented strategies and tactics are described, including risk mitigation measures such as urban planning adaptations and seismic hazard mapping.
Spiral Tissue Microarrays as Next Evolutionary Step in the High-density Tissue Microarray Technology
Authors: Uemura Takeshi , Chirieac Lucian , Fukuoka Junya , Hofer Matthias , Hori Takashi , Tanaka Tomonori , Tominaga Sayaka , Ohsawa Ryo
Published: July 2019

Tissue microarray (TMA) is a well-established technique that connects basic research with clinical applications that allow the validation of many pathobiologic events from gene expression dysregulation to genomic aberrations. However, conventional TMAs have several limitations such as limited representation of tissue heterogeneity, destruction of donor tissue blocks due to coring and usage of particular specimens that have limited evaluable material (tissue from thin specimens or needle biopsies). We have developed a novel method, which we termed "Spiral TMA" that generates TMAs that allow for improved representation of the donor tissue while keeping the architectural details of the donor block intact. This technology is ideal for specimens with limited tissue without the need to punch holes into the original block and therefore preserving the tissue integrity. In this report, we describe the methodology of constructing Spiral TMA and demonstrate the validation of tumor representation and tissue heterogeneity by comparing Spiral TMA to conventional TMA using immunohistochemical staining to EGFR and CK7.
Controlling sap-sucking insect pests with recombinant endophytes expressing plant lectin
Authors: Zhao Xiuyun , Qi Gaofu , Zhang Xianfang , Lan Nan , Ma Xinrong
Published: July 2019

We developed a novel pest management strategy, which uses endophytes to express anti-pest plant lectins. Fungal endophyte of Chaetomium globosum YY-11 with anti-fungi activities was isolated from rape seedlings, and bacterial endophytes of SJ-10 (Enterobacter sp.) and WB (Bacillus subtilis) were isolated from rice seedlings. Pinellia ternate agglutinin gene was cloned into SJ-10 and WB for expression by a shuttle vector, and YY-11 was mediated by Agrobacterium tumefaciens. Positive transformants were evaluated using PCR and Western blot assay. Recombinant endophytes colonized most of crops, and resistance of rice seedlings, which were inoculated with the recombinant endophytic bacteria, to white backed planthoppers was dramatically enhanced by decreasing the survival and fecundity of white backed planthoppers. Rape inoculated with recombinant endophytic fungi significantly inhibited the growth and reproduction of aphids. Recombinant endophytes expressing PTA may endow hosts with resistance against sap-sucking pests.
Lengthening of 3'UTR Increases Morphological Complexity in Animal Evolution
Authors: Chen Cho-Yi , Chen Shui-Tein , Juan Hsueh-Fen , Huang Hsuan-Cheng
Published: July 2019

By analyzing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 3' untranslated regions (3'UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 3'UTRs together with a commensurate expansion in post-transcriptional regulation can contribute to the emergence of new cell types during animal evolution.
Visualization of Minute Mechanical-Excitation/Relaxation Wave-front Propagation in Myocardial Tissue
Authors: Kanai Hiroshi , Tanaka Motonao
Published: July 2019

Unlike the case of skeletal muscle, the direction of myocardial contraction does not coincide with the direction of work necessary to eject the intraventricular blood, contributing to great complexity of the wall deformation sequence of cardiac contraction. The advent of advanced techniques (CT^1^, MRI^2,3^, SPECT^4^, echocardiology^5-9^, electrocardiography^10^, and magnetocardiography^11,12^) has enabled to the evaluation of cardiac function and disorders by the measurement of blood flow, pressure, electrical reaction process, and other factors. However, complexity of the contraction sequence is still not fully understood because the dynamic mechanical excitation process, which directly correlates with contraction, cannot be accurately measured based on these electro-magnetic phenomena. Here, developing and using a noninvasive novel imaging modality with high temporal and spatial resolutions^13-17^, we show that the propagation of the mechanical wave-front occurs at the beginning of each cardiac contraction and relaxation sequence for the first time. The former occurs about 60 ms prior to the ordinarily accepted onset time of the contraction (R-wave of the electrocardiogram). From the apical side of the interventricular septum, close to the terminal of the Purkinje fibers (specialized to carry contraction impulses), a minute velocity component with an amplitude of several tenth micrometers is generated and propagates sequentially to the entire left ventricle, that is, it propagates from the apex to the base of the posterior wall, and then from the base to the apex of the septum, with a propagation speed of 3-9 m/s. The latter occurs at the end of the first heart sound at the apical side and propagates to the base side with a speed of 0.6 m/s. These physiological findings, unlike the widely accepted myocardial excitation process, have potential for accurate assessment of myocardial tissue damage in coronary disease and cardiomyopathy. This dynamic measurement modality is also applicable to various tissues in biology.
A Study of prevalence of malnutrition in government School children in the field area of Azad nagar Bangalore, India
Authors: Hasan Izhar
Published: July 2019

Malnutrition is a problem at varying proportions in developing countries, and anthropometry is a simple tool to assess its magnitude in children. This study was aimed at identifying the prevalence of malnutrition among 500 children of govt schols of Azad Nagar, bangalore south Asia. The value of using various field based formulae and of various anthropometric indicators used for classification of malnutrition was also studied. The study was focused on children aged 8-14 years studying in class 1st to 8th in govt schools. Anthropometric data and eating practices of children were collected with the help of a pretested questionnaire and food intake diary. Selected anthropometric measurements were taken using standard techniques. Their Body Mass Index (B.M.I) for age was calculated and compared with WHO (2007) standards. Compared to WHO standards, mean BMI of school children in Azad Nagar and its surrounding area was inferior at all ages. The prevalence of malnutrition was 68%, males recorded a relatively high high rate of malnutrition 57.94% (197) than females 42.06% (143). The study reveals that the average of govt school children in Azad Nagar are underweighted. Poor nutrition of children do not only affects the cognitive development of children but also likely to reduce the work capacity in future.
Homochirality through Photon-Induced Melting of RNA/DNA: the Thermodynamic Dissipation Theory of the Origin of Life
Authors: Michaelian Karo
Published: July 2019

The homochirality of the molecules of life has been a vexing problem with no generally accepted solution to date. Since a racemic mixture of chiral nucleotides frustrates the extension and replication of RNA and DNA, understanding the origin of homochirality has important implications to the investigation of the origin of life. Theories on the origin of life have generally elected to presume an abiotic mechanism giving rise to a large prebiotic enantiomer enrichment. Although a number of such mechanism have been suggested, none has enjoyed sufficient plausibility or relevance to be generally accepted. Here we suggest a novel solution to the homochirality problem based on a recently proposed thermodynamic dissipation theory for the origin of life. The ultraviolet absorption and dissipation characteristics of RNA/DNA point to their origin as photoautorophs, their replication assisted by UV light and temperature, and acting as catalysts for the global water cycle. Homochirality is suggested to have been incorporated gradually into the emerging life as a result of asymmetric right- over left-handed photon-induced denaturation of RNA/DNA occurring when Archean sea surface temperatures became close to the denaturing temperatures of RNA/DNA. This differential denaturing success would have been promoted by the somewhat right-handed circularly polarized submarine light of the late afternoon when surface water temperatures are highest, and a negative circular dichroism band extending from 220 nm up to 260 nm for small segments of RNA/DNA. A numerical model is presented demonstrating the efficacy of such a mechanism in procuring 100% homochirality of RNA or DNA from an original racemic solution in less than 500 Archean years assuming a photon absorption threshold for replication representing the hydrogen bonding energy between complementary strands. Because cholesteric D-nucleic acids have greater affinity for L-amino acids due to a positive structural complementarity, and because D-RNA/DNA+L-amino acid complexes also have a negative circular dichroism band between 200 - 300 nm, the homochirality of amino acids can also be explained by the theory.
Antibody-antigen interactions: What is the required time to equilibrium?
Authors: Andersson Karl , Björkelund Hanna , Malmqvist Magnus
Published: July 2019

The use of antibodies is widespread in many areas including in-vivo and in-vitro diagnostics, quantitative analysis in research laboratories and as therapeutic substances. Since the methods for generation of antibodies has improved and regularly results in high-affinity interactions, the standard assays used for quantification of the interaction properties should be revisited because they do not necessarily produce accurate results. Here we show that in several cases, the affinity determination of strongly binding antibodies will be inherently difficult when using standard procedures, due to impractically long incubation times. Real-time kinetic analysis is often the only realistic alternative for affinity determination.
An innovative method for the biological control of Alternanthera philoxeroides
Authors: Cao Yusong , Wang Huiming
Published: July 2019

Biological invasion has become a serious global environmental problems and been considered as an important component of global change^1-2^. Invasions by alien species can have an impact at several levels of ecological complexity from genes to ecosystems^3-4^. Invasive alien species had seriously threated the biodiversity and natural ecosystems in China^5^, and caused economic losses by more than US$7 billion every year^6^. Alternanthera philoxeroides, commonly known as Alligator weed, is an invasive amphibious plant^7^. The effect of physical methods such as mechanical or artificial salvage, removal of A. philoxeroides were very limited. Moreover, these measure should be carried out very carefully or would easy lead to its rebound^8^. The mainly biological control methods of A.philoxeroides is the introduction of natural enemies including Arcola malloi and Amynothrips andersoni^9^. However, the introduction of natural enemies had little control effect on A. philoxeroides especially in terrestrial conditions, where the stems of A. philoxeroides lignified^9-12^. Here we found that Humulus Scandens (H. japonicus) can better inhibit the invasion of A. philoxeroides by means of interspecific competition which could be an ideal biological control method to control the invasion of A. philoxeroides.
Autosegregation of enzyme loci Me1 and Gpi2 in agamospermous progenies of triploid sugarbeet plants
Authors: Levites Evgenii , Kirikovich Svetlana
Published: July 2019

Ratios of malic-enzyme (ME1) and glucosephosphate isomerase (GPI2) phenotypic classes were studied in agamospermous progenies of triploid sugar beet plants. It was shown that the ratio of enzymes phenotypic classes quite well accords with the calculations based on the supposition about reduplication of chromosome sites carrying alleles of enzyme loci accompanied by a loss of excessive allelic copies in the first cell division under embryogenesis. Polyteny – conditioned allelic dose increase leads to the occurrence of alleles – absent in the initial parent – at a certain frequency in the developing progeny. The notions of “meiotic autosegregation” and “mitotic autosegregation” – typical of meiotic and mitotic agamospermy, respectively, – were introduced; the term locus “polygenotype” characterizing the allelic composition of locus, number of chromosomes and a copies number of chromatides sites carrying marker-locus alleles in the cell before entering embryogenesis was also introduced.
Neural Substrates of Chronic Pain in the Thalamocortical Circuit
Authors: Zippo Antonio , Storchi Riccardo , Valente Maurizio , Caramenti Gian Carlo , Biella Gabriele
Published: July 2019

Chronic pain (CP), a pathological condition with a large repertory of signs and symptoms, has no recognizable neural functional common hallmark shared by its diverse expressions. The aim of the present research was to identify potential dynamic markers shared in CP models, by using simultaneous electrophysiological extracellular recordings from the rat ventrobasal thalamus and the primary somatosensory cortex. We have been able to extract a neural signature attributable solely to CP, independent from of the originating conditions. This study showed disrupted functional connectivity and increased redundancy in firing patterns in CP models versus controls, and interpreted these signs as a neural signature of CP. In a clinical perspective, we envisage CP as disconnection syndrome and hypothesize potential novel therapeutic appraisal.
The disease mutation A77V in Ryanodine receptor RyR2 induces changes in energy conduction pathways in the protein
Authors: Erman Burak , Walpoth Nazan
Published: July 2019

Energetically responsive residues of the 217 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. These residues lie along a hydrogen bonded path through the protein. The evolutionarily conserved residues of the protein are all located on this path or in its close proximity. All of the residues of the path are either located on the two Mir domains of the protein or are hydrogen bonded to them. Two calcium binding residues, E171 and E173, are proposed as potential binding residues, based on insights gained from the elastic net analysis of another calcium channel receptor, the inositol 1,4,5-triphosphate receptor, IP3R. Analysis of the disease causing A77V mutated RyR2 showed that the path is disrupted by the loss of energy responsiveness of certain residues.
Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection
Authors: Kolody B C , McCrow J P , Allen L Zeigler , Aylward F O , Fontanez K M , Moustafa A , Moniruzzaman M , Chavez F P , Scholin C A , Allen E E , Worden A Z , Delong E F , Allen A E
Published: July 2019

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
F-box protein FBXO30 mediates retinoic acid receptor γ ubiquitination and regulates BMP signaling in neural tube defects
Authors: Cheng Xiyue , Pei Pei , Yu Juan , Zhang Qin , Li Dan , Xie Xiaolu , Wu Jianxin , Wang Shan , Zhang Ting
Published: July 2019

Retinoic acid (RA), an active derivative of vitamin A, is critical for the neural system development. During the neural development, the RA/RA receptor (RAR) pathway suppresses BMP signaling-mediated proliferation and differentiation of neural progenitor cells. However, how the stability of RAR is regulated during neural system development and how BMP pathway genes expression in neural tissue from human fetuses affected with neural tube defects (NTDs) remain elusive. Here, we report that FBXO30 acts as an E3 ubiquitin ligase and targets RARγ for ubiquitination and proteasomal degradation. In this way, FBXO30 positively regulates BMP signaling in mammalian cells. Moreover, RA treatment leads to suppression of BMP signaling by reducing the level of FBXO30 in mammalian cells and in mouse embryos with NTDs. In samples from human NTDs with high levels of retinol, downregulation of BMP target genes was observed, along with aberrant FBXO30 levels. Collectively, our results demonstrate that RARγ levels are controlled by FBXO30-mediated ubiquitination and that FBXO30 is a key regulator of BMP signaling. Furthermore, we suggest a novel mechanism by which high-retinol levels affect the level of FBXO30, which antagonizes BMP signaling during early stage development.
Translationally controlled tumor protein (TCTP) plays a pivotal role in cardiomyocyte survival through a Bnip3-dependent mechanism
Authors: Cai Wenqian , Fujita Takayuki , Hidaka Yuko , Jin Huiling , Suita Kenji , Shigeta Mayo , Kiyonari Hiroshi , Umemura Masanari , Yokoyama Utako , Sadoshima Junichi , Ishikawa Yoshihiro
Published: July 2019

Prevention of cardiomyocyte death is an important therapeutic strategy for heart failure. In this study, we focused on translationally controlled tumor protein (TCTP), a highly conserved protein that is expressed ubiquitously in mammalian tissues, including heart. TCTP plays pivotal roles in survival of certain cell types, but its function in cardiomyocytes has not been examined. We aimed to clarify the role of TCTP in cardiomyocyte survival and the underlying mechanism. Here, we demonstrated that downregulation of TCTP with siRNA induced cell death of cardiomyocytes with apoptotic and autophagic features, accompanied with mitochondrial permeability transition pore (mPTP) opening. TCTP loss did not induce cell death of cardiac fibroblasts. Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (Bnip3) was found to mediate the TCTP-loss-induced cardiomyocyte death. In exploring the clinical significance of the TCTP expression in the heart, we found that DOX treatment markedly downregulated the protein expression of TCTP in cultured cardiomyocytes and in mouse heart tissue. Exogenous rescue of TCTP expression attenuated DOX-induced cardiomyocyte death. In mice, cardiomyocyte-specific overexpression of TCTP resulted in decreased susceptibility to DOX-induced cardiac dysfunction, accompanied with attenuated induction of Bnip3. Dihydroartemisinin, a pharmacological TCTP inhibitor, induced development of heart failure and cardiomyocyte death in control mice, but not in mice with cardiomyocyte-specific TCTP overexpression. Our findings revealed TCTP has a pivotal role in cardiomyocyte survival, at least in part through a Bnip3-dependent mechanism. TCTP could be considered as a candidate therapeutic target to prevent DOX-induced heart failure.
Dysregulated calcium homeostasis prevents plasma membrane repair in Anoctamin 5/TMEM16E-deficient patient muscle cells
Authors: Chandra Goutam , Defour Aurelia , Mamchoui Kamel , Pandey Kalpana , Mishra Soumya , Mouly Vincent , Sreetama SenChandra , Mahad Ahmad Mohammad , Mahjneh Ibrahim , Morizono Hiroki , Pattabiraman Nagarajan , Menon Anant K. , Jaiswal Jyoti K.
Published: July 2019

Autosomal recessive mutations in Anoctamin 5 (ANO5/TMEM16E), a member of the transmembrane 16 (TMEM16) family of Ca2+-activated ion channels and phospholipid scramblases, cause adult-onset muscular dystrophies (limb girdle muscular dystrophy 2L (LGMD2L) and Miyoshi Muscular Dystrophy (MMD3). However, the molecular role of ANO5 is unclear and ANO5 knockout mouse models show conflicting requirements of ANO5 in muscle. To study the role of ANO5 in human muscle cells we generated a myoblast line from a MMD3-patient carrying the c.2272C>T mutation, which we find causes the mutant protein to be degraded. The patient myoblasts exhibit normal myogenesis, but are compromised in their plasma membrane repair (PMR) ability. The repair deficit is linked to the poor ability of the endoplasmic reticulum (ER) to clear cytosolic Ca2+ increase caused by focal plasma membrane injury. Expression of wild-type ANO5 or pharmacological prevention of injury-triggered cytosolic Ca2+ overload enable injured patient muscle cells to repair. A homology model of ANO5 shows that several of the known LGMD2L/MMD3 patient mutations line the transmembrane region of the protein implicated in its channel activity. These results point to a role of cytosolic Ca2+ homeostasis in PMR, indicate a role for ANO5 in ER-mediated cytosolic Ca2+ uptake and identify normalization of cytosolic Ca2+ homeostasis as a potential therapeutic approach to treat muscular dystrophies caused by ANO5 deficit.
Relationship between duration and extent of oedema and visual acuity outcome with ranibizumab in diabetic macular oedema: A post hoc analysis of Protocol I data
Authors: Sadda Srinivas R. , Campbell Joanna , Dugel Pravin U. , Holekamp Nancy M. , Kiss Szilárd , Loewenstein Anat , Augustin Albert J. , Shih Vanessa , Xu Xiaoshu , Wykoff Charles C. , Whitcup Scott M.
Published: July 2019

Background/objectives

This post hoc analysis explores the relationship between residual oedema exposure after ranibizumab treatment initiation and long-term visual acuity outcome in eyes with centre-involved diabetic macular oedema (DMO).

Subjects/methods

Eyes randomised to the ranibizumab + prompt or deferred laser treatment arms in the Protocol I trial and with observed central retinal thickness (CRT) readings at baseline and ≥1 follow-up visits (n = 367) were stratified by 1) oedema duration (number of study visits with CRT ≥ 250 µm during the first 52 weeks of ranibizumab treatment); and 2) oedema extent (amount of excess CRT [≥ 250 µm] at each study visit, averaged over the first 52 weeks). Associations between measures of residual oedema and best-corrected visual acuity (BCVA) were assessed in multiple regression analyses.

Results

Oedema duration and oedema extent during the first 52 weeks of ranibizumab treatment showed significant negative associations with BCVA improvement at weeks 52, 104 and 156. Eyes with the most persistent oedema gained (mean) 4.4 (95% CI 0.1─8.7) fewer Early Treatment Diabetic Retinopathy Study (ETDRS) letters at week 156 than eyes with the least persistent oedema (P = 0.044). Eyes with the greatest amount of oedema gained (mean) 9.3 (95% CI 4.0─14.5) fewer ETDRS letters at week 156 than eyes with the least amount of oedema (P < 0.001).

Conclusions

Macular oedema exposure over the first 52 weeks of ranibizumab treatment is a negative prognostic factor for long-term visual acuity improvement in centre-involved DMO.
Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin
Authors: Nass Kovacs Gabriela , Colletier Jacques-Philippe , Grünbein Marie Luise , Yang Yang , Stensitzki Till , Batyuk Alexander , Carbajo Sergio , Doak R. Bruce , Ehrenberg David , Foucar Lutz , Gasper Raphael , Gorel Alexander , Hilpert Mario , Kloos Marco , Koglin Jason E. , Reinstein Jochen , Roome Christopher M. , Schlesinger Ramona , Seaberg Matthew , Shoeman Robert L. , Stricker Miriam , Boutet Sébastien , Haacke Stefan , Heberle Joachim , Heyne Karsten , Domratcheva Tatiana , Barends Thomas R. M. , Schlichting Ilme
Published: July 2019

Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.
The post-abscission midbody is an intracellular signaling organelle that regulates cell proliferation
Authors: Peterman Eric , Gibieža Paulius , Schafer Johnathon , Skeberdis Vytenis Arvydas , Kaupinis Algirdas , Valius Mindaugas , Heiligenstein Xavier , Hurbain Ilse , Raposo Graca , Prekeris Rytis
Published: July 2019

Once thought to be a remnant of cell division, the midbody (MB) has recently been shown to have roles beyond its primary function of orchestrating abscission. Despite the emerging roles of post-abscission MBs, how MBs accumulate in the cytoplasm and signal to regulate cellular functions remains unknown. Here, we show that extracellular post-abscission MBs can be internalized by interphase cells, where they reside in the cytoplasm as a membrane-bound signaling structure that we have named the MBsome. We demonstrate that MBsomes stimulate cell proliferation and that MBsome formation is a phagocytosis-like process that depends on a phosphatidylserine/integrin complex, driven by actin-rich membrane protrusions. Finally, we show that MBsomes rely on dynamic actin coats to slow lysosomal degradation and propagate their signaling function. In summary, MBsomes may sometimes serve as intracellular organelles that signal via integrin and EGFR-dependent pathways to promote cell proliferation and anchorage-independent growth and survival.
Mixed topological semimetals driven by orbital complexity in two-dimensional ferromagnets
Authors: Niu Chengwang , Hanke Jan-Philipp , Buhl Patrick M. , Zhang Hongbin , Plucinski Lukasz , Wortmann Daniel , Blügel Stefan , Bihlmayer Gustav , Mokrousov Yuriy
Published: July 2019

The concepts of Weyl fermions and topological semimetals emerging in three-dimensional momentum space are extensively explored owing to the vast variety of exotic properties that they give rise to. On the other hand, very little is known about semimetallic states emerging in two-dimensional magnetic materials, which present the foundation for both present and future information technology. Here, we demonstrate that including the magnetization direction into the topological analysis allows for a natural classification of topological semimetallic states that manifest in two-dimensional ferromagnets as a result of the interplay between spin-orbit and exchange interactions. We explore the emergence and stability of such mixed topological semimetals in realistic materials, and point out the perspectives of mixed topological states for current-induced orbital magnetism and current-induced domain wall motion. Our findings pave the way to understanding, engineering and utilizing topological semimetallic states in two-dimensional spin-orbit ferromagnets.