Value of serial ultrasound imaging in conservative management of epididymo-cutaneous fistula in a person with cervical spinal cord injury.

Epididymo-cutaneous fistula was seen in a person with cervical spinal cord injury and neuropathic bladder. This patient developed left epididymitis; then he formed an abscess superficial to the tail of the epididymis, which burst open to the skin discharging pus; subsequently, this progressed to epididymo-cutaneous fistula. A few drops of urine would leak through the fistula. The carers kept a dressing over the fistula to collect the small amount of urine leak and changed the dressing daily. This patient's carers squeezed any subcutaneous collection and drained the pus through the fistula. Serial ultrasound imaging of the scrotum was performed to guide the clinical management: (1) any subcutaneous abscess detected by the ultrasound scan was drained promptly; (2) ultrasound scans confirmed absence of any pathology in the testis; (3) the course of the disease was monitored as chronic epididymitis with echogenic debris in epididymal tail progressed to development of epididymo-cutaneous fistula and later to a chronic fistula with a matured tract. The serial scans revealed thickened tail of the left epididymis with heterogenous echo texture with no abscess formation, which encouraged the continuation of conservative management over a 5-year period while maintaining good quality of life. At the last follow-up in June 2022, leakage of urine from the epididymo-cutaneous fistula was observed very infrequently (once a month).

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.

We describe a graphical system for automatically generating multiple 2D diagrams of ligand-protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond interaction patterns and hydrophobic contacts between the ligand(s) and the main-chain or side-chain elements of the protein. The system is able to plot, in the same orientation, related sets of ligand-protein interactions. This facilitates popular research tasks, such as analyzing a series of small molecules binding to the same protein target, a single ligand binding to homologous proteins, or the completely general case where both protein and ligand change.

Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19.

Effective agents to treat coronavirus infection are urgently required, not only to treat COVID-19, but to prepare for future outbreaks. Repurposed anti-virals such as remdesivir and human anti-inflammatories such as barcitinib have received emergency approval but their overall benefits remain unclear. Vaccines are the most promising prospect for COVID-19, but will need to be redeveloped for any future coronavirus outbreak. Protecting against future outbreaks requires the identification of targets that are conserved between coronavirus strains and amenable to drug discovery. Two such targets are the main protease (Mpro) and the papain-like protease (PLpro) which are essential for the coronavirus replication cycle. We describe the discovery of two non-antiviral therapeutic agents, the caspase-1 inhibitor SDZ 224015 and Tarloxotinib that target Mpro and PLpro, respectively. These were identified through extensive experimental screens of the drug repurposing ReFRAME library of 12,000 therapeutic agents. The caspase-1 inhibitor SDZ 224015, was found to be a potent irreversible inhibitor of Mpro (IC50 30 nM) while Tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor, is a sub micromolar inhibitor of PLpro (IC50 300 nM, Ki 200 nM) and is the first reported PLpro inhibitor with drug-like properties. SDZ 224015 and Tarloxotinib have both undergone safety evaluation in humans and hence are candidates for COVID-19 clinical evaluation.

A randomized controlled trial of real versus sham acupuncture for basal thumb joint arthritis.

We report a single-blinded randomized controlled trial comparing acupuncture to sham (non-penetrating) needling for relief of symptoms of basal thumb joint arthritis. Seventy acupuncture naive patients with basal thumb joint arthritis were randomized to receive true acupuncture or sham needling with 35 patients in each arm. Blinded baseline and post-treatment assessments included visual analogue pain scores for different grips and movement. Function was assessed using the Nelson questionnaire. Both groups showed statistically and clinically significant improvements in pain at week one post-treatment compared with baseline, but there was no difference between the treatment groups. The pain relief was comparable with published data for some standard treatments. Acupuncture did not perform better than sham needling in this study, indicating that pain relief may have been achieved through non-specific mechanisms. Level of evidence: I.

Getting the most from PSI-BLAST.

Most biologists now conduct sequence searches as a matter of course. But how do we know that a relationship predicted by a homology search is a true, rather than false, hit with the same score? Many biologists design their own experiments with exquisite care yet still assume that results from programs with more than 20 adjustable parameters are 100% reliable. This article explains some of the key steps in getting the most from PSI-Blast, one of the most popular and powerful homology search programs currently available.

Inferring function using patterns of native disorder in proteins.

Natively unstructured regions are a common feature of eukaryotic proteomes. Between 30% and 60% of proteins are predicted to contain long stretches of disordered residues, and not only have many of these regions been confirmed experimentally, but they have also been found to be essential for protein function. In this study, we directly address the potential contribution of protein disorder in predicting protein function using standard Gene Ontology (GO) categories. Initially we analyse the occurrence of protein disorder in the human proteome and report ontology categories that are enriched in disordered proteins. Pattern analysis of the distributions of disordered regions in human sequences demonstrated that the functions of intrinsically disordered proteins are both length- and position-dependent. These dependencies were then encoded in feature vectors to quantify the contribution of disorder in human protein function prediction using Support Vector Machine classifiers. The prediction accuracies of 26 GO categories relating to signalling and molecular recognition are improved using the disorder features. The most significant improvements were observed for kinase, phosphorylation, growth factor, and helicase categories. Furthermore, we provide predicted GO term assignments using these classifiers for a set of unannotated and orphan human proteins. In this study, the importance of capturing protein disorder information and its value in function prediction is demonstrated. The GO category classifiers generated can be used to provide more reliable predictions and further insights into the behaviour of orphan and unannotated proteins.

abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction.

abYsis is a web-based antibody research system that includes an integrated database of antibody sequence and structure data. The system can be interrogated in numerous ways-from simple text and sequence searches to sophisticated queries that apply 3D structural constraints. The publicly available version includes pre-analyzed sequence data from the European Molecular Biology Laboratory European Nucleotide Archive (EMBL-ENA) and Kabat as well as structure data from the Protein Data Bank. A researcher's own sequences can also be analyzed through the web interface. A defining characteristic of abYsis is that the sequences are automatically numbered with a series of popular schemes such as Kabat and Chothia and then annotated with key information such as complementarity-determining regions and potential post-translational modifications. A unique aspect of abYsis is a set of residue frequency tables for each position in an antibody, allowing "unusual residues" (those rarely seen at a particular position) to be highlighted and decisions to be made on which mutations may be acceptable. This is especially useful when comparing antibodies from different species. abYsis is useful for any researcher specializing in antibody engineering, especially those developing antibodies as drugs. abYsis is available at www.abysis.org.

The complement of enzymatic sets in different species.

We present here a comprehensive analysis of the complement of enzymes in a large variety of species. As enzymes are a relatively conserved group there are several classification systems available that are common to all species and link a protein sequence to an enzymatic function. Enzymes are therefore an ideal functional group to study the relationship between sequence expansion, functional divergence and phenotypic changes. By using information retrieved from the well annotated SWISS-PROT database together with sequence information from a variety of fully sequenced genomes and information from the EC functional scheme we have aimed here to estimate the fraction of enzymes in genomes, to determine the extent of their functional redundancy in different domains of life and to identify functional innovations and lineage specific expansions in the metazoa lineage. We found that prokaryote and eukaryote species differ both in the fraction of enzymes in their genomes and in the pattern of expansion of their enzymatic sets. We observe an increase in functional redundancy accompanying an increase in species complexity. A quantitative assessment was performed in order to determine the degree of functional redundancy in different species. Finally, we report a massive expansion in the number of mammalian enzymes involved in signalling and degradation.

SCOPEC: a database of protein catalytic domains.

MOTIVATION: Domains are the units of protein structure, function and evolution. It is therefore essential to utilize knowledge of domains when studying the evolution of function, or when assigning function to genome sequence data. For this purpose, we have developed a database of catalytic domains, SCOPEC, by combining structural domain information from SCOP, full-length sequence information from Swiss-Prot, and verified functional information from the Enzyme Classification (EC) database. Two major problems need to be overcome to create a database of domain-function relationships; (1) for sequences, EC numbers are typically assigned to whole sequences rather than the functional unit, and (2) The Protein Data Bank (PDB) structures elucidated from a larger multi-domain protein will often have EC annotation although the relevant catalytic domain may lie elsewhere. RESULTS: SCOPEC entries have high quality enzyme assignments; having passed both computational and manual checks. SCOPEC currently contains entries for 75% of all EC annotations in the PDB. Overall, EC number is fairly well conserved within a superfamily, even when the proteins are distantly related. Initial analysis is encouraging; suggesting that there is a 50:50 chance of conserved function in distant homologues first detected by a third iteration PSI-BLAST search. Therefore, we envisage that a knowledge-based approach to function assignment using the domain-EC relationships in SCOPEC will gain a marked improvement over this base line. AVAILABILITY: The SCOPEC database is a valuable resource in the analysis and prediction of protein structure and function. It can be obtained or queried at our website http://www.enzome.com

Prioritizing the proteome: identifying pharmaceutically relevant targets.

Considerable attention is now being placed on prioritizing the proteome as the point of delivery for genomic information. Some of the challenges faced in prioritizing efforts from a pharmaceutical perspective, when presented with an incomplete proteome picture, are described. Examples of pharmaceutically relevant proteins are used to illustrate an informatics-based analysis of the proteome using knowledge of known drug targets. We show how results can be maximized by linking informatics approaches to experimental techniques and describe methods that can be used for prioritization within unprecedented protein families using, for example, single nucleotide polymorphism data and knowledge of disease pathways.

Elastic intramedullary nailing in unstable fractures of the paediatric tibial diaphysis: a systematic review.

PURPOSE: The majority of paediatric tibial fractures can be managed conservatively. However, there is a small but significant group of patients that require surgical intervention for several indications, most notably, unstable fractures. There are various surgical options, each with its own advantages and risks. This review establishes the current available evidence for the use of elastic intramedullary nails in this group. METHODS: A systematic review of the currently available literature was performed. The relevant studies were then critically appraised. RESULTS: Seven applicable retrospective case series were identified, with the outcomes from a total of 210 (range 16-60) patients considered. The mean time to union ranged from 7 to 21 weeks. Reported complications included small numbers each of delayed union, non-union, malunion, leg length discrepancy and infection. CONCLUSIONS: There is only a small body of evidence currently published on this topic. The evidence published so far concludes that elastic intramedullary nailing represents an effective and reliable method to treat an unstable fracture of the tibial diaphysis in the paediatric patient, where conservative management is not appropriate.

Pediatric advanced appendicitis: open versus laparoscopic approach.

PURPOSE: Optimal surgical approach for advanced pediatric appendicectomy remains controversial. We compare the open versus the laparoscopic approach. METHODS: Retrospective case notes review of children operated on for advanced appendicitis between January 2005 and July 2006 was undertaken for length of hospital stay, operating time, wound complications, need for further surgery, and hospital readmission. RESULTS: Forty children were included, 17 were treated with open approach and 23 with laparoscopic approach. There was no conversion from laparoscopic to open approach. Overall complication rate, length of hospital stay, and need for further surgery were similar in both groups. The mean operative time was longer in the laparoscopic group. Wound complications occurred more in the open group. Readmission for gastrointestinal obstruction was noted in the laparoscopic group. CONCLUSIONS: Laparoscopic approach is safe for advanced appendicitis in children. The outcomes are comparable in both study groups.

Acute radial artery ischemia following therapeutic steroid injection.

Intra-arterial corticosteroid injection at the wrist can have devastating consequences. Anatomic arterial variation of the hand can lead to atypical presentation. A careful history and examination, with appropriate investigations, can lead to an accurate diagnosis in such difficult cases.

Early blood profiles of virus infection in a monkey model for Lassa fever.

Acute arenavirus disease in primates, like Lassa hemorrhagic fever in humans, begins with flu-like symptoms and leads to death approximately 2 weeks after infection. Our goal was to identify molecular changes in blood that are related to disease progression. Rhesus macaques (Macaca mulatta) infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV) provide a model for Lassa virus infection of humans. Blood samples taken before and during the course of infection were used to monitor gene expression changes that paralleled disease onset. Changes in blood showed major disruptions in eicosanoid, immune response, and hormone response pathways. Approximately 12% of host genes alter their expression after LCMV infection, and a subset of these genes can discriminate between virulent and non-virulent LCMV infection. Major transcription changes have been given preliminary confirmation by quantitative PCR and protein studies and will be valuable candidates for future validation as biomarkers for arenavirus disease.

Effective function annotation through catalytic residue conservation.

Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology searches, by providing an opportunity to transfer functional information between related proteins, have become the de facto way to address this. Although a single, well annotated, close relationship will often facilitate sufficient annotation, this situation is not always the case, particularly if mutations are present in important functional residues. When only distant relationships are available, the transfer of function information is more tenuous, and the likelihood of encountering several well annotated proteins with different functions is increased. The consequence for a researcher is a range of candidate functions with little way of knowing which, if any, are correct. Here, we address the problem directly by introducing a computational approach to accurately identify and segregate related proteins into those with a functional similarity and those where function differs. This approach should find a wide range of applications, including the interpretation of genomics/proteomics data and the prioritization of targets for high-throughput structure determination. The method is generic, but here we concentrate on enzymes and apply high-quality catalytic site data. In addition to providing a series of comprehensive benchmarks to show the overall performance of our approach, we illustrate its utility with specific examples that include the correct identification of haptoglobin as a nonenzymatic relative of trypsin, discrimination of acid-d-amino acid ligases from a much larger ligase pool, and the successful annotation of BioH, a structural genomics target.

Is 'big biology' a commercial enterprise?

Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, in the USA, Europe and Japan, and highlights some issues to be considered when deciding whether particular research belongs in a company rather than an academic setting.

GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures.

GENIUS II is an automated database system in which open reading frames (ORFs) in complete genomes are assigned to known protein three-dimensional (3D) structures. The system uses the multiple intermediate sequence search method in which query and target sequences are linked by intermediate sequences gathered by PSI-BLAST search. By applying the system to 129 complete genomes, 43.8% on average of the ORFs in the genomes were assigned to known 3D structures and the results are available for free at GENIUS II web site.

Application of high-throughput computing in bioinformatics.

We describe the challenges faced when developing a Linux/PC-based cluster to apply bioinformatics algorithms to the rapidly increasing raw genomics data available. The calculations, which take around two months to complete, result in a powerful resource that can be used for data mining--most obviously for the human genome. Our current infrastructure consists of a 1314 node cluster with 1734 processors supporting both production and research. This paper highlights the problems in achieving high data throughput with such systems and shows that raw computer power is only one component of a complex problem.