PSICalc: a novel approach to identifying and ranking critical non-proximal interdependencies within the overall protein structure.

Motivation: AlphaFold has been a major advance in predicting protein structure, but still leaves the problem of determining which sub-molecular components of a protein are essential for it to carry out its function within the cell. Direct coupling analysis predicts two- and three-amino acid contacts, but there may be essential interdependencies that are not proximal within the 3D structure. The problem to be addressed is to design a computational method that locates and ranks essential non-proximal interdependencies within a protein involving five or more amino acids, using large, multiple sequence alignments (MSAs) for both globular and intrinsically unstructured proteins. Results: We developed PSICalc (Protein Subdomain Interdependency Calculator), a laptop-friendly, pattern-discovery, bioinformatics software tool that analyzes large MSAs for both structured and unstructured proteins, locates both proximal and non-proximal inter-dependent sites, and clusters them into pairwise (second order), third-order and higher-order clusters using a k-modes approach, and provides ranked results within minutes. To aid in visualizing these interdependencies, we developed a graphical user interface that displays these subdomain relationships as a polytree graph. To demonstrate, we provide examples of both proximal and non-proximal interdependencies documented for eukaryotic topoisomerase II including between the unstructured C-terminal domain and the N-terminal domain. Availability and implementation: https://github.com/jdeweeselab/psicalc-package. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Clarifying the Mechanism of Copper(II) α-(N)-Heterocyclic Thiosemicarbazone Complexes on DNA Topoisomerase IIα and IIß.

Topoisomerase II is a nuclear enzyme involved in the maintenance of DNA and is an effective anticancer drug target. However, several clinical topoisomerase II-targeted agents display significant off-target toxicities and adverse events. Thus, it is important to continue characterizing compounds with activity against topoisomerase II. We previously analyzed α-(N)-heterocyclic thiosemicarbazone copper(II) complexes against human topoisomerase IIα (TOP2A), but humans also express topoisomerase IIß (TOP2B), which has distinct functional roles. Therefore, we examined two α-(N)-heterocyclic thiosemicarbazone copper [Cu(II)] complexes for activity against TOP2B in a purified system. The Cu(II) complexes, Cu(APY-ETSC)Cl and Cu(BZP-ETSC)Cl, were examined using plasmid DNA cleavage, supercoiled DNA relaxation, enzyme inactivation, protein cross-linking, DNA ligation, and ATP hydrolysis assays with TOP2B to determine whether these compounds act similarly against both enzymes. Both of the Cu(II) thiosemicarbazone (Cu-TSC) complexes we tested disrupted the function of TOP2B in a way similar to the effect on TOP2A. In particular, TOP2B DNA cleavage activity is increased in the presence of these compounds, while the relaxation and ATPase activities are inhibited. Further, both Cu-TSCs stabilize the N-terminal DNA clamp of TOP2A and TOP2B and rapidly inactivate TOP2B when the compounds are present before DNA. Our data provide evidence that the Cu-TSC complexes we tested utilize a similar mechanism against both isoforms of the enzyme. This mechanism may involve interaction with the ATPase domain of TOP2A and TOP2B outside of the ATP binding pocket. Additionally, these data support a model of TOP2 function where the ATPase domain communicates with the DNA cleavage/ligation domain.

Structural and Metal Ion Effects on Human Topoisomerase IIα Inhibition by α-(N)-Heterocyclic Thiosemicarbazones.

Our previous research has shown that α-(N)-heterocyclic thiosemicarbazone (TSC) metal complexes inhibit human topoisomerase IIα (TopoIIα), while the ligands without metals do not. To find out the structural elements of TSC that are important for inhibiting TopoIIα, we have synthesized two series of α-(N)-heterocyclic TSCs with various substrate ring segments, side chain substitutions, and metal ions, and we have examined their activities in TopoIIα-mediated plasmid DNA relaxation and cleavage assays. Our goal is to explore the structure-activity relationship of α-(N)-heterocyclic TSCs and their effect on TopoIIα. Our data suggest that, similar to Cu(II)-TSCs, Pd(II)-TSC complexes inhibit plasmid DNA relaxation mediated by TopoIIα. In TopoIIα-mediated plasmid DNA cleavage assays, the Cu(II)-TSC complexes induce higher levels of DNA cleavage than their Pd(II) counterparts. The Cu(II)-TSC complexes with methyl, ethyl, and tert-butyl substitutions are slightly more effective than those with benzyl and phenyl groups. The α-(N)-heterocyclic ring substrates of the TSCs, including benzoylpyridine, acetylpyridine, and acetylthiazole, do not exhibit a significant difference in TopoIIα-mediated DNA cleavage. Our data suggest that the metal ion of TSC complexes plays a predominant role in inhibition of TopoIIα, the side chain substitution of the terminal nitrogen plays a secondary role, while the substrate ring segment has the least effect. Our molecular modeling data support the biochemical data, which together provide a mechanism by which Cu(II)-TSC complexes stabilize TopoIIα-mediated cleavage complexes.

Geospatial blockchain: promises, challenges, and scenarios in health and healthcare.

A PubMed query run in June 2018 using the keyword 'blockchain' retrieved 40 indexed papers, a reflection of the growing interest in blockchain among the medical and healthcare research and practice communities. Blockchain's foundations of decentralisation, cryptographic security and immutability make it a strong contender in reshaping the healthcare landscape worldwide. Blockchain solutions are currently being explored for: (1) securing patient and provider identities; (2) managing pharmaceutical and medical device supply chains; (3) clinical research and data monetisation; (4) medical fraud detection; (5) public health surveillance; (6) enabling truly public and open geo-tagged data; (7) powering many Internet of Things-connected autonomous devices, wearables, drones and vehicles, via the distributed peer-to-peer apps they run, to deliver the full vision of smart healthy cities and regions; and (8) blockchain-enabled augmented reality in crisis mapping and recovery scenarios, including mechanisms for validating, crediting and rewarding crowdsourced geo-tagged data, among other emerging use cases. Geospatially-enabled blockchain solutions exist today that use a crypto-spatial coordinate system to add an immutable spatial context that regular blockchains lack. These geospatial blockchains do not just record an entry's specific time, but also require and validate its associated proof of location, allowing accurate spatiotemporal mapping of physical world events. Blockchain and distributed ledger technology face similar challenges as any other technology threatening to disintermediate legacy processes and commercial interests, namely the challenges of blockchain interoperability, security and privacy, as well as the need to find suitable and sustainable business models of implementation. Nevertheless, we expect blockchain technologies to get increasingly powerful and robust, as they become coupled with artificial intelligence (AI) in various real-word healthcare solutions involving AI-mediated data exchange on blockchains.

HU-331 and Oxidized Cannabidiol Act as Inhibitors of Human Topoisomerase IIα and ß.

Topoisomerase II is a critical enzyme in replication, transcription, and the regulation of chromatin topology. Several anticancer agents target topoisomerases in order to disrupt cell growth. Cannabidiol is a major non-euphoriant, pharmacologically active component of cannabis. Previously, we examined the cannabidiol derivative HU-331 in order to characterize the mechanism of the compound against topoisomerase IIα. In this current work, we explore whether cannabidiol (CBD) impacts topoisomerase II activity, and we additionally examine the activity of these compounds against topoisomerase IIß. CBD does not appear to strongly inhibit DNA relaxation and is not a poison of topoisomerase II DNA cleavage. However, oxidation of CBD allows this compound to inhibit DNA relaxation by topoisomerase IIα and ß without poisoning DNA cleavage. Additionally, we found that oxidized CBD, similar to HU-331, inhibits ATP hydrolysis and can result in inactivation of topoisomerase IIα and ß. We also determined that oxidized CBD and HU-331 are both able to stabilize the N-terminal clamp of topoisomerase II. Taken together, we conclude that while CBD does not have significant activity against topoisomerase II, both oxidized CBD and HU-331 are active against both isoforms of topoisomerase II. We hypothesize that oxidized CBD and HU-331 act against the enzyme through interaction with the N-terminal ATPase domain. According to the model we propose, topoisomerase II inactivation may result from a decrease in the ability of the enzyme to bind to DNA when the compound is bound to the N-terminus.

Examination of the Impact of Copper(II) α-(N)-Heterocyclic Thiosemicarbazone Complexes on DNA Topoisomerase IIα.

Type II DNA topoisomerases resolve topological knots and tangles in DNA that result from routine cellular processes and are effective targets for anticancer therapeutics. To this end, thiosemicarbazones have been identified as having the ability to kill cancer cells from several cell lines. Literature evidence suggests that at least some thiosemicarbazones have an impact on topoisomerase II activity. However, the mechanism is not as clearly defined. Therefore, we set out to analyze the activity of four α-(N)-heterocyclic thiosemicarbazone compounds against topoisomerase IIα. The ligands, acetylpyridine-ethylthiosemicarbazone (APY-ETSC) and acetylpyrazine-methylthiosemicarbazone (APZ-MTSC), and their copper(II) [Cu(II)] complexes [Cu(APY-ETSC)Cl] and [Cu(APZ-MTSC)Cl] were examined for the ability to impact the catalytic cycle of human topoisomerase IIα. Both [Cu(APY-ETSC)Cl] and [Cu(APZ-MTSC)Cl] were more effective at inhibiting DNA relaxation compared with the ligands alone. Further, both [Cu(APY-ETSC)Cl] and [Cu(APZ-MTSC)Cl] increased double-stranded DNA cleavage levels without inhibiting topoisomerase IIα-mediated DNA ligation. The Cu(II) complexes inactivate enzyme activity over time suggesting a critical interaction with the enzyme. Additionally, we found that the Cu(II)-thiosemicarbazone complexes do not significantly impact DNA cleavage by the catalytic core of the enzyme. This evidence is supported by the fact that both [Cu(APY-ETSC)Cl] and [Cu(APZ-MTSC)Cl], and to a lesser extent the ligands, inhibit topoisomerase IIα-mediated ATP hydrolysis. Based upon kinetic analysis, the Cu(II) complexes appear to be noncompetitive inhibitors of the ATPase domain of topoisomerase IIα. Taken together, our results provide evidence that Cu(II) complexes of α-(N)-heterocyclic thiosemicarbazones catalytically inhibit the enzyme through the ATPase domain but also promote double-stranded DNA cleavage by the enzyme.

Elbow isokinetic strength characteristics among collegiate baseball players.

OBJECTIVES: To compare the bilateral strength characteristics of the wrist flexors, extensors, pronators, and supinators among baseball players. DESIGN: Cross-sectional. SETTING: Laboratory. PARTICIPANTS: 30 collegiate baseball players with no recent history of upper extremity injury. MAIN OUTCOME MEASURES: Bilateral pronation, supination, wrist flexion, and wrist extension peak torque (PT) and peak torque to body weight (PT/BW) strength were measured at speeds of 90 and 180°/second. RESULTS: Paired t-tests showed that the throwing arm of baseball players produced significantly less PT/BW strength for supination at 90°/second compared to the non-throwing arm (P = .001). The throwing arm produced significantly more PT/BW strength for pronation (P = .001) at 180°/second compared to the non-throwing arm. Furthermore, the throwing arm had more PT and PT/BW strength for wrist extension (P < .005) at 180°/second. Conversely, the throwing arm had less PT and PT/BW strength for supination (P < .004) and wrist flexion (P < .004) at 180°/second compared to the non-throwing arm. CONCLUSIONS: Significant bilateral strength differences exist in pronation, supination, wrist flexion, and wrist extension among collegiate baseball players. With the steady increase in ulnar collateral ligament injuries of the elbow among baseball players and the proven resistance to valgus force provided by the flexor-pronator mass of the elbow, the results of this study may prove beneficial in the prevention, evaluation, and rehabilitation of such dysfunctions.

Anal cancer with cerebral metastasis: a case report.

Carcinoma of the anal canal is a relatively rare cancer with a low propensity for metastasis. A literature review identifies two cases of brain metastases from anal cancer. The authors present the case of a 63-year-old female with poorly differentiated squamous cell carcinoma of the anal canal who presented with a solitary dural-based enhancing lesion of the right parietal area. The patient underwent craniectomy and tumor resection. Histopathology confirmed the cerebral lesion to be a poorly differentiated squamous cell carcinoma, consistent with the known primary tumor of the anal canal. Although exceptionally rare, the presence of a cerebral lesion in a patient with carcinoma of the anal canal should raise the possibility of metastatic disease. Treatment decisions in patients with newly diagnosed dural-based enhancing lesions and known anal cancer should bear in mind the possibility of metastatic disease.

Radiographic assessment of snap-shunt failure: report of 2 cases.

Accurate assessment of imaging studies in patients with ventriculoperitoneal shunts can be aided by empirical findings. The authors characterize an objective measurement easily performed on head CT scans with the goal of producing clear evidence of shunt fracture or disconnection in patients with a snap shunt-type system. The authors describe 2 cases of ventriculoperitoneal shunt failure involving a fracture and a disconnection associated with a snap-shunt assembly. In both cases the initial clinical symptoms were not convincing for shunt malfunction, and the interpretation of the CT finding failed to immediately identify the abnormality. As the clinical picture became more convincing for shunt malfunction, each patient subsequently underwent successful shunt revision. The authors reviewed the CT scans of 10 patients with an intact and functioning snap-shunt system to characterize the normal appearance of the snap-shunt connection. On CT scans the distance between the radiopaque portion of the ventricular catheter and the radiopaque portion of the reservoir dome measures an average of 4.72 mm (range 4.6-4.9 mm, 95% CI 4.63-4.81 mm). In the authors' patient with a fractured ventricular catheter, this interval measured 7.8 mm, and in the patient with a disconnection it measured 7.7 mm. In comparison with the range of normal values, a radiolucent interval significantly greater than 4.9 mm should promptly raise concern for a disconnected or fractured shunt in this system. This measurement may prove particularly useful when serial imaging is not readily available.

The acute effects of sleeper stretches on shoulder range of motion.

CONTEXT: The deceleration phase of the throwing motion creates large distraction forces at the shoulder, which may result in posterior shoulder tightness and ensuing alterations in shoulder range of motion (ROM) and may result in an increased risk of shoulder injury. Researchers have hypothesized that various stretching options increase this motion, but few data on the effectiveness of treating such tightness are available. OBJECTIVE: To evaluate the acute effects of "sleeper stretches" on shoulder ROM. DESIGN: Descriptive with repeated measures. SETTING: Biomechanics laboratory and 2 separate collegiate athletic training facilities. PATIENTS OR OTHER PARTICIPANTS: Thirty-three National Collegiate Athletic Association Division I baseball players (15 pitchers, 18 position players; age = 19.8 +/- 1.3 years, height = 184.7 +/- 6.4 cm, mass = 84.8 +/- 7.7 kg) and 33 physically active male college students (age = 20.1 +/- 0.6 years, height = 179.6 +/- 6.6 cm, mass = 83.4 +/- 11.3 kg) who reported no recent participation (within 5 years) in overhead athletic activities. INTERVENTION(S): Range-of-motion measurements of the dominant shoulder were assessed before and after completion of 3 sets of 30-second passive sleeper stretches among the baseball players. The ROM measurements in the nonthrower group were taken using identical methods as those in the baseball group, but this group did not perform any stretch or movement between measurements. MAIN OUTCOME MEASURE(S): Internal and external glenohumeral rotation ROM and posterior shoulder motion (glenohumeral horizontal adduction). RESULTS: In the baseball group, posterior shoulder tightness, internal rotation ROM, and external rotation ROM were -3.5 degrees +/- 7.7 degrees , 43.8 degrees +/- 9.5 degrees , and 118.6 degrees +/- 10.9 degrees , respectively, before the stretches and were -1.2 degrees +/- 8.8 degrees , 46.9 degrees +/- 9.8 degrees , and 119.2 degrees +/- 11.0 degrees , respectively, after the stretches. These data revealed increases in posterior shoulder motion (P = .01, effect size = 0.30) and in internal shoulder rotation (P = .003, effect size = 0.32) after application of the stretches. No other differences were observed in the baseball group, and no differences were noted in the nonthrower group. CONCLUSIONS: Based on our results, the sleeper stretches produced a statistically significant acute increase in posterior shoulder flexibility. However, this change in motion may not be clinically significant.

Torsion of a lumbar nerve root schwannoma.

We report a very rare case of a lumbar nerve root schwannoma presenting with torsion and infarction. The patient was a 16-year-old male presenting with severe low back pain and urinary retention following an aggressive game of hockey. Subsequent MRI of the lumbar spine revealed a nonenhancing lumbar intradural lesion at the level of L3. The patient was taken to the operating room where he underwent a bilateral L2 and L3 laminectomy and gross total resection of an intradural nerve root tumor, which appeared to have undergone torsion and infarction. Subsequent histopathological examination of the surgical specimen verified the diagnosis of infarcted schwannoma. This is a unique case of lumbar nerve root schwannoma, with atypical MRI findings, presenting with infarction due to torsion of the involved nerve root.

Numerical chromosomal aberrations in the early life-history stages of a marine tubeworm, Pomatoceros lamarckii (Polychaeta: Serpulidae).

The marine environment provides a sink for a host of toxic chemicals, directly or inadvertently, released as a result of human activity. Some of these chemicals have the potential to act as aneugens, substances that cause numerical chromosomal aberrations (NCAs). NCAs are one of the most important classes of genetic abnormality and are implicated in a variety of deleterious effects, including premature ageing, birth defects and cancer. Clearly, any increase in the incidence of these agents in the marine environment poses a risk to the indigenous biota and its predators, including man. In this paper, we describe our recent success with applying the fluorescence in situ hybridisation technique (FISH) to detect NCAs in the interphase cell nuclei of Pomatoceros lamarckii, a common rocky shore invertebrate. Given the lack of requirement for any detailed cytogenetic knowledge, the method holds considerable promise for laboratory and field studies in general, and should lend itself to automated screening protocols, where large numbers of cells can be screened rapidly, for example, using a flow cytometer. When exposed either under acute or chronic (viz. adult) exposure conditions, colchicine and di-butylphthalate (DBP) (a widely-used plasticiser), two recognised aneugens, induced significant increases in the levels of NCAs, in the dose range 1 x 10(-6)-5 x 10(-6) M, in both four to eight cell embryo stages and 24 h-old larvae. In keeping with the severely debilitating effects of this class of agent, an inverse correlation was observed between the induced levels of NCAs and larval fitness based on the results of a standard 48-h larval bioassay.