Target highlights in CASP13: Experimental target structures through the eyes of their authors.

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.

Cancer-associated mesothelial cells are regulated by the anti-Müllerian hormone axis.

Cancer-associated mesothelial cells (CAMCs) in the tumor microenvironment are thought to promote growth and immune evasion. We find that, in mouse and human ovarian tumors, cancer cells express anti-Müllerian hormone (AMH) while CAMCs express its receptor AMHR2, suggesting a paracrine axis. Factors secreted by cancer cells induce AMHR2 expression during their reprogramming into CAMCs in mouse and human in vitro models. Overexpression of AMHR2 in the Met5a mesothelial cell line is sufficient to induce expression of immunosuppressive cytokines and growth factors that stimulate ovarian cancer cell growth in an AMH-dependent way. Finally, syngeneic cancer cells implanted in transgenic mice with Amhr2-/- CAMCs grow significantly slower than in wild-type hosts. The cytokine profile of Amhr2-/- tumor-bearing mice is altered and their tumors express less immune checkpoint markers programmed-cell-death 1 (PD1) and cytotoxic T lymphocyte-associated protein 4 (CTLA4). Taken together, these data suggest that the AMH/AMHR2 axis plays a critical role in regulating the pro-tumoral function of CAMCs in ovarian cancer.

The multifunctional histone-like protein Lsr2 protects mycobacteria against reactive oxygen intermediates.

Mycobacterium tuberculosis has evolved a number of strategies to survive within the hostile environment of host phagocytes. Reactive nitrogen and oxygen intermediates (RNI and ROI) are among the most effective antimycobacterial molecules generated by the host during infection. Lsr2 is a M. tuberculosis protein with histone-like features, including the ability to regulate a variety of transcriptional responses in mycobacteria. Here we demonstrate that Lsr2 protects mycobacteria against ROI in vitro and during macrophage infection. Furthermore, using macrophages derived from NOS(-/-) and Phox(-/-) mice, we demonstrate that Lsr2 is important in protecting against ROI but not RNI. The protection provided by Lsr2 protein is not the result of its ability to either bind iron or scavenge hydroxyl radicals. Instead, electron microscopy and DNA-binding studies suggest that Lsr2 shields DNA from reactive intermediates by binding bacterial DNA and physically protecting it. Thus, Lsr2 appears to be a unique protein with both histone-like properties and protective features that may be central to M. tuberculosis pathogenesis. In addition, evidence indicates that lsr2 is an essential gene in M. tuberculosis. Because of its essentiality, Lsr2 may represent an excellent candidate as a drug target.

Effect of high temperature and the presence of stone-wales defects on the mechanical behavior of a single wall carbon nanotube under tension and compression.

On the basis of molecular dynamics simulation, a zigzag (7, 0) SWCNT is examined under axial tension and compression to observe its mechanical behavior and fracture pattern in the absence and presence of Stone-Wales (SW) defects coupled with the variation of temperature. A defect-free tube is subjected to tensile or compressive stresses at different temperatures. Then SW defects are introduced into it and stress is applied with the increase of temperature. The defective and defect-free tubes show different fracture patterns with increasing temperature showing significant changes in their mechanical properties. Compression of the tube also reveals interesting changes in its buckling behavior with variation of temperature and inclusion of defects.

Three-photon-induced four-photon absorption and nonlinear refraction in ZnO quantum dots.

Three-photon-induced four-photon absorption via excited-state absorption and self-defocusing nonlinear refraction are reported for the first time, to our knowledge, in ZnO quantum dots with average sizes of 2.0+/-0.1 nm with 1064 nm radiation from a Q-switched Nd:YAG laser at a peak intensity of 2.5 GW/cm(2). By employing the three-level two-step model, the experimental results can be explained quite satisfactorily.

Three-dimensional structure of the nicotinic acetylcholine receptor and location of the major associated 43-kD cytoskeletal protein, determined at 22 A by low dose electron microscopy and x-ray diffraction to 12.5 A.

The three-dimensional structure of the nicotinic acetylcholine receptor (AChR) from Torpedo californica, crystallized both before and after removal of associated proteins, most notably the main 43-kD cytoskeletal protein that interacts both with AChR and actin, is determined to a resolution of 22 A. This is the first structural analysis where the 43-kD protein has been removed from the sample before crystallization. Thus, it provides the most reliable assessment of what constitutes the structure of the minimal five subunit AChR complex, and, by comparison with the native membrane, of the location of the 43-kD cytoskeletal protein. Image reconstruction of two-dimensional crystals includes information from electron images of up to +/- 52 degrees tilted specimens of latticed AChR. Hybrid density maps that include x-ray diffraction perpendicular to the membrane to 12.5 A resolution were used and eliminate some of the distortions introduced in maps based only on electron microscopic analyses. Comparison of the difference Fourier density maps between AChR with its normal complement of associated proteins, and without them shows that the main density, assigned to the actin-binding 43-kD component is closely associated with the lipid bilayer as well as with the cytoplasmic domain of the AChR. It binds beside the AChR, not beneath it as suggested by others (C. Toyoshima and N. Unwin 1988. Nature [Lond.]. 336:237-240). There is good agreement between the volumes of density for structural components and expected volumes based on their molecular weight. Acetylcholine receptors aggregate in the absence of any cytoskeletal proteins, suggesting that the AChR alone is sufficient to encode and stabilize clustering, and perhaps to do so during synaptogenesis. The main 43-kD component may play a role in location and rate of association of AChR. We show that the disulfide bond that cross-links delta-delta chains of adjacent pentamers in about 80% of AChR, is not required to stabilize the lattice of AChR. Latticed tube structures are stable indefinitely. The lattices described here have 20% less volume of lipid than those originally obtained and characterized by J. Kistler and R. M. Stroud (1981. Proc. Natl. Acad. Sci. USA. 78:3678-3682), or those subsequently characterized by A. Brisson and P. N. T. Unwin (1984. J. Cell Biol. 99:1202-1211) and A. Brisson and P. N. T. Unwin (1985. Nature (Lond.). 315:474-477).

EDXRF analysis of municipal solid waste using (109)Cd source.

Elemental compositions of municipal solid waste (MSW) samples have been analyzed using the non-destructive energy dispersive X-ray fluorescence (EDXRF) technique. The samples were collected from three different dumping sites of urban and suburban areas of the city of Kolkata, West Bengal, India. The EDXRF spectrometer consisted of a (109)Cd radioactive source and a Si (Li) detector. To check the reliability of the system, NIST Standard Reference Material-1648 UPM had been analyzed and it was found that within the experimental errors, our results agree quite well with the certified and non-certified values. The elemental compositions of all the three MSW samples were subsequently estimated using the same procedure. The matrix effects were estimated following the emission-transmission method. It was observed that except Fe, all the elements from Ti to Pb show concentration levels higher by a factor of 2-7 than the ecological screening values where as in the case of Fe, this factor varies from 100 to 200.

A gene expression signature distinguishes innate response and resistance to proteasome inhibitors in multiple myeloma.

Extensive interindividual variation in response to chemotherapy is a major stumbling block in achieving desirable efficacy in the treatment of cancers, including multiple myeloma (MM). In this study, our goal was to develop a gene expression signature that predicts response specific to proteasome inhibitor (PI) treatment in MM. Using a well-characterized panel of human myeloma cell lines (HMCLs) representing the biological and genetic heterogeneity of MM, we created an in vitro chemosensitivity profile in response to treatment with the four PIs bortezomib, carfilzomib, ixazomib and oprozomib as single agents. Gene expression profiling was performed using next-generation high-throughput RNA-sequencing. Applying machine learning-based computational approaches including the supervised ensemble learning methods Random forest and Random survival forest, we identified a 42-gene expression signature that could not only distinguish good and poor PI response in the HMCL panel, but could also be successfully applied to four different clinical data sets on MM patients undergoing PI-based chemotherapy to distinguish between extraordinary (good and poor) outcomes. Our results demonstrate the use of in vitro modeling and machine learning-based approaches to establish predictive biomarkers of response and resistance to drugs that may serve to better direct myeloma patient treatment options.

In stent restenosis: bane of the stent era.

The long term outcome of stent implantation is affected by a process called in stent restenosis (ISR). Multiple contributory factors have been identified, but clear understanding of the overall underlying mechanism remains an enigma. ISR progresses through several different phases and involves numerous cellular and molecular constituents. Platelets and macrophages play a central role via vascular smooth muscle cell migration and proliferation in the intima to produce neointimal hyperplasia, which is pathognomic of ISR. Increased extracellular matrix formation appears to form the bulk of the neointimal hyperplasia tissue. Emerging evidence of the role of inflammatory cytokines and suppressors of cytokine signalling make this an exciting and novel field of antirestenosis research. Activation of Akt pathway triggered by mechanical stretch may also be a contributory factor to ISR formation. Prevention of ISR appears to be a multipronged attack as no therapeutic "magic bullet" exists to block all the processes in one go.

A comparison of stent-induced stenosis in coronary and peripheral arteries.

BACKGROUND AND OBJECTIVES: Restenosis is a complication of interventional procedures such as angioplasty and stenting, often limiting the success of these procedures. Knowledge regarding the relative behaviour of different arteries after these procedures is limited, despite the extensive use of different vascular models. Although the results from studies using different vessels are analysed to predict the behaviour of coronary arteries and other vasculature, direct controlled comparisons between different arteries are necessary for a better understanding of the differential response to restenosis. METHODS: This study examines the response to stenting in coronary and internal iliac arteries as characterised by intimal hyperplasia and restenosis. In a swine model of in-stent stenosis, coronary arteries exhibited higher levels of intimal hyperplasia and per cent stenosis than internal iliac arteries. RESULTS: After normalisation for injury score, coronary arteries were found to undergo 47% more intimal hyperplasia (p<0.05), whereas per cent stenosis normalised for injury score tended to be higher (p = 0.01). Other measurements reflecting post-stenting intimal hyperplasia (maximal intimal thickness, medial area) did not exhibit significant differences between the artery groups. CONCLUSIONS: These results show that coronary vessels are more prone to develop significant intimal hyperplasia and subsequent restenosis than internal iliac vessels. A better insight into how different arteries and arterial components behave is important in understanding and developing newer and better therapeutic measures for restenosis.

Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

Multiple myeloma (MM) is characterized by significant genetic diversity at subclonal levels that have a defining role in the heterogeneity of tumor progression, clinical aggressiveness and drug sensitivity. Although genome profiling studies have demonstrated heterogeneity in subclonal architecture that may ultimately lead to relapse, a gene expression-based prediction program that can identify, distinguish and quantify drug response in sub-populations within a bulk population of myeloma cells is lacking. In this study, we performed targeted transcriptome analysis on 528 pre-treatment single cells from 11 myeloma cell lines and 418 single cells from 8 drug-naïve MM patients, followed by intensive bioinformatics and statistical analysis for prediction of proteasome inhibitor sensitivity in individual cells. Using our previously reported drug response gene expression profile signature at the single-cell level, we developed an R Statistical analysis package available at https://github.com/bvnlabSCATTome, SCATTome (single-cell analysis of targeted transcriptome), that restructures the data obtained from Fluidigm single-cell quantitative real-time-PCR analysis run, filters missing data, performs scaling of filtered data, builds classification models and predicts drug response of individual cells based on targeted transcriptome using an assortment of machine learning methods. Application of SCATT should contribute to clinically relevant analysis of intratumor heterogeneity, and better inform drug choices based on subclonal cellular responses.

Chondroitin 4-sulfate: comparison of the structures of the potassium and sodium salts.

Analysis of the X-ray diffraction pattern from an oriented, polycrystalline fiber of a potassium chondroitin 4-sulfate proteoglycan shows that the polysaccharide chains have a left-handed 3-fold helical secondary structure stabilized by intra- and intermolecular hydrogen bonds. Two antiparallel chains pass through each trigonal unit cell, which has dimensions a = b = 1.385 nm, c = 2.776 nm and space group symmetry P3(2)21. The cations and water molecules in the crystals are not all periodic and only one potassium ion and four water molecules per disaccharide were located by difference Fourier methods. Sodium chondroitin 4-sulfate forms an analogous structure with polyanions of similar geometry. However, the packing arrangements in the two salts are quite different, presumably because of the different co-ordination preference of K+ and Na+. Thus the relatively small differences between these two cations are greatly amplified by the idiosyncratic polymer networks they promote.

Hyaluronic acid: molecular conformation and interactions in the tetragonal form of the potassium salt containing extended chains.

X-ray diffraction data were used to determine the detailed crystal structure of a tetragonal form of potassium hyaluronate containing relatively extended 4-fold helical chains (rise per disaccharide h = 0.95 nm). The polysaccharide chains are left-handed (4(3] helices. Two antiparallel chains pack in a tetragonal unit cell (a = b = 0.996 nm, c = 3.788 nm) with P4(3)2(1)2 space group symmetry. The chain conformations are stabilized intramolecularly by O4-O5 hydrogen bonds across the beta(1 leads to 3) linkage and by a pair of intermolecular hydrogen bonds per disaccharide between adjacent antiparallel chains. Fourier difference synthesis revealed one potassium ion and two water molecules per disaccharide. Six polyanion oxygen atoms from three neighboring chains together with one of these water molecules form the co-ordination polyhedra. Further stability is brought about through inter- and intrachain water bridges involving both water molecules. The probable reason for the stability of this extended allomorph is discussed in terms of the preferred co-ordination geometry of the potassium ion.

Hyaluronic acid double helix.

The hyaluronic acid double helix, contrary to an earlier visualization, probably incorporates extensively hydrogen-bonded chains and is pinned together by carboxyl-carboxylate hydrogen bonds and water bridges. Transient interactions between stiffened chain segments provided by the formation of double-helical loops could give rise to the characteristic viscoelastic properties of hyaluronic acid solutions.

Three-dimensional fold of the human AQP1 water channel determined at 4 A resolution by electron crystallography of two-dimensional crystals embedded in ice.

Here, we present a three-dimensional (3D) density map of deglycosylated, human erythrocyte aquaporin 1 (AQP1) determined at 4 A resolution in plane and approximately 7 A resolution perpendicular to the bilayer. The map was calculated by analyzing images and electron diffraction patterns recorded from tilted (up to 60 degrees ), ice-embedded, frozen-hydrated 2D crystals of AQP1 in lipid bilayer membranes. This map significantly extends the findings related to the folding of the AQP1 polypeptide chain determined by us at a lower, 7 A by approximately 20 A, resolution. The solvent-accessible volume within a monomer has a vestibular architecture, with a narrow, approximately 6.5 A diameter constriction near the center of the bilayer, where the location of the water-selective channel is postulated to exist. The clearly resolved densities for the transmembrane helices display the protrusions expected for bulky side-chains. The density in the interior of the helix barrel (putative NPA box region) is better resolved compared to our previous map, suggesting clearer linkage to some of the helices, and it may harbor short stretches of alpha-helix. At the bilayer extremities, densities for some of the inter-helix hydrophilic loops are visible. Consistent with these observed inter-helix connections, possible models for the threading of the AQP1 polypeptide chain are presented. A preferred model is deduced that agrees with the putative locations of a group of aromatic residues in the amino acid sequence and in the 3D density map.

Hyaluronic acid: molecular conformations and interactions in the orthorhombic and tetragonal forms containing sinuous chains.

The conformation, packing and probable mode of cation binding have been determined for compact potassium hyaluronate chains (average rise per disaccharide h = 0.89 nm) organized in an orthorhombic unit cell (a = 1.173 nm, b = 0.925 nm, c = 3.542 nm). The space group symmetry is P2(1)2(1)2(1) and the unit cell contains two antiparallel polysaccharide chains that are disturbed 4(3) helices. Each chain is stabilized intramolecularly by four hydrogen bonds and between adjacent antiparallel chains there are two intermolecular hydrogen bonds per crystallographic tetrasaccharide repeat. Fourier difference synthesis revealed two potassium ions and two water molecules in each asymmetric unit. Both potassium ions show octahedral co-ordination geometries and link adjacent antiparallel polysaccharide chains. The water molecules provide further intermolecular association through water bridges. A comparison of this potassium hyaluronate structure with the orthorhombic and tetragonal sodium hyaluronate structures containing similar compact hyaluronate chains revealed that the apparently isomorphous orthorhombic sodium and potassium salts did not have the same packing arrangements. The relative orientations of the sinuous hyaluronate chains in the sodium and potassium salts are about 90 degrees apart. The locations of the cations and hence the coordination schemes of K+ and Na+ are therefore very different. These analyses have delineated, for the first time, how hyaluronate chains can respond differentially to two different monovalent cations.

Dermatan sulfate: molecular conformations and interactions in the condensed state.

The molecular conformations and manner of aggregation has been determined for three allomorphs of the connective tissue polysaccharide dermatan sulfate by analysis of X-ray diffraction from oriented, polycrystalline fibers of sodium salts. One allomorph is unique among glycosaminoglycans in having right-handed (8(3)) helical chains. Two such chains pack antiparallel in a tetragonal unit cell (a = b = 1.267 nm, c = 7.353 nm) with P4(3)2(1)2 space group symmetry. The 3(2) chains of the second allomorph are organized in a trigonal unit cell (a = b = 1.460 nm, c = 2.823 nm, space group symmetry P3(2)21) containing two left-handed antiparallel polysaccharide molecules. (The chirality of this allomorph has been assumed to be the same as in other 3-fold glycosaminoglycan helices, since discrimination between 3(1) and 3(2) symmetries was found not to be possible.) The archiral 2(1) helices of the third allomorph, pack probably in an orthorhombic unit cell (a = 1.151 nm, b = 1.065 nm, c = 1.878 nm, space group symmetry P2(1)2(1)2(1)) that contains again two antiparallel polymer molecules. Each dermatan sulfate chain is stabilized intramolecularly by O3-O5 hydrogen bonds across the beta (1 leads to 4) linkage. There are two intermolecular hydrogen bonds per tetrasaccharide repeat in the tetragonal structure and two per disaccharide in the trigonal structure. Fourier difference syntheses indicated equivalents of four sodium ions per tetrasaccharide and two sodium ions per disaccharide in the tetragonal and trigonal structures, respectively. The cations are either partially or fully hydrated and link dermatan sulfate chains either intra- or intermolecularly by involving besides other polyanion oxygen atoms, carboxylate and sulfate oxygen atoms. The probable mode of packing in the orthorhombic structure indicates a pair of hydrogen bonds between adjacent antiparallel polysaccharide chains and suggests plausible cationic sites in the unit cell.

Comparing 2-year outcomes of anterior cruciate ligament reconstruction using either patella-tendon or semitendinosus-tendon autografts: a non-randomised prospective study.

PURPOSE: To compare the results of anterior cruciate ligament (ACL) reconstructions using either a patella-tendon autograft or a semitendinosus-tendon autograft. METHODS: Based on surgeon experience and preference, 68 patients underwent ACL reconstruction using either a quadruple-strand semitendinosus autograft (n = 34) or a central one-third bone-patella tendon-bone autograft (n = 34). Each patient was assessed preoperatively and postoperatively at 3, 6, and 24 months using the International Knee Documentation Committee (IKDC) knee score, Biodex muscle strength and endurance testing, and the KT1000 instrumented arthrometer test of knee laxity to anterior translation. All assessments at the 2-year follow-up were performed by the same physician and physiotherapist. RESULTS: While ACL reconstruction improved knee stability and IKDC knee scores significantly, there was no statistically significant difference between semitendinosus- and patella-tendon autograft reconstructions in terms of long-term knee score or laxity to anterior translation. Semitendinosus graft reconstruction was associated with less donor-site morbidity and hamstring weakness. Meniscectomy was associated with poorer long-term knee scores. CONCLUSION: ACL reconstruction is associated with a significantly better IKDC knee score and laxity measurement at 2-year follow-up. However, we were unable to demonstrate a significantly better long-term outcome in knee score or laxity to anterior translation with either a patella-tendon autograft or a semitendinosus-tendon autograft.