bluuebunny/crossref_metadata_2025 huggingface dataset:
General derivation of the Green's functions for the atomic approach of the Anderson model: application to a single electron transistor (SET)
Authors: Foglio M. E. , Lobo T. , Figueira M. S.
Published: August 2012

We consider the cumulant expansion of the periodic Anderson model (PAM) in the case of a finite electronic correlation U, employing the hybridization as perturbation, and obtain a formal expression of the exact one-electron Green's function (GF). This expression contains effective cumulants that are as difficult to calculate as the original GF, and the atomic approach consists in substituting the effective cumulants by the ones that correspond to the atomic case, namely by taking a conduction band of zeroth width and local hybridization. In a previous work (T. Lobo, M. S. Figueira, and M. E. Foglio, Nanotechnology 21, 274007 (2010)10.1088/0957-4484/21/27/274007) we developed the atomic approach by considering only one variational parameter that is used to adjust the correct height of the Kondo peak by imposing the satisfaction of the Friedel sum rule. To obtain the correct width of the Kondo peak in the present work, we consider an additional variational parameter that guarantees this quantity. The two constraints now imposed on the formalism are the satisfaction of the Friedel sum rule and the correct Kondo temperature. In the first part of the work, we present a general derivation of the method for the single impurity Anderson model (SIAM), and we calculate several density of states representative of the Kondo regime for finite correlation U, including the symmetrical case. In the second part, we apply the method to study the electronic transport through a quantum dot (QD) embedded in a quantum wire (QW), which is realized experimentally by a single electron transistor (SET). We calculate the conductance of the SET and obtain a good agreement with available experimental and theoretical results.
Minirhizotron imaging reveals that nodulation of field-grown soybean is enhanced by free-air CO2 enrichment only when combined with drought stress
Authors: Gray Sharon B. , Strellner Reid S. , Puthuval Kannan K. , Ng Christopher , Shulman Ross E. , Siebers Matthew H. , Rogers Alistair , Leakey Andrew D. B.
Published: August 2012

The rate of N2 fixation by a leguminous plant is a product of the activity of individual nodules and the number of nodules. Initiation of new nodules and N2 fixation per nodule are highly sensitive to environmental conditions. However, the effects of global environmental change on nodulation in the field are largely unknown. It is also unclear whether legumes regulate nodulation in response to environment solely by varying root production or also by varying nodule density per unit of root length. This study utilised minirhizotron imaging as a novel in situ method for assessing the number, size and distribution of nodules in field-grown soybean (Glycine max (L.) Merr.) exposed to elevated atmospheric CO2 ([CO2]) and reduced precipitation. We found that nodule numbers were 134–229% greater in soybeans grown at elevated [CO2] in combination with reduced precipitation, and this response was driven by greater nodule density per unit of root length. The benefits of additional nodules were probably offset by an unfavourable distribution of nodules in shallow, dry soil in reduced precipitation treatment under elevated [CO2] but not ambient [CO2]. In fact, significant decreases in seed and leaf nitrogen concentration also occurred only in elevated [CO2] with reduced precipitation. This study demonstrates the potential of minirhizotron imaging to reveal previously uncharacterised changes in nodule production and distribution in response to global environmental change.
Co-expressed peJK genes of lobster (Jasus edwardsii)
Authors: Schadich Ermin , Mason Drusilla , Sin Frank
Published: August 2012

Previous studies have shown that the two novel genes of southern rock lobster (Jasus edwardsii) named peJK2 and peJK3 are implicated in eyestalk hormonal regulation of the lobster moult cycle. Northern blot, in situ hybridisation studies and sequence analyses showed that their putative products might be transmembrane proteins associated with cell signal transduction of hormonal signals in the eyestalk during the intermoult phase of the moult cycle. The aim of this study was to analyse coexpression of peJK genes in different J. edwardsii tissues. Using reverse transcriptase–polymerase chain reaction (RT-PCR), the expression of peJK genes was analysed in seven different tissues (eyestalk, brain, epidermis, hepatopancreas, gill, muscle and heart) of an intermoult lobster. During RT-PCR analysis, a novel sequence was isolated, and was named peJK4. It shares 88% and 86% sequence identity with peJK2 and peJK3 respectively. The peJK2 and peJK4 genes are expressed in all tested tissues. Sequence analyses of the predicted peJK2 and peJK4 proteins revealed two common signal transduction motifs, transmembrane helices and protein kinase C. These results showed that the peJK genes of J. edwardsii are a complex group of genes and possibly involved in different signal transduction pathways.
Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia
Authors: Luck Naomi L. , Thomas Kristen C. , Morin-Adeline Victoria E. , Barwick Sophie , Chong Amanda Y. , Carpenter Eliza L. , Wan LinXiao , Willet Cali E. , Langford-Salisbury Shannan M. , Abdelsayd Mary , Ang Rachel A. , Atkinson Sarah J. , Barcelo Fabian G. , Booth Melanie E. , Bradbury Emma J. , Branighan Thomas L. , Brown Jennifer , Castillo Lesley E. , Chandler Nichola D. , Chong Josephine Y. , Collits Kimberly J. , Cook Emma , Cruz Rachel E. , Farrugia Claire A. , Fletcher Jessica L. , Fletcher Sophie , Gamaliel Nicole S. , Gurr Jessica F. , Hallett Nathan J. , Hargreaves Grace , Harris Teresa , Hollings Samantha , Hopcroft Ryan L. , Johinke Danielle , Kern Pippa L. , Kiddell Jane L. , Kilby Kristen E. , Kragic Borjana , Kwan Jacqueline H. , Lee Joseph I. , Liang Jennifer M. , Lillie Mette C. , Lui Belle C. , Luk Sharon W. , Lun Kwok H. , Marshall Kate L. , Marzec Jolanta A. , Masters Kellie T. , Mazurkijevic Laura J. , Medlock Jeremy , Meoli Christopher , Morris Katrina M. , Noh Yvonne H. , Okazaki Hana , Orourke Tamara J. , Payne Elyssa M. , Powell Dean J. , Quinlivan Antonia R. , Reeves Thomas J. , Robson Kate , Robson Kate L. , Royle Leah J. , Stevenson Ryan , Sellens Teigan , Sun ZiChen , Sutton Amanda L. , Swan Amelia , Tang Jason M. , Tinker Jarrod E. , Tomlinson Suzanne C. , Wilkin Tessa , Wright Amanda L. , Xiao Sam T. , Yang Jessica , Yee Christine , Jaratlerdsiri Weerachai , Isberg Sally R. , Miles Lee , Higgins Damien , Lane Amanda , Gongora Jaime
Published: August 2012

The saltwater crocodile is distributed throughout south-east Asia and Australia. In Australia, it is most abundant in the Northern Territory and Queensland, where it is sustainably farmed for its skins and meat. The aim of this study was to elucidate the relationships and genetic structure among saltwater crocodiles from the Northern Territory of Australia using mitochondrial control region sequences from 61 individuals, representing nine river basins and six of unknown origin, as well as published sequences from other regions. Eight mitochondrial control region haplotypes were identified among both published and novel sequences. Three of the haplotypes appear to be restricted to specimens from northern Australia, with a single haplotype being the most widely dispersed across all river basins. Although Analysis of Molecular Variance provides some support for differentiation among river basins, the frequency of shared haplotypes among these geographical units and median-joining network analysis do not support a clear genetic structure or phylogeographic pattern for saltwater crocodiles in the Northern Territory. The results of this study will assist in furthering our understanding of the genetic diversity of wild saltwater crocodile populations used for ranching in the Northern Territory, as well as providing a framework for assessing the origin of unknown specimens in the future.
Strategies to alleviate original antigenic sin responses to influenza viruses
Authors: Kim Jin Hyang , Davis William G. , Sambhara Suryaprakash , Jacob Joshy
Published: August 2012

Original antigenic sin is a phenomenon wherein sequential exposure to closely related influenza virus variants reduces antibody (Ab) response to novel antigenic determinants in the second strain and, consequently, impairs the development of immune memory. This could pose a risk to the development of immune memory in persons previously infected with or vaccinated against influenza. Here, we explored strategies to overcome original antigenic sin responses in mice sequentially exposed to two closely related hemagglutinin 1 neuraminidase 1 (H1N1) influenza strains A/PR/8/34 and A/FM/1/47. We found that dendritic cell–activating adjuvants [Bordetella pertussistoxin (PT) or CpG ODN or a squalene-based oil-in-water nanoemulsion (NE)], upon administration during the second viral exposure, completely protected mice from a lethal challenge and enhanced neutralizing-Ab titers against the second virus. Interestingly, PT and NE adjuvants when administered during the first immunization even prevented original antigenic sin in subsequent immunization without any adjuvants. As an alternative to using adjuvants, we also found that repeated immunization with the second viral strain relieved the effects of original antigenic sin. Taken together, our studies provide at least three ways of overcoming original antigenic sin.
Aging of biogenic secondary organic aerosol via gas-phase OH radical reactions
Authors: Donahue Neil M. , Henry Kaytlin M. , Mentel Thomas F. , Kiendler-Scharr Astrid , Spindler Christian , Bohn Birger , Brauers Theo , Dorn Hans P. , Fuchs Hendrik , Tillmann Ralf , Wahner Andreas , Saathoff Harald , Naumann Karl-Heinz , Möhler Ottmar , Leisner Thomas , Müller Lars , Reinnig Marc-Christopher , Hoffmann Thorsten , Salo Kent , Hallquist Mattias , Frosch Mia , Bilde Merete , Tritscher Torsten , Barmet Peter , Praplan Arnaud P. , DeCarlo Peter F. , Dommen Josef , Prévôt Andre S.H. , Baltensperger Urs
Published: August 2012

The Multiple Chamber Aerosol Chemical Aging Study (MUCHACHAS) tested the hypothesis that hydroxyl radical (OH) aging significantly increases the concentration of first-generation biogenic secondary organic aerosol (SOA). OH is the dominant atmospheric oxidant, and MUCHACHAS employed environmental chambers of very different designs, using multiple OH sources to explore a range of chemical conditions and potential sources of systematic error. We isolated the effect of OH aging, confirming our hypothesis while observing corresponding changes in SOA properties. The mass increases are consistent with an existing gap between global SOA sources and those predicted in models, and can be described by a mechanism suitable for implementation in those models.
Dysfunction of the auditory thalamus in developmental dyslexia
Authors: Díaz Begoña , Hintz Florian , Kiebel Stefan J. , von Kriegstein Katharina
Published: August 2012

Developmental dyslexia, a severe and persistent reading and spelling impairment, is characterized by difficulties in processing speech sounds (i.e., phonemes). Here, we test the hypothesis that these phonological difficulties are associated with a dysfunction of the auditory sensory thalamus, the medial geniculate body (MGB). By using functional MRI, we found that, in dyslexic adults, the MGB responded abnormally when the task required attending to phonemes compared with other speech features. No other structure in the auditory pathway showed distinct functional neural patterns between the two tasks for dyslexic and control participants. Furthermore, MGB activity correlated with dyslexia diagnostic scores, indicating that the task modulation of the MGB is critical for performance in dyslexics. These results suggest that deficits in dyslexia are associated with a failure of the neural mechanism that dynamically tunes MGB according to predictions from cortical areas to optimize speech processing. This view on task-related MGB dysfunction in dyslexics has the potential to reconcile influential theories of dyslexia within a predictive coding framework of brain function.
Influenza virus binds its host cell using multiple dynamic interactions
Authors: Sieben Christian , Kappel Christian , Zhu Rong , Wozniak Anna , Rankl Christian , Hinterdorfer Peter , Grubmüller Helmut , Herrmann Andreas
Published: August 2012

Influenza virus belongs to a wide range of enveloped viruses. The major spike protein hemagglutinin binds sialic acid residues of glycoproteins and glycolipids with dissociation constants in the millimolar range [Sauter NK, et al. (1992)
Biochemistry
31:9609–9621], indicating a multivalent binding mode. Here, we characterized the attachment of influenza virus to host cell receptors using three independent approaches. Optical tweezers and atomic force microscopy-based single-molecule force spectroscopy revealed very low interaction forces. Further, the observation of sequential unbinding events strongly suggests a multivalent binding mode between virus and cell membrane. Molecular dynamics simulations reveal a variety of unbinding pathways that indicate a highly dynamic interaction between HA and its receptor, allowing rationalization of influenza virus–cell binding quantitatively at the molecular level.
Rapid divergence and expansion of the X chromosome in papaya
Authors: Gschwend Andrea R. , Yu Qingyi , Tong Eric J. , Zeng Fanchang , Han Jennifer , VanBuren Robert , Aryal Rishi , Charlesworth Deborah , Moore Paul H. , Paterson Andrew H. , Ming Ray
Published: August 2012

X chromosomes have long been thought to conserve the structure and gene content of the ancestral autosome from which the sex chromosomes evolved. We compared the recently evolved papaya sex chromosomes with a homologous autosome of a close relative, the monoecious
Vasconcellea monoica
, to infer changes since recombination stopped between the papaya sex chromosomes. We sequenced 12
V. monoica
bacterial artificial chromosomes, 11 corresponding to the papaya X-specific region, and 1 to a papaya autosomal region. The combined
V. monoica
X-orthologous sequences are much shorter (1.10 Mb) than the corresponding papaya region (2.56 Mb). Given that the
V. monoica
genome is 41% larger than that of papaya, this finding suggests considerable expansion of the papaya X; expansion is supported by a higher repetitive sequence content of the X compared with the papaya autosomal sequence. The alignable regions include 27 transcript-encoding sequences, only 6 of which are functional X/
V. monoica
gene pairs. Sequence divergence from the
V. monoica
orthologs is almost identical for papaya X and Y alleles; the
Carica
-
Vasconcellea
split therefore occurred before the papaya sex chromosomes stopped recombining, making
V. monoica
a suitable outgroup for inferring changes in papaya sex chromosomes. The papaya X and the hermaphrodite-specific region of the Y
h
chromosome and
V. monoica
have all gained and lost genes, including a surprising amount of changes in the X.
A paradoxical teratogenic mechanism for retinoic acid
Authors: Lee Leo M. Y. , Leung Chun-Yin , Tang Walfred W. C. , Choi Heung-Ling , Leung Yun-Chung , McCaffery Peter J. , Wang Chi-Chiu , Woolf Adrian S. , Shum Alisa S. W.
Published: August 2012

Retinoic acid, an active metabolite of vitamin A, plays essential signaling roles in mammalian embryogenesis. Nevertheless, it has long been recognized that overexposure to vitamin A or retinoic acid causes widespread teratogenesis in rodents as well as humans. Although it has a short half-life, exposure to high levels of retinoic acid can disrupt development of yet-to-be formed organs, including the metanephros, the embryonic organ which normally differentiates into the mature kidney. Paradoxically, it is known that either an excess or a deficiency of retinoic acid results in similar malformations in some organs, including the mammalian kidney. Accordingly, we hypothesized that excess retinoic acid is teratogenic by inducing a longer lasting, local retinoic acid deficiency. This idea was tested in an established in vivo mouse model in which exposure to excess retinoic acid well before metanephric rudiments exist leads to failure of kidney formation several days later. Results showed that teratogen exposure was followed by decreased levels of
Raldh
transcripts encoding retinoic acid-synthesizing enzymes and increased levels of
Cyp26a1
and
Cyp26b1
mRNAs encoding enzymes that catabolize retinoic acid. Concomitantly, there was significant reduction in retinoic acid levels in whole embryos and kidney rudiments. Restoration of retinoic acid levels by maternal supplementation with low doses of retinoic acid following the teratogenic insult rescued metanephric kidney development and abrogated several extrarenal developmental defects. This previously undescribed and unsuspected mechanism provides insight into the molecular pathway of retinoic acid-induced teratogenesis.
Postsynaptic dysfunction is associated with spatial and object recognition memory loss in a natural model of Alzheimer’s disease
Authors: Ardiles Álvaro O. , Tapia-Rojas Cheril C. , Mandal Madhuchhanda , Alexandre Frédéric , Kirkwood Alfredo , Inestrosa Nibaldo C. , Palacios Adrian G.
Published: August 2012

Alzheimer’s disease (AD) is an age-related neurodegenerative disorder associated with progressive memory loss, severe dementia, and hallmark neuropathological markers, such as deposition of amyloid-β (Aβ) peptides in senile plaques and accumulation of hyperphosphorylated tau proteins in neurofibrillary tangles. Recent evidence obtained from transgenic mouse models suggests that soluble, nonfibrillar Aβ oligomers may induce synaptic failure early in AD. Despite their undoubted value, these transgenic models rely on genetic manipulations that represent the inherited and familial, but not the most abundant, sporadic form of AD. A nontransgenic animal model that still develops hallmarks of AD would be an important step toward understanding how sporadic AD is initiated. Here we show that starting between 12 and 36 mo of age, the rodent
Octodon degus
naturally develops neuropathological signs of AD, such as accumulation of Aβ oligomers and phosphorylated tau proteins. Moreover, age-related changes in Aβ oligomers and tau phosphorylation levels are correlated with decreases in spatial and object recognition memory, postsynaptic function, and synaptic plasticity. These findings validate
O. degus
as a suitable natural model for studying how sporadic AD may be initiated.
MUC1 mucin stabilizes and activates hypoxia-inducible factor 1 alpha to regulate metabolism in pancreatic cancer
Authors: Chaika Nina V. , Gebregiworgis Teklab , Lewallen Michelle E. , Purohit Vinee , Radhakrishnan Prakash , Liu Xiang , Zhang Bo , Mehla Kamiya , Brown Roger B. , Caffrey Thomas , Yu Fang , Johnson Keith R. , Powers Robert , Hollingsworth Michael A. , Singh Pankaj K.
Published: August 2012

Aberrant glucose metabolism is one of the hallmarks of cancer that facilitates cancer cell survival and proliferation. Here, we demonstrate that MUC1, a large, type I transmembrane protein that is overexpressed in several carcinomas including pancreatic adenocarcinoma, modulates cancer cell metabolism to facilitate growth properties of cancer cells. MUC1 occupies the promoter elements of multiple genes directly involved in glucose metabolism and regulates their expression. Furthermore, MUC1 expression enhances glycolytic activity in pancreatic cancer cells. We also demonstrate that MUC1 expression enhances in vivo glucose uptake and expression of genes involved in glucose uptake and metabolism in orthotopic implantation models of pancreatic cancer. The MUC1 cytoplasmic tail is known to activate multiple signaling pathways through its interactions with several transcription factors/coregulators at the promoter elements of various genes. Our results indicate that MUC1 acts as a modulator of the hypoxic response in pancreatic cancer cells by regulating the expression/stability and activity of hypoxia-inducible factor-1α (HIF-1α). MUC1 physically interacts with HIF-1α and p300 and stabilizes the former at the protein level. By using a ChIP assay, we demonstrate that MUC1 facilitates recruitment of HIF-1α and p300 on glycolytic gene promoters in a hypoxia-dependent manner. Also, by metabolomic studies, we demonstrate that MUC1 regulates multiple metabolite intermediates in the glucose and amino acid metabolic pathways. Thus, our studies indicate that MUC1 acts as a master regulator of the metabolic program and facilitates metabolic alterations in the hypoxic environments that help tumor cells survive and proliferate under such conditions.
Evolutionary trajectories explain the diversified evolution of isogamy and anisogamy in marine green algae
Authors: Togashi Tatsuya , Bartelt John L. , Yoshimura Jin , Tainaka Kei-ichi , Cox Paul Alan
Published: August 2012

The evolution of anisogamy (the production of gametes of different size) is the first step in the establishment of sexual dimorphism, and it is a fundamental phenomenon underlying sexual selection. It is believed that anisogamy originated from isogamy (production of gametes of equal size), which is considered by most theorists to be the ancestral condition. Although nearly all plant and animal species are anisogamous, extant species of marine green algae exhibit a diversity of mating systems including both isogamy and anisogamy. Isogamy in marine green algae is of two forms: isogamy with extremely small gametes and isogamy with larger gametes. Based on disruptive selection for fertilization success and zygote survival (theory of Parker, Baker, and Smith), we explored how environmental changes can contribute to the evolution of such complex mating systems by analyzing the stochastic process in the invasion simulations of populations of differing gamete sizes. We find that both forms of isogamy can evolve from other isogamous ancestors through anisogamy. The resulting dimensionless analysis accounts for the evolutionary stability of all types of mating systems in marine green algae, even in the same environment. These results imply that evolutionary trajectories as well as the optimality of gametes/zygotes played an important role in the evolution of gamete size.
Bodywide skipping of exons 45–55 in dystrophic
mdx52
mice by systemic antisense delivery
Authors: Aoki Yoshitsugu , Yokota Toshifumi , Nagata Tetsuya , Nakamura Akinori , Tanihata Jun , Saito Takashi , Duguez Stephanie M. R. , Nagaraju Kanneboyina , Hoffman Eric P. , Partridge Terence , Takeda Shin'ichi
Published: August 2012

Duchenne muscular dystrophy (DMD), the commonest form of muscular dystrophy, is caused by lack of dystrophin. One of the most promising therapeutic approaches is antisense-mediated elimination of frame-disrupting mutations by exon skipping. However, this approach faces two major hurdles: limited applicability of each individual target exon and uncertain function and stability of each resulting truncated dystrophin. Skipping of exons 45–55 at the mutation hotspot of the
DMD
gene would address both issues. Theoretically it could rescue more than 60% of patients with deletion mutations. Moreover, spontaneous deletions of this specific region are associated with asymptomatic or exceptionally mild phenotypes. However, such multiple exon skipping of exons 45–55 has proved technically challenging. We have therefore designed antisense oligo (AO) morpholino mixtures to minimize self- or heteroduplex formation. These were tested as conjugates with cell-penetrating moieties (vivo-morpholinos). We have tested the feasibility of skipping exons 45–55 in
H2K-mdx52
myotubes and in
mdx52
mice, which lack exon 52. Encouragingly, with mixtures of 10 AOs, we demonstrated skipping of all 10 exons in vitro, in
H2K-mdx52
myotubes and on intramuscular injection into
mdx52
mice. Moreover, in
mdx52
mice in vivo, systemic injections of 10 AOs induced extensive dystrophin expression at the subsarcolemma in skeletal muscles throughout the body, producing up to 15% of wild-type dystrophin protein levels, accompanied by improved muscle strength and histopathology without any detectable toxicity. This is a unique successful demonstration of effective rescue by exon 45–55 skipping in a dystrophin-deficient animal model.
North African Jewish and non-Jewish populations form distinctive, orthogonal clusters
Authors: Campbell Christopher L. , Palamara Pier F. , Dubrovsky Maya , Botigué Laura R. , Fellous Marc , Atzmon Gil , Oddoux Carole , Pearlman Alexander , Hao Li , Henn Brenna M. , Burns Edward , Bustamante Carlos D. , Comas David , Friedman Eitan , Pe'er Itsik , Ostrer Harry
Published: August 2012

North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian, Djerban, and Libyan) and comparison with other Jewish and non-Jewish groups demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture. Two major subgroups were identified by principal component, neighbor joining tree, and identity-by-descent analysis—Moroccan/Algerian and Djerban/Libyan—that varied in their degree of European admixture. These populations showed a high degree of endogamy and were part of a larger Ashkenazi and Sephardic Jewish group. By principal component analysis, these North African groups were orthogonal to contemporary populations from North and South Morocco, Western Sahara, Tunisia, Libya, and Egypt. Thus, this study is compatible with the history of North African Jews—founding during Classical Antiquity with proselytism of local populations, followed by genetic isolation with the rise of Christianity and then Islam, and admixture following the emigration of Sephardic Jews during the Inquisition.
Perception of climate change
Authors: Hansen James , Sato Makiko , Ruedy Reto
Published: August 2012

“Climate dice,” describing the chance of unusually warm or cool seasons, have become more and more “loaded” in the past 30 y, coincident with rapid global warming. The distribution of seasonal mean temperature anomalies has shifted toward higher temperatures and the range of anomalies has increased. An important change is the emergence of a category of summertime extremely hot outliers, more than three standard deviations (3σ) warmer than the climatology of the 1951–1980 base period. This hot extreme, which covered much less than 1% of Earth’s surface during the base period, now typically covers about 10% of the land area. It follows that we can state, with a high degree of confidence, that extreme anomalies such as those in Texas and Oklahoma in 2011 and Moscow in 2010 were a consequence of global warming because their likelihood in the absence of global warming was exceedingly small. We discuss practical implications of this substantial, growing, climate change.
Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels
Authors: Margariti Andriana , Winkler Bernhard , Karamariti Eirini , Zampetaki Anna , Tsai Tsung-neng , Baban Dilair , Ragoussis Jiannis , Huang Yi , Han Jing-Dong J. , Zeng Lingfang , Hu Yanhua , Xu Qingbo
Published: August 2012

The generation of induced pluripotent stem (iPS) cells is an important tool for regenerative medicine. However, the main restriction is the risk of tumor development. In this study we found that during the early stages of somatic cell reprogramming toward a pluripotent state, specific gene expression patterns are altered. Therefore, we developed a method to generate partial-iPS (PiPS) cells by transferring four reprogramming factors (OCT4, SOX2, KLF4, and c-MYC) to human fibroblasts for 4 d. PiPS cells did not form tumors in vivo and clearly displayed the potential to differentiate into endothelial cells (ECs) in response to defined media and culture conditions. To clarify the mechanism of PiPS cell differentiation into ECs, SET translocation (myeloid leukemia-associated) (SET) similar protein (SETSIP) was indentified to be induced during somatic cell reprogramming. Importantly, when PiPS cells were treated with VEGF, SETSIP was translocated to the cell nucleus, directly bound to the VE-cadherin promoter, increasing vascular endothelial-cadherin (VE-cadherin) expression levels and EC differentiation. Functionally, PiPS-ECs improved neovascularization and blood flow recovery in a hindlimb ischemic model. Furthermore, PiPS-ECs displayed good attachment, stabilization, patency, and typical vascular structure when seeded on decellularized vessel scaffolds. These findings indicate that reprogramming of fibroblasts into ECs via SETSIP and VEGF has a potential clinical application.
Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3
Authors: Zheng Yupeng , Sweet Steve M. M. , Popovic Relja , Martinez-Garcia Eva , Tipton Jeremiah D. , Thomas Paul M. , Licht Jonathan D. , Kelleher Neil L.
Published: August 2012

We have developed a targeted method to quantify all combinations of methylation on an H3 peptide containing lysines 27 and 36 (H3K27-K36). By using stable isotopes that separately label the histone backbone and its methylations, we tracked the rates of methylation and demethylation in myeloma cells expressing high vs. low levels of the methyltransferase MMSET/WHSC1/NSD2. Following quantification of 99 labeled H3K27-K36 methylation states across time, a kinetic model converged to yield 44 effective rate constants qualifying each methylation and demethylation step as a function of the methylation state on the neighboring lysine. We call this approach MS-based measurement and modeling of histone methylation kinetics (M4K). M4K revealed that, when dimethylation states are reached on H3K27 or H3K36, rates of further methylation on the other site are reduced as much as 100-fold. Overall, cells with high MMSET have as much as 33-fold increases in the effective rate constants for formation of H3K36 mono- and dimethylation. At H3K27, cells with high MMSET have elevated formation of K27me1, but even higher increases in the effective rate constants for its reversal by demethylation. These quantitative studies lay bare a bidirectional antagonism between H3K27 and H3K36 that controls the writing and erasing of these methylation marks. Additionally, the integrated kinetic model was used to correctly predict observed abundances of H3K27-K36 methylation states within 5% of that actually established in perturbed cells. Such predictive power for how histone methylations are established should have major value as this family of methyltransferases matures as drug targets.
Viroid RNA redirects host DNA ligase 1 to act as an RNA ligase
Authors: Nohales María-Ángeles , Flores Ricardo , Daròs José-Antonio
Published: August 2012

Viroids are a unique class of noncoding RNAs: composed of only a circular, single-stranded molecule of 246–401 nt, they manage to replicate, move, circumvent host defenses, and frequently induce disease in higher plants. Viroids replicate through an RNA-to-RNA rolling-circle mechanism consisting of transcription of oligomeric viroid RNA intermediates, cleavage to unit-length strands, and circularization. Though the host RNA polymerase II (redirected to accept RNA templates) mediates RNA synthesis and a type-III RNase presumably cleavage of
Potato spindle tuber viroid
(PSTVd) and closely related members of the family Pospiviroidae, the host enzyme catalyzing the final circularization step, has remained elusive. In this study we propose that PSTVd subverts host DNA ligase 1, converting it to an RNA ligase, for the final step. To support this hypothesis, we show that the tomato (
Solanum lycopersicum
L.) DNA ligase 1 specifically and efficiently catalyzes circularization of the genuine PSTVd monomeric linear replication intermediate opened at position G95–G96 and containing 5′-phosphomonoester and 3′-hydroxyl terminal groups. Moreover, we also show a decreased PSTVd accumulation and a reduced ratio of monomeric circular to total monomeric PSTVd forms in
Nicotiana benthamiana
Domin plants in which the endogenous DNA ligase 1 was silenced. Thus, in a remarkable example of parasitic strategy, viroids reprogram for their replication the template and substrate specificity of a DNA-dependent RNA polymerase and a DNA ligase to act as RNA-dependent RNA polymerase and RNA ligase, respectively.
Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly
Authors: Chernyatina Anastasia A. , Nicolet Stefan , Aebi Ueli , Herrmann Harald , Strelkov Sergei V.
Published: August 2012

Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) “rod” domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.
Interkingdom metabolic transformations captured by microbial imaging mass spectrometry
Authors: Moree Wilna J. , Phelan Vanessa V. , Wu Cheng-Hsuan , Bandeira Nuno , Cornett Dale S. , Duggan Brendan M. , Dorrestein Pieter C.
Published: August 2012

In polymicrobial infections, microbes can interact with both the host immune system and one another through direct contact or the secretion of metabolites, affecting disease progression and treatment options. The thick mucus in the lungs of patients with cystic fibrosis is highly susceptible to polymicrobial infections by opportunistic pathogens, including the bacterium
Pseudomonas aeruginosa
and the fungus
Aspergillus fumigatus
. Unravelling the hidden molecular interactions within such polymicrobial communities and their metabolic exchange processes will require effective enabling technologies applied to model systems. In the present study, MALDI-TOF and MALDI-FT-ICR imaging mass spectrometry (MALDI-IMS) combined with MS/MS networking were used to provide insight into the interkingdom interaction between
P. aeruginosa
and
A. fumigatus
at the molecular level. The combination of these technologies enabled the visualization and identification of metabolites secreted by these microorganisms grown on agar. A complex molecular interplay was revealed involving suppression, increased production, and biotransformation of a range of metabolites. Of particular interest is the observation that
P. aeruginosa
phenazine metabolites were converted by
A. fumigatus
into other chemical entities with alternative properties, including enhanced toxicities and the ability to induce fungal siderophores. This work highlights the capabilities of MALDI-IMS and MS/MS network analysis to study interkingdom interactions and provides insight into the complex nature of polymicrobial metabolic exchange and biotransformations.
Cyclin-dependent kinase 8 mediates chemotherapy-induced tumor-promoting paracrine activities
Authors: Porter Donald C. , Farmaki Elena , Altilia Serena , Schools Gary P. , West Deborah K. , Chen Mengqian , Chang Bey-Dih , Puzyrev Anatoliy T. , Lim Chang-uk , Rokow-Kittell Rebecca , Friedhoff Lawrence T. , Papavassiliou Athanasios G. , Kalurupalle Swathi , Hurteau Gregory , Shi Jun , Baran Phil S. , Gyorffy Balazs , Wentland Mark P. , Broude Eugenia V. , Kiaris Hippokratis , Roninson Igor B.
Published: August 2012

Conventional chemotherapy not only kills tumor cells but also changes gene expression in treatment-damaged tissues, inducing production of multiple tumor-supporting secreted factors. This secretory phenotype was found here to be mediated in part by a damage-inducible cell-cycle inhibitor p21 (CDKN1A). We developed small-molecule compounds that inhibit damage-induced transcription downstream of p21. These compounds were identified as selective inhibitors of a transcription-regulating kinase CDK8 and its isoform CDK19. Remarkably, p21 was found to bind to CDK8 and stimulate its kinase activity. p21 and CDK8 also cooperate in the formation of internucleolar bodies, where both proteins accumulate. A CDK8 inhibitor suppresses damage-induced tumor-promoting paracrine activities of tumor cells and normal fibroblasts and reverses the increase in tumor engraftment and serum mitogenic activity in mice pretreated with a chemotherapeutic drug. The inhibitor also increases the efficacy of chemotherapy against xenografts formed by tumor cell/fibroblast mixtures. Microarray data analysis revealed striking correlations between CDK8 expression and poor survival in breast and ovarian cancers. CDK8 inhibition offers a promising approach to increasing the efficacy of cancer chemotherapy.
Diphthamide modification on eukaryotic elongation factor 2 is needed to assure fidelity of mRNA translation and mouse development
Authors: Liu Shihui , Bachran Christopher , Gupta Pradeep , Miller-Randolph Sharmina , Wang Hailun , Crown Devorah , Zhang Yi , Wein Alexander N. , Singh Rajat , Fattah Rasem , Leppla Stephen H.
Published: August 2012

To study the role of the diphthamide modification on eukaryotic elongation factor 2 (eEF2), we generated an eEF2 Gly717Arg mutant mouse, in which the first step of diphthamide biosynthesis is prevented. Interestingly, the Gly717-to-Arg mutation partially compensates the eEF2 functional loss resulting from diphthamide deficiency, possibly because the added +1 charge compensates for the loss of the +1 charge on diphthamide. Therefore, in contrast to mouse embryonic fibroblasts (MEFs) fromOVCA1−/−mice,eEF2G717R/G717RMEFs retain full activity in polypeptide elongation and have normal growth rates. Furthermore,eEF2G717R/G717Rmice showed milder phenotypes thanOVCA1−/−mice (which are 100% embryonic lethal) and a small fraction survived to adulthood without obvious abnormalities. Moreover,eEF2G717R/G717R/OVCA1−/−double mutant mice displayed the milder phenotypes of theeEF2G717R/G717Rmice, suggesting that the embryonic lethality ofOVCA1−/−mice is due to diphthamide deficiency. We confirmed that the diphthamide modification is essential for eEF2 to prevent −1 frameshifting during translation and show that the Gly717-to-Arg mutation cannot rescue this defect.
Human superoxide dismutase 1 (hSOD1) maturation through interaction with human copper chaperone for SOD1 (hCCS)
Authors: Banci Lucia , Bertini Ivano , Cantini Francesca , Kozyreva Tatiana , Massagni Chiara , Palumaa Peep , Rubino Jeffrey T. , Zovo Kairit
Published: August 2012

Copper chaperone for superoxide dismutase 1 (SOD1), CCS, is the physiological partner for the complex mechanism of SOD1 maturation. We report an in vitro model for human CCS-dependent SOD1 maturation based on the study of the interactions of human SOD1 (hSOD1) with full-length WT human CCS (hCCS), as well as with hCCS mutants and various truncated constructs comprising one or two of the protein’s three domains. The synergy between electrospray ionization mass spectrometry (ESI-MS) and NMR is fully exploited. This is an in vitro study of this process at the molecular level. Domain 1 of hCCS is necessary to load hSOD1 with Cu(I), requiring the heterodimeric complex formation with hSOD1 fostered by the interaction with domain 2. Domain 3 is responsible for the catalytic formation of the hSOD1 Cys-57–Cys-146 disulfide bond, which involves both hCCS Cys-244 and Cys-246 via disulfide transfer.
Two-year survey comparing earthquake activity and injection-well locations in the Barnett Shale, Texas
Authors: Frohlich Cliff
Published: August 2012

Between November 2009 and September 2011, temporary seismographs deployed under the EarthScope USArray program were situated on a 70-km grid covering the Barnett Shale in Texas, recording data that allowed sensing and locating regional earthquakes with magnitudes 1.5 and larger. I analyzed these data and located 67 earthquakes, more than eight times as many as reported by the National Earthquake Information Center. All 24 of the most reliably located epicenters occurred in eight groups within 3.2 km of one or more injection wells. These included wells near Dallas–Fort Worth and Cleburne, Texas, where earthquakes near injection wells were reported by the media in 2008 and 2009, as well as wells in six other locations, including several where no earthquakes have been reported previously. This suggests injection-triggered earthquakes are more common than is generally recognized. All the wells nearest to the earthquake groups reported maximum monthly injection rates exceeding 150,000 barrels of water per month (24,000 m
3
/mo) since October 2006. However, while 9 of 27 such wells in Johnson County were near earthquakes, elsewhere no earthquakes occurred near wells with similar injection rates. A plausible hypothesis to explain these observations is that injection only triggers earthquakes if injected fluids reach and relieve friction on a suitably oriented, nearby fault that is experiencing regional tectonic stress. Testing this hypothesis would require identifying geographic regions where there is interpreted subsurface structure information available to determine whether there are faults near seismically active and seismically quiescent injection wells.
Overexpression of the
Hspa13
(
Stch
) gene reduces prion disease incubation time in mice
Authors: Grizenkova Julia , Akhtar Shaheen , Hummerich Holger , Tomlinson Andrew , Asante Emmanuel A. , Wenborn Adam , Fizet Jérémie , Poulter Mark , Wiseman Frances K. , Fisher Elizabeth M. C. , Tybulewicz Victor L. J. , Brandner Sebastian , Collinge John , Lloyd Sarah E.
Published: August 2012

Prion diseases are fatal neurodegenerative disorders that include bovine spongiform encephalopathy (BSE) and scrapie in animals and Creutzfeldt-Jakob disease (CJD) in humans. They are characterized by long incubation periods, variation in which is determined by many factors including genetic background. In some cases it is possible that incubation time may be directly correlated to the level of gene expression. To test this hypothesis, we combined incubation time data from five different inbred lines of mice with quantitative gene expression profiling in normal brains and identified five genes with expression levels that correlate with incubation time. One of these genes,
Hspa13
(
Stch
), is a member of the Hsp70 family of ATPase heat shock proteins, which have been previously implicated in prion propagation. To test whether
Hspa13
plays a causal role in determining the incubation period, we tested two overexpressing mouse models. The Tc1 human chromosome 21 (
Hsa21
) transchromosomic mouse model of Down syndrome is trisomic for many
Hsa21
genes including
Hspa13
and following Chandler/Rocky Mountain Laboratory (RML) prion inoculation, shows a 4% reduction in incubation time. Furthermore, a transgenic model with eightfold overexpression of mouse
Hspa13
exhibited highly significant reductions in incubation time of 16, 15, and 7% following infection with Chandler/RML, ME7, and MRC2 prion strains, respectively. These data further implicate Hsp70-like molecular chaperones in protein misfolding disorders such as prion disease.
Cultural transmission of social essentialism
Authors: Rhodes Marjorie , Leslie Sarah-Jane , Tworek Christina M.
Published: August 2012

Social essentialism entails the belief that certain social categories (e.g., gender, race) mark fundamentally distinct kinds of people. Essentialist beliefs have pernicious consequences, supporting social stereotyping and contributing to prejudice. How does social essentialism develop? In the studies reported here, we tested the hypothesis that generic language facilitates the cultural transmission of social essentialism. Two studies found that hearing generic language about a novel social category diverse for race, ethnicity, age, and sex led 4-y-olds and adults to develop essentialist beliefs about that social category. A third study documented that experimentally inducing parents to hold essentialist beliefs about a novel social category led them to produce more generic language when discussing the category with their children. Thus, generic language facilitates the transmission of essentialist beliefs about social categories from parents to children.
Assembly and subunit stoichiometry of the functional helicase-primase (primosome) complex of bacteriophage T4
Authors: Jose Davis , Weitzel Steven E. , Jing Debra , von Hippel Peter H.
Published: August 2012

Physical biochemical techniques are used to establish the structure, subunit stoichiometry, and assembly pathway of the primosome complex of the bacteriophage T4 DNA replication system. Analytical ultracentrifugation and fluorescence anisotropy methods show that the functional T4 primosome consists of six gp41 helicase subunits that assemble into a hexagon, driven by the binding of six NTPs (or six nonhydrolyzable GTPγS analogues) that are located at and stabilize the intersubunit interfaces, together with a single tightly bound gp61 primase subunit. Assembling the components of the primosome onto a model DNA replication fork is a multistep process, but equilibrium cannot be reached along all mixing pathways. Producing a functional complex requires that the helicase hexamer be assembled in the presence of the DNA replication fork construct prior to the addition of the primase to avoid the formation of metastable DNA-protein aggregates. The gp41 helicase hexamer binds weakly to fork DNA in the absence of primase, but forms a much more stable primosome complex that expresses full and functional helicase (and primase) activities when bound to a gp61 primase subunit at a helicase:primase subunit ratio of 6∶1. The presence of additional primase subunits does not change the molecular mass or helicase activity of the primosome, but significantly inhibits its primase activity. We develop both an assembly pathway and a minimal mechanistic model for the structure and function of the T4 primosome that are likely to be relevant to the assembly and function of the replication primosome subassemblies of higher organisms as well.