bluuebunny/crossref_metadata_2025 huggingface dataset:
Widespread late Cenozoic increase in erosion rates across the interior of eastern Tibet constrained by detrital low‐temperature thermochronometry
Authors: Duvall Alison R. , Clark Marin K. , Avdeev Boris , Farley Kenneth A. , Chen Zhengwei
Published: May 2012

New detrital low‐temperature thermochronometry provides estimates of long‐term erosion rates and the timing of initiation of river incision from across the interior of the Tibetan Plateau. We use the erosion history of this region to evaluate proposed models of orogenic development as well as regional climatic events. Erosion histories of the externally drained portion of the east‐central Tibetan Plateau are recorded in modern river sands from major rivers across a transect that spans >750 km and covers a region with no published thermochronometric ages. Individual grains from eight catchments were analyzed for apatite (U‐Th)/He and fission track thermochronometry. A wide distribution in ages that, in most cases, spans the entire Cenozoic and Late Mesozoic eras requires a long period of slow or no erosion with a relative increase in erosion rate toward the present. We apply a recently developed methodology for inversion of detrital thermochronometric data for three specified erosion scenarios: constant erosion rate, two‐stage erosion history, and three‐stage erosion history. Modeling results suggest that rates increase by at least an order of magnitude between 11 and 4 Ma following a period of slow erosion across the studied catchments. Synchroneity in accelerated erosion across the whole of the Tibetan Plateau rather than a spatial or temporal progression challenges the widely held notion that the plateau evolved as a steep, northward‐propagating topographic front, or that south to north precipitation gradients exert a primary control on erosion rates. Instead, we suggest that accelerated river incision late in the orogen's history relates to regional‐scale uplift that occurred in concert with eastern expansion of the plateau.
Convergence of the Indian and Eurasian plates under eastern Tibet revealed by seismic tomography
Authors: Zhang Heng , Zhao Dapeng , Zhao Junmeng , Xu Qiang
Published: May 2012

A three‐dimensional P wave velocity model of the crust and upper mantle down to 400‐km depth beneath eastern Tibet is obtained using many temporary seismic stations of the ASCENT project and the Namche Barwa Broadband Seismic Network. We collected 16,508 arrival times of P, Pn and Pg phases from 573 local and regional earthquakes and 7,450 P wave arrivals from seismograms of 435 teleseismic events. Our high‐quality data set enables us to reconstruct the 3‐D velocity structure under eastern Tibet in more detail than the previous studies. In the shallow depth, our results show that the low velocity zones are not interconnected well (no wide‐spread low velocity zones), which may reflect the complex pattern of material flowing in the study region. Below the Moho, we find that the Indian lithospheric mantle underthrusts sub‐horizontally under eastern Tibet, and the extent of the northward advancing Indian lithosphere decreases from west to east. In the north, the Asian lithospheric mantle is detected under the vicinity of the Qaidam Basin. Between the Indian and Asian lithospheric mantles, there is an obvious low‐velocity anomaly which may reflect an upwelling mantle diapir.
Relationship of maximum tropical cyclone intensity to sea surface temperature and tropical cyclone heat potential in the North Pacific Ocean
Authors: Wada Akiyoshi , Usui Norihisa , Sato Kanako
Published: May 2012

We investigated whether the maximum intensity of tropical cyclones (TC) in the North Pacific Ocean depends on sea surface temperature (SST) and tropical cyclone heat potential (TCHP). The study used reanalysis data sets for both the oceans and atmosphere: daily, 10‐day, and monthly oceanic data sets; six‐hour and monthly atmospheric data sets; and a daily satellite SST data set, for the July‐to‐October season from 2002 to 2005. For each TC, we summed TCHP from the time of genesis to the time of first reaching a minimum central pressure (MCP), to obtain an accumulated TCHP. In a linear regression analysis, the relationship between maximum TC intensity and accumulated TCHP differed between the eastern and western Pacific: high values of accumulated TCHP were needed before a TC attained a certain MCP in the western Pacific. In addition, the background convective available potential energy (CAPE) value was nearly four times larger in the western Pacific than in the eastern Pacific. The static stability was also 6.5% lower, the inertial stability 29.7% higher, and the size of tropical cyclones 38.2% larger in the western Pacific than in the eastern Pacific. The result indicated a deeper Rossby penetration depth and stronger TC in the western Pacific. Finally, we validated the TCHP values derived from three oceanic reanalysis data sets by using Argo profiling float observations. We found that use of only the daily data can reproduce the cooling effect of a passage of a TC, which caused a decrease in the TCHP values.
Distinct and redundant roles of the non-muscle myosin II isoforms and functional domains
Authors: Wang Aibing , Ma Xuefei , Conti Mary Anne , Adelstein Robert S.
Published: May 2012

We propose that the in vivo functions of NM II (non-muscle myosin II) can be divided between those that depend on the N-terminal globular motor domain and those less dependent on motor activity but more dependent on the C-terminal domain. The former, being more dependent on the kinetic properties of NM II to translocate actin filaments, are less amenable to substitution by different NM II isoforms, whereas the in vivo functions of the latter, which involve the structural properties of NM II to cross-link actin filaments, are more amenable to substitution. In light of this hypothesis, we examine the ability of NM II-A, as well as a motor-compromised form of NM II-B, to replace NM II-B and rescue neuroepithelial cell–cell adhesion defects and hydrocephalus in the brain of NM II-B-depleted mice. We also examine the ability of NM II-B as well as chimaeric forms of NM II (II-A head and II-B tail and vice versa) to substitute for NM II-A in cell–cell adhesions in II-A-ablated mice. However, we also show that certain functions, such as neuronal cell migration in the developing brain and vascularization of the mouse embryo and placenta, specifically require NM II-B and II-A respectively.
Mitotic motors and chromosome segregation: the mechanism of anaphase B
Authors: Brust-Mascher Ingrid , Scholey Jonathan M.
Published: May 2012

Anaphase B spindle elongation plays an important role in chromosome segregation. In the present paper, we discuss our model for anaphase B in Drosophila syncytial embryos, in which spindle elongation depends on an ip (interpolar) MT (microtubule) sliding filament mechanism generated by homotetrameric kinesin-5 motors acting in concert with poleward ipMT flux, which acts as an ‘on/off’ switch. Specifically, the pre-anaphase B spindle is maintained at a steady-state length by the balance between ipMT sliding and ipMT depolymerization at spindle poles, producing poleward flux. Cyclin B degradation at anaphase B onset triggers: (i) an MT catastrophe gradient causing ipMT plus ends to invade the overlap zone where ipMT sliding forces are generated; and (ii) the inhibition of ipMT minus-end depolymerization so flux is turned ‘off’, tipping the balance of forces to allow outward ipMT sliding to push apart the spindle poles. We briefly comment on the relationship of this model to anaphase B in other systems.
Messengers, motors and mysteries: sorting of eukaryotic mRNAs by cytoskeletal transport
Authors: Bullock Simon L.
Published: May 2012

It has become increasingly apparent in recent years that the subcellular localization of specific mRNAs is a prevalent method for spatially controlling gene expression. In most cases, targeting of mRNAs is mediated by transport along cytoskeletal filaments by molecular motors. However, the means by which specific messages are recognized and linked to the motors are poorly understood. Here, I will provide an overview of recent progress in elucidating the molecular mechanisms and principles of mRNA transport, including several studies highlighting the co-operation of different motors during the localization process. Important outstanding questions will also be highlighted.
Cytoplasmic dynein
Authors: Allan Victoria J.
Published: May 2012

The organization and function of eukaryotic cells rely on the action of many different molecular motor proteins. Cytoplasmic dynein drives the movement of a wide range of cargoes towards the minus ends of microtubules, and these events are needed, not just at the single-cell level, but are vital for correct development. In the present paper, I review recent progress on understanding dynein's mechanochemistry, how it is regulated and how it binds to such a plethora of cargoes. The importance of a number of accessory factors in these processes is discussed.
Function and regulation of Saccharomyces cerevisiae myosins-I in endocytic budding
Authors: Giblin Jonathan , Fernández-Golbano Isabel María , Idrissi Fatima-Zahra , Geli María Isabel
Published: May 2012

Myosins-I are widely expressed actin-dependent motors which bear a phospholipid-binding domain. In addition, some members of the family can trigger Arp2/3 complex (actin-related protein 2/3 complex)-dependent actin polymerization. In the early 1990s, the development of powerful genetic tools in protozoa and mammals and discovery of these motors in yeast allowed the demonstration of their roles in membrane traffic along the endocytic and secretory pathways, in vacuole contraction, in cell motility and in mechanosensing. The powerful yeast genetics has contributed towards dissecting in detail the function and regulation of Saccharomyces cerevisiae myosins-I Myo3 and Myo5 in endocytic budding from the plasma membrane. In the present review, we summarize the evidence, dissecting their exact role in membrane budding and the molecular mechanisms controlling their recruitment and biochemical activities at the endocytic sites.
Rab GTPases and microtubule motors
Authors: Horgan Conor P. , McCaffrey Mary W.
Published: May 2012

Rab proteins are a family of small GTPases which, since their initial identification in the late 1980s, have emerged as master regulators of all stages of intracellular trafficking processes in eukaryotic cells. Rabs cycle between distinct conformations that are dependent on their guanine-nucleotide-bound status. When active (GTP-bound), Rabs are distributed to the cytosolic face of specific membranous compartments where they recruit downstream effector proteins. Rab–effector complexes then execute precise intracellular trafficking steps, which, in many cases, include vesicle motility. Microtubule-based kinesin and cytoplasmic dynein motor complexes are prominent among the classes of known Rab effector proteins. Additionally, many Rabs associate with microtubule-based motors via effectors that act as adaptor molecules that can simultaneously associate with the GTP-bound Rab and specific motor complexes. Thus, through association with motor complexes, Rab proteins can allow for membrane association and directional movement of various vesicular cargos along the microtubule cytoskeleton. In this mini-review, we highlight the expanding repertoire of Rab/microtubule motor protein interactions, and, in doing so, present an outline of the multiplicity of transport processes which result from such interactions.
Co-operative transport by molecular motors
Authors: Berger Florian , Keller Corina , Müller Melanie J.I. , Klumpp Stefan , Lipowsky Reinhard
Published: May 2012

Intracellular transport is often driven co-operatively by several molecular motors, which may belong to one or several motor species. Understanding how these motors interact and what co-ordinates and regulates their movements is a central problem in studies of intracellular transport. A general theoretical framework for the analysis of such transport processes is described, which enables us to explain the behaviour of intracellular cargos by the transport properties of individual motors and their interactions. We review recent advances in the theoretical description of motor co-operativity and discuss related experimental results.
Measurement and meaning of markers of reactive species of oxygen, nitrogen and sulfur in healthy human subjects and patients with inflammatory joint disease
Authors: Winyard Paul G. , Ryan Brent , Eggleton Paul , Nissim Ahuva , Taylor Emma , Lo Faro Maria Letizia , Burkholz Torsten , Szabó-Taylor Katalin E. , Fox Bridget , Viner Nick , Haigh Richard C. , Benjamin Nigel , Jones Andrew M. , Whiteman Matthew
Published: May 2012

Reactive species of oxygen, nitrogen and sulfur play cell signalling roles in human health, e.g. recent studies have shown that increased dietary nitrate, which is a source of RNS (reactive nitrogen species), lowers resting blood pressure and the oxygen cost of exercise. In such studies, plasma nitrite and nitrate are readily determined by chemiluminescence. At sites of inflammation, such as the joints of RA (rheumatoid arthritis) patients, the generation of ROS (reactive oxygen species) and RNS overwhelms antioxidant defences and one consequence is oxidative/nitrative damage to proteins. For example, in the inflamed joint, increased RNS-mediated protein damage has been detected in the form of a biomarker, 3-nitrotyrosine, by immunohistochemistry, Western blotting, ELISAs and MS. In addition to NO•, another cell-signalling gas produced in the inflamed joint is H2S (hydrogen sulfide), an RSS (reactive sulfur species). This gas is generated by inflammatory induction of H2S-synthesizing enzymes. Using zinc-trap spectrophotometry, we detected high (micromolar) concentrations of H2S in RA synovial fluid and levels correlated with clinical scores of inflammation and disease activity. What might be the consequences of the inflammatory generation of reactive species? Effects on inflammatory cell-signalling pathways certainly appear to be crucial, but in the current review we highlight the concept that ROS/RNS-mediated protein damage creates neoepitopes, resulting in autoantibody formation against proteins, e.g. type-II collagen and the complement component, C1q. These autoantibodies have been detected in inflammatory autoimmune diseases.
Analysis of oxidized and chlorinated lipids by mass spectrometry and relevance to signalling
Authors: Spickett Corinne M. , Fauzi Norsyahida Mohd
Published: May 2012

Oxidized and chlorinated phospholipids are generated under inflammatory conditions and are increasingly understood to play important roles in diseases involving oxidative stress. MS is a sensitive and informative technique for monitoring phospholipid oxidation that can provide structural information and simultaneously detect a wide variety of oxidation products, including chain-shortened and -chlorinated phospholipids. MSn technologies involve fragmentation of the compounds to yield diagnostic fragment ions and thus assist in identification. Advanced methods such as neutral loss and precursor ion scanning can facilitate the analysis of specific oxidation products in complex biological samples. This is essential for determining the contributions of different phospholipid oxidation products in disease. While many pro-inflammatory signalling effects of oxPLs (oxidized phospholipids) have been reported, it has more recently become clear that they can also have anti-inflammatory effects in conditions such as infection and endotoxaemia. In contrast with free radical-generated oxPLs, the signalling effects of chlorinated lipids are much less well understood, but they appear to demonstrate mainly pro-inflammatory effects. Specific analysis of oxidized and chlorinated lipids and the determination of their molecular effects are crucial to understanding their role in disease pathology.
Cysteine residues as catalysts for covalent peptide and protein modification: a role for thiyl radicals?
Authors: Schöneich Christian
Published: May 2012

Cysteine thiyl radicals engage in reversible intramolecular hydrogen-transfer reactions with amino acid residues in peptides and proteins. These reactions can be experimentally demonstrated through covalent hydrogen–deuterium exchange when experiments are carried out in 2H2O. To this end, hydrogen-transfer reactions have been observed between cysteine thiyl radicals and glycine, alanine, serine, valine and leucine in both model peptides and a protein, insulin. The relevance of such reactions for protein oxidation under conditions of oxidative stress is discussed.
Contemporary techniques for detecting and identifying proteins susceptible to reversible thiol oxidation
Authors: Burgoyne Joseph R. , Eaton Philip
Published: May 2012

Elevated protein oxidation is a widely reported hallmark of most major diseases. Historically, this ‘oxidative stress’ has been considered causatively detrimental, as the protein oxidation events were interpreted simply as damage. However, recent advances have changed this antiquated view; sensitive methodology for detecting and identifying proteins susceptible to oxidation has revealed a fundamental role for this modification in physiological cell signalling during health. Reversible protein oxidation that is dynamically coupled with cellular reducing systems allows oxidative protein modifications to regulate protein function, analogous to phosphoregulation. However, the relatively labile nature of many reversible protein oxidation states hampers the reliable detection and identification of modified proteins. Consequently, specialized methods to stabilize protein oxidation in combination with techniques to detect specific types of modification have been developed. Here, these techniques are discussed, and their sensitivity, selectivity and ability to reliably identify reversibly oxidized proteins are critically assessed.
Thiol regulation of pro-inflammatory cytokines and innate immunity: protein S-thiolation as a novel molecular mechanism
Authors: Coppo Lucia , Ghezzi Pietro
Published: May 2012

Inflammation or inflammatory cytokines and oxidative stress have often been associated, and thiol antioxidants, particularly glutathione, have often been seen as possible anti-inflammatory mediators. However, whereas several cytokine inhibitors have been approved for drug use in chronic inflammatory diseases, this has not happened with antioxidant molecules. We outline the complexity of the role of protein thiol–disulfide oxidoreduction in the regulation of immunity and inflammation, the underlying molecular mechanisms (such as protein glutathionylation) and the key enzyme players such as Trx (thioredoxin) or Grx (glutaredoxin).
Free radicals and redox signalling in T-cells during chronic inflammation and ageing
Authors: Griffiths Helen R. , Dunston Christopher R. , Bennett Stuart J. , Grant Melissa M. , Phillips Darren C. , Kitas George D.
Published: May 2012

During chronic inflammation and ageing, the increase in oxidative stress in both intracellular and extracellular compartments is likely to influence local cell functions. Redox changes alter the T-cell proteome in a quantitative and qualitative manner, and post-translational modifications to surface and cytoplasmic proteins by increased reactive species can influence T-cell function. Previously, we have shown that RA (rheumatoid arthritis) T-cells exhibit reduced ROS (reactive oxygen species) production in response to extracellular stimulation compared with age-matched controls, and basal ROS levels [measured as DCF (2′,7′-dichlorofluorescein) fluorescence] are lower in RA T-cells. In contrast, exposing T-cells in vitro to different extracellular redox environments modulates intracellular signalling and enhances cytokine secretion. Together, these data suggest that a complex relationship exists between intra- and extra-cellular redox compartments which contribute to the T-cell phenotype.
Mechanisms and consequences of oxidative damage to extracellular matrix
Authors: Kennett Eleanor C. , Chuang Christine Y. , Degendorfer Georg , Whitelock John M. , Davies Michael J.
Published: May 2012

Considerable evidence exists for oxidative damage to extracellular materials during multiple human pathologies. Unlike cells, the extracellular compartment of most biological tissues is less well protected against oxidation than intracellular sites in terms of the presence of both antioxidants (low molecular mass and enzymatic) and repair enzymes. The extracellular compartment may therefore be subject to greater oxidative stress, marked alterations in redox balance and an accumulation of damage due to slow turnover and/or poor repair. The nature and consequences of damage to ECM (extracellular matrix) are poorly understood, despite the growing realization that changes in matrix structure not only have structural consequences, but also play a key role in the regulation of cellular adhesion, proliferation, migration and cell signalling. The ECM also plays a key role in cytokine and growth factor binding, and matrix modifications would therefore be expected to alter these parameters. In the present study, we review mechanisms of oxidative damage to ECM, resulting changes in matrix structure and how this affects cellular behaviour. The role of such damage in the development and progression of inflammatory diseases is also discussed with particular reference to cardiovascular disease.
Electrochemical and optical sensing of reactive oxygen species: pathway to an integrated intracellular and extracellular measurement platform
Authors: Manning Philip , McNeil Calum J.
Published: May 2012

A comprehensive understanding of ROS (reactive oxygen species)-dependent cellular interaction requires the previously unmet ability to simultaneously monitor the intra- and extra-cellular environments. The present review assesses the potential of novel electrochemical and fluorescent-based nanosensor approaches to address the limitations of existing techniques for ROS analysis. Data generated by these new approaches have already contributed significantly to current understanding of the roles that these species play in various in vitro scenarios. However, integration of these novel approaches has the potential to offer, for the first time, the unparalleled ability to measure simultaneously and in real-time ROS flux in both the intra- and extra-cellular environments.
Application of proteomics in the mechanistic study of traditional Chinese medicine
Authors: Liu Xuan , Guo De-An
Published: May 2012

Systems biology is considered to be the possible technology that could bring breakthroughs in the study of TCM (traditional Chinese medicine). Proteomics, as one of the major components of systems biology, has been used in the mechanistic study of TCM, providing some interesting results. In the present paper, we review the current application of proteomics in the mechanistic study of TCM. Proteomics technologies and strategies that might be used in the future to improve study of TCM are also discussed.
Towards a structural understanding of drug and peptide transport within the proton-dependent oligopeptide transporter (POT) family
Authors: Newstead Simon
Published: May 2012

One of the principal aims of modern drug design is the targeted delivery of drugs within the body, such as to the central nervous system, combined with their exclusion from the liver and kidneys, which break down foreign molecules and subsequently eliminate them. Many of the commonly prescribed drugs are transported into cells and across the plasma membrane via endogenous membrane transporters, whose principal roles are the uptake of essential nutrients for metabolism. In many cases, such drug transport is serendipitous as they are simply mistaken as ‘natural’ compounds. Many of these transporters could, however, be targeted more efficiently, improving drug absorption, distribution and retention. The molecular details of these drug–transporter interactions, however, are at best poorly understood, in large part through the absence of any high-resolution structural information. To address this issue, we recently determined the structure of a prokaryotic peptide transporter, PepTSo from Shewanella oneidensis, which shares a high degree of sequence similarity and functional characteristics with the human PepT1 and PepT2 proteins. PepT1 and PepT2 contribute significantly to the oral bioavailability and pharmacokinetic properties of a number of important drug families, including antibiotics, antivirals and anticancer agents. The crystal structure of PepTSo provides the first high-resolution model of a drug importer and provides the starting point for understanding drug and peptide transport within the human body.
Towards structure-based protein drug design
Authors: Zhang Changsheng , Lai Luhua
Published: May 2012

Structure-based drug design for chemical molecules has been widely used in drug discovery in the last 30 years. Many successful applications have been reported, especially in the field of virtual screening based on molecular docking. Recently, there has been much progress in fragment-based as well as de novo drug discovery. As many protein–protein interactions can be used as key targets for drug design, one of the solutions is to design protein drugs based directly on the protein complexes or the target structure. Compared with protein–ligand interactions, protein–protein interactions are more complicated and present more challenges for design. Over the last decade, both sampling efficiency and scoring accuracy of protein–protein docking have increased significantly. We have developed several strategies for structure-based protein drug design. A grafting strategy for key interaction residues has been developed and successfully applied in designing erythropoietin receptor-binding proteins. Similarly to small-molecule design, we also tested de novo protein-binder design and a virtual screen of protein binders using protein–protein docking calculations. In comparison with the development of structure-based small-molecule drug design, we believe that structure-based protein drug design has come of age.
Non-homologous end-joining partners in a helical dance: structural studies of XLF–XRCC4 interactions
Authors: Wu Qian , Ochi Takashi , Matak-Vinkovic Dijana , Robinson Carol V. , Chirgadze Dimitri Y. , Blundell Tom L.
Published: May 2012

XRCC4 (X-ray cross-complementation group 4) and XLF (XRCC4-like factor) are two essential interacting proteins in the human NHEJ (non-homologous end-joining) pathway that repairs DNA DSBs (double-strand breaks). The individual crystal structures show that the dimeric proteins are homologues with protomers containing head domains and helical coiled-coil tails related by approximate two-fold symmetry. Biochemical, mutagenesis, biophysical and structural studies have identified the regions of interaction between the two proteins and suggested models for the XLF–XRCC4 complex. An 8.5 Å (1 Å=0.1 nm) resolution crystal structure of XLF–XRCC4 solved by molecular replacement, together with gel filtration and nano-ESI (nano-electrospray ionization)–MS results, demonstrates that XLF and XRCC4 dimers interact through their head domains and form an alternating left-handed helical structure with polypeptide coiled coils and pseudo-dyads of individual XLF and XRCC4 dimers at right angles to the helical axis.
Genes encoding WFDC- and Kunitz-type protease inhibitor domains: are they related?
Authors: Lundwall Åke , Clauss Adam
Published: May 2012

We have previously demonstrated that the genes of SCPs (semen coagulum proteins) and the WFDC (whey acidic protein four-disulfide core)-type protease inhibitor elafin are homologous in spite of lacking similarity between their protein products. This led to the discovery of a locus on human chromosome 20, encompassing genes of the SCPs, SEMG1 (semenogelin I) and SEMG2, and 14 genes containing the sequence motif that is characteristic of WFDC-type protease inhibitors. We have now identified additional genes at the locus that are similarly organized, but which give rise to proteins containing the motif of Kunitz-type protease inhibitors. Here, we discuss the evolution of genes encoding SCPs and describe mechanisms by which they and genes with Kunitz motifs might have evolved from genes with WFDC motifs. We can also demonstrate an expansion of the WFDC locus with 0.6 Mb in the cow. The region, which seems to be specific to ruminants, contains several genes and pseudogenes with Kunitz motifs, one of which is the much-studied BPTI (bovine pancreatic trypsin inhibitor).
Biological functions of the WAP domain-containing multidomain proteins WFIKKN1 and WFIKKN2
Authors: Kondás Katalin , Szláma György , Nagy Alinda , Trexler Mária , Patthy László
Published: May 2012

WFIKKN1 and WFIKKN2 are two closely related multidomain proteins consisting of a WAP (whey acidic protein)-, a follistatin-, an immunoglobulin-, two Kunitz-type protease inhibitor-domains and an NTR domain (netrin domain). Recent experiments have shown that both WFIKKN1 and WFIKKN2 bind myostatin and GDF11 (growth and differentiation factor 11) with high affinity and are potent antagonists of these growth factors. Structure–function studies on WFIKKN proteins have revealed that their interactions with GDF8 and GDF11 are mediated primarily by the follistatin and NTR domains.
Immunotherapy of prostate cancer: identification of new treatments and targets for therapy, and role of WAP domain-containing proteins
Authors: Galustian Christine , Vyakarnam Annapurna , Elhage Oussama , Hickman Oliver , Dasgupta Prokar , Smith Richard A.
Published: May 2012

Prostate adenocarcinoma is present in over 80% of men over the age of 80 and is by far the most common cancer of men. Although radical prostatectomy is curative in early disease, the risks of incontinence and impotence can affect the quality of life of patients. Early intervention with localized immunotherapy represents a potential solution as lymphocyte infiltration does occur in prostate cancer lesions, and immunotherapy with dendritic cell vaccines can significantly increase survival in late stage disease. However, lymphocytic infiltrates in the cancerous prostates have an anergic character arising from the suppressive effects of the microenvironment resulting from a conversion of effector cells into regulatory T-cells. Although TGFβ (transforming growth factor β) and IL-10 (interleukin-10) are known to be strong suppressor molecules associated with prostate cancer, they are among many possible suppressive factors. We discuss the possible role of alternative suppressor molecules, including the WAP (whey acidic protein) homologue ps20 that is expressed on prostate stroma and other WAP domain-containing proteins in the immunosuppressive prostate cancer milieu and discuss novel immunotherapeutic strategies to combat this disease.
SLPI and trappin-2 as therapeutic agents to target airway serine proteases in inflammatory lung diseases: current and future directions
Authors: Zani Marie-Louise , Tanga Annabelle , Saidi Ahlame , Serrano Hélène , Dallet-Choisy Sandrine , Baranger Kévin , Moreau Thierry
Published: May 2012

It is now clear that NSPs (neutrophil serine proteases), including elastase, Pr3 (proteinase 3) and CatG (cathepsin G) are major pathogenic determinants in chronic inflammatory disorders of the lungs. Two unglycosylated natural protease inhibitors, SLPI (secretory leucocyte protease inhibitor) and elafin, and its precursor trappin-2 that are found in the lungs, have therapeutic potential for reducing the protease-induced inflammatory response. This review examines the multifaceted roles of SLPI and elafin/trappin-2 in the context of their possible use as inhaled drugs for treating chronic lung diseases such as CF (cystic fibrosis) and COPD (chronic obstructive pulmonary disease).
Functional studies of eppin
Authors: O'Rand Michael G. , Widgren Esther E. , Hamil Katherine G. , Silva Erick J. , Richardson Richard T.
Published: May 2012

Our laboratory has characterized EPPIN [epididymal protease inhibitor; SPINLW1] as a novel gene on human chromosome 20q12-13.2, which encodes a cysteine-rich protein of 133 amino acids with a calculated molecular mass of 15.283 kDa, containing both Kunitz-type and WAP (whey acidic protein)-type four-disulfide core consensus sequences. Eppin is secreted by Sertoli cells in the testis and epididymal epithelial cells; it is predominantly a dimer, although multimers often exist, and in its native form eppin is found on the human sperm surface complexed with LTF (lactotransferrin) and clusterin. During ejaculation SEMG (semenogelin) from the seminal vesicles binds to the eppin protein complex, initiating a series of events that define eppin's function. Eppin's functions include (i) modulating PSA (prostate-specific antigen) enzyme activity, (ii) providing antimicrobial protection and (iii) binding SEMG thereby inhibiting sperm motility. As PSA hydrolyses SEMG in the ejaculate coagulum, spermatozoa gain progressive motility. We have demonstrated that eppin is essential for fertility because immunization of male monkeys with recombinant eppin results in complete, but reversible, contraception. To exploit our understanding of eppin's function, we are developing compounds that inhibit eppin–SEMG interaction and mimic anti-eppin, inhibiting sperm motility. These compounds should have potential as a male contraceptive.
Aging and longevity of yeast colony populations: metabolic adaptation and differentiation
Authors: Váchová Libuše , Palková Zdena
Published: May 2012

Yeast multicellular colonies possess several traits that are absent from individual yeasts. These include the ability to synchronize colony population development and adapt its metabolism to different environmental changes, such as nutrient depletion. This, together with cell diversification to cell variants with distinct metabolic and other properties, contributes to the main goal of the colony population: to achieve longevity. In this respect, a benefit to individual cells is subordinated to the benefit to the whole population, exhibiting a kind of altruistic behaviour. For example, some colony cells located at particular positions undergo regulated cell dying and provide components to other cells located in more propitious areas. The enhancement of techniques that enable the in vivo investigation of three-dimensional spatiotemporal colony development may lead to new discoveries on metabolic differentiation and regulation in the near future.
Apoptosis-like programmed cell death in the grey mould fungus Botrytis cinerea: genes and their role in pathogenicity
Authors: Shlezinger Neta , Doron Adi , Sharon Amir
Published: May 2012

A considerable number of fungal homologues of human apoptotic genes have been identified in recent years. Nevertheless, we are far from being able to connect the different pieces and construct a primary structure of the fungal apoptotic regulatory network. To get a better picture of the available fungal components, we generated an automatic search protocol that is based on protein sequences together with a domain-centred approach. We used this protocol to search all the available fungal databases for domains and homologues of human apoptotic proteins. Among all known apoptotic domains, only the BIR [baculovirus IAP (inhibitor of apoptosis protein) repeat] domain was found in fungi. A single protein with one or two BIR domains is present in most (but not all) fungal species. We isolated the BIR-containing protein from the grey mould fungus Botrytis cinerea and determined its role in apoptosis and pathogenicity. We also isolated and analysed BcNMA, a homologue of the yeast NMA11 gene. Partial knockout or overexpression strains of BcBIR1 confirmed that BcBir1 is anti-apoptotic and this activity was assigned to the N′-terminal part of the protein. Plant infection assays showed that the fungus undergoes massive PCD (programmed cell death) during early stages of infection. Further studies showed that fungal virulence was fully correlated with the ability of the fungus to cope with plant-induced PCD. Together, our result show that BcBir1 is a major regulator of PCD in B. cinerea and that proper regulation of the host-induced PCD is essential for pathogenesis in this and other similar fungal pathogens.
Mitochondrial quality control by the ubiquitin–proteasome system
Authors: Taylor Eric B. , Rutter Jared
Published: May 2012

Mitochondria perform multiple functions critical to the maintenance of cellular homoeostasis and their dysfunction leads to disease. Several lines of evidence suggest the presence of a MAD (mitochondria-associated degradation) pathway that regulates mitochondrial protein quality control. Internal mitochondrial proteins may be retrotranslocated to the OMM (outer mitochondrial membrane), multiple E3 ubiquitin ligases reside at the OMM and inhibition of the proteasome causes accumulation of ubiquitinated proteins at the OMM. Reminiscent of ERAD [ER (endoplasmic reticulum)-associated degradation], Cdc48 (cell division cycle 42)/p97 is recruited to stressed mitochondria, extracts ubiquitinated proteins from the OMM and presents ubiquitinated proteins to the proteasome for degradation. Recent research has provided mechanistic insights into the interaction of the UPS (ubiquitin–proteasome system) with the OMM. In yeast, Vms1 [VCP (valosin-containing protein) (p97)/Cdc48-associated mitochondrial-stress-responsive 1] protein recruits Cdc48/p97 to the OMM. In mammalian systems, the E3 ubiquitin ligase parkin regulates the recruitment of Cdc48/p97 to mitochondria, subsequent mitochondrial protein degradation and mitochondrial autophagy. Disruption of the Vms1 or parkin systems results in the hyper-accumulation of ubiquitinated proteins at mitochondria and subsequent mitochondrial dysfunction. The emerging MAD pathway is important for the maintenance of cellular and therefore organismal viability.
Mitophagy, mitochondrial dynamics and the general stress response in yeast
Authors: Müller Matthias , Reichert Andreas S.
Published: May 2012

Autophagy is a fundamental cellular process promoting survival under various environmental stress conditions. Selective types of autophagy have gained much interest recently as they are involved in specific quality control mechanisms removing, for example, aggregated proteins or dysfunctional mitochondria. This is considered to counteract the development of a number of neurodegenerative disorders and aging. Here we review the role of mitophagy and mitochondrial dynamics in ensuring quality control of mitochondria. In particular, we provide possible explanations why mitophagy in yeast, in contrast with the situation in mammals, was found to be independent of mitochondrial fission. We further discuss recent findings linking these processes to nutrient sensing pathways and the general stress response in yeast. In particular, we propose a model for how the stress response protein Whi2 and the Ras/PKA (protein kinase A) signalling pathway are possibly linked and thereby regulate mitophagy.
Vacuole–mitochondrial cross-talk during apoptosis in yeast: a model for understanding lysosome–mitochondria-mediated apoptosis in mammals
Authors: Sousa Maria João , Azevedo Flávìa , Pedras Ana , Marques Carolina , Coutinho Olga P. , Preto Ana , Gerós Hernâni , Chaves Susana R. , Côrte-Real Manuela
Published: May 2012

The yeast apoptosis field emerged with the finding that key components of the apoptotic machinery are conserved in these simple eukaryotes. Thus it became possible to exploit these genetically tractable organisms to improve our understanding of the intricate mechanisms of cell death in higher eukaryotes and of severe human diseases associated with apoptosis dysfunctions. Early on, it was recognized that a mitochondria-mediated apoptotic pathway showing similarities to the mammalian intrinsic pathway was conserved in yeast. Recently, lysosomes have also emerged as central players in mammalian apoptosis. Following LMP (lysosomal membrane permeabilization), lysosomal proteases such as cathepsins B, D and L are released into the cytosol and can trigger a mitochondrial apoptotic cascade. CatD (cathepsin D) can also have anti-apoptotic effects in some cellular types and specific contexts. Nonetheless, the mechanisms underlying LMP and the specific role of cathepsins after their release into the cytosol remain poorly understood. We have recently shown that yeast vacuoles, membrane-bound acidic organelles, which share many similarities to plant vacuoles and mammalian lysosomes, are also involved in the regulation of apoptosis and that the vacuolar protease Pep4p, orthologue of the human CatD, is released from the vacuole into the cytosol in response to acetic acid. Here, we discuss how the conservation of cell-death regulation mechanisms in yeast by the lysosome-like organelle and mitochondria may provide new insights into the understanding of the complex interplay between the mitochondria and lysosome-mediated signalling routes during mammalian apoptosis.
Achievements and perspectives in yeast acetic acid-induced programmed cell death pathways
Authors: Guaragnella Nicoletta , Antonacci Lucia , Passarella Salvatore , Marra Ersilia , Giannattasio Sergio
Published: May 2012

The use of non-mammalian model organisms, including yeast Saccharomyces cerevisiae, can provide new insights into eukaryotic PCD (programmed cell death) pathways. In the present paper, we report recent achievements in the elucidation of the events leading to PCD that occur as a response to yeast treatment with AA (acetic acid). In particular, ROS (reactive oxygen species) generation, cyt c (cytochrome c) release and mitochondrial function and proteolytic activity will be dealt with as they vary along the AA-PCD time course by using both wild-type and mutant yeast cells. Two AA-PCD pathways are described sharing common features, but distinct from one another with respect to the role of ROS and mitochondria, the former in which YCA1 acts upstream of cyt c release and caspase-like activation in a ROS-dependent manner and the latter in which cyt c release does not occur, but caspase-like activity increases, in a ROS-independent manner.
Farnesol-induced cell death in the filamentous fungus Aspergillus nidulans
Authors: Dinamarco Taísa Magnani , Goldman Maria Helena S. , Goldman Gustavo Henrique
Published: May 2012

FOH (farnesol), a non-sterol isoprenoid produced by dephosphorylation of farnesyl pyrophosphate, has been shown to inhibit proliferation and induce apoptosis. We have been using Aspergillus nidulans and FOH as a model system and cell death stimulus, respectively, aiming to understand by which means filamentous fungi are driven towards cell death. Here, we review some of our findings about FOH-induced cell death in A. nidulans.
Retinoic acid promotes proliferation of chicken primordial germ cells via activation of PI3K/Akt‐mediated NF‐κB signalling cascade
Authors: Yu Minli , Ge Chutian , Zeng Weidong , Mi Yuling , Zhang Caiqiao
Published: May 2012

As embryonic progenitors for the gametes, PGCs (primordial germ cells) proliferate and develop under strict regulation of numerous intrinsic and external factors. As the most active natural metabolite of vitamin A, all‐trans RA (retinoic acid) plays pivotal roles in regulating development of various cells. The proliferating action of RA on PGCs was investigated along with the intracellular PI3K (phosphoinositide 3‐kinase)/Akt (protein kinase B; also known as Akt)‐mediated NF‐κB (nuclear factor κB) signalling cascade. The results show that RA significantly promoted PGC proliferation in a dose‐ and time‐dependent manner, confirmed by BrdU (bromodeoxyuridine) incorporation and cell cycle analysis. However, this promoting effect was attenuated by sequential inhibitors of LY294002 for PI3K, KP372‐1 for Akt and SN50 for NF‐κB respectively. Western blot analysis showed increased Akt phosphorylation (Ser473) of PGCs after stimulation with RA, but this was abolished by LY294002 or KP372‐1. Treatment with RA increased expression of NF‐κB and decreased IκBα (inhibitory κBα) expression, which were inhibited by SN50. Blockade of PI3K or Akt activity inhibited NF‐κB translocation from the cytoplasm to the nucleus. Finally, mRNA expression of cell cycle regulating genes [cyclin D1 and E, CDK6 (cyclin‐dependent kinase 6) and CDK2] was up‐regulated in the RA‐treated cells. This stimulation was also markedly retarded by combined treatment with LY294002, KP372‐1 and SN50. These results suggest that RA activates the PI3K/Akt and NF‐κB signalling cascade to promote proliferation of the cultured chicken PGCs.
Asymmetrically expressed
axin
required for anterior development in
Tribolium
Authors: Fu Jinping , Posnien Nico , Bolognesi Renata , Fischer Tamara D. , Rayl Parker , Oberhofer Georg , Kitzmann Peter , Brown Susan J. , Bucher Gregor
Published: May 2012

Canonical Wnt signaling has been implicated in an AP axis polarizing mechanism in most animals, despite limited evidence from arthropods. In the long-germ insect,
Drosophila
, Wnt signaling is not required for global AP patterning, but in short-germ insects including
Tribolium castaneum
, loss of Wnt signaling affects development of segments in the growth zone but not those defined in the blastoderm. To determine the effects of ectopic Wnt signaling, we analyzed the expression and function of
axin
, which encodes a highly conserved negative regulator of the pathway. We found
Tc-axin
transcripts maternally localized to the anterior pole in freshly laid eggs. Expression spread toward the posterior pole during the early cleavage stages, becoming ubiquitous by the time the germ rudiment formed.
Tc-axin
RNAi produced progeny phenotypes that ranged from mildly affected embryos with cuticles displaying a graded loss of anterior structures, to defective embryos that condensed at the posterior pole in the absence of serosa. Altered expression domains of several blastodermal markers indicated anterior expansion of posterior fates. Analysis of other canonical Wnt pathway components and the expansion of
Tc-caudal
expression, a Wnt target, suggest that the effects of
Tc-axin
depletion are mediated through this pathway and that Wnt signaling must be inhibited for proper anterior development in
Tribolium
. These studies provide unique evidence that canonical Wnt signaling must be carefully regulated along the AP axis in an arthropod, and support an ancestral role for Wnt activity in defining AP polarity and patterning in metazoan development.
Detection of an autoreactive T-cell population within the polyclonal repertoire that undergoes distinct autoimmune regulator (Aire)-mediated selection
Authors: Taniguchi Ruth T. , DeVoss Jason J. , Moon James J. , Sidney John , Sette Alessandro , Jenkins Marc K. , Anderson Mark S.
Published: May 2012

The autoimmune regulator (Aire) plays a critical role in central tolerance by promoting the display of tissue-specific antigens in the thymus. To study the influence of Aire on thymic selection in a physiological setting, we used tetramer reagents to detect autoreactive T cells specific for the Aire-dependent tissue-specific antigen interphotoreceptor retinoid-binding protein (IRBP), in the polyclonal repertoire. Two class II tetramer reagents were designed to identify T cells specific for two different peptide epitopes of IRBP. Analyses of the polyclonal T-cell repertoire showed a high frequency of activated T cells specific for both IRBP tetramers in Aire−/−mice, but not in Aire+/+mice. Surprisingly, although one tetramer-binding T-cell population was efficiently deleted in the thymus in an Aire-dependent manner, the second tetramer-binding population was not deleted and could be detected in both the Aire−/−and Aire+/+T-cell repertoires. We found that Aire-dependent thymic deletion of IRBP-specific T cells relies on intercellular transfer of IRBP between thymic stroma and bone marrow-derived antigen-presenting cells. Furthermore, our data suggest that Aire-mediated deletion relies not only on thymic expression of IRBP, but also on proper antigen processing and presentation of IRBP by thymic antigen-presenting cells.