Bacterial diversity and activity along a salinity gradient in soda lakes of the Kulunda Steppe (Altai, Russia)

Here we describe the diversity and activity of sulfate reducing bacteria along a salinity gradient in four different soda lakes from the Kulunda Steppe (South East Siberia, Russia). For this purpose, a combination of culture-dependent and independent techniques was applied. The general bacterial and SRB diversity were analyzed by denaturing gradient gel electrophoresis (DGGE) targeting the 16S rDNA gene. DNA was used to detect the microbial populations that were present in the soda lake sediments, whereas ribosomal RNA was used as a template to obtain information on those that were active. Individual DGGE bands were sequenced and a phylogenetic analysis was performed. In addition, the overall activity of SRB was obtained by measuring the sulfate reduction rates (SRR) and their abundance was estimated by serial dilution. Our results showed the presence of minor, but highly active microbial populations, mostly represented by members of the Proteobacteria. Remarkably high SRR were measured at hypersaline conditions (200 g L⁻¹). A relatively high viable count indicated that sulfate reducing bacteria could be highly active in hypersaline soda lakes. Furthermore, the increase of sodium carbonate/bicarbonate seemed to affect the composition of the microbial community in soda lakes, but not the rate of sulfate reduction.     

Estrogen receptor subtype β2 is involved in neuromast development in zebrafish (Danio rerio) larvae

Estrogens are known to play a role in both reproductive and non-reproductive functions in mammals. Estrogens and their receptors are involved in the development of the central nervous system (brain development, neuronal survival and differentiation) as well as in the development of the peripheral nervous system (sensory-motor behaviors). In order to decipher possible functions of estrogens in early development of the zebrafish sensory system, we investigated the role of estrogen receptor β₂ (ERβ₂) by using a morpholino (MO) approach blocking erβ₂ RNA translation. We further investigated the development of lateral line organs by cell-specific labeling, which revealed a disrupted development of neuromasts in morphants. The supporting cells developed and migrated normally. Sensory hair cells, however, were absent in morphants' neuromasts. Microarray analysis and subsequent in situ hybridizations indicated an aberrant activation of the Notch signaling pathway in ERβ₂ morphants. We conclude that signaling via ERβ₂ is essential for hair cell development and may involve an interaction with the Notch signaling pathway during cell fate decision in the neuromast maturation process.     

Discourses,Power Negotiations and Indigenous Political Organization in Forest Partnerships: The Case of Selva de Matavén,Colombia

While much research on forest partnerships hitherto has been focused mainly on the drivers behind their formation, the kind of actors and deals involved, and the factors that promote or hinder their success, much less attention has been paid to the dynamic relationships and processes inherent in these partnerships. Based on the study of a partnership process in an indigenous reservation in Colombian Amazonia covering a variety of projects, this paper seeks to fill part of this lacuna by analyzing the partnership as a dynamic ‘discursive battlefield,’ in which objectives and actions are being constantly negotiated. Actors in the Matavén partnership strategically incorporate discursive elements in order to pursue their own interests while also endorsing those that ensure the continuation of collaboration. We conclude that discourses are embedded in partnership micro-politics. On the one hand, discursive shifts occur as a reflection of power balances at given moments. On the other hand, discourses constitute indispensable resources with the potential to both enhance individual actor’s negotiating power and to create opportunities for compromise. Within an ongoing discursive tension between ‘conservation’ and ‘indigenous autonomy,’ flexible notions such as ‘territorial ordering’ prove to be successful in allowing space for manoeuvre and granting conceptual coherence to shifts occurring ‘on the ground.’     

Hypoxia and stem cell‐based engineering of mesenchymal tissues

Stem cells have the ability for prolonged self‐renewal and differentiation into mature cells of various lineages, which makes them important cell sources for tissue engineering applications. Their remarkable ability to replenish and differentiate in vivo is regulated by both intrinsic and extrinsic cellular mechanisms. The anatomical location where the stem cells reside, known as the “stem cell niche or microenvironment,” provides signals conducive to the maintenance of definitive stem cell properties. Physiological condition including oxygen tension is an important component of the stem cell microenvironment and has been shown to play a role in regulating both embryonic and adult stem cells. This review focuses on oxygen as a signaling molecule and the way it regulates the stem cells' development into mesenchymal tissues in vitro. The physiological relevance of low oxygen tension as an environmental parameter that uniquely benefits stem cells' expansion and maintenance is described along with recent findings on the regulatory effects of oxygen on embryonic stem cells and adult mesenchymal stem cells. The relevance to tissue engineering is discussed in the context of the need to specifically regulate the oxygen content in the cellular microenvironment in order to optimize in vitro tissue development. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Molecular basis of the anti-cancer effects of histone deacetylase inhibitors

Histone deacetylase inhibitors comprise a variety of natural and synthetic compounds, which have in common that they inhibit enzymes that mediate the removal of acetyl groups from a range of proteins, including nucleosomal histones. Histone deacetylase inhibitors have anti-cancer activities in vitro and in vivo and are used in the clinic for the treatment of advanced cutaneous T cell lymphoma. The molecular pathways targeted by these compounds are discussed with an emphasis on the effects of these compounds on retinoic acid signaling.     

Structure and Function of a Novel Type of ATP-dependent Clp Protease

The Clp protease is conserved among eubacteria and most eukaryotes, and uses ATP to drive protein substrate unfolding and translocation into a chamber of sequestered proteolytic active sites. The main constitutive Clp protease in photosynthetic organisms has evolved into a functionally essential and structurally intricate enzyme. The model Clp protease from the cyanobacterium Synechococcus consists of the HSP100 molecular chaperone ClpC and a mixed proteolytic core comprised of two distinct subunits, ClpP3 and ClpR. We have purified the ClpP3/R complex, the first for a Clp proteolytic core comprised of heterologous subunits. The ClpP3/R complex has unique functional and structural features, consisting of twin heptameric rings each with an identical ClpP3₃ClpR₄ configuration. As predicted by its lack of an obvious catalytic triad, the ClpR subunit is shown to be proteolytically inactive. Interestingly, extensive modification to ClpR to restore proteolytic activity to this subunit showed that its presence in the core complex is not rate-limiting for the overall proteolytic activity of the ClpCP3/R protease. Altogether, the ClpP3/R complex shows remarkable similarities to the 20 S core of the proteasome, revealing a far greater degree of convergent evolution than previously thought between the development of the Clp protease in photosynthetic organisms and that of the eukaryotic 26 S proteasome.Proteases perform numerous tasks vital for cellular homeostasis in all organisms. Much of the selective proteolysis within living cells is performed by multisubunit chaperone-protease complexes. These proteases all share a common two-component architecture and mode of action, with one of the best known examples being the proteasome in archaebacteria, certain eubacteria, and eukaryotes (1).The 20 S proteasome is a highly conserved cylindrical structure composed of two distinct types of subunits, α and β. These are organized in four stacked heptameric rings, with two central β-rings sandwiched between two outer α-rings. Although the α- and β-protein sequences are similar, it is only the latter that is proteolytic active, with a single Thr active site at the N terminus. The barrel-shaped complex is traversed by a central channel that widens up into three cavities. The catalytic sites are positioned in the central chamber formed by the β-rings, adjacent to which are two antechambers conjointly built up by β- and α-subunits. In general, substrate entry into the core complex is essentially blocked by the α-rings, and thus relies on the associating regulatory partner, PAN and 19 S complexes in archaea and eukaryotes, respectively (1). Typically, the archaeal core structure is assembled from only one type of α- and β-subunit, so that the central proteolytic chamber contains 14 catalytic active sites (2). In contrast, each ring of the eukaryotic 20 S complex has seven distinct α- and β-subunits. Moreover, only three of the seven β-subunits in each ring are proteolytically active (3). Having a strictly conserved architecture, the main difference between the 20 S proteasomes is one of complexity. In mammalian cells, the three constitutive active subunits can even be replaced with related subunits upon induction by γ-interferon to generate antigenic peptides presented by the class 1 major histocompatibility complex (4).Two chambered proteases architecturally similar to the proteasome also exist in eubacteria, HslV and ClpP. HslV is commonly thought to be the prokaryotic counterpart to the 20 S proteasome mainly because both are Thr proteases. A single type of HslV protein, however, forms a proteolytic chamber consisting of twin hexameric rather than heptameric rings (5). Also displaying structural similarities to the proteasome is the unrelated ClpP protease. The model Clp protease from Escherichia coli consists of a proteolytic ClpP core flanked on one or both sides by the ATP-dependent chaperones ClpA or ClpX (6). The ClpP proteolytic chamber is comprised of two opposing homo-heptameric rings with the catalytic sites harbored within (7). ClpP alone displays only limited peptidase activity toward short unstructured peptides (8). Larger native protein substrates need to be recognized by ClpA or ClpX and then translocated in an unfolded state into the ClpP proteolytic chamber (9, 10). Inside, the unfolded substrate is bound in an extended manner to the catalytic triads (Ser-97, His-122, and Asp-171) and degraded into small peptide fragments that can readily diffuse out (11). Several adaptor proteins broaden the array of substrates degraded by a Clp protease by binding to the associated HSP100 partner and modifying its protein substrate specificity (12, 13). One example is the adaptor ClpS that interacts with ClpA (EcClpA) and targets N-end rule substrates for degradation by the ClpAP protease (14).Like the proteasome, the Clp protease is found in a wide variety of organisms. Besides in all eubacteria, the Clp protease also exist in mammalian and plant mitochondria, as well as in various plastids of algae and plants. It also occurs in the unusual plastid in Apicomplexan protozoan (15), a family of parasites responsible for many important medical and veterinary diseases such as malaria. Of all these organisms, photobionts have by far the most diverse array of Clp proteins. This was first apparent in cyanobacteria, with the model species Synechococcus elongatus having 10 distinct Clp proteins, four HSP100 chaperones (ClpB1–2, ClpC, and ClpX), three ClpP proteins (ClpP1–3), a ClpP-like protein termed ClpR, and two adaptor proteins (ClpS1–2) (16). Of particular interest is the ClpR variant, which has protein sequence similarity to ClpP but appears to lack the catalytic triad of Ser-type proteases (17). This diversity of Clp proteins is even more extreme in photosynthetic eukaryotes, with at least 23 different Clp proteins in the higher plant Arabidopsis thaliana, most of which are plastid-localized (18).We have recently shown that two distinct Clp proteases exist in Synechococcus, both of which contain mixed proteolytic cores. The first consists of ClpP1 and ClpP2 subunits, and associates with ClpX, whereas the other has a proteolytic core consisting of ClpP3 and ClpR that binds to ClpC, as do the two ClpS adaptors (19). Of these proteases, it is the more constitutively abundant ClpCP3/R that is essential for cell viability and growth (20, 21). It is also the ClpP3/R complex that is homologous to the single type in eukaryotic plastids, all of which also have ClpC as the chaperone partner (16). In algae and plants, however, the complexity of the plastidic Clp proteolytic core has evolved dramatically. In Arabidopsis, the core complex consists of five ClpP and four ClpR paralogs, along with two unrelated Clp proteins unique to higher plants (22). Like ClpP3/R, the plastid Clp protease in Arabidopsis is essential for normal growth and development, and appears to function primarily as a housekeeping protease (23, 24).One of the most striking developments in the Clp protease in photosynthetic organisms and Apicomplexan parasites is the inclusion of ClpR within the central proteolytic core. Although this type of Clp protease has evolved into a vital enzyme, little is known about its activity or the exact role of ClpR within the core complex. To address these points we have purified the intact Synechococcus ClpP3/R proteolytic core by co-expression in E. coli. The recombinant ClpP3/R forms a double heptameric ring complex, with each ring having a specific ClpP3/R stoichiometry and arrangement. Together with ClpC, the ClpP3/R complex degrades several polypeptide substrates, but at a rate considerably slower than that by the E. coli ClpAP protease. Interestingly, although ClpR is shown to be proteolytically inactive, its inclusion in the core complex is not rate-limiting to the overall activity of the ClpCP3/R protease. In general, the results reveal remarkable similarities between the evolutionary development of the Clp protease in photosynthetic organisms and the eukaryotic proteasome relative to their simpler prokaryotic counterparts.     

Convergence of IL-1β and VDR Activation Pathways in Human TLR2/1-Induced Antimicrobial Responses

Antimicrobial effector mechanisms are central to the function of the innate immune response in host defense against microbial pathogens. In humans, activation of Toll-like receptor 2/1 (TLR2/1) on monocytes induces a vitamin D dependent antimicrobial activity against intracellular mycobacteria. Here, we report that TLR activation of monocytes triggers induction of the defensin beta 4 gene (DEFB4), requiring convergence of the IL-1β and vitamin D receptor (VDR) pathways. TLR2/1 activation triggered IL-1β activity, involving the upregulation of both IL-1β and IL-1 receptor, and downregulation of the IL-1 receptor antagonist. TLR2/1L induction of IL-1β was required for upregulation of DEFB4, but not cathelicidin, whereas VDR activation was required for expression of both antimicrobial genes. The differential requirements for induction of DEFB4 and cathelicidin were reflected by differences in their respective promoter regions; the DEFB4 promoter had one vitamin D response element (VDRE) and two NF-κB sites, whereas the cathelicidin promoter had three VDREs and no NF-κB sites. Transfection of NF-κB into primary monocytes synergized with 1,25D3 in the induction of DEFB4 expression. Knockdown of either DEFB4 or cathelicidin in primary monocytes resulted in the loss of TLR2/1-mediated antimicrobial activity against intracellular mycobacteria. Therefore, these data identify a novel mechanism of host defense requiring the induction of IL-1β in synergy with vitamin D activation, for the TLR-induced antimicrobial pathway against an intracellular pathogen.     

O6-methylguanine DNA methyltransferase and p53 status predict temozolomide sensitivity in human malignant glioma cells

Temozolomide (TMZ) is a methylating agent which prolongs survival when administered during and after radiotherapy in the first-line treatment of glioblastoma and which also has significant activity in recurrent disease. O6-methylguanine DNA methyltransferase (MGMT) is a DNA repair enzyme attributed a role in cancer cell resistance to O6-alkylating agent-based chemotherapy. Using a panel of 12 human glioma cell lines, we here defined the sensitivity to TMZ in acute cytotoxicity and clonogenic survival assays in relation to MGMT, mismatch repair and p53 status and its modulation by dexamethasone, irradiation and BCL-X(L). We found that the levels of MGMT expression were a major predictor of TMZ sensitivity in human glioma cells. MGMT activity and clonogenic survival after TMZ exposure are highly correlated (p < 0.0001, r2 = 0.92). In contrast, clonogenic survival after TMZ exposure does not correlate with the expression levels of the mismatch repair proteins mutS homologue 2, mutS homologue 6 or post-meiotic segregation increased 2. The MGMT inhibitor O6-benzylguanine sensitizes MGMT-positive glioma cells to TMZ whereas MGMT gene transfer into MGMT-negative cells confers protection. The antiapoptotic BCL-X(L) protein attenuates TMZ cytotoxicity in MGMT-negative LNT-229 but not in MGMT-positive LN-18 cells. Neither ionizing radiation (4 Gy) nor clinically relevant concentrations of dexamethasone modulate MGMT activity or TMZ sensitivity. Abrogation of p53 wild-type function strongly attenuates TMZ cytotoxicity. Conversely, p53 mimetic agents designed to stabilize the wild-type conformation of p53 sensitize glioma cells for TMZ cytotoxicity. Collectively, these results suggest that the determination of MGMT expression and p53 status will help to identify glioma patients who will or will not respond to TMZ.     

Optimizing the medium perfusion rate in bone tissue engineering bioreactors

There is a critical need to increase the size of bone grafts that can be cultured in vitro for use in regenerative medicine. Perfusion bioreactors have been used to improve the nutrient and gas transfer capabilities and reduce the size limitations inherent to static culture, as well as to modulate cellular responses by hydrodynamic shear. Our aim was to understand the effects of medium flow velocity on cellular phenotype and the formation of bone‐like tissues in three‐dimensional engineered constructs. We utilized custom‐designed perfusion bioreactors to culture bone constructs for 5 weeks using a wide range of superficial flow velocities (80, 400, 800, 1,200, and 1,800 µm/s), corresponding to estimated initial shear stresses ranging from 0.6 to 20 mPa. Increasing the flow velocity significantly affected cell morphology, cell–cell interactions, matrix production and composition, and the expression of osteogenic genes. Within the range studied, the flow velocities ranging from 400 to 800 µm/s yielded the best overall osteogenic responses. Using mathematical models, we determined that even at the lowest flow velocity (80 µm/s) the oxygen provided was sufficient to maintain viability of the cells within the construct. Yet it was clear that this flow velocity did not adequately support the development of bone‐like tissue. The complexity of the cellular responses found at different flow velocities underscores the need to use a range of evaluation parameters to determine the quality of engineered bone. Bioeng. 2011; 108:1159–1170. © 2010 Wiley Periodicals, Inc.     

Age Effects on Mediolateral Balance Control

BackgroundAge-related balance impairments, particularly in mediolateral direction (ML) may cause falls. Sufficiently sensitive and reliable ML balance tests are, however, lacking. This study is aimed to determine (1) the effect of age on and (2) the reliability of ML balance performance using Center of Mass (CoM) tracking.MethodsBalance performance of 19 young (26±3 years) and 19 older (72±5 years) adults on ML-CoM tracking tasks was compared. Subjects tracked predictable and unpredictable target displacements at increasing frequencies with their CoM by shifting their weight sideward. Phase-shift (response delay) and gain (amplitude difference) between the CoM and target in the frequency domain were used to quantify performance. Thirteen older and all young adults were reassessed to determine reliability of balance performance measures. In addition, all older adults performed a series of clinical balance tests and conventional posturography was done in a sub-sample.ResultsPhase-shift and gain dropped below pre-determined thresholds (−90 degrees and 0.5) at lower frequencies in the older adults and were even lower below these frequencies than in young adults. Performance measures showed good to excellent reliability in both groups. All clinical scores were close to the maximum and no age effect was found using posturography. ML balance performance measures exhibited small but systematic between-session differences indicative of learning.ConclusionsThe ability to accurately perform ML-CoM tracking deteriorates with age. ML-CoM tracking tasks form a reliable tool to assess ML balance in young and older adults and are more sensitive to age-related impairment than posturography and clinical tests.