bluuebunny/crossref_metadata_2025_split huggingface dataset:
Icebergs boost phytoplankton growth in the Southern Ocean
Authors: Schwarz Jill , Schodlok Michael 
Published: July 2019

AbstractIcebergs which calve from the Antarctic ice shelves and drift in the Southern Ocean deliver fresh water, dust and minerogenic particles to the surface ocean along the iceberg's path. Each of these components may have an effect on growth conditions for phytoplankton, as might the mechanical effects of the iceberg keel disturbing the water. Although anecdotal evidence and small-scale surveys suggest that drifting icebergs increase local primary production, no large-scale studies have reported on this possibility in detail. A combination of satellite and automated iceberg tracking data presented here shows that the probability of increased surface phytoplankton biomass was two-fold higher in the wake of a tracked iceberg compared to background biomass fluctuations. Only during the month of February were the effects of icebergs on surface biomass likely to be negative. These results confirm icebergs as a factor affecting phytoplankton in the Southern Ocean and highlight the need for detailed process studies so that responses to future changes in the Antarctic ice sheets may be predicted.
Preincision Processing of Cyclobutane Pyrimidine Dimers in Escherichia coli
Authors: Paul Sunirmal , Hashimoto Mitsumasa , Bhanot Opinder , Kow Yoke , Tang Moon-shong 
Published: July 2019

AbstractIn both prokaryotes and eukaryotes cyclobutane pyrimidine dimers (CPD) formed by UV-irradiation are repaired mainly by the nucleotide excision repair (NER) pathway. Evidence has been presented that CPDs are repaired more rapidly and efficiently in vivo than when using purified NER components in vitro, and raises the possibility that CPD can be processed at the preincision stage before being removed by NER pathway. We investigated this hypothesis in E. coli cells and found that the phosphodiester bonds in CPDs are indeed incised (for the sake of simplicity we term this result as CPD*) in a time-dependent fashion in NER-proficient cells. This CPD preincision processing also occurs in NER-deficient uvrB- and uvrC-, but not in uvrA-mutant cells, and in endonuclease V (nfi) mutant cells. Introduction of the nfi mutation into wild type or uvrB-mutant cells results in disablement of CPD to CPD* conversion and enhances UV sensitization to the level of uvrA-mutant cells. We found that in a reconstituted in vitro system, that purified UvrA and Nfi are necessary but not sufficient to convert CPD to CPD*. A UvrC homologous protein, Cho, is also needed for this conversion. In addition, we found that Nfi does not bind to UV-irradiated DNA, suggesting that UvrA and Cho proteins may function as matchmakers for Nfi-CPD binding, which consequently results in the conversion of CPD to CPD*. We further demonstrated that CPD*, but not CPD, can allow efficient translesion bypass synthesis with accuracy. We thus have elucidated a new CPD preincision processing mechanism and genes involved in this process. The biological significance of these findings is discussed elsewhere (another manuscript in preparation).
Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology
Authors: Gibson Frank , Overton Paul , Smulders Tom , Schultz Simon , Eglen Stephen , Ingram Colin , Panzeri Stefano , Bream Phil , Sernagor Evelyne , Cunningham Mark , Adams Christopher , Echtermeyer Christoph , Simonotto Jennifer , Kaiser Marcus , Swan Daniel , Fletcher Marty , Lord Phillip 
Published: July 2019

AbstractThis module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).
Pancreas islets in metabolic signaling - focus on the β-cell
Authors: Suckale Jakob , Solimena Michele 
Published: July 2019

AbstractTaken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and flow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve changes in transcription. Glucose increases protein synthesis in the [beta] cell overall and especially that of some secretory proteins including insulin. This effect may be mediated through recognition of RNA motifs in the untranslated regions of those messengers. Failure of essential molecular components of the nutrient sensing system due to mutation or weakness paired with cellular stress can lead to dysfunctions, which on a larger scale manifest as diseases like diabetes mellitus.
Requirement of RIZ1 for cancer prevention by methyl-balanced diet
Authors: Zhou Wenyun , Alonso Sergio , Takai Daisaku , Lu Shelly , Yamamoto Fumiichiro , Perucho Manuel , Huang Shi 
Published: July 2019

AbstractThe typical Western diet is not balanced in methyl nutrients that regulate the level of the methyl donor S-adenosylmethionine (SAM) and its derivative metabolite S-adenosylhomocysteine (SAH), which in turn may control the activity of certain methyltransferases. Feeding rodents with amino acid defined and methyl-imbalanced diet decreases hepatic SAM and causes liver cancers. RIZ1 (PRDM2 or KMT8) is a tumor suppressor and functions in transcriptional repression by methylating histone H3 lysine 9. Here we show that a methyl-balanced diet conferred additional survival benefits compared to a tumor-inducing methyl-imbalanced diet only in mice with wild type RIZ1 but not in mice deficient in RIZ1. While absence of RIZ1 was tumorigenic in mice fed the balanced diet, its presence did not prevent tumor formation in mice fed the imbalanced diet. Unlike most of its related enzymes, RIZ1 was upregulated by methyl-balanced diet. Methyl-balanced diet did not fully repress oncogenes such as c-Jun in the absence of RIZ1. The data identify RIZ1 as a critical target of methyl-balanced diet in cancer prevention. The molecular understanding of dietary carcinogenesis may help people make informed choices on diet, which may greatly reduce the incidence of cancer.
Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Authors: Witzany Guenther 
Published: July 2019

AbstractCommunicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing.	In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe the main categories of sign-mediated interactions between bacterial and non-bacterial organisms, and between bacteria of the same or related species. In a third stage I will focus on the relationship between bacteria and their obligate settlers, i.e. viruses. We will see that bacteria are important hosts for multiviral colonisation and virally-determined order of nucleic acid sequences.
Compressibility of Calcium Nitride to 137 Kb
Authors: Bucknum Michael 
Published: July 2019

AbstractA compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study of the equation of state of calcium nitride reported in the literature.
Compressibility of Calcium Nitride to 137 Kb
Authors: Bucknum Michael 
Published: July 2019

Abstract[alpha]-Ca3N2 as an opaque, red-brown crystalline powder lying in the cubic Ia-3 space group, was placed into a specially designed glove box under nitrogen atmosphere, along with powdered f.c.c. Au, and carefully loaded within the [beta]-brass gasket of a conventional high pressure diamond anvil cell (DAC). The powdered samples were then sealed under nitrogen atmosphere to a pressure of 8.40 Kb and taken to Cornell High Energy Synchrotron Source where conventional Debeye-Scherrer diffraction photographs were recorded at 8.40, 91.0 and 137 Kb. The pressure of the sample was monitored by using the equation of state of Au, and no phase change from the Ia-3 structure was observed in the sample of powdered [alpha]-Ca3N2 up to a pressure of 137 Kb, although the red-brown powder was observed to undergo a slight band gap broadening as the opaque powder became a slightly yellow-like tinged transparent phase above 8.40 Kb. A compressibility curve and a bulk modulus for [alpha]-Ca3N2 are derived from the data presented herein.
Barlow-Hall in vitro Evolution Protocol
Authors: Hall Barry , Barlow Miriam 
Published: July 2019

AbstractThe Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly applicable to predicting the evolution of target genes in nature. This detailed protocol includes the procedure itself and, as Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells.
Overexpression of an isoform of AML1 in acute leukemia and its potential role in leukemogenesis
Authors: Liu Xiangrong , Zhang Qing , Zhang Dong-er , Zhou Chunlin , Xing Haiyan , Tian Zhen , Rao Qing , Wang Min , Wang Jianxiang 
Published: July 2019

AbstractAML1/RUNX1 is a critical transcription factor in hematopoietic cell differentiation and proliferation. From the AML1 gene, at least three isoforms, AML1a, AML1b and AML1c, are produced through alternative splicing. AML1a interferes with the function of AML1b/1c, which are often called AML1. In the current study, we found a higher expression level of AML1a in ALL patients in comparison to the controls. Additionally, AML1a represses transcription from promotor of macrophage-colony simulating factor receptor (M-CSFR) mediated by AML1b, indicating that AML1a antagonized the effect of AML1b. In order to investigate the role of AML1a in hematopoiesis and leukemogenesis in vivo, bone marrow mononuclear cells (BMMNCs) from mice were transduced with AML1a and transplanted into lethally irradiated mice, which develop lymphoblastic leukemia after transplantation. Taken together, these results indicate that overexpression of AML1a may be an important contributing factor to leukemogenesis.
The Genetic Signature of Perineuronal Oligodendrocytes
Authors: Szuchet Sara , Nielsen Joseph , Lovas Gabor , Martinez de Velasco Javier , Maric Dragan , Hudson Lynn 
Published: July 2019

AbstractOligodendrocytes in the central nervous system can be categorized as precursors, myelin-forming, and non-myelinating perineuronal cells. The function of perineuronal oligodendrocytes is unknown; it was proposed that following injury, they may remyelinate denuded axons. We investigated these cells' potential. A combination of cell-specific tags, microarray technology and bioinformatics tools to identify gene expression differences between these subpopulations allowed us to capture the genetic signature of perineuronal oligodendrocytes. Here we report that perineuronal oligodendrocytes are configured for a dual role. As cells that embrace neuronal somata, they integrate a repertoire of transcripts designed to create their own code for communicating with neurons. But they maintain a reservoir of untranslated transcripts encoding the major myelin proteins for - we speculate - a demyelinating episode. We posit that the signature molecules, PDGFR-[alpha][beta] cytokine PDGF-CC, and transcription factor Pea3, used - among others - to define the non-myelinating phenotype, may be critical for mounting a myelinating programme during demyelination. Harnessing this capability is of therapeutic value for diseases such as multiple sclerosis. This is the first molecular characterization of an elusive neural cell.
Atmospheric hypoxia limits selection for large body size in insects
Authors: Klok C Jaco , Harrison Jon 
Published: July 2019

AbstractRecent geological models indicate a marked increase in atmospheric oxygen partial pressure (aPO~2~) to 32 kPa in the Permo-Carboniferous (approx. 300 million years ago), subsequently falling to 13 kPa in the Triassic^1^.These aPO~2~ changes have been hypothesized to cause multiple major evolutionary events^2^ including the appearance and subsequent extinction of giant insects and other taxa^3, 4^. Patterns of increasing tracheal investment in larger insects support this hypothesis^5^, as do observations of positive relationships between aPO~2~ and body size in single- or multi-generational experiments with Drosophila melanogaster and other insects^6^. Large species likely result from many generations of selection for large body size driven by predation, competition or sexual selection^7^. Thus a crucial question is whether aPO~2~ influences the capacity of such selection to increase insect size. We tested that possibility by selecting for large body size in five Drosophila melanogaster populations for 11 generations in hypoxic (10 kPa), normoxic (21 kPa) and hyperoxic (40 kPa) aPO~2~, followed by three generations of normoxia without size selection to test for evolved responses. Average body sizes increased by 15% during 11 generations of size selection in 21 and 40 kPa aPO~2~ flies and even stronger responses were observed for the flies in the largest quartile of body masses. However, flies selected for large size in 10 kPa aPO~2~ had strongly reduced sizes compared to those in higher aPO~2~. Upon return to normoxia, all flies had similar, enlarged sizes relative to the starting populations. These results demonstrated that positive size selection had equivalent genetic effects on all flies independent of aPO~2~, but that hypoxia provided a physical constraint on body size even in a relatively small insect under strong selection for larger mass. Our data support the hypothesis that Triassic hypoxia may have contributed to a reduction in insect size.
Why are women smaller than men? When anthropology meets evolutionary biology
Authors: Touraille Priscille , Gouyon Pierre-Henri 
Published: July 2019

AbstractThere are large variations of size among humans but in all populations, men are larger on average than women. For most biologists this fact can be easily explained by the same processes that explain the size dimorphism in large mammals in general and in apes in particular. Due to fights between males for the possession of females, sexual selection has favoured bigger males. Indeed, this factor certainly explains why males are selected for being large but lets aside the question of selection on the female side. Actually, it has been shown that larger females are also favoured by natural selection. This is particularly relevant for women because their probability of dying when giving birth is then reduced. In this paper, the common view that size dimorphism in humans results from the fact that the advantage of being big is stronger for men than for women is challenged by another hypothesis, namely that the difference results from a difference of cost rather than from a difference of benefits. The cost of being big would be higher in women simply because, under gender hierarchical regimes found in all cultures, men are allocated the best food. The interaction between evolutionary forces and cultural practices could then lead to this disadaptive situation.
Green Fluorescent Protein (GFP) in Vector Systems Played Sense Role of Epigenetic in Plants
Authors: El-Shemy Hany , Khalafalla Mutasim , Ishimoto Masao 
Published: July 2019

AbstractThe green fluorescent protein (GFP) of jellyfish (Aequorea victoria) has significant advantages over other reporter genes, because expression can be detected in living cells without any substrates. Recently, epigenetic phenomena are important to consider in plant biotechnology experiments for elucidate unknown mechanism. Therefore, soybean immature cotyledons were generated embryogenesis cells and engineered with two different gene constructs (pHV and pHVS) using gene gun method. Both constructs contain a gene conferring resistance to hygromycin (hpt) as a selective marker and a modified glycinin (11S globulin) gene (V3-1) as a target. However, sGFP(S65T) as a reporter gene was used only in pHVS as a reporter gene for study the relation between using sGFP(S65T) and gene silencing phenomena. Fluorescence microscopic was used for screening after the selection of hygromycin, identified clearly the expression of sGFP(S65T) in the transformed soybean embryos bombarded with the pHVS construct. Protein analysis was used to detect gene expression overall seeds using SDS-PAGE. Percentage of gene down regulation was highly in pHV construct compared with pHVS. Thus, sGFP(S65T) as a reporter gene in vector system may be play useful role for transgenic evaluation and avoid gene silencing in plants for the benefit of plant transformation system.
Trichoplax, the simplest known animal, contains an estrogen-related receptor: Implications for the evolution of vertebrate and invertebrate estrogen receptors
Authors: Baker Michael 
Published: July 2019

AbstractAlthough, as their names imply, vertebrate and invertebrate estrogen receptors [ERs] and estrogen-related receptors [ERRs] are related transcription factors, their evolutionary relationships to each other are not fully understood. We searched recently sequenced genome of Trichoplax, the simplest known animal, and genomes from three lophotrochozoans: Capitella, a worm, Helobdella robusta, a leech, and Lottia gigantea, a snail, to elucidate the origins and evolution of ERs and ERRs. BLAST found an ERR in Trichoplax, but no ER. BLAST searches of the lophotrochozaons found ERRs in all three and invertebrate ERs in Capitella and Lottia, but not in Helobdella. These database searches and a phylogenetic analyses indicate that invertebrate ERs arose in a protostome, and vertebrate ERs arose later in deuterostome.
An optimized energy potential can predict SH2 domain-peptide interactions
Authors: Wunderlich Zeba , Mirny Leonid 
Published: July 2019

AbstractPeptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are members of large protein domain families. Members of these families are often quite similar to each other, but each domain recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein domains. The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family. Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically. Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical origin of domain-peptide specificity. We develop an energy model, inspired by protein folding, based on interactions between the amino acid positions in the domain and peptide. We use this model to successfully predict which SH2 domains and peptides interact and uncover the positions in each that are important for specificity. The energy model is general enough that it can be applied to other members of the SH2 family or to new peptides, and the cross-validation results suggest that these energy calculations will be useful for predicting binding interactions. It can also be adapted to study other PRM families, predict optimal peptides for a given SH2 domain, or study other biological interactions, e.g. protein-DNA interactions.
Biocommunication of Fungal Organisms
Authors: Witzany Guenther 
Published: July 2019

AbstractThe development and growth of fungal organisms depend on successful communication processes (a) within the organism and between organisms, (b) with the same or related species and (c) with non-related organisms. In order to generate an appropriate response behaviour, fungal organisms must also be able to (d) correctly interpret meaningful information from the abiotic environment. However, these communication and interpretation processes can also fail. In such cases the overall results can induce disease-causing and even lethal consequences for the organism.	This review will not enrich the knowledge of specialists in fungal research, but will demonstrate to a broader readership the different levels of fungal communication and how versatile fungal communicative competences really are. Interestingly, certain rules of fungal communication are very similar to those of animals, while others resemble those of plants. The correspondence between all three eukaryotic kingdoms has two aspects: (1) the context determines the meaning of trans-, inter- and intra-organismic (inter- and intracellular) communication, while (2) differences in abiotic and biotic signal perception determine the content arrangement of response behaviour.
D-aspartate exerts an opposing role upon age-dependent NMDAR-related synaptic plasticity and memory decay
Authors: Errico Francesco , Nistico’ Robert , D’Aniello Antimo , Sivilia Sandra , Giustizieri Michela , Napolitano Francesco , Topo Enza , Bernardi Giorgio , Calza Laura , Mercuri Nicola , Usiello Alessandro 
Published: July 2019

AbstractIn the present study, we demonstrated that D-aspartate acts as an in vitro and in vivo neuromodulatory molecule upon hippocampal NMDAR transmission. Accordingly, we showed that this D-amino acid, widely expressed during embryonic phase, was able to strongly influence hippocampus-related functions at adulthood. Thus, while up-regulated levels of D-aspartate increased LTP and spatial memory in four-month old adult mice, the prolonged deregulation of this molecule in thirteen-month old animals induced a substantial acceleration of age-dependent decay of synaptic plasticity and cognitive functions. Moreover, we highlighted a role for D-aspartate in enhancing NMDAR-dependent synaptic plasticity through an inducible &quot;turn-on/turn-off-like mechanism&quot;. Strikingly, we also showed that D-aspartate, when administered to aged mice, strongly rescued their physiological synaptic decay and attenuated their cognitive deterioration. In conclusion, our data suggest a tantalizing hypothesis for which this in-embryo-occurring D-amino acid, might disclose plasticity windows in the aging brain.