bluuebunny/crossref_metadata_2025 huggingface dataset:
The oldest Asian record of Anthropoidea
Authors: Bajpai Sunil , Kay Richard F. , Williams Blythe A. , Das Debasis P. , Kapur Vivesh V. , Tiwari B. N.
Published: August 2008

Undisputed anthropoids appear in the fossil record of Africa and Asia by the middle Eocene, about 45 Ma. Here, we report the discovery of an early Eocene eosimiid anthropoid primate from India, namedAnthrasimias, that extends the Asian fossil record of anthropoids by 9–10 million years. A phylogenetic analysis of 75 taxa and 343 characters of the skull, postcranium, and dentition ofAnthrasimiasand living and fossil primates indicates the basal placement ofAnthrasimiasamong eosimiids, confirms the anthropoid status of Eosimiidae, and suggests that crown haplorhines (tarsiers and monkeys) are the sister clade of Omomyoidea of the Eocene, not nested within an omomyoid clade. Co-occurence of Anthropoidea, Omomyoidea, and Adapoidea makes it evident that peninsular India was an important center for the diversification of primates of modern aspect (euprimates) in the early Eocene. Adaptive reconstructions indicate that early anthropoids were mouse–lemur-sized (≈75 grams) and consumed a mixed diet of fruit and insects. Eosimiids bear little adaptive resemblance to later Eocene-early Oligocene African Anthropoidea.
Evasion of peptide, but not lipid antigen presentation, through pathogen-induced dendritic cell maturation
Authors: Hava David L. , van der Wel Nicole , Cohen Nadia , Dascher Christopher C. , Houben Diane , León Luis , Agarwal Sandeep , Sugita Masahiko , van Zon Maaike , Kent Sally C. , Shams Homayoun , Peters Peter J. , Brenner Michael B.
Published: August 2008

Dendritic cells (DC) present lipid and peptide antigens to T cells on CD1 and MHC Class II (MHCII), respectively. The relative contribution of these systems during the initiation of adaptive immunity after microbial infection is not characterized. MHCII molecules normally acquire antigen and rapidly traffic from phagolysosomes to the plasma membrane as part of DC maturation, whereas CD1 molecules instead continually recycle between these sites before, during, and after DC maturation. We find that in
Mycobacterium tuberculosis
(Mtb)-infected DCs, CD1 presents antigens quickly. Surprisingly, rapid DC maturation results in early failure and delay in MHCII presentation. Whereas both CD1b and MHCII localize to bacterial phagosomes early after phagocytosis, MHCII traffics from the phagosome to the plasma membrane with a rapid kinetic that can precede antigen availability and loading. Thus, rather than facilitating antigen presentation, a lack of coordination in timing may allow organisms to use DC maturation as a mechanism of immune evasion. In contrast, CD1 antigen presentation occurs in the face of Mtb infection and rapid DC maturation because a pool of CD1 molecules remains available on the phagolysosome membrane that is able to acquire lipid antigens and deliver them to the plasma membrane.
Shear-induced reorganization of renal proximal tubule cell actin cytoskeleton and apical junctional complexes
Authors: Duan Yi , Gotoh Nanami , Yan Qingshang , Du Zhaopeng , Weinstein Alan M. , Wang Tong , Weinbaum Sheldon
Published: August 2008

In this study, we demonstrate that fluid shear stress (FSS)-induced actin cytoskeletal reorganization and junctional formation in renal epithelial cells are nearly completely opposite the corresponding changes in vascular endothelial cells (ECs) [Thi MM
et al.
(2004)
Proc Natl Acad Sci USA
101:16483–16488]. Mouse proximal tubule cells (PTCs) were subjected to 5 h of FSS (1 dyn/cm
2
) to investigate the dynamic responses of the cytoskeletal distribution of filamentous actin (F-actin), ZO-1, E-cadherin, vinculin, and paxillin to FSS. Immunofluorescence analysis revealed that FSS caused basal stress fiber disruption, more densely distributed peripheral actin bands (DPABs), and the formation of both tight junctions (TJs) and adherens junctions (AJs). A dramatic reinforcement of vinculin staining was found at the cell borders as well as the cell interior. These responses were abrogated by the actin-disrupting drug, cytochalasin D. To interpret these results, we propose a “junctional buttressing” model for PTCs in which FSS enables the DPABs, TJs, and AJs to become more tightly connected. In contrast, in the “bumper-car” model for ECs, all junctional connections were severely disrupted by FSS. This “junctional buttressing” model explains why a FSS of only 1/10 of that used in the EC study can cause a similarly dramatic, cytoskeletal response in these tall, cuboidal epithelial cells; and why junctional buttressing between adjacent cells may benefit renal epithelium in maximizing flow-activated, brush border-dependent, transcellular salt and water reabsorption.
Architecture and inherent robustness of a bacterial cell-cycle control system
Authors: Shen Xiling , Collier Justine , Dill David , Shapiro Lucy , Horowitz Mark , McAdams Harley H.
Published: August 2008

A closed-loop control system drives progression of the coupled stalked and swarmer cell cycles of the bacterium
Caulobacter crescentus
in a near-mechanical step-like fashion. The cell-cycle control has a cyclical genetic circuit composed of four regulatory proteins with tight coupling to processive chromosome replication and cell division subsystems. We report a hybrid simulation of the coupled cell-cycle control system, including asymmetric cell division and responses to external starvation signals, that replicates mRNA and protein concentration patterns and is consistent with observed mutant phenotypes. An asynchronous sequential digital circuit model equivalent to the validated simulation model was created. Formal model-checking analysis of the digital circuit showed that the cell-cycle control is robust to intrinsic stochastic variations in reaction rates and nutrient supply, and that it reliably stops and restarts to accommodate nutrient starvation. Model checking also showed that mechanisms involving methylation-state changes in regulatory promoter regions during DNA replication increase the robustness of the cell-cycle control. The hybrid cell-cycle simulation implementation is inherently extensible and provides a promising approach for development of whole-cell behavioral models that can replicate the observed functionality of the cell and its responses to changing environmental conditions.
Human mitochondrial RNA polymerase primes lagging-strand DNA synthesis
in vitro
Authors: Wanrooij Sjoerd , Fusté Javier Miralles , Farge Géraldine , Shi Yonghong , Gustafsson Claes M. , Falkenberg Maria
Published: August 2008

The mitochondrial transcription machinery synthesizes the RNA primers required for initiation of leading-strand DNA synthesis in mammalian mitochondria. RNA primers are also required for initiation of lagging-strand DNA synthesis, but the responsible enzyme has so far remained elusive. Here, we present a series of observations that suggests that mitochondrial RNA polymerase (POLRMT) can act as lagging-strand primase in mammalian cells. POLRMT is highly processive on double-stranded DNA, but synthesizes RNA primers with a length of 25 to 75 nt on a single-stranded template. The short RNA primers synthesized by POLRMT are used by the mitochondrial DNA polymerase γ to initiate DNA synthesis
in vitro
. Addition of mitochondrial single-stranded DNA binding protein (mtSSB) reduces overall levels of primer synthesis, but stimulates primer-dependent DNA synthesis. Furthermore, when combined, POLRMT, DNA polymerase γ, the DNA helicase TWINKLE, and mtSSB are capable of simultaneous leading- and lagging-strand DNA synthesis
in vitro
. Based on our observations, we suggest that POLRMT is the lagging-strand primase in mammalian mitochondria.
Biphasic requirement for geranylgeraniol in hippocampal long-term potentiation
Authors: Kotti Tiina , Head Daphne D. , McKenna Charles E. , Russell David W.
Published: August 2008

Mice deficient in cholesterol 24-hydroxylase exhibit reduced rates of cholesterol synthesis and other non-sterol isoprenoids that arise from the mevalonate pathway. These metabolic abnormalities, in turn, impair learning in the whole animal and hippocampal long-term potentiation (LTP)
in vitro
. Here, we report pharmacogenetic experiments in hippocampal slices from wild-type and mutant mice that characterize the dependence of LTP on the non-sterol isoprenoid, geranylgeraniol. Addition of geranylgeraniol to slices from 24-hydroxylase knockout mice restores LTP to wild-type levels; however, farnesol, a chemically related compound, does not substitute for geranylgeraniol nor does another animal model of impaired LTP (apolipoprotein E deficiency) respond to this isoprenoid. The requirement for geranylgeraniol is independent of acute protein isoprenylation as judged in experiments employing cell-permeable inhibitors of protein farnesyl transferase and geranylgeranyl transferase enzymes and in mutant mice hypomorphic for geranylgeranyltransferase II. Time course studies show that geranylgeraniol acts within 5 min and at 2 different times during the establishment of LTP: just before electrical stimulation and approximately 15 min thereafter. Localized delivery of geranylgeraniol to the dendritic trees of CA1 hippocampal neurons via the recording electrode is sufficient to restore LTP in slices from 24-hydroxylase knockout mice. We conclude that geranylgeraniol acts specifically and quickly to affect LTP in the Schaffer collaterals of the hippocampus.
Specific mutations within the AT-rich region of a plasmid replication origin affect either origin opening or helicase loading
Authors: Rajewska Magdalena , Kowalczyk Lukasz , Konopa Grazyna , Konieczny Igor
Published: August 2008

Prokaryotic and eukaryotic replicons possess a distinctive region containing a higher than average number of adenine and thymine residues (the AT-rich region) where, during the process of replication initiation, the initial destabilization (opening) of the double helix takes place. In many prokaryotic origins, this region consists of repeated 13-mer motifs whose function has not yet been specified. Here we identify specific mutations within the 13-mer sequences of the broad-host-range plasmid RK2 that can result in defective origin opening or that do not affect opening but induce defects in helicase loading. We also show that after the initial recruitment of helicase at the DnaA-box sequences of the plasmid origin, the helicase is translocated to the AT-rich region in a reaction requiring specific sequence of the 13-mers and appropriate facing of the origin motifs. Our results demonstrate that specific sequences within the AT-rich region of a replication origin are required for either origin opening or helicase loading.
Glial Fibrillary Acidic Protein Filaments Can Tolerate the Incorporation of Assembly-compromised GFAP-δ, but with Consequences for Filament Organization and αB-Crystallin Association
Authors: Perng Ming-Der , Wen Shu-Fang , Gibbon Terry , Middeldorp Jinte , Sluijs Jacqueline , Hol Elly M. , Quinlan Roy A.
Published: August 2008

The glial fibrillary acidic protein (GFAP) gene is alternatively spliced to give GFAP-α, the most abundant isoform, and seven other differentially expressed transcripts including GFAP-δ. GFAP-δ has an altered C-terminal domain that renders it incapable of self-assembly in vitro. When titrated with GFAP-α, assembly was restored providing GFAP-δ levels were kept low (∼10%). In a range of immortalized and transformed astrocyte derived cell lines and human spinal cord, we show that GFAP-δ is naturally part of the endogenous intermediate filaments, although levels were low (∼10%). This suggests that GFAP filaments can naturally accommodate a small proportion of assembly-compromised partners. Indeed, two other assembly-compromised GFAP constructs, namely enhanced green fluorescent protein (eGFP)-tagged GFAP and the Alexander disease–causing GFAP mutant, R416W GFAP both showed similar in vitro assembly characteristics to GFAP-δ and could also be incorporated into endogenous filament networks in transfected cells, providing expression levels were kept low. Another common feature was the increased association of αB-crystallin with the intermediate filament fraction of transfected cells. These studies suggest that the major physiological role of the assembly-compromised GFAP-δ splice variant is as a modulator of the GFAP filament surface, effecting changes in both protein– and filament–filament associations as well as Jnk phosphorylation.
Rapid Turnover Rate of Phosphoinositides at the Front of Migrating MDCK Cells
Authors: Nishioka Teruko , Aoki Kazuhiro , Hikake Kazuhiro , Yoshizaki Hisayoshi , Kiyokawa Etsuko , Matsuda Michiyuki
Published: August 2008

Phosphoinositides (PtdInss) play key roles in cell polarization and motility. With a series of biosensors based on Förster resonance energy transfer, we examined the distribution and metabolism of PtdInss and diacylglycerol (DAG) in stochastically migrating Madin-Darby canine kidney (MDCK) cells. The concentrations of phosphatidylinositol (4,5)-bisphosphate, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), phosphatidylinositol (3,4)-bisphosphate, and DAG were higher at the plasma membrane in the front of the cell than at the plasma membrane of the rear of the cell. The difference in the concentrations of PtdInss was estimated to be less than twofold between the front and rear of the migrating MDCK cells. To decode the spatial activities of PtdIns metabolic enzymes from the obtained concentration maps of PtdInss, we developed a one-dimensional reaction diffusion model of PtdIns metabolism. In this model, the activities of phosphatidylinositol monophosphate 5-kinase, phosphatidylinositol 3-kinase, phospholipase C, and PIP3 5-phosphatases were higher at the plasma membrane of the front than at the plasma membrane of the rear of the cell. This result suggests that, although the difference in the steady-state level of PtdInss is less than twofold, PtdInss were more rapidly turned over at the front than the rear of the migrating MDCK cells.
Cyclic Guanosine Monophosphate-dependent Protein Kinase I Promotes Adhesion of Primary Vascular Smooth Muscle Cells
Authors: Weinmeister Pascal , Lukowski Robert , Linder Stefan , Traidl-Hoffmann Claudia , Hengst Ludger , Hofmann Franz , Feil Robert
Published: August 2008

The cyclic guanosine monophosphate (cGMP)/cGMP-dependent protein kinase type I (cGKI) pathway regulates many cellular functions. The current study shows that 8-Br-cGMP stimulates the number of attached primary but not that of subcultured murine vascular smooth muscle cells (VSMCs). These effects of 8-Br-cGMP require the presence of cGKI. In agreement with previous studies, cGKI inhibited the number of cells in repeatedly passaged murine VSMCs. Activation of the cGMP/cGKI pathway in freshly isolated primary VSMCs slightly decreased apoptosis and strongly increased cell adhesion. The stimulation of cell adhesion by cGKI involves an inhibition of the RhoA/Rho kinase pathway and increased exposure of β1and β3integrins on the cell surface. Together, these results identify a novel proadhesive function of cGMP/cGKI signaling in primary VSMCs and suggest that the opposing effects of this pathway on VSMC number depend on the phenotypic context of the cells.
Regulation of Early Endosomal Entry by theDrosophilaTumor Suppressors Rabenosyn and Vps45
Authors: Morrison Holly A. , Dionne Heather , Rusten Tor Erik , Brech Andreas , Fisher William W. , Pfeiffer Barret D. , Celniker Susan E. , Stenmark Harald , Bilder David
Published: August 2008

The small GTPase Rab5 has emerged as an important regulator of animal development, and it is essential for endocytic trafficking. However, the mechanisms that link Rab5 activation to cargo entry into early endosomes remain unclear. We show here that Drosophila Rabenosyn (Rbsn) is a Rab5 effector that bridges an interaction between Rab5 and the Sec1/Munc18-family protein Vps45, and we further identify the syntaxin Avalanche (Avl) as a target for Vps45 activity. Rbsn and Vps45, like Avl and Rab5, are specifically localized to early endosomes and are required for endocytosis. Ultrastructural analysis of rbsn, Vps45, avl, and Rab5 null mutant cells, which show identical defects, demonstrates that all four proteins are required for vesicle fusion to form early endosomes. These defects lead to loss of epithelial polarity in mutant tissues, which overproliferate to form neoplastic tumors. This work represents the first characterization of a Rab5 effector as a tumor suppressor, and it provides in vivo evidence for a Rbsn–Vps45 complex on early endosomes that links Rab5 to the SNARE fusion machinery.
PK/DB: database for pharmacokinetic properties and predictive in silico ADME models
Authors: Moda Tiago L. , Torres Leonardo G. , Carrara Alexandre E. , Andricopulo Adriano D.
Published: August 2008

Summary: The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, blood–brain barrier and water solubility).

Availability:  http://www.pkdb.ifsc.usp.br

Contact:  aandrico@if.sc.usp.br
ZOOM! Zillions of oligos mapped
Authors: Lin Hao , Zhang Zefeng , Zhang Michael Q. , Ma Bin , Li Ming
Published: August 2008

Motivation: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts.

Results: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15× coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.

Availability: ZOOM is freely available to non-commercial users at http://www.bioinfor.com/zoom

Contact:  bma@csd.uwo.ca, mli@uwaterloo.ca
Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines
Authors: Larson Marilynn A. , Bressani Rafael , Sayood Khalid , Corn Jacob E. , Berger James M. , Griep Mark A. , Hinrichs Steven H.
Published: August 2008

The placement of the extreme thermophile Aquifex aeolicus in the bacterial phylogenetic tree has evoked much controversy. We investigated whether adaptations for growth at high temperatures would alter a key functional component of the replication machinery, specifically DnaG primase. Although the structure of bacterial primases is conserved, the trinucleotide initiation specificity for A. aeolicus was hypothesized to differ from other microbes as an adaptation to a geothermal milieu. To determine the full range of A. aeolicus primase activity, two oligonucleotides were designed that comprised all potential trinucleotide initiation sequences. One of the screening templates supported primer synthesis and the lengths of the resulting primers were used to predict possible initiation trinucleotides. Use of trinucleotide-specific templates demonstrated that the preferred initiation trinucleotide sequence for A. aeolicus primase was 5′-d(CCC)-3′. Two other sequences, 5′-d(GCC)-3′ and d(CGC)-3′, were also capable of supporting initiation, but to a much lesser degree. None of these trinucleotides were known to be recognition sequences used by other microbial primases. These results suggest that the initiation specificity of A. aeolicus primase may represent an adaptation to a thermophilic environment.
A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress
Authors: Kimura Junko , Nguyen Su Tien , Liu Hanshao , Taira Naoe , Miki Yoshio , Yoshida Kiyotsugu
Published: August 2008

Evasion from apoptotic cell death is a characteristic of cancer; genes that modulate this process may be optimal for therapeutic attack. Identifying key regulators of apoptosis is thus a central goal in cancer therapy. Here, we describe a loss-of-function screen that uses RNA interference libraries to identify genes required for induction of apoptosis. We used a short-hairpin RNA expressing vector with high gene-expression silencing activity that contained fetal brain cDNAs. Survived cells from genotoxic stress were isolated to determine knockdown of molecules that are crucial for induction of apoptosis. We identified TBP-associated factor 1 (TAF1), a gene previously implicated as an essential component of transcription machinery. Depletion of TAF1 was associated with substantial attenuation of apoptosis induced by oxidative as well as genotoxic stress. Microarray analysis further demonstrated that a number of genes were transcriptionally declined in cells silenced for TAF1. Surprisingly, knocking down TAF1 exhibited a marked decrease in p27Kip1 expression, allowing cells resistant from oxidative stress-induced apoptosis. These results suggest that TAF1 regulates apoptosis by controlling p27Kip1 expression. Our system provides a novel approach to identifying candidate genes that modulate apoptosis.
The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets
Authors: García-Mayoral María Flor , Díaz-Moreno Irene , Hollingworth David , Ramos Andres
Published: August 2008

K-homology (KH) splicing regulator protein (KSRP) is a multi-domain RNA-binding protein that regulates different steps of mRNA metabolism, from mRNA splicing to mRNA decay, interacting with a broad range of RNA sequences. To understand how KSRP recognizes its different RNA targets it is necessary to define the general rules of KSRP– RNA interaction. We describe here a complete scaffold-independent analysis of the RNA-binding potential of the four KH domains of KSRP. The analysis shows that KH3 binds to the RNA with a significantly higher affinity than the other domains and recognizes specifically a G-rich target. It also demonstrates that the other KH domains of KSRP display different sequence preferences explaining the broad range of targets recognized by the protein. Further, KSRP shows a strong negative selectivity for sequences containing several adjacent Cytosines limiting the target choice of KSRP within single-stranded RNA regions. The in-depth analysis of the RNA-binding potential of the KH domains of KSRP provides us with an understanding of the role of low sequence specificity domains in RNA recognition by multi-domain RNA-binding proteins.
An intronic microRNA silences genes that are functionally antagonistic to its host gene
Authors: Barik Sailen
Published: August 2008

MicroRNAs (miRNAs) are short noncoding RNAs that down-regulate gene expression by silencing specific target mRNAs. While many miRNAs are transcribed from their own genes, nearly half map within introns of ‘host’ genes, the significance of which remains unclear. We report that transcriptional activation of apoptosis-associated tyrosine kinase (AATK), essential for neuronal differentiation, also generates miR-338 from an AATK gene intron that silences a family of mRNAs whose protein products are negative regulators of neuronal differentiation. We conclude that an intronic miRNA, transcribed together with the host gene mRNA, may serve the interest of its host gene by silencing a cohort of genes that are functionally antagonistic to the host gene itself.
Emergency Medical Consequence Planning and Management for National Special Security Events After September 11: Boston 2004
Authors: Kade Kristy A. , Brinsfield Kathryn H. , Serino Richard A. , Savoia Elena , Koh Howard K.
Published: August 2008

The post-September 11 era has prompted unprecedented attention to medical preparations for national special security events (NSSE), requiring extraordinary planning and coordination among federal, state, and local agencies. For an NSSE, the US Secret Service (USSS) serves as the lead agency for all security operations and coordinates with relevant partners to provide for the safety and welfare of participants. For the 2004 Democratic National Convention (DNC), designated an NSSE, the USSS tasked the Boston Emergency Medical Services (BEMS) of the Boston Public Health Commission with the design and implementation of health services related to the Convention. In this article, we describe the planning and development of BEMS’ robust 2004 DNC Medical Consequence Management Plan, addressing the following activities: public health surveillance, on-site medical care, surge capacity in the event of a mass casualty incident, and management of federal response assets. Lessons learned from enhanced medical planning for the 2004 DNC may serve as an effective model for future mass gathering events. (Disaster Med Public Health Preparedness. 2008;2:166–173)
MultipleMONOPTEROS-Dependent Pathways Are Involved in Leaf Initiation
Authors: Schuetz Mathias , Berleth Thomas , Mattsson Jim
Published: August 2008

Initiation of leaves at the flanks of the shoot apical meristem occurs at sites of auxin accumulation and pronounced expression of auxin-inducible PIN-FORMED1 (PIN) genes, suggesting a feedback loop to progressively focus auxin in concrete spots. Because PIN expression is regulated by auxin response factor activity, including MONOPTEROS (MP), it appeared possible that MP affects leaf formation as a positive regulator of PIN genes and auxin transport. Here, we analyze a novel, completely leafless phenotype arising from simultaneous interference with both auxin signaling and auxin transport. We show that mp pin1 double mutants, as well as mp mutants treated with auxin-efflux inhibitors, display synergistic abnormalities not seen in wild type regardless of how strongly auxin transport was reduced. The synergism of abnormalities indicates that the role of MP in shoot meristem organization is not limited to auxin transport regulation. In the mp mutant background, auxin transport inhibition completely abolishes leaf formation. Instead of forming leaves, the abnormal shoot meristems dramatically increase in size, harboring correspondingly enlarged expression domains of CLAVATA3 and SHOOTMERISTEMLESS, molecular markers for the central stem cell zone and the complete meristem, respectively. The observed synergism under conditions of auxin efflux inhibition was further supported by an unrestricted PIN1 expression in mp meristems, as compared to a partial restriction in wild-type meristems. Auxin transport-inhibited mp meristems also lacked detectable auxin maxima. We conclude that MP promotes the focusing of auxin and leaf initiation in part through pathways not affected by auxin efflux inhibitors.
Mitochondrial mRNA Polymorphisms in Different Arabidopsis Accessions
Authors: Forner Joachim , Hölzle Angela , Jonietz Christian , Thuss Sabine , Schwarzländer Markus , Weber Bärbel , Meyer Rhonda C. , Binder Stefan
Published: August 2008

In our analysis of 5′ and 3′ end formation in plant mitochondria, we compared the major transcript ends of all mitochondrial protein-coding genes between the three Arabidopsis (Arabidopsis thaliana) accessions Columbia (Col), C24, and Landsberg erecta (Ler). Differences between transcript patterns were found for seven genes. For atp6-2, no transcripts at all were detected in Ler. This and further analyses suggest that the atp6-2 gene arrangement is absent from the mitochondrial DNA of this accession. All other transcript polymorphisms are attributed to variations at the 5′ termini and were consistently observed in all tissues investigated. mRNA phenotyping of reciprocal Col/Ler, Col/C24, and Ler/C24 F1 hybrids revealed the differing transcript patterns of ccmC to be inherited maternally, suggesting these to arise from differences in the mitochondrial DNA. Biparental inheritance was observed for the polymorphic transcripts of nad4, nad9, ccmB, and rpl5, indicating these differences to be caused by nuclear-encoded trans-factors. Deviant transcript patterns were tested in further accessions and were found in at least three additional accessions. Detailed examination of the nad4 and the nad9 transcripts demonstrates that the respective polymorphisms affect the major mRNAs of these genes. This study shows that natural genetic variation in Arabidopsis can also affect mitochondrial mRNA end processing. These variations can now be used to identify the nuclear genes responsible, as well as the mitochondrial cis-elements required, for 5′ end generation of mitochondrial transcripts.
Generation of Hydrogen Peroxide in Chloroplasts of Arabidopsis Overexpressing Glycolate Oxidase as an Inducible System to Study Oxidative Stress
Authors: Fahnenstich Holger , Scarpeci Telma E. , Valle Estela M. , Flügge Ulf-Ingo , Maurino Verónica G.
Published: August 2008

Arabidopsis (Arabidopsis thaliana) overexpressing glycolate oxidase (GO) in chloroplasts accumulates both hydrogen peroxide (H2O2) and glyoxylate. GO-overexpressing lines (GO plants) grown at 75 μmol quanta m−2 s−1 show retarded development, yellowish rosettes, and impaired photosynthetic performance, while at 30 μmol quanta m−2 s−1, this phenotype virtually disappears. The GO plants develop oxidative stress lesions under photorespiratory conditions but grow like wild-type plants under nonphotorespiratory conditions. GO plants coexpressing enzymes that further metabolize glyoxylate but still accumulate H2O2 show all features of the GO phenotype, indicating that H2O2 is responsible for the GO phenotype. The GO plants can complete their life cycle, showing that they are able to adapt to the stress conditions imposed by the accumulation of H2O2 during the light period. Moreover, the data demonstrate that a response to oxidative stress is installed, with increased expression and/or activity of known oxidative stress-responsive components. Hence, the GO plants are an ideal noninvasive model system in which to study the effects of H2O2 directly in the chloroplasts, because H2O2 accumulation is inducible and sustained perturbations can reproducibly be provoked by exposing the plants to different ambient conditions.
Dicaesium hexamercury heptasulfide
Authors: Bugaris Daniel E. , Ibers James A.
Published: August 2008

The title compound, Cs2Hg6S7, crystallizes in a new structure type that is closely related to that of K2Zn6O7. The structure comprises a three-dimensional mercury sulfide network that is composed of channels. These channels, which are along [001], are of two different diameters. The crystal structure contains one Cs, two Hg, and three S atoms in the asymmetric unit. The Cs, one Hg, and one S atom are at sites of symmetry m, whereas a second S atom is at a site of symmetry 2mm. The Hg atoms are bound to the S atoms in both three- and four-coordinate geometries. The caesium cations occupy the central spaces of the larger diameter channels and exhibit a coordination number of 7.
Tetra-μ-2,5-difluorobenzoato-bis[(2,2′-bipyridine)(2,5-difluorobenzoato)gadolinium(III)]
Authors: Li Sheng , Zhang Fu-Li , Tang Kun , Ma Yuan-Fang
Published: August 2008

In the centrosymmetric title compound, [Gd2(C7H3F2O2)6(C10H8N2)2], the asymmetric unit comprises one cation chelated by two 2,5-difluorobenzoate and one 2,2′-bipyridine. Two cations are linked into dimers via three bridging carboxylate groups from three 2,5-difluorobenzoic acid units. The GdIII ion is nine-coordinated by seven O atoms and two N atoms.
catena-Poly[[[μ-cyanido-1:2κ2
C:N-tricyanido-1κ3
C-bis(ethylenediamine)-2κ4
N,N′-copper(II)iron(II)]-μ-cyanido-κ2
C:N-[bis(ethylenediamine-κ2
N,N′)copper(II)]-μ-cyanido-κ2
N:C] 4.5-hydrate]
Authors: Liu Hongling , Wang Daqi
Published: August 2008

The asymmetric unit of the title compound, {[Cu2Fe(CN)6(C2H8N2)4]·4.5H2O}
n
, consists of two [Cu(C2H8N2)2]2+ cations, one [Fe(CN)6]4− anion, four water molecules and a half water molecule that lies on a twofold rotation axis. The FeII atom is coordinated by six C atoms from three terminal and three doubly bridging CN− ligands. The bridging CN− ligands connect the anion to a five-coordinate [Cu(C2H8N2)2]2+ cation and to two symmetry-related six-coordinate [Cu(C2H8N2)2]2+ cations, forming a one-dimensional polymer in the ab plane. Intermolecular hydrogen bonds connect the polymer units into a three-dimensional network.
catena-Poly[[tetrakis(μ2-acetato-κ2
O:O′)dicopper(II)(Cu—Cu)]-μ2-acetato-κ2
O:O′-[bis[μ2-3-(dimethylamino)propan-1-olato]-κ2
N,O:O;κ2
O:N,O-bis[(tetrahydrofuran-κO)copper(II)]]-μ2-acetato-κ2
O:O′]
Authors: Shahid Muhammad , Mazhar Muhammad , Helliwell Madeleine , Akhtar Javeed , Ahmad Kibriya
Published: August 2008

The title complex, [Cu4(C5H12NO)2(C2H3O2)6(C4H8O)2]
n
, consists of dinuclear [Cu2(C5H12NO)2(THF)2] (THF is tetrahydrofuran) and [Cu2(CH3COO)4] units linked through acetate ions, generating parallel one-dimensional polymeric chains propagating in the [1\overline{1}0] direction. In the first dinuclear unit, CuII ions related by inversion symmetry are bridged by two 3-(dimethylamino)propan-1-olate ligands. Likewise, a pair of inversion-related CuII ions are bridged by four acetate groups. The crystallographically independent Cu centers are linked to one another by a single bridging acetate group, generating an infinite chain. The distorted square-pyramidal coordination of the first metal center is completed with an apical THF molecule, with a long Cu—O bond length of 2.476 (5) Å. The geometry around the other metal atom is close to octahedral, and the Cu...Cu separation in this unit is 2.652 (1) Å. The distance between the metal centers in the first dinuclear unit is considerably longer [3.068 (1) Å], suggesting little or no bonding interaction. The Cu...Cu separation between two acetate-bridged independent Cu centers is 4.860 (2) Å. The THF molecule has methylene groups disordered over two positions, with occupancies of 0.608 (13) and 0.392 (13).
{μ-N-[(Diphenylphosphino)methyl]pyridin-2-amine-κ2
N
1:P}bis{[2-(2,2′-bipyridin-6-yl)phenyl-κ3
N,N′,C
1]platinum(II)} bis(perchlorate)
Authors: Du Xiang-Dang , Mo Juan , Li Xin-Sheng , Pan Yu-Shan , Zhang Su-Mei
Published: August 2008

The title compound, [Pt2(C16H11N2)2(C18H17N2P)](ClO4)2, contains two PtII atoms, bridged by an N-[(diphenylphosphino)methyl]pyridin-2-amine (dppmp) ligand. One Pt atom is coordinated by one P atom from the dppmp ligand, and one C atom and two N atoms from a 6-phenyl-2,2′-bipyridine (pbpy) ligand in a square-planar geometry. The other Pt atom is coordinated by one N atom from the dppmp ligand, and one C atom and two N atoms from another pbpy ligand in a square-planar geometry. There are intramolecular π–π interactions between the pbpy ligands, with a centroid–centroid distance of 3.62 (1) Å between two pyridyl rings. The oxygen atoms of both perchlorate anions are disordered, each over two different positions [occupanicies 0.49 (3)/0.51 (3) and 0.48 (2)/0.52 (2)].
Bis(4,6-diaminopyrimidin-2-yl) disulfide dimethyl sufoxide disolvate
Authors: Papastavrou Ephthymia , Shakhatreh Saleh , Akrivos Pericles D. , Gdaniec Maria
Published: August 2008

The title compound, C8H10N8S2·2C2H6SO, was obtained unintentionally during an attempt to prepare a thiolate derivative of trimethyltin. The complete disulfide molecule is generated by twofold rotation symmetry and the C—S—S—C torsion angle around the S—S bond is −85.70 (10)°. The molecules are connected via N—H...N hydrogen bonds into strongly corrugated layers parallel to (001), generating an R
2
2(8) motif. The solvent molecule, which exhibits minor disorder of its S atom [site occupancies = 0.9591 (18) and 0.0409 (18)], is linked to this layer via a pair of N—H...O interactions.
N-(2,6-Diisopropylphenyl)formamide
Authors: Chitanda Jackson M. , Quail J. Wilson , Foley Stephen R.
Published: August 2008

The title compound, C13H19NO, exhibits a non-planar structure in which the 2,6-diisopropylphenyl ring is tilted at a dihedral angle of 77.4 (1)° with respect to the formamide group. This is the largest dihedral angle known among structurally characterized formamides. The molecules are linked via N—H...O hydrogen bonds, forming infinite chains which run along the b-axis directions.
3-Ethyl 5-methyl 2-hydroxy-6-methyl-4-(4-nitrophenyl)-2-trifluoromethyl-1,2,3,4-tetrahydropyridine-3,5-dicarboxylate
Authors: Yu Chen-Xia , Qian Pei-Li , Ping Jia-Jing , Yao Chang-Sheng
Published: August 2008

In the title compound, C18H19F3N2O7, the tetrahydropyridine ring adopts a half-chair conformation. The nitro group is disordered over two sites with occupancies of 0.780 (15) and 0.220 (15). An intramolecular N—H...F hydrogen bond is observed in the molecular structure. The molecules are linked into a two-dimensional network parallel to (100) by O—H...O, N—H...O and C—H...O hydrogen bonds.
Tetra-μ-benzoato-bis[(3-methylquinoline)copper(II)](Cu—Cu)
Authors: Park Byeong Kwon , Jang Kyung-Hwan , Kim Pan-Gi , Kim Cheal , Kim Youngmee
Published: August 2008

In the title compound, [Cu2(C7H5O2)4(C10H9N)2], the paddle-wheel-type dinuclear complex molecule contains four bridging benzoate groups and two terminal 3-methylquinoline ligands. The asymmetric unit contains one and a half molecules with a total of three independent Cu atoms; there is an inversion center at the mid-point of the Cu...Cu bond in one molecule. The octahedral coordination of each Cu atom, with four O atoms in the equatorial plane, is completed by an N atom of a 3-methylquinoline ligand [Cu—N = 2.190 (4)–2.203 (3) Å] and by another Cu atom [Cu...Cu = 2.667 (1) and 2.6703 (7) Å]. The Cu atoms are all ca 0.22 Å out of the plane of the four bonded O atoms.
3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl)prop-2-en-1-one
Authors: Fun Hoong-Kun , Chantrapromma Suchada , Patil P. S. , Dharmaprakash S. M.
Published: August 2008

The title chalcone derivative, C13H8ClFOS, crystallized as an inversion twin with two independent molecules in the asymmetric unit. The thiophene rings in both molecules are disordered over two sites: the ratios of occupancies for the major and minor components in the two molecules are 0.820 (2):0.180 (2) and 0.853 (2):0.147 (2). The dihedral angles between the major and minor components of the thiophene and benzene rings are 1.13 (18) and 2.2 (6)°, respectively, in one molecule, with corresponding values 6.09 (17) and 1.3 (6)° in the other. Weak intramolecular C—H...O and C—H...F interactions involving the prop-2-en-1-one group generate an S(5)S(5) ring motif, whereas a weak intramolecular C—H...Cl contact generates an S(6) ring motif. In the crystal structure, molecules of both the major and minor components are linked into infinite one-dimensional chains along the b axis. The crystal structure is stabilized by weak C—H...O, C—H...F, C—H...Cl and C—H...π interactions.
2,2′-[1,1′-(Hexane-1,6-diyldioxydinitrilo)diethylidyne]diphenol
Authors: Dong Wen-Kui , He Xue-Ni , Sun Yin-Xia , Xu Li , Tong Jun-Feng
Published: August 2008

The molecule of the title compound, C22H28N2O2, lies across an inversion centre with one half-molecule in the asymmetric unit. The molecule adopts an E configuration with respect to the azomethine C=N bond and the imino group is coplanar with the aromatic ring. Within the molecule, the planar units are parallel, but extend in opposite directions from the hexamethylene bridge. There are intramolecular O—H...N hydrogen bonds between the hydroxyl groups and the oxime N atoms. There are also weak intermolecular C—H...O bonds that link each molecule to two others, forming chains along the a axis.
{μ-N,N′-Bis[(E)-4-pyridylmethylidene]naphthalene-1,5-diamine}bis[dichlorido(dimethyl sulfide)platinum(II)]
Authors: Huh Hyun Sue , Lee Soon W.
Published: August 2008

The title dinuclear platinum compound, [Pt2Cl4(C22H16N4)(C2H6S)2], with a long bridging bipyridyl-type ligand, is centrosymmetric and the PtII cation shows a slightly distorted square-planar coordination geometry. The Cl ligands are trans to each other, with a Cl—Pt—Cl angle of 178.83 (8)°. The pyridine ring forms a dihedral angle of 48.8 (2)° with the planar PtCl2SN unit. Within the molecule, the distance between Pt atoms is 20.262 (5) Å and the N...N separation between the terminal pyridyl rings is 16.23 (1)Å.
N,N′-Bis[2-chloro-5-(trifluoromethyl)benzylidene]ethane-1,2-diamine
Authors: Fun Hoong-Kun , Kia Reza
Published: August 2008

The molecule of the title Schiff base compound, C18H12Cl2F6N2, adopts an E configuration with respect to the azomethine C=N bond. Intramolecular C—H...F (× 2) and C—H...Cl (× 2) hydrogen bonds generate S(5) ring motifs. The imino group is coplanar with the aromatic ring. Within the molecule, the planar units are parallel, but extend in opposite directions from the methylene bridge, as indicated by the dihedral angle between the two benzene rings of 3.74 (6)°. The interesting features of the crystal structure are weak intermolecular Cl...N and F...F interactions, with distances of 2.9192 (11) and 3.2714 (10) Å, respectively, which are shorter than the sum of the van der Waals radii of the relevent atoms. These interactions link neighbouring molecules into dimers which are stacked down the b axis.
Ethyl 4-{2,6-dichloro-4-[3-(2,6-difluorobenzoyl)ureido]phenoxy}butanoate
Authors: Liu Yin-Hong , Li Fang-Shi , Li Yi , Yu Da-Sheng , Lu Chui
Published: August 2008

The title compound, C20H18Cl2F2N2O5, is considered to belong to the fourth generation of insecticides with properties such as high selectivity, low acute toxicity for mammals and high biological activity. An intramolecular N—H...O hydrogen bond results in the formation of a six-membered ring. In the crystal structure, intermolecular N—H...O and C—H...F hydrogen bonds link the molecules.
2-(6-Methyl-2-pyridyl)-1,1-diphenylethanol
Authors: Gu Wei-Jin , Wang Bing-Xiang
Published: August 2008

The title compound, C20H19NO, was prepared from 2,6-lutidine and benzophenone. There are two symmetry-independent molecules in the asymmetric unit. Each molecule is involved in one intramolecular O—H...N hydrogen bond. In the crystal structure, helical chains are formed along the b axis by weak π–π interactions between neighbouring molecules [centroid–centroid distances between the pyridyl rings of the two independent molecules = 4.041 (3) and 4.051 (3) Å].
2,2′-Dimethoxybiphenyl
Authors: Nakaema Kosuke , Okamoto Akiko , Maruyama Satoshi , Noguchi Keiichi , Yonezawa Noriyuki
Published: August 2008

The molecule of the title compound, C14H14O2, lies on a crystallographic twofold axis perpendicular to the central C—C bond; there is one half-molecule in the asymmetric unit. The angle between the least-squares planes of the two aromatic rings is 66.94 (7)°. The methoxy group, with a twist angle of 10.69 (8)°, is slightly out of the plane of the benzene ring. In the crystal structure, C—H...π interactions are observed between adjacent molecules along the c-axis direction.
N-[(3,5-Dimethylpyrazol-1-yl)methyl]phthalimide
Authors: Wang Su-Qing , Jian Fang-Fang , Liu Huan-Qiang
Published: August 2008

The title compound {systematic name: 2-[(3,5-dimenthylpyrazol-1-yl)methyl]isoindole-1,3-dione}, C14H13N3O2, was prepared by reaction of N-(bromomethyl)phthalimide and 3,5-dimethylpyrazole in chloroform solution. The molecular structure and packing are stabilized by intramolecular C—H...O hydrogen-bonding and C—H...π interactions.
Hexacarbonyltechnetium(I) perchlorate
Authors: Gurzhiy V. V. , Miroslavov A. E. , Sidorenko G. V. , Lumpov A. A. , Krivovichev S. V. , Suglobov D. N.
Published: August 2008

The title compound, [Tc(CO)6]ClO4, was synthesized by the reaction of [TcCl(CO)5] with AgClO4, followed by acidification with HClO4 under a CO atmosphere. The [Tc(CO)6]+ cation has close to idealized octahedral geometry, with the bond angles between cis-CO groups close to 90° and the Tc—C bond lengths in the range 2.025 (3)–2.029 (3)Å. The perchlorate anion is disordered over two crystallographically equivalent half-occupied positions. The Tc atom in the [Tc(CO)6]+ cation is located on an inversion centre.
Pentacarbonyl-2κ5
C-chlorido-1κCl-bis[1(η5)-cyclopentadienyl][μ-oxido(phenyl)methylene-1:2κ2
O:C]hafnium(IV)tungsten(0)
Authors: Esterhuysen Catharine , Nel I. B. Jacques , Cronje Stephanie
Published: August 2008

The title compound, [HfW(C5H5)2(C7H5O)Cl(CO)5] or [W(CO)5(C7H5O){Hf(C5H5)2Cl}], contains two metal centres, with a (tungstenpentacarbonyl)oxyphenylcarbene unit coordinated to a hafnocene chloride. The Hf—O—C angle is nearly linear, and the C=O distance is slightly shorter than for equivalent alkoxycarbenes. One of the cyclopentadienyl (Cp) rings undergoes an offset face-to-face π–π interaction [3.495 (7) Å] with the symmetry-related Cp ring of a neighbouring molecule.
Bis(2,6-dimethylpyridinium) hexachloridoplatinate(IV)
Authors: Amani Vahid , Rahimi Rahmatollah , Khavasi Hamid Reza
Published: August 2008

The asymmetric unit of the title compound, (C7H10N)2[PtCl6], contains one independent protonated 2,6-dimethylpyridinium cation and half of a centrosymmetric [PtCl6]2− anion. The Pt atom has an octahedral coordination. In the crystal structure, intermolecular N—H...Cl and C—H...Cl hydrogen bonds result in the formation of a supramolecular structure. There is a π–π contact between the pyridine rings [centroid–centroid distance = 4.235 (1) Å].
N-(Hydroxymethyl)ibogaine
Authors: Jarraya Raoudha Mezghani , Bouaziz Amira , Hamdi Besma , Ben Salah Abdelhamid , Damak Mohamed
Published: August 2008

The title compound (systematic name: 16-hydroxymethyl-12-methoxyibogamine), C21H28N2O2, was prepared by reaction of ibogaine with a formaldehyde–acetic acid solution (pH = 4). The crystal structure of this new product, belonging to the iboga indole family, is stabilized by an intermolecular O—H...N hydrogen bond. The identity of the compound was confirmed by one- and two-dimensional NMR spectroscopic techniques.
Barium zinc diarsenate
Authors: Đordević Tamara
Published: August 2008

The title compound, BaZnAs2O7, belongs to the family of isotypic series of compounds adopting the general formula M12+
M22+
X
2O7 (M12+ = Ca, Sr, Ba or Pb; M22+ = Mg, Cr, Mn, Fe, Co, Ni, Cu, Zn or Cd; X = P or As). Suitable single crystals were prepared under hydrothermal conditions. The framework structure is characterized by corner-sharing ZnO5 square pyramids and As2O7 groups where the Zn atoms occupy channels. X-ray diffraction analysis of single crystals twinned by non-merohedry [twin plane is (100)] yielded formula BaZnAs2O7. Raman spectra confirmed the presence of a non-linear As—O—As linkage.