Advances in structure-activity relationships of HDAC inhibitors as HIV latency-reversing agents

INTRODUCTION

HIV-infected cells may rebound due to the existence of the silent HIV-infected memory CD4+ T cells (HIV latency). This HIV latency makes the disease almost incurable. In latency, the integrated proviral DNA of HIV is transcriptionally silenced partly due to the activity of histone deacetylases (HDACs). Hence, inhibition of HDAC is considered a prime target for HIV latency reversal.

AREAS COVERED

A brief biology and function of HDACs have been discussed to identify key points to design HDAC inhibitors (HDACis). This article summarizes recent achievements in the development of HDACis to achieve HIV latency reversal. Structure-activity relationships (SARs) of some series of compounds were also explored.

EXPERT OPINION

Depletion of the HIV reservoir is the only way to end this deadly epidemic. HDACis are latency-reversing agents (LRA) that can be used to 'shock' the latently infected CD4+ T cells to induce them to produce viral proteins. It is interesting to note that HDAC3, which is extensively expressed in resting T cells, is specifically preferred by benzamide-containing HDACis for inhibition. Thus, the benzamide class of compounds should be explored. Nevertheless, more data on selective HDAC inhibition is needed for further development of HDACis in HIV latency reversal.

Enhanced expression of recombinant proteins in Escherichia coli by co-expression with Vibrio parahaemolyticus CsgG, a pore-forming protein of the curli biogenesis pathway

AIM

To test whether engineered nanopores on the outer membrane (OM) of Escherichia coli can increase expression of heterologous proteins by making additional nutrients available to the host.

METHODS AND RESULTS

Outer membrane nanopores were generated by expressing recombinant Vibrio parahaemolyticus CsgG (rVpCsgG), which spontaneously assembles into a pore-forming channel on the OM, allowing spontaneous diffusion of small chemical entities from the exterior. Protein expression was probed using a reporter protein, sfGFP, expressed on a second compatible plasmid. OM pore formation was shown by acquired erythromycin sensitivity in cells transformed with rVpCsgG, influx of propidium iodide as well as by surface localization of recombinant CsgG by immunogold-labeled transmission electron microscopy. Expression of recombinant CsgG showed increased growth and also enhanced expression of sfGFP in minimal medium and is due to both enhanced transcription as well as translation. Similar enhancement of expression was also observed for a number of different proteins of different origin, sizes and nature.

CONCLUSIONS

Our findings clearly demonstrate that engineered nanopores on the OM of E. coli enhance expression of different heterologous proteins in minimal medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

Vibrio parahaemolyticus CsgG β-nanopore mediated co-expression strategy to improve recombinant protein expression is fully compatible with other methods of protein expression enhancement, and therefore can be a useful tool in biotechnology particularly for whole-cell bio-transformations for production of secondary metabolite.

Preliminary results for the 19F(ρ,α)16O reaction cross section measured at INFN-LNS

The 19F(ρ,α)16O reaction is an important fluorine destruction chan- nel in the proton-rich outer layers of asymptotic giant branch (AGB) stars and it might also play a role in hydrogen-deficient post-AGB star nucleosynthesis. At present, theoretical models overproduce F abundances in AGB stars with re-spect to the observed values, thus calling for further investigation of the nuclear reaction rates involved in the production and destruction of fluorine. In the last years, new direct and indirect measurements improved significantly the knowl- edge of 19F(ρ,α)16O cross section at deeply sub-Coulomb energies (below 0.8 MeV). However, those data are larger by a factor of 1.4 with respect the previ- ous data reported in the NACRE compilation in the energy region 0.6-0.8 MeV. Using the Large High resolution Array of Silicons for Astrophysics (LHASA), we performed a new direct measurement of the 19F(ρ,α)16O. The goal of this experiment is to reduce the uncertainties in the nuclear reaction rate of the 19F(ρ,α)16O reaction. Here, experimental details, the calibration procedure and angular distributions are presented.

Conversion of clinically isolated syndrome to multiple sclerosis: a prospective multi-center study in Eastern India

Background

In White populations more than 60% of clinically isolated syndrome (CIS) convert to multiple sclerosis (MS) on a long-term follow-up; several predictors for conversion have been identified.

Objective

This study aimed to determine the conversion rate and the predictors of conversion from CIS to MS (McDonald 2010) among Indians. The other objective was to evaluate the diagnostic accuracy of the new McDonald 2017 criteria in prediction of a second clinical attack.

Methods

Clinical and demographic data of CIS cohorts were collected. Baseline investigations included cerebrospinal magnetic resonance imaging (MRI) with contrast and cerebrospinal fluid (CSF) testing for oligoclonal band (OCB). Follow-up clinical and MRI examinations were performed annually for at least 24 months.

Results

Of the 82 subjects (age range 15-58 years), 36 (43.9%) converted to MS; 31/82 (37.8%) converted in 24 months. The predictors for conversion were earlier age of onset, CSF-OCB, cerebral MRI T2 lesion count, and periventricular and juxtacortical location of lesions. Twenty-two (26.83%) CIS fulfilled the McDonald MS 2017 criteria at baseline.

Conclusion

In this first prospective study of CIS in India, the risk factors for conversion are similar but the conversion rate to MS is lower than that in the western nations.

Demonstration of acid and water recovery systems: Applicability and operational challenges in Indian metal finishing SMEs

Diffusion dialysis, acid retardation and nanofiltration plants were acquired from Europe and demonstrated in several Indian metal finishing companies over a three year period. These companies are primarily small and medium enterprises (SMEs). Free acid recovery rate from spent pickling baths using diffusion dialysis and retardation was in the range of 78-86% and 30-70% respectively. With nanofiltration, 80% recovery rate of rinse water was obtained. The demonstrations created awareness among the metal finishing companies to reuse resources (acid/water) from the effluent streams. However, lack of efficient oil separators, reliable chemical analysis and trained personnel as well as high investment cost limit the application of these technologies. Local manufacturing, plant customization and centralized treatment are likely to encourage the uptake of such technologies in the Indian metal finishing sector.

Prompt fission gamma-ray emission spectral data for 239Pu(n,f) using fast directional neutrons from the LICORNE neutron source

Prompt fission gamma-ray spectra (PFGS) have been measured for the 239Pu(n,f) reaction using fast neutrons at Ēn=1.81 MeV produced by the LICORNE directional neutron source. The setup makes use of LaBr3 scintillation detectors and PARIS phoswich detectors to measure the emitted prompt fission gamma rays (PFG). The mean multiplicity, average total energy release per fission and average energy of photons are extracted from the unfolded PFGS. These new measurements provide complementary information to other recent work on thermal neutron induced fission of 239Pu and spontaneous fission of 252Cf.

Gamma-beam photofission experiments at ELI-NP: The future is emerging

At the Extreme Light Infrastructure - Nuclear Physics facility (ELI-NP), high-power laser systems together with high-brilliance gamma beams are the main research tools. The status of the construction of the facility is reported. The emerging photofission experimental program with brilliant gamma beams at ELI-NP is presented with emphasis on the prepared day-one experiments. The physics cases of the flagship experiments at ELI-NP are discussed, as well as the related instruments which are under construction for their realization.

Endoscopic sensing of alveolar pH

Previously unobtainable measurements of alveolar pH were obtained using an endoscope-deployable optrode. The pH sensing was achieved using functionalized gold nanoshell sensors and surface enhanced Raman spectroscopy (SERS). The optrode consisted of an asymmetric dual-core optical fiber designed for spatially separating the optical pump delivery and signal collection, in order to circumvent the unwanted Raman signal generated within the fiber. Using this approach, we demonstrate a ~100-fold increase in SERS signal-to-fiber background ratio, and demonstrate multiple site pH sensing with a measurement accuracy of ± 0.07 pH units in the respiratory acini of an ex vivo ovine lung model. We also demonstrate that alveolar pH changes in response to ventilation.

Contribution of efflux pumps in fluroquinolone resistance in multi-drug resistant nosocomial isolates of Pseudomanas aeruginosa from a tertiary referral hospital in north east India

BACKGROUND

Pseudomonas aeruginosa is one of the leading opportunistic pathogen and its ability to acquire resistance against series of antimicrobial agents confine treatment option for nosocomial infections. Increasing resistance to fluroquinolone (FQ) agents has further worsened the scenario. The major mechanism of resistance to FQs includes mutation in FQs target genes in bacteria (DNA gyrase and/or topoisomerases) and overexpression of antibiotic efflux pumps.

OBJECTIVE

We have investigated the role of efflux pump mediated FQ resistance in nosocomial isolates of P. aeruginosa from a tertiary referral hospital in north eastern part of India.

MATERIALS AND METHODS

A total of 234 non-duplicate, consecutive clinical isolates of P. aeruginosa were obtained from a tertiary referral hospital of north-east India. An efflux pump inhibitor (EPI), carbonyl cyanide m-chlorophenylhydrazone (CCCP) based method was used for determination of efflux pump activity and multiplex polymerase chain reaction (PCR) was performed for molecular characterisation of efflux pump. Minimum inhibitory concentration (MIC) reduction assay was also performed for all the isolates.

RESULTS AND CONCLUSION

A total number of 56 (23%) have shown efflux mediated FQ resistance. MexAB-OprM efflux system was predominant type. This is the first report of efflux pump mediated FQ resistance from this part of the world and the continued emergence of these mutants with such high MIC range from this part of the world demands serious awareness, diagnostic intervention, and proper therapeutic option.

Magnetic Interactions at the Nanoscale in Trilayer Titanates

We report on the phase diagram of competing magnetic interactions at the nanoscale in engineered ultrathin trilayer heterostructures of LaTiO_{3}/SrTiO_{3}/YTiO_{3}, in which the interfacial inversion symmetry is explicitly broken. Combined atomic layer resolved scanning transmission electron microscopy with electron energy loss spectroscopy and electrical transport have confirmed the formation of a spatially separated two-dimensional electron liquid and high density two-dimensional localized magnetic moments at the LaTiO_{3}/SrTiO_{3} and SrTiO_{3}/YTiO_{3} interfaces, respectively. Resonant soft x-ray linear dichroism spectroscopy has demonstrated the presence of orbital polarization of the conductive LaTiO_{3}/SrTiO_{3} and localized SrTiO_{3}/YTiO_{3} electrons. Our results provide a route with prospects for exploring new magnetic interfaces, designing a tunable two-dimensional d-electron Kondo lattice, and potential spin Hall applications.

A scalable label-free approach to separate human pluripotent cells from differentiated derivatives

The broad capacity of pluripotent human embryonic stem cells (hESC) to grow and differentiate demands the development of rapid, scalable, and label-free methods to separate living cell populations for clinical and industrial applications. Here, we identify differences in cell stiffness, expressed as cell elastic modulus (CEM), for hESC versus mesenchymal progenitors, osteoblast-like derivatives, and fibroblasts using atomic force microscopy and data processing algorithms to characterize the stiffness of cell populations. Undifferentiated hESC exhibited a range of CEMs whose median was nearly three-fold lower than those of differentiated cells, information we exploited to develop a label-free separation device based on the principles of tangential flow filtration. To test the device's utility, we segregated hESC mixed with fibroblasts and hESC-mesenchymal progenitors induced to undergo osteogenic differentiation. The device permitted a throughput of 10(6)-10(7) cells per min and up to 50% removal of specific cell types per single pass. The level of enrichment and depletion of soft, pluripotent hESC in the respective channels was found to rise with increasing stiffness of the differentiating cells, suggesting CEM can serve as a major discriminator. Our results demonstrate the principle of a scalable, label-free, solution for separation of heterogeneous cell populations deriving from human pluripotent stem cells.

Gingival fibroblasts resist apoptosis in response to oxidative stress in a model of periodontal diseases

Periodontal diseases are classified as inflammation affecting the supporting tissue of teeth, which eventually leads to tooth loss. Mild reversible gingivitis and severe irreversible periodontitis are the most common periodontal diseases. Periodontal pathogens initiate the diseases. The bacterial toxin, lipopolysaccharide (LPS), triggers the inflammatory response and leads to oxidative stress. However, the progress of oxidative stress in periodontal diseases is unknown. The purpose of this study is to examine oxidative stress and cell damage in gingivitis and periodontitis. Our results showed that LPS increases reactive oxygen species (ROS) accumulation in gingival fibroblast (GF). However, oxidative stress resulting from excessive ROS did not influence DNA damage and cell apoptosis within 24 h. The mechanism may be related to the increased expression of DNA repair genes, Ogg1, Neil1 and Rad50. Detection of apoptosis-related proteins also showed anti-apoptotic effects and pro-apoptotic effects were balanced. The earliest damage appeared in DNA when increased γH2AX, an early biomarker for DNA damage, was detected in the LPS group after 48 h. Later, when recurrent inflammation persisted, 8-OHdG, a biomarker for oxidative stress was much higher in periodontitis model compared to the control in vivo. Staining of 8-OHdG in human periodontitis specimens confirmed the results. Furthermore, TUNEL staining of apoptotic cells indicated that the periodontitis model induced more cell apoptosis in gingival tissue. This suggested GF could resist early and acute inflammation (gingivitis), which was regarded as reversible, but recurrent and chronic inflammation (periodontitis) led to permanent cell damage and death.

Near-room-temperature colossal magnetodielectricity and multiglass properties in partially disordered La2NiMnO6

We report magnetic, dielectric, and magnetodielectric responses of the pure monoclinic bulk phase of partially disordered La2NiMnO6, exhibiting a spectrum of unusual properties and establish that this compound is an intrinsically multiglass system with a large magnetodielectric coupling (8%-20%) over a wide range of temperatures (150-300 K). Specifically, our results establish a unique way to obtain colossal magnetodielectricity, independent of any striction effects, by engineering the asymmetric hopping contribution to the dielectric constant via the tuning of the relative-spin orientations between neighboring magnetic ions in a transition-metal oxide system. We discuss the role of antisite (Ni-Mn) disorder in emergence of these unusual properties.

Friction Reduction in Metal on Metal Hip Joint

In the world, approximately 800,000 total hip replacements are implanted, while, at least 50,000 hip replacements are performed in the United Kingdom each year. Orthopaedic surgeons have traditionally delayed joint replacement surgery in patients younger than 60 due to its limited survivorship time and biological effect inside the human body. The highest percentage (71%) hip joint failure was caused by aseptic loosening of the femoral and acetabular components and the war rate and debris are the accepted causes of that aseptic loosening. The wear particles, either ion or stable form, can react with proteins and change the pH value of albumin solutions inside the human body, causing damage to the DNA resulting in genotoxicity. There has been a great deal of research into the materials, dimension of the prosthesis, surface roughness, and lubrication effect by surface coating. But it is very rare to apply surface texture technique to a metallic prosthesis bearing surface although it has proven very successful in many engineering applications including automobile industry due to secondary lubrication effect and hydrodynamic effect. A TE 77 high frequency friction simulator has been used for the experiment where specimens were manufactured with 50 mm diameters and 50μm clearance. A dynamic loading was applied synchronized with Hip CD 98 while the temperature was controlled at 37°C. The output data including friction coefficient, friction force and contact pot were recorded in connected computer via COMPEND 2000 software. The surfaces were inspected after and before test under scanning electronic microscopy. The plateau honed surfaces were produced on the moving specimens with controlled load, speed and various grade of emery paper using a specially designed tool. The friction coefficient was recorded 0.035 for the honing surface which was made by 30 kg laod and 60 emery paper, 0.04 for the honing surface profile made by 30 kg load and 150 emery paper and 0.06 for plane surface after one million cycles. The rest of surfaces profiled surface were broken down before one million cycles. That made a conclusion that plateau honing surface made with 30 kg load and 60 emery paper was best surface texture profile (45° honed angle, 40±10μm width and 35±10μm depth honing) for the metal on metal hip prosthesis. The comparison experiment was continue for plane surface and plateau honing surface of 60 emery paper and 30 kg load up to one and half millions cycles. It was found that the friction coefficient (0.03) was further reduced 0.005 after one and half million cycles for plateau honing surface but it was increased nearly double (0.065) for plane surface. The static friction coefficient was also reduced 38% in case of that plateau honing surface. The contact pot profile which is an indicator of fluid film thickness was noticed higher in plateau honing surface. This was evidence that the lubrication distribution was better in plateau honed surface which should provide longer life of joint, reduce wear and improves acceptability of metal on metal hip joints.

Digestive enzymes and metabolic profile of Labeo rohita fingerlings fed diets with different crude protein levels

Labeo rohita, commonly called rohu is one of the most important fish species for aquaculture in India. Digestive enzyme response and metabolic profile of fingerling L. rohita to different dietary crude protein (CP) levels (viz. 25, 30, 35 and 40%) were studied in an attempt to optimize a practical diet formulation for this species. After 45 days of feeding, activity of digestive enzymes and metabolite concentrations were assayed. Amylase, lipase and alkaline phosphatase (ALP) activities were not influenced by the dietary protein, but proteolytic and acid phosphatase (ACP) activities varied (P<0.05) between the treatments. Proteolytic activity showed a second order polynomial relationship with dietary crude protein (CP) as Y = 0.0734X(2) + 4.937X - 68.37, r(2)=0.97. A positive correlation was observed between dietary CP and amylase (r(2)=0.78). All the metabolites except muscle glucose showed significant change corresponding to the dietary protein levels. Glucose and glycogen levels corresponded to the dietary carbohydrate levels. Muscle and plasma pyruvic acid increased as the crude protein in the diet increased, whereas liver pyruvic acid showed the opposite trend. Muscle protein content was not affected by dietary CP. Protein fractions in plasma (total protein, albumin and globulin) showed maximum values in 30% CP fed group. It is concluded that proteolytic activity and ACP are the major digestive enzymes responsive to dietary CP in L. rohita fingerlings. Considering the cost effectiveness of the diet, and based on liver and plasma free amino acid levels and plasma protein fractions, 30% crude protein is recommended as the optimal dietary protein for L. rohita fingerlings.

Visual inspection with acetic acid and cytology in the early detection of cervical neoplasia in Kolkata, India

Visual inspection of the cervix after application of 3-5% acetic acid (VIA) is a potential alternative to cytology for screening in low-resource countries. The present study evaluated the performance of VIA, magnified visual inspection after application of acetic acid (VIAM), and cytology in the detection of high-grade cervical cancer precursor lesions in Kolkata (Calcutta) and suburbs in eastern India. Trained health workers with college education concurrently screened 5881 women aged 30-64 years with VIA, VIAM, and conventional cervical cytology. Detection of well-defined, opaque acetowhite lesions close to the squamocolumnar junction; well-defined, circumorificial acetowhite lesions; or dense acetowhitening of ulceroproliferative growth on the cervix constituted a positive VIA or VIAM. Cytology was considered positive if reported as mild dysplasia or worse lesions. All screened women (N = 5881) were evaluated by colposcopy, and biopsies were directed in those with colposcopic abnormalities (N = 1052, 17.9%). The final diagnosis was based on histology (if biopsies had been taken) or colposcopic findings, which allowed direct estimation of sensitivity, specificity, and predictive values. Moderate or severe dysplasia or carcinoma in situ (CIN 2-3 disease) was considered as true positive disease for the calculation of sensitivity, specificity, and predictive values of screening tests. 18.7%, 17.7% and 8.2% of the women tested positive for VIA, VIAM, and cytology. One hundred twenty two women had a final diagnosis of CIN 2-3 lesions. The sensitivities of VIA and VIAM to detect CIN 2-3 lesions were 55.7% and 60.7%, respectively; the specificities were 82.1% and 83.2%, respectively. The sensitivity and specificity of cytology were 29.5% and 92.3%, respectively. All the tests were associated with negative predictive values above 98%. VIA and VIAM had significantly higher sensitivity than cytology in our study; the specificity of cytology was higher than that of VIA and VIAM.

Visual inspection with acetic acid and cytology in the early detection of cervical neoplasia in Kolkata, India

Visual inspection of the cervix after application of 3–5% acetic acid (VIA) is a potential alternative to cytology for screening in low-resource countries. The present study evaluated the performance of VIA, magnified visual inspection after application of acetic acid (VIAM), and cytology in the detection of high-grade cervical cancer precursor lesions in Kolkata (Calcutta) and suburbs in eastern India. Trained health workers with college education concurrently screened 5881 women aged 30–64 years with VIA, VIAM, and conventional cervical cytology. Detection of well-defined, opaque acetowhite lesions close to the squamocolumnar junction; well-defined, circumorificial acetowhite lesions; or dense acetowhitening of ulceroproliferative growth on the cervix constituted a positive VIA or VIAM. Cytology was considered positive if reported as mild dysplasia or worse lesions. All screened women (N = 5881) were evaluated by colposcopy, and biopsies were directed in those with colposcopic abnormalities (N = 1052, 17.9%). The final diagnosis was based on histology (if biopsies had been taken) or colposcopic findings, which allowed direct estimation of sensitivity, specificity, and predictive values. Moderate or severe dysplasia or carcinoma in situ (CIN 2–3 disease) was considered as true positive disease for the calculation of sensitivity, specificity, and predictive values of screening tests. 18.7%, 17.7% and 8.2% of the women tested positive for VIA, VIAM, and cytology. One hundred twenty two women had a final diagnosis of CIN 2–3 lesions. The sensitivities of VIA and VIAM to detect CIN 2–3 lesions were 55.7% and 60.7%, respectively; the specificities were 82.1% and 83.2%, respectively. The sensitivity and specificity of cytology were 29.5% and 92.3%, respectively. All the tests were associated with negative predictive values above 98%. VIA and VIAM had significantly higher sensitivity than cytology in our study; the specificity of cytology was higher than that of VIA and VIAM.

Bacterial adhesins: structural studies reveal chaperone function and pilus biogenesis

During the past year, remarkable progress has been made in understanding how periplasmic chaperones fold and protect protein modules that are destined for assembly into adhesive pili in Gram-negative bacteria. The first two three-dimensional structures of complexes of periplasmic chaperones with substrate pilus subunits have revealed much about the structural basis for chaperone-mediated folding and aggregation prevention, and have provided insight into the structure of adhesive pili.

Chaperone-assisted pilus assembly and bacterial attachment

Bacterial pili assembled by the chaperone-usher pathway can mediate microbial attachment, an early step in the establishment of an infection, by binding specifically to sugars present in host tissues. Recent work has begun to reveal the structural basis both of chaperone function in the biogenesis of these pili and of bacterial attachment.

Percutaneous cuffed catheter insertion by nephrologists

The use of Dacron cuff double-lumen permanent catheters for hemodialysis has become more common in the dialysis unit as patients await for creation or maturation of a permanent hemoaccess for various reasons. Placement of these catheters is often done by surgeons. Nephrologists skilled in the placement of temporary central vein accesses can extend their skill to placement of cuff catheters with the current available peel-away insertion technique. Data are presented on the percutaneous placement of 77 Dacron cuff permanent catheters by 4 nephrologists in two medical centers in a nonoperating room setting with minimal complications.

Advanced glycation end products: a Nephrologist's perspective

Advanced glycation end products (AGEs) are a heterogeneous group of molecules that accumulate in plasma and tissues with advancing age, diabetes, and renal failure. There is emerging evidence that AGEs are potential uremic toxins and may have a role in the pathogenesis of vascular and renal complications associated with diabetes and aging. AGEs are formed when a carbonyl of a reducing sugar condenses with a reactive amino group in target protein. These toxic molecules interact with specific receptors and elicit pleiotropic responses. AGEs accelerate atherosclerosis through cross-linking of proteins, modification of matrix components, platelet aggregation, defective vascular relaxation, and abnormal lipoprotein metabolism. In vivo and in vitro studies indicate that AGEs have a vital role in the pathogenesis of diabetic nephropathy and the progression of renal failure. The complications of normal aging, such as loss of renal function, Alzheimer's disease, skin changes, and cataracts, may also be mediated by progressive glycation of long-lived proteins. AGEs accumulate in renal failure as a result of decreased excretion and increased generation resulting from oxidative and carbonyl stress of uremia. AGE-modified beta(2)-microglobulin is the principal pathogenic component of dialysis-related amyloidosis in patients undergoing dialysis. Available dialytic modalities are not capable of normalizing AGE levels in patients with end-stage renal disease. A number of reports indicated that restoration of euglycemia with islet-cell transplantation normalized and prevented further glycosylation of proteins. Aminoguanidine (AGN), a nucleophilic compound, not only decreases the formation of AGEs but also inhibits their action. A number of studies have shown that treatment with AGN improves neuropathy and delays the onset of retinopathy and nephropathy. N-Phenacylthiazolium bromide is a prototype AGE cross-link breaker that reacts with and can cleave covalent AGE-derived protein cross-links. Thus, there is an exciting possibility that the complications of diabetes, uremia, and aging may be prevented with these novel agents.

Pseudo-symmetry characterization and refinement of a trigonal crystal form of naphthalene 1,2-dioxygenase

Two trigonal crystal structures of naphthalene 1,2-dioxygenase from Pseudomonas sp. NCIB 9816-4 have been refined at 2.6 A resolution. The space group is R3, with four heterodimers in the asymmetric unit. The crystallographic threefold axis coincides with the symmetry axis of the active molecule, a mushroom-shaped alpha(3)beta(3) hexamer. The crystal is formed by symmetrical contacts between the hexamers on three different interaction surfaces, one on the beta-subunit and the other two on the alpha--subunits. Nickel ions mediate one of the alpha-subunit interactions. The two other types of packing contacts sustain two interlaced and almost independent crystal patterns with significantly different temperature factors. The space group of the individual crystal patterns is R32, with the corresponding twofold axes parallel to each other. The interactions between the crystal patterns separate the two parallel twofolds, eliminating the twofold symmetry for the whole crystal. The differences in temperature factors among the molecules in the asymmetric unit have been refined and are different for the two refined structures. An analysis of the structure factors of the pseudo-equivalent reflections showed that their differences lie in their phases and not in their amplitudes, suggesting that R(merge) is not an appropriate indicator for revealing the correct point group.

Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding

The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound. This compound appears to be an indole adduct, which in Escherichia coli is derived from tryptophan present in the rich culture medium. An indole-dioxygen adduct has been built which fits the electron density convincingly. Support for this interpretation was obtained from crystals of the enzyme purified from cells grown in the absence of tryptophan which had an empty substrate pocket. These types of crystals were soaked in indole solutions and the position of indole in this complex was similar to the corresponding part in the modelled indole-oxygen adduct. This suggests that a peroxide bound to iron end-on attacks the substrate and forms this intermediate. The substrate position has implications for the substrate specificity of the enzyme. Docking studies with indole, naphthalene and biphenyl inside the substrate pocket of NDO suggest the presence of subpockets where the one close to the active site iron is reserved for the binding of the aromatic ring which is hydroxylated upon catalysis. The plausible location for the binding of dioxygen is between this pocket and the catalytic iron. This is in accordance with the enantiospecificity of the products.

Stereoisomeric selectivity of human deoxyribonucleoside kinases

Deoxynucleoside kinases catalyze the 5'-phosphorylation of 2'-deoxyribonucleosides with nucleoside triphosphates as phosphate donors. One of the cellular kinases, deoxycytidine kinase (dCK), has been shown to phosphorylate several L-nucleosides that are efficient antiviral agents. In this study we investigated the potentials of stereoisomers of the natural deoxyribonucleoside to serve as substrates for the recombinant cellular deoxynucleoside kinases. The cytosolic thymidine kinase exhibited a strict selectivity and phosphorylated only beta-D-Thd, while the mitochondrial thymidine kinase (TK2) and deoxyguanosine kinase (dGK) as well as dCK all had broad substrate specificities. TK2 phosphorylated Thd and dCyd stereoisomers in the order: beta-D- > or = beta-L- >> alpha-D- > or = alpha-L-isomer. dCK activated both enantiomers of beta-dCyd, beta-dGuo, and beta-dAdo with similar efficiencies, and alpha-D-dCyd also served as a substrate. dGK phosphorylated the beta-dGuo enantiomers with no preference for the ribose configuration; alpha-L-dGuo was also phosphorylated, and beta-L-dAdo and beta-L-dCyd were substrates but showed reduced efficiencies. The anomers of the 2',3'-dideoxy-D-nucleosides (ddNs) were tested, and TK2 and dCK retained their low selectivities. Unexpectedly, alpha-dideoxycytidine (ddC) was a 3-fold better substrate for dCK than beta-ddC. Similarly, alpha-dideoxythymidine (ddT) was a better substrate for TK2 than beta-ddT. dGK did not accept any D-ddNs. Thus, TK2, dCK, and dGK, similar to herpes simplex virus type 1 thymidine kinase (HSV-1 TK), showed relaxed stereoselectivities, and these results substantiate the functional similarities within this enzyme family. Docking simulations with the Thd isomers and the active site of HSV-1 TK showed that the viral enzyme may in some respects serve as a model for studying the substrate specificities of the cellular enzymes.

X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli

Type 1 pili-adhesive fibers expressed in most members of the Enterobacteriaceae family-mediate binding to mannose receptors on host cells through the FimH adhesin. Pilus biogenesis proceeds by way of the chaperone/usher pathway. The x-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli at 2.5 angstrom resolution reveals the basis for carbohydrate recognition and for pilus assembly. The carboxyl-terminal pilin domain of FimH has an immunoglobulin-like fold, except that the seventh strand is missing, leaving part of the hydrophobic core exposed. A donor strand complementation mechanism in which the chaperone donates a strand to complete the pilin domain explains the basis for both chaperone function and pilus biogenesis.

A conserved structural element in horse and mouse IGF2 genes binds a methylation sensitive factor

The equine IGF2 gene has been cloned and characterised. It spans a 9 kb region, which is substantially less than the corresponding human gene. Three coding exons and three untranslated leader exons, all highly homologous to those in other species, were identified. Downstream of the polyadenylation site in exon 6, a dinucleotide repeat sequence was identified. Three putative promoters (P1-P3) were localised in the 5' region of the gene. RNase protection analysis revealed two active promoters in fetal tissues, P2 and P3, whereas P3 was the only promoter active in adult tissues. This represents a transcriptional pattern different from that in humans or rodents. A novel structural element, an inverted repeat, is predicted in the 3' region of the IGF2 gene. This repeat is conserved between species and located in a region which is differentially methylated in the human and mouse genes and might therefore be involved in the imprinting mechanism. The inverted repeat acquires a stem-loop structure in vitro with a hybrid A/B-DNA conformation in the stem area. Both in horse and mouse, a methylation-sensitive protein binds this structure with a strong requirement for the loop area. Furthermore, the protein might be developmentally regulated.

Drug-induced nephrotoxicity

Drug-induced renal dysfunction is not an uncommon event, which can cause significant morbidity and can be easily overlooked. Many medications can lead to renal dysfunction through various mechanisms. The most common medications or classes of medications along with their clinical presentations are discussed in this article. As can be noted, many drugs can cause nephropathy in more than one way. Because it is difficult to discuss nephrotoxicities of every reported medication, Tables 1, 2, and 3 are provided; although these tables are by no means comprehensive, they may serve as further reference. This article is intended to provide a broad overview of the spectrum of presentation associated with drug-induced nephrotoxicity to guide the clinician to familiarity with this entity.

IgA multiple myeloma presenting as Henoch-Schönlein purpura/polyarteritis nodosa overlap syndrome

We report the unusual case of a man with a 5-year history of relapsing Henoch-Schonlein purpura (HSP) and macroscopic polyarteritis nodosa (PAN) as early manifestations of IgA kappa multiple myeloma. The glomeruli contained monoclonal IgA kappa deposits, without other immunoglobulins or lambda light chains. Glomerular deposits lacked the usual electron density but could be demonstrated by immunoelectron microscopy. Multisystem large vessel vasculitis (antineutrophil cytoplasmic antibody negative) produced aneurysms of renal and hepatic arteries, whereas small vessel vasculitis affected the skin and glomeruli, producing a symptom complex of HSP with dermal and glomerular deposits of IgA. We conclude that HSP/overlap syndrome may be the initial manifestation of IgA myeloma and should be considered within the spectrum of monoclonal IgA deposition disease.

Correlation of venography, venous pressure, and hemoaccess function

We analyzed the anatomic features of both grafts and fistulas and correlated these features with access function. We also attempted to determine venous pressures predicting access dysfunction (critical venous pressures) at various blood flow rates (BFRs). Therefore, accesses of 46 chronic hemodialysis patients were studied by venography in a prospective fashion. We defined the incidences of various lesions and the effects of venous collaterals on graft function, and determined critical venous pressures at various BFRs. Eighty-three percent of the accesses had outflow obstruction. Five types of anatomic lesions were identified. The incidences were venous stenosis of the draining vein immediately proximal to the venous anastomosis, 36.4%; central vein, 23.6%; venous anastomosis, 25.5%; arterial anastomosis, 10.9%; and intragraft hyperplasia, 3.6%. Twelve patients had multiple lesions. When the homogenous polytetrafluoroethylene arm graft population was studied for the effect of venous collaterals, we found that venous collaterals conferred protection but did not prevent graft failure. Venous pressure measurements were good predictors of access failure at the lower BFRs. Venous pressures increased with increasing BFRs. A critical venous pressure of 145 mm Hg was found for a BFR of 250 mL/min. At a BFR of 300 mL/min, the critical venous pressure was 170 mm Hg. A critical venous pressure could not be found for a BFR of 400 mL/min.

Evaluation of coronary artery disease by dipyridamole echocardiography test

Role of oral dipyridamole echocardiography test (DET) was evaluated in 50 patients with effort angina. All patients underwent coronary angiography, the day after oral DET. The echo studies were performed at rest and 65 +/- 15 minutes after 300 mg of oral dipyridamole. Segmental wall motion was analysed in a 16 segment model and a wall motion score index (WMSI) was generated for the entire left ventricle both at rest and following the drug. WMSI was significantly higher after oral dipyridamole, (p < 0.001) compared to resting condition with increased sensitivity (86% vs 74%). When results of DET were compared with coronary angiography, the correlation of WMSI was statistically significant in three vessel disease (p < 0.001), two vessel disease (p < 0.001) as well as for left anterior descending lesions (p < 0.001). However, it was insignificant for single vessel disease, viz, right coronary artery and circumflex artery. Thus we conclude that oral DET is a safe, inexpensive, sensitive and non-exercise dependent method for demonstrating myocardial ischaemia with high diagnostic accuracy.