Bacterial diversity in an industrial wastewater bioreactor

Industrial wastewater bioreactors are potentially important sources of novel biocatalysts. However, the microbial populations in these bioreactors are not well characterized. The microbial community in an industrial wastewater bioreactor was surveyed by extracting DNA from a sample of activated sludge, followed by PCR amplification and sequencing of cloned 16S rRNA genes. A total of 407 cloned 16S rRNA gene sequences were compared with 88 bacterial isolates cultured from the same sample of sludge using a variety of standard media. Most of the bacteria detected by the PCR-based approach were -subdivision Proteobacteria, whereas most of the cultured bacteria were -subdivision Proteobacteria. Only a few types of bacteria were detected by both approaches. These observations indicate that multiple techniques are necessary to characterize the microbial diversity in any complex ecosystem.     

Modelling Metal Complexes of Calixarene Esters and Phosphine Oxides Using Molecular Mechanics

This paper focuses on the molecular modelling of a number of calixarene ester and phosphine oxide metal ion complexes. Monte Carlo conformational searches, in conjunction with the Merck Molecular Force Field, were carried out using Spartan SGI Version 5.0.1. running on Silicon Graphics O2 workstations. In the case of the calix[4]arene tetraesters, the optimised models strongly suggest that the selectivity of these ligands is strongly related to the eight-fold nature of the coordination with the Na⁺ ion, while coordination with the Li⁺ ion, for example, is merely three-fold. This feature of eight-fold coordination is also observed in the models of the complexes formed by the calix[4]arene tetraphosphine oxides with calcium. However, whereas the eight-fold coordination is unique to the model of the TPOL:Ca²⁺ complex among the ions modelled, this mode of coordination occurs for TPOS with sodium and potassium, in addition to calcium. This concurs with the observation that calcium selectivity is obtained with ion selective electrodes based on TPOL but not TPOS. Though the cavity in the calix[5]arenes PPOL and PPOLx and the calix[6]arene HPOL, in their uncomplexed form, are much larger than that of the corresponding calix[4]arenes, the pattern of selectivity is the same – the ligands are selective for calcium. The models of the complexes of these larger calixarenes, such as PPOL:Ca²⁺, strongly suggest that the reason for this similarity is that four of the available phosphine oxide groups complex with the calcium ion, and the others are forced away from the cavity region for steric reasons. The resulting eight-fold coordination, is therefore, similar to that of the calix[4]arenes studied.Electronic Supplementary Material available.     

Gross,histological and ultrastructural morphology of the aglomerular kidney in the lined seahorse Hippocampus erectus

Histologic evaluation of the renal system in the lined seahorse Hippocampus erectus reveals a cranial kidney with low to moderate cellularity, composed of a central dorsal aorta, endothelial lined capillary sinusoids, haematopoietic tissue, fine fibrovascular stroma, ganglia and no nephrons. In comparison, the caudal kidney is moderately to highly cellular with numerous highly convoluted epithelial lined tubules separated by interlacing haematopoietic tissue, no glomeruli, fine fibrovascular stroma, numerous capillary sinusoids, corpuscles of Stannius and clusters of endocrine cells adjacent to large calibre vessels. Ultrastructural evaluation of the renal tubules reveals minimal variability of the tubule epithelium throughout the length of the nephron and the majority of tubules are characterized by epithelial cells with few apical microvilli, elaborate basal membrane infolding, rare electron dense granules and abundant supporting collagenous matrix.     

Subunit Interactions and Requirements for Inhibition of the Yeast V1-ATPase

Disassembly of the yeast V-ATPase into cytosolic V₁ and membrane V₀ sectors inactivates MgATPase activity of the V₁-ATPase. This inactivation requires the V₁ H subunit (Parra, K. J., Keenan, K. L., and Kane, P. M. (2000) J. Biol. Chem. 275, 21761–21767), but its mechanism is not fully understood. The H subunit has two domains. Interactions of each domain with V₁ and V₀ subunits were identified by two-hybrid assay. The B subunit of the V₁ catalytic headgroup interacted with the H subunit N-terminal domain (H-NT), and the C-terminal domain (H-CT) interacted with V₁ subunits B, E (peripheral stalk), and D (central stalk), and the cytosolic N-terminal domain of V₀ subunit Vph1p. V₁-ATPase complexes from yeast expressing H-NT are partially inhibited, exhibiting 26% the MgATPase activity of complexes with no H subunit. The H-CT domain does not copurify with V₁ when expressed in yeast, but the bacterially expressed and purified H-CT domain inhibits MgATPase activity in V₁ lacking H almost as well as the full-length H subunit. Binding of full-length H subunit to V₁ was more stable than binding of either H-NT or H-CT, suggesting that both domains contribute to binding and inhibition. Intact H and H-CT can bind to the expressed N-terminal domain of Vph1p, but this fragment of Vph1p does not bind to V₁ complexes containing subunit H. We propose that upon disassembly, the H subunit undergoes a conformational change that inhibits V₁-ATPase activity and precludes V₀ interactions.V-ATPases are ubiquitous proton pumps responsible for compartment acidification in all eukaryotic cells (1, 2). These pumps couple hydrolysis of cytosolic ATP to proton transport into the lysosome/vacuole, endosomes, Golgi apparatus, clathrin-coated vesicles, and synaptic vesicles. Through their role in organelle acidification, V-ATPases are linked to cellular functions as diverse as protein sorting and targeting, zymogen activation, cytosolic pH homeostasis, and resistance to multiple types of stress (3). They are also recruited to the plasma membrane of certain cells, where they catalyze proton export (4, 5).V-ATPases are evolutionarily related to ATP synthases of bacteria and mitochondria and consist of two multisubunit complexes, V₁ and V₀, which contain the sites for ATP hydrolysis and proton transport, respectively. Like the ATP synthase (F-ATPase), V-ATPases utilize a rotational catalytic mechanism. ATP binding and hydrolysis in the three catalytic subunits of the V₁ sector generate sequential conformational changes that drive rotation of a central stalk (6–8). The central stalk subunits are connected to a ring of proteolipid subunits in the V₀ sector that bind protons to be transported. The actual transport is believed to occur at the interface of the proteolipids and V₀ subunit a. Rotational catalysis will be productive in proton transport only if V₀ subunit a is held stationary, whereas the proteolipid ring rotates (8). This “stator function” resides in a single peripheral stalk in F-ATPases (9, 10), but is distributed among up to three peripheral stalks in V-ATPases (11–13). The peripheral stator stalks link V₀ subunit a to the catalytic headgroup and ensures that there is rotation of the central stalk complex relative to the V₀ a subunit and catalytic headgroup.Eukaryotic V-ATPases are highly conserved in both their overall structure and the sequences of individual subunits. Although homologs of most subunits of eukaryotic V-ATPases are present in archaebacterial V-ATPases (also known as A-ATPases), the C and H subunits are unique to eukaryotes. Both subunits have been localized at the interface of the V₁ and V₀ sectors, suggesting that they are positioned to play a critical role in structural and functional interaction between the two sectors (14–16). The yeast C and H subunits are the only eukaryotic V-ATPase subunits for which x-ray crystal structures are available (17, 18). The structure of the C subunit revealed an elongated “dumbbell-shaped” molecule, with foot, head, and neck domains (18). The structure of the H subunit indicated two domains. The N-terminal 348 amino acids fold into a series of HEAT repeats and are connected by a 4-amino acid linker to a C-terminal domain containing amino acids 352–478 (17). These two domains have partially separable functions in the context of the assembled V-ATPase (19). Complexes containing only the N-terminal domain of the H subunit (H-NT)² supported some ATP hydrolysis but little or no proton pumping in isolated vacuolar vesicles (19, 20). The C-terminal domain (H-CT) assembled with the rest of the V-ATPase in the absence of intact subunit H, but supported neither ATPase nor proton pumping activity (19). However, co-expression of the H-NT and H-CT domains results in assembly of both sectors with the V-ATPase and allows increased ATP-driven proton pumping in isolated vacuolar vesicles. These results suggest that the H-NT and H-CT domains play distinct and complementary roles even when the two domains are not covalently attached.In addition to their role as dedicated proton pumps, eukaryotic V-ATPases are also distinguished from F-ATPases and archaeal V-ATPases in their regulation. Eukaryotic V-ATPases are regulated in part by reversible disassembly of the V₁ complex from the V₀ complex (1, 21, 22). In yeast, disassembly of previously assembled complexes occurs in response to glucose deprivation, and reassembly is rapidly induced by glucose readdition to glucose-deprived cells. Disassembly down-regulates pump activity, and both the disassembled sectors are inactivated. Inhibition of ATP hydrolysis in free V₁ sectors is particularly critical, because release of an active ATPase into the cytosol could deplete cytosolic ATP stores. This inhibition is dependent in part on the H subunit. V₁ complexes isolated from vma13Δ mutants, which lack the H subunit gene (V₁(-H) complexes) have MgATPase activity. Consistent with a physiological role for H subunit inhibition of V₁, heterozygous diploids containing elevated levels of free V₁ complexes without subunit H have severe growth defects (23). V₁ complexes containing subunit H have no MgATPase activity, but retain some CaATPase activity, suggesting a role for nucleotides in inhibition (24, 25). Consistent with such a role, both the CaATPase activity of native V₁ and the MgATPase activity of V₁(-H) complexes are lost within a few minutes of nucleotide addition (24).A number of points of interaction between the H subunit and the V₁ and V₀ complexes have been identified through two-hybrid assays, binding of expressed proteins, and cross-linking experiments. These experiments have indicated that the H subunit binds to V₁ subunits E and G of the V-ATPase peripheral stalks (26, 27), the catalytic subunit (V₁ subunit A) (28), regulatory V₁ subunit B (15), and the N-terminal domain of subunit a (28). Recently, Jeffries and Forgac (29) have found that cysteines introduced into the C-terminal domain of subunit H can be cross-linked to subunit F in isolated V₁ sectors via a 10-Å cross-linking reagent.In this work, we examine both the subunit-subunit interactions and functional roles of the H-NT and H-CT domains in inhibition of V₁-ATPase activity. When expressed in yeast cells lacking subunit H, H-NT can be isolated with cytosolic V₁ complexes, but H-CT cannot. We find that both of these domains contribute to inhibition of ATPase activity, but that stable binding to V₁ and full inhibition of activity requires both domains. We also find that the H-CT can bind to the cytosolic N-terminal domain of V₀ subunit Vph1p (Vph1-NT) in isolation, but does not support tight binding of Vph1-NT to isolated V₁ complexes.     

Sonographic evaluation of thyroid morphology during different reproductive events in female Indo‐Pacific bottlenose dolphins,Tursiops aduncus

Thyroid morphology and function are likely affected by the cyclic hormonal environment during different reproductive events in females. The present study was undertaken to evaluate the variation of thyroid morphology at different reproductive events (anestrus, estrus, lactation, and pregnancy) in a captive group of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) measured using sonography. Sonographic examinations of the thyroid gland and ovaries in nine sexually mature female subjects were performed weekly for 2.5 yr. A generalized linear mixed model was used to estimate the effects of the reproductive events for thyroid volume. Reproductive event was found to be a significant predictor for thyroid volume measurement and significant variation in thyroid volume was found between different reproductive events. A significantly larger thyroid volume in lactating females was observed when compared with estrous and anestrous females, possibly due to the high energy requirements and milk production during lactation. Taken together, thyroid volume variation during different reproductive events in female dolphins should be considered so as to obtain a diagnostically meaningful assessment when conducting routine examinations.     

A unique binding epitope for salvinorin A, a non-nitrogenous kappa opioid receptor agonist

Salvinorin A is a potent kappa opioid receptor (KOP) agonist with unique structural and pharmacological properties. This non-nitrogenous ligand lacks nearly all the structural features commonly associated with opioid ligand binding and selectivity. This study explores the structural basis to salvinorin A binding and selectivity using a combination of chimeric and single-point mutant opioid receptors. The experiments were designed based on previous models of salvinorin A that locate the ligand within a pocket formed by transmembrane (TM) II, VI, and VII. More traditional sites of opioid recognition were also explored, including the highly conserved aspartate in TM III (D138) and the KOP selectivity site E297, to determine the role, if any, that these residues play in binding and selectivity. The results indicate that salvinorin A recognizes a cluster of residues in TM II and VII, including Q115, Y119, Y312, Y313, and Y320. Based on the position of these residues within the receptor, and prior study on salvinorin A, a model is proposed that aligns the ligand vertically, between TM II and VII. In this orientation, the ligand spans residues that are spaced one to two turns down the face of the helices within the receptor cavity. The ligand is also in close proximity to EL-2 which, based on chimeric data, is proposed to play an indirect role in salvinorin A binding and selectivity.