Five computational developability guidelines for therapeutic antibody profiling.

Therapeutic mAbs must not only bind to their target but must also be free from "developability issues" such as poor stability or high levels of aggregation. While small-molecule drug discovery benefits from Lipinski's rule of five to guide the selection of molecules with appropriate biophysical properties, there is currently no in silico analog for antibody design. Here, we model the variable domain structures of a large set of post-phase-I clinical-stage antibody therapeutics (CSTs) and calculate in silico metrics to estimate their typical properties. In each case, we contextualize the CST distribution against a snapshot of the human antibody gene repertoire. We describe guideline values for five metrics thought to be implicated in poor developability: the total length of the complementarity-determining regions (CDRs), the extent and magnitude of surface hydrophobicity, positive charge and negative charge in the CDRs, and asymmetry in the net heavy- and light-chain surface charges. The guideline cutoffs for each property were derived from the values seen in CSTs, and a flagging system is proposed to identify nonconforming candidates. On two mAb drug discovery sets, we were able to selectively highlight sequences with developability issues. We make available the Therapeutic Antibody Profiler (TAP), a computational tool that builds downloadable homology models of variable domain sequences, tests them against our five developability guidelines, and reports potential sequence liabilities and canonical forms. TAP is freely available at opig.stats.ox.ac.uk/webapps/sabdab-sabpred/TAP.php.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.

SAbPred: a structure-based antibody prediction server.

SAbPred is a server that makes predictions of the properties of antibodies focusing on their structures. Antibody informatics tools can help improve our understanding of immune responses to disease and aid in the design and engineering of therapeutic molecules. SAbPred is a single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens. The server is available at http://opig.stats.ox.ac.uk/webapps/sabpred.

Toward monitoring and estimating the size of the HFO-contaminated seabed around a shipwreck using MBES backscatter data.

Despite a progressive reduction of oil spills caused by the activity of maritime transportation, the latent sources of pollution still exist. Although the harmful impact of heavy fuel oil (HFO) on the marine environment is widely known, many shipwrecks cause contamination of the surrounding areas. In this paper, an approach to monitor the area of the HFO spill around a shipwreck is made using a bottom backscattering strength (BBS) obtained by a multibeam echosounder (MBES). As a case study, the s/s Stuttgart wreck located in the Gulf of Gdansk (Poland) is verified. Two different measurement campaigns have been carried out in shallow waters using low (190 kHz) and high (420 kHz) MBES frequency. The results indicate that the polluted area around s/s Stuttgart was estimated at 49.1 ha, which is around 18.3% more in comparison to the geological surveys made four years earlier.

Structurally Mapping Antibody Repertoires.

Every human possesses millions of distinct antibodies. It is now possible to analyze this diversity via next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell receptors that are indicative of the antibody repertoire. In this paper, we enrich these large-scale sequence datasets with structural information. Enriching a sequence with its structural data allows better approximation of many vital features, such as its binding site and specificity. Here, we describe the structural annotation of antibodies pipeline that maps the outputs of large Ig-seq experiments to known antibody structures. We demonstrate the viability of our protocol on five separate Ig-seq datasets covering ca. 35 m unique amino acid sequences from ca. 600 individuals. Despite the great theoretical diversity of antibodies, we find that the majority of sequences coming from such studies can be reliably mapped to an existing structure.

Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania.

The indigenous populations of the South Pacific experience a high burden of rheumatic heart disease (RHD). Here we report a genome-wide association study (GWAS) of RHD susceptibility in 2,852 individuals recruited in eight Oceanian countries. Stratifying by ancestry, we analysed genotyped and imputed variants in Melanesians (607 cases and 1,229 controls) before follow-up of suggestive loci in three further ancestral groups: Polynesians, South Asians and Mixed or other populations (totalling 399 cases and 617 controls). We identify a novel susceptibility signal in the immunoglobulin heavy chain (IGH) locus centring on a haplotype of nonsynonymous variants in the IGHV4-61 gene segment corresponding to the IGHV4-61*02 allele. We show each copy of IGHV4-61*02 is associated with a 1.4-fold increase in the risk of RHD (odds ratio 1.43, 95% confidence intervals 1.27-1.61, P=4.1 × 10-9). These findings provide new insight into the role of germline variation in the IGH locus in disease susceptibility.

Loblolly pine and slash pine responses to acute aluminum and acid exposures.

In response to concerns about aluminum and HCl exposure associated with rocket motor testing and launches, survival and growth of full-sib families of loblolly pine (Pinus taeda L.) and slash pine (Pinus elliottii Engelm.) were evaluated in a nursery bed experiment. Each species was exposed to a single soil application of aluminum chloride (0.33 M AlCl(3), pH 2.5), hydrochloric acid (0.39 M HCl, pH 0.6) or water, with or without mycorrhizal inoculation with Pisolithus tinctorius (Coker and Couch). After 20 weeks without inoculation, survival in AlCl(3) and HCl treatments averaged 52% for loblolly pine and 72% for slash pine. Inoculation improved survival of loblolly pine, receiving HCl from 49 to 73%, and of those receiving AlCl3, from 55 to 90%. Inoculation also resulted in improved survival and growth of individual families in AlCl(3), but not in HCl treatments. Results illustrate the relative resistance of both pine species to the acute treatments supplied, the improvement in resistance associated with mycorrhizal inoculation and the importance of field testing, following hydroponic screening, to verify the resistance to soil-supplied stresses.

Millimeter scale variations in the isotopic composition of vein sulphide minerals in the Kupferschiefer deposits, Lubin area, SW Poland.

A slice of black shale rock cut by various metal sulphide veins of different generations from the Kupferschiefer deposits of Lubin, Poland was subjected to bombardment in a Laser Microprobe Combustion Reactor to produce SO2 for S-isotope analyses. The delta34S values ranged from-22 to-29 per thousand consistent with previous findings using conventional IRMS and attributable to primary generation of H2S by bacterial sulphate reduction. Systematic trends in delta34S values of a few per mil over distances of the order of mm attest to low temperatures of mineralization with accompanying change in the isotope composition of the fluids due to kinetic or equilibrium isotope fractionation.

Length-independent structural similarities enrich the antibody CDR canonical class model.

Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach. To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ∼20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.

Aluminum fractions in root tips of slash pine and loblolly pine families differing in Al resistance.

Aluminum (Al) distribution among several cellular fractions was investigated in root tips of seedlings of one Al-resistant and one Al-sensitive family of slash pine (Pinus elliottii Engelm.) and loblolly pine (Pinus taeda L.) grown in nutrient solution containing 100 microM AlCl3 (pH 4) for 167 h. Aluminum present in 5-mm-long root tips was fractionated into cell-wall-labile (desorbed in 0.5 mM citric acid), cell-wall-bound (retained after filtering disrupted cells through 20-microm mesh) and symplasmic (filtrate following cell disruption) fractions. When averaged across both species, 12% of Al absorbed by root tips appeared in the symplasmic fraction and 88% in the apoplasmic fraction (55% as cell-wall-labile, and 33% as cell-wall-bound). On a fresh mass basis, total Al in root tips was lower in loblolly pine than in slash pine, lower in the Al-resistant slash pine family than in the Al-sensitive slash pine family, and lower in the Al-resistant families than in the Al-sensitive families across species. Although the data support the hypothesis that Al-resistant plants limit Al uptake to root apices, they do not exclude other mechanisms of Al resistance. Differential Al resistance between the species and between slash pine families may also be associated with the size of the total non-labile and cell-wall-labile Al fractions, respectively. We were unable to identify the basis for differential Al resistance in loblolly pine.

[Aspiration thrombectomy during percutaneous coronary intervention in a patient with cardiogenic shock caused by left main occlusion]. / Zastosowanie trombektomii aspiracyjneju pacjenta we wstrzasie kardiogennym z niedroznoscia pnia lewej tetnicy wiencowej.

CASE STUDY: 56-year-old male patient in cardiogenic shock with a large thrombus in LM, succesfully treated by PTCA with aspiration thrombectomy. FOLLOW-UP: 9 months control angiography.

Temperature controller for thermal ionization mass spectrometry.

We describe the use of a simple voltage stabilizer that controls the filament temperature (T(f)) in the ion source of a thermal ionization mass spectrometer. The filament voltage (V(f)) is measured by means of a separate pair of wires connected inside of the ion source in parallel to the wires supplying power. It has been demonstrated that V(f) is directly proportional to T(f) in a wide range of filament temperature. The T(f) value is solely controlled by the reference voltage (V(r)) that can be manually selected from a voltage divider or by means of a computer. Digital signals from the computer in the form of a series of pulses are transmitted opto-electronically and subsequently converted to analog signals. The temperature controller described here was successfully applied for analysis of potassium concentration by the isotope dilution method.