Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer

Head and neck squamous cell carcinoma is the sixth most common cancer worldwide and has high heterogeneity and unsatisfactory outcomes. To better characterize the tumor progression trajectory, we perform single-cell RNA sequencing of normal tissue, precancerous tissue, early-stage, advanced-stage cancer tissue, lymph node, and recurrent tumors tissue samples. We identify the transcriptional development trajectory of malignant epithelial cells and a tumorigenic epithelial subcluster regulated by TFDP1. Furthermore, we find that the infiltration of POSTN+ fibroblasts and SPP1+ macrophages gradually increases with tumor progression; their interaction or interaction with malignant cells also gradually increase to shape the desmoplastic microenvironment and reprogram malignant cells to promote tumor progression. Additionally, we demonstrate that during lymph node metastasis, exhausted CD8+ T cells with high CXCL13 expression strongly interact with tumor cells to acquire more aggressive phenotypes of extranodal expansion. Finally, we delineate the distinct features of malignant epithelial cells in primary and recurrent tumors, providing a theoretical foundation for the precise selection of targeted therapy for tumors at different stages. In summary, the current study offers a comprehensive landscape and deep insight into epithelial and microenvironmental reprogramming throughout initiation, progression, lymph node metastasis and recurrence of head and neck squamous cell carcinoma.

[Best evidence summary of prevention strategies for pressure injury in adult hospitalized burn patients]

Objective: To summarize the best evidence of prevention strategies for pressure injury in adult hospitalized burn patients. Methods: A bibliometric approach was used. Systematic searches were carried out to retrieve the published evidence of prevention strategies for pressure injury in adult hospitalized burn patients in the official websites of relevant academic organizations such as International Society for Burn injury, American Burn Association, and Japanese Dermatology Association, National Pressure Injury Advisory Panel, European Pressure Injury Advisory Panel, Pan Pacific Pressure Injury Alliance International Guidelines Website, foreign language databases such as UpToDate, BMJ Best Practice, MedSci, Joanna Briggs Institute Evidence-Based Practice Database, Cochrane Library, Web of Science, Embase, and PubMed, and Chinese databases such as China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang Database, and China Clinical Guidelines Library. The literature types include clinical decision-making, evidence summary, guidelines, systematic review, and expert consensus. The search time was till February 21st, 2023. Two researchers independently screened the literature and evaluated the quality, and other researchers extracted and graded the evidence according to the topic. Results: A total of 10 papers were included, including 6 evidence summaries, 3 guidelines, and 1 expert consensus, all with high literature quality. After extracting evidence and classifying, 27 pieces of best evidences were summarized from three aspects, including prevention training and supervision, risk assessment, and prevention measures of pressure injury. Conclusions: A total of 27 pieces of best evidences of prevention strategies for pressure injury in adult hospitalized burn patients were summarized from 3 aspects. Medical workers can follow the best evidence and give personalized prevention strategies according to the specific condition of adult hospitalized burn patients to reduce the incidence of pressure injury.

[Associations between different levels of blood pressure and risk of prediabetes]

Objective: To explore sex and rural-urban differences in the associations of different blood pressure levels with the risk of prediabetes. Methods: We used a multi-stage stratified cluster random sampling method to investigate 21 637 residents aged ≥18 years from 10 survey areas in Hubei province in 2020. The data on questionnaire, physical measurements, and laboratory indicators of the participants were collected. The associations of different blood pressure levels with risk of prediabetes by sex and regions were analyzed using multivariate logistic regressions after complex weighting. Results: A total of 16 111 subjects were included. The prevalence (95%CI) of prediabetes, impaired fasting glucose (IFG), impaired glucose tolerance (IGT), and IFG complicated with IGT were 25.1% (14.4%-35.9%), 12.7% (3.2%-22.1%), 8.1% (6.3%-9.8%), and 4.4% (2.3%-6.5%), respectively. After multivariate adjustment, the risk of prediabetes, IFG, IGT, and IFG complicated with IGT increased with the increment of blood pressure (both P for trend <0.05). The positive dose-response relationships between blood pressure levels and risk of prediabetes were also significant among male, urban, and rural residents (both P for trend <0.05), and the interactions between sex and blood pressure showed significant associations for risk of prediabetes and IGT (both P for interaction <0.05). Conclusions: Higher blood pressure levels were associated with an increased risk of prediabetes. The association with prediabetes was stronger in males, but no significant difference was found between urban and rural residents. More distinctive and effective prevention and control strategies should be developed for different populations.

Quality matters: low-density lipoprotein electronegativity but not quantity determines mortality risk in acute coronary syndromes

Background

Changes in the protein composition of low-density lipoprotein (LDL) particles induce a shift in their electronegativity, a phenomenon implicated in both pro-inflammatory and pro-atherogenic signalling (1). While high levels of LDL foster the build-up of atherosclerotic plaques, and as such the susceptibility for the development of acute coronary syndromes (ACS), LDL levels assessed at the time of presentation fail to associate with fatal events following the index event (2). Experimental data suggest that altered LDL electronegativity exerts functional effects on both the myocardium and vasculature (1,3).

Purpose

We aimed to study the association between LDL electronegativity, assessed at the time of acute presentation, and all-cause mortality following the index ACS.

Methods

We designed a case-cohort study in 2'619 ACS patients prospectively recruited in the investigator-driven, multicentre SPUM-ACS study (ClinicalTrials.gov Identifier: NCT01000701). Plasma LDL levels were quantified at baseline and LDL was chromatographically resolved into 5 subfractions (L1-L5), with the L1/L5 ratio serving as a proxy for overall LDL electronegativity. By employing least-squares ordinary regression models determinants of plasma L1, L5, and the L1/5 ratio were studied, and the association with mortality of both LDL levels and its electronegativity were estimated using weighted Cox regression models.

Results

Cases and controls showed similar lipid profiles, but distinct LDL electronegativity, demonstrated by an increase in the L1/L5 ratio in cases vs. controls (P&lt;0.05; Fig. 1). The highest-ranked determinants of the L1/L5 ratio were total cholesterol, LDL, high-density lipoprotein, age and triglycerides. Higher L1/L5 ratios were associated with increased risk all-cause and cardiovascular death at both 30-day (adjusted [adj.] hazard ratio [HR], 2.35, 95% confidence interval [CI], 1.81–3.03, and 2.37, 95% CI, 1.83–3.07, per standard-deviation [SD] increase) and 1-year intervals (adj. HR, 1.88, 95% CI 1.43–2.46, and 1.81, 95% CI 1.36–2.42 per SD increase). In contrast, LDL levels were not associated with these outcomes, neither at 30-day (adj. HR, 1.20, 95% CI, 0.64–2.24, and 1.20, 95% CI, 0.64–2.56 per SD increase) nor 1-year intervals (adj. HR, 1.35, 95% CI, 0.69–2.63, and 1.25, 95% CI 0.56–2.78 per SD increase). These associations were independent of age, sex, cardiometabolic risk factors and baseline risk, as assessed by the updated GRACE score. When compared with established risk factors (hsTnT levels, BMI, Killip class, eGFR, LDL levels), the L1/L5 ratio superseded several risk factors as an independent predictor for fatal events following ACS (Fig. 2).

Conclusions

In contemporary patients with ACS, LDL electronegativity independently predicts fatal events after the acute event, while LDL levels do not. Our results suggest that LDL quality rather than quantity provides predictive utility for premature death within 1 year after the index ACS.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Swiss National Science FoundationSwiss Heart FoundationTheodor-Ida Herzog StiftungFoundation for Cardiovascular Research – Zurich Heart House

[Nursing care of one patient with neuromyelitis optica spectrum disorders complicated with pressure ulcers]

On February 11, 2019, a 37-year-old female patient with neuromyelitis optica spectrum disorders was admitted to the Second Affiliated Hospital of Zhejiang University School of Medicine, and her acute osteomyelitis was caused by infection of multiple pressure ulcer wounds with Staphylococcus aureus. The patient was diagnosed and treated with multidisciplinary cooperation. The nurses focused on the strict observation of the syndrome of neuromyelitis optica spectrum disorders during hormone reduction therapy, guarded against the rebound of condition, implemented wound care in stages according to the diagnosis and treatment plan, maintained effective drainage, ensured appropriate negative pressure, and strengthened nutrition to promote wound healing. After active treatment and careful nursing care, the patient recovered and was discharged on the 39th day after admission.

[Evidence summary for postoperative hypothermia rewarming in adults with severe burns]

Objective: To retrieve, evaluate, and summarize the best evidence for postoperative hypothermia rewarming in adults with severe burns. Methods: Foreign language databases including Cochrane Library, Joanna Briggs Institute Evidence-Based Health Care Center Database, PubMed, Ovid-Medline, BMJ Best Practice, and Web of Science were retrieved with the search terms of " severe burn/major burn/severe degree burn" , " hypothermia/warming intervention/hypothermia/temperature/body temperature change" , and " postoperative /perioperative/peri-operative/post-operative" and Chinese databases including Chinese Journal Full-Text Database, Wanfang Database, and VIP Database were retrieved with the search terms of "//" , "/" , and "" to obtain all the publicly published evidence for postoperative hypothermia rewarming in adults with severe burns from the establishment of each database to April 2018, including systematic evaluations, guidelines, expert consensus, evidence summary, and original research closely related to the evidence. The literatures were screened and evaluated for their quality, the evidences were extracted from them, evaluated, classified in order to summarize the best evidences. Results: A total of 8 literatures were included, including one systematic evaluation, three guidelines, one expert consensus, and three evidence summaries. Finally, the best evidences in 8 aspects including the body temperature monitoring site, body temperature monitoring frequency, surface heating, in vivo heating, rewarming start, multi-strategy rewarming, equipment, and personnel training were summarized. Conclusions: Based in the evidence-based nursing method, this study retrieves and evaluates the literature, summarizes the evidence analysis and evaluation, and obtains the best evidences of postoperative hypothermia rewarming in adult patients with severe burns, which provides a strong reference for the clinical implementation of rewarming.

[Nursing of one patient with extremely severe burn-blast combined injury complicated with acute kidney injury caused by dust explosion]

On January 31, 2018, a 21-year-old male patient with extremely severe burn-blast combined injury complicated with acute kidney injury caused by dust explosion of crospovidone was admitted to the Second Affiliated Hospital of Zhejiang University School of Medicine. The following nursing measures were carried out, aiming at the condition of the patient. We strengthened the management of fluid intake and output volume, prevented hypothermia and unplanned disembarkation during the period of continuous renal replacement therapy with burn shock and acute kidney injury. For traumatic pneumothorax, we took a good care of the closed chest drainage tube and implemented a ventilation strategy of low tide and low positive end expiratory pressure. During the infection with carbapenem-resistant Klebsiella pneumoniae, the environmental disinfection of the care unit was optimized and polymyxin B drug care was done. After 71 days of comprehensive treatment and nursing care, the patient recovered and was discharged from hospital. This case suggests that, in view of the renal function and lung function of patients with extremely severe burn-blast combined injury, individualized treatment and nursing measures are helpful to improve the cure rate and prognosis.

[Practice of nosocomial infection management in burn department based on the American hospital evaluation standard of the Joint Commission International]

Objective: To explore the role of continuous quality improvement measures based on the American hospital evaluation standard of the Joint Commission International (JCI) in prevention and control of nosocomial infection in Burn Department of the Second Affiliated Hospital of Zhejiang University School of Medicine (hereinafter referred to as the author' s department). Methods: From 2013 to 2018, based on 11 JCI standards related to infection prevention and control and the current situation of the author' s department, more than 50 doctors, nurses, and nursing assistants from the author' s department participated in continuous improvement of the three-level management system of nosocomial infection in the author' s department, focusing on implementing of management of patient with multidrug resistant bacteria infection, optimizing the infection control management of instrument and cloth, and implementing target management on 5 indicators such as hand hygiene implementation rate, and carrying out inspection, quality management, and improvement on 11 items of prevention and control of nosocomial infection. The implementation rate of hand hygiene from 2013 to 2018 and the accuracy rate of hand hygiene from 2016 to 2018 of medical staff in the author' s department, and incidences of catheter-related bloodstream infection (CRBSI) of central venous, catheter-associated urinary tract infection (CAUTI), and ventilator associated pneumonia (VAP) of burn intensive care unit in the author's department from 2013 to 2018 were monitored.The following 7 indicators were monitored from 2013 to 2018, including false negative rate of nosocomial infection, incidence of hyperglycemia during intensive insulin treatment for severely burned patients, the implementation rate of CRBSI preventive measures, the specification rate of surface fixation of indwelling catheter, the implementation rate of VAP preventive measures, the accuracy rate of bed temperature during the use of suspended bed, and the implementation rate of hand hygiene of standardized training medical staff in the author' s department before and after improvement. Data were statistically analyzed with chi-square test. Results: The implementation rate of hand hygiene of medical staff in the author' s department was 88.0%-89.5% from 2013 to 2018, the correct rate of hand hygiene of medical staff in the author' s department was 95.10%-97.35%, and both reached the target values. The incidences of CRBSI in 2015, VAP in 2017, and CAUTI in 2013, 2014, and 2017 of burn intensive care unit failed to reach the respective target value and reached the respective target value after quality improvement, and the above-mentioned 3 indicators reached the respective target value in other years. From 2013 to 2018, the false negative rate of nosocomial infection and the incidence of hyperglycemia during intensive insulin treatment of severely burned patients in the author' s department after improvement were significantly lower than those before improvement (χ(2)=24.50, 4.74, P<0.05 or P<0.01), the implementation rate of CRBSI preventive measures, the specification rate of surface fixation of indwelling catheter, the implementation rate of VAP preventive measures, and the accuracy rate of bed temperature during the use of suspended bed after improvement in the author' s department were significantly higher than those before improvement (χ(2)=13.78, 6.50, 20.37, 13.92, P<0.05 or P<0.01), and the implementation rate of hand hygiene of standardized training medical staff in the author' s department after improvement was similar to that before improvement (χ(2)=1.71, P>0.05). Conclusions: The introduction of JCI standard can improve the implementation rate and accuracy rate of hand hygiene of medical staff in burn department, reduce the incidences of CRBSI, CAUTI, and VAP, and improve the effect of prevention and control of nosocomial infection in burn department.

[Treatment and nursing of one patient with burns on perineal region and complicated by secondary multiple organ injuries by exposing to paraquat fluid]

On March 18, 2016, one 53 years old man with burns on perineal region and complicated by secondary multiple organ injuries by exposing to paraquat fluid was admitted to our department. Comprehensive treatment measures including protective mechanical ventilation, intensive care, vacuum sealing drainage, anti-infection, and organ protection were conducted sequentially. Through 33 days of comprehensive treatment and nursing, the patient's condition substantially improved and he left hospital. This case presents that paraquat fluid absorption through skin and mucosa can also lead to severe systemic poisoning, and multiple organ protection is the key to improve the prognosis of this patient.

3-D imaging, illustration, and quantitation of enteric glial network in transparent human colon mucosa

BACKGROUND

Enteric glia form a network in the intestinal mucosa and have been suggested to engage in multidirectional interactions with the epithelium, blood vessels, nerves, and immune system. However, due to the dispersed nature of the glial network, standard histology cannot provide a global view of the network architecture. We prepared transparent human colon mucosa for three-dimensional (3-D) confocal microscopy with S100B immunostaining to reveal the location-dependent glial network for qualitative and quantitative analyses.

METHODS

Full-thickness human colons were acquired from colectomies performed for colorectal cancer. We targeted the mucosa away from the tumor site to characterize the glial network morphology. Optical clearing (use of immersion solution to reduce scattering) was applied to generate transparent specimens for deep-tissue microscopy.

KEY RESULTS

Two features of the glial network were seen: (i) A dense glial population resides at the crypt base/mucosal boundary in contact with the lymphatic vessels, and (ii) from the base, the glial network elongates along the crypt axis with peri-cryptic and peri-vascular connections toward the opening. We quantified the mucosal glia as the S100B-positive cells with at least two processes extending from the cell body. Examples of the global and in-depth imaging of adenoma were given to illustrate the morphological correlation between the loss of glial fibers and the aberrant crypts.

CONCLUSIONS & INFERENCES

We have established a useful approach for 3-D imaging, panoramic illustration, and quantitation of the enteric glia in the human colon mucosa to help characterize their roles with mucosal components in health and disease.

Room temperature SnO2 thin film gas sensor fabricated on Si nanospikes

The SnO2 thin film CO gas sensors have been fabricated on silicon nanostructured surface made using a femtosecond pulsed laser irradiation. The measurement shows a significant response to the CO gas at room temperature. While a SnO2 sensor fabricated on a flat surface shows no response when CO gas exists at room temperature. The high area/volume ratio and sharp structures of the nanospikes enhance the sensitivity of SnO2 at room temperature.

How well can the accuracy of comparative protein structure models be predicted?

Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for predicting the Calpha root-mean-squared deviation (RMSD) and native overlap (NO3.5A) errors of a model in the absence of its native structure. In contrast to most traditional assessment scores that merely predict one model is more accurate than others, this approach quantifies the error in an absolute sense, thus helping to determine whether or not the model is suitable for intended applications. The assessment relies on a model-specific scoring function constructed by a support vector machine. This regression optimizes the weights of up to nine features, including various sequence similarity measures and statistical potentials, extracted from a tailored training set of models unique to the model being assessed: If possible, we use similarly sized models with the same fold; otherwise, we use similarly sized models with the same secondary structure composition. This protocol predicts the RMSD and NO3.5A errors for a diverse set of 580,317 comparative models of 6174 sequences with correlation coefficients (r) of 0.84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71.

Comparative protein structure modeling using MODELLER

Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.

Comparative protein structure modeling using Modeller

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.

Protein structure modeling with MODELLER

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

Statistical potential for assessment and prediction of protein structures

Protein structures in the Protein Data Bank provide a wealth of data about the interactions that determine the native states of proteins. Using the probability theory, we derive an atomic distance-dependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein Energy, or DOPE). DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. The DOPE potential was extracted from a nonredundant set of 1472 crystallographic structures. We tested DOPE and five other scoring functions by the detection of the native state among six multiple target decoy sets, the correlation between the score and model error, and the identification of the most accurate non-native structure in the decoy set. For all decoy sets, DOPE is the best performing function in terms of all criteria, except for a tie in one criterion for one decoy set. To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo-electron microscopy mass density maps combined with comparative protein structure modeling, DOPE was incorporated into the modeling package MODELLER-8.

Structural modeling of protein interactions by analogy: application to PSD-95

We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of comparative modeling based on a template complex and protein docking, with a greater applicability than comparative modeling and a higher accuracy than docking. It relies on structurally defined interactions of each of the complex components, or their homologs, with any other protein, irrespective of its fold. For each component, its known binding modes with other proteins of any fold are collected and expanded by the known binding modes of its homologs. These modes are then used to restrain conventional molecular docking, resulting in a set of binary domain complexes that are subsequently ranked by geometric complementarity and a statistical potential. The method is evaluated by predicting 20 binary complexes of known structure. It is able to correctly identify the binding mode in 70% of the benchmark complexes compared with 30% for protein docking. We applied comparative patch analysis to model the complex of the third PSD-95, DLG, and ZO-1 (PDZ) domain and the SH3-GK domains in the PSD-95 protein, whose structure is unknown. In the first predicted configuration of the domains, PDZ interacts with SH3, leaving both the GMP-binding site of guanylate kinase (GK) and the C-terminus binding cleft of PDZ accessible, while in the second configuration PDZ interacts with GK, burying both binding sites. We suggest that the two alternate configurations correspond to the different functional forms of PSD-95 and provide a possible structural description for the experimentally observed cooperative folding transitions in PSD-95 and its homologs. More generally, we expect that comparative patch analysis will provide useful spatial restraints for the structural characterization of an increasing number of binary and higher-order protein complexes.

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations

In order to investigate the level of representation required to simulate folding and predict structure, we test the ability of a variety of reduced representations to identify native states in decoy libraries and to recover the native structure given the advanced knowledge of the very broad native Ramachandran basin assignments. Simplifications include the removal of the entire side-chain or the retention of only the Cbeta atoms. Scoring functions are derived from an all-atom statistical potential that distinguishes between atoms and different residue types. Structures are obtained by minimizing the scoring function with a computationally rapid simulated annealing algorithm. Results are compared for simulations in which backbone conformations are sampled from a Protein Data Bank-based backbone rotamer library generated by either ignoring or including a dependence on the identity and conformation of the neighboring residues. Only when the Cbeta atoms and nearest neighbor effects are included do the lowest energy structures generally fall within 4 A of the native backbone root-mean square deviation (RMSD), despite the initial configuration being highly expanded with an average RMSD > or = 10 A. The side-chains are reinserted into the Cbeta models with minimal steric clash. Therefore, the detailed, all-atom information lost in descending to a Cbeta-level representation is recaptured to a large measure using backbone dihedral angle sampling that includes nearest neighbor effects and an appropriate scoring function.

Protein complex compositions predicted by structural similarity

Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain—porcine α–amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE ().

MODBASE: a database of annotated comparative protein structure models and associated resources

MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, ), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, ) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, ).

A simple method for faster nonbonded force evaluations

Accurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent "dielectric constant" in implicit solvent models. Benchmarks are provided for the all-atom, implicit solvent dynamics of Met-enkephalin, the villin headpiece, the B1 domain of protein-G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look-up tables for other implicit solvent models such as the generalized Born models.

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

The populations and transitions between Ramachandran basins are studied for combinations of the standard 20 amino acids in monomers, dimers and trimers using an implicit solvent Langevin dynamics algorithm and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates are influenced by the nearest neighbor's conformation and identity, contrary to the Flory isolated-pair hypothesis. This conclusion is robust to the choice of force-field, even though the use of different force-fields produces large variations in the populations and inter-conversion rates between the dominant helical, extended beta, and polyproline II basins. The computed variation of conformational and dynamical properties with different force-fields exceeds the difference between explicit and implicit solvent calculations using the same force-field. For all force-fields, the inter-basin transitions exhibit a directional dependence, with most transitions going through extended beta conformation, even when it is the least populated basin. The implications of these results are discussed in the context of estimates for the backbone entropy of single residues, and for the ability of all-atom simulations to reproduce experimental protein folding data.

Folding and misfolding of the papillomavirus E6 interacting peptide E6ap

All-atom Langevin dynamics simulations have been performed to study the folding pathways of the 18-residue binding domain fragment E6ap of the human papillomavirus E6 interacting peptide. Six independent folding trajectories, with a total duration of nearly 2 micros, all lead to the same native state in which the E6ap adopts a fluctuating alpha-helix structure in the central portion (Ser-4-Leu-13) but with very flexible N and C termini. Simulations starting from different core configurations exhibit the E6ap folding dynamics as either a two- or three-state folder with an intermediate misfolded state. The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) is well conserved in the native-state structure but absent in the intermediate structure, suggesting that the leucine core is not only essential for the binding activity of E6ap but also important for the stability of the native structure. The free energy landscape reveals a significant barrier between the basins separating the native and misfolded states. We also discuss the various underlying forces that drive the peptide into its native state.

Inhibitory mechanisms of kinetin, a plant growth-promoting hormone, in platelet aggregation

Kinetin has been shown to have anti-aging effects on several different systems including plants and human cells. The aim of this study was to examine the detailed inhibitory mechanisms of kinetin in platelet aggregation. In this study, kinetin concentration-dependently (50-150 microM) inhibited platelet aggregation in human platelets stimulated by agonists. Kinetin (70 and 150 microM) also concentration-dependently inhibited intracellular Ca2+ mobilization and phosphoinositide breakdown in platelets stimulated by collagen (1 microg/ml). Kinetin (70 and 150 microM) significantly inhibited thromboxane A2 formation stimulated by collagen (1 microg/ml) and arachidonic acid (60 microM) in human platelets. In addition, kinetin (70 and 150 microM) significantly increased the formation of cyclic AMP. Intracellular pH values were measured spectrofluorometrically using the fluorescent probe BCECF-AM in platelets. The thrombin-evoked increase in pHi was markedly inhibited in the presence of kinetin (70 and 150 microM). Rapid phosphorylation of a platelet protein of molecular weight (Mr) 47000 (P47), a marker of protein kinase C activation, was triggered by collagen (1 microg/ml). This phosphorylation was inhibited by kinetin (70 and 150 microM). In conclusion, these results indicate that the anti-platelet activity of kinetin may be involved in the following pathways: kinetin's effects may initially be due to inhibition of the activation of phospholipase C and the Na+/H+ exchanger. This leads to lower intracellular Ca2+ mobilization, followed by inhibition of TxA2 formation and then increased cyclic AMP formation, followed by a further inhibition of the Na+/H+ exchanger, ultimately resulting in markedly decreased intracellular Ca2+ mobilization and phosphorylation of P47. These results suggest that kinetin has an effective anti-platelet effect and that it may be a potential therapeutic agent for arterial thrombosis.

The hyperaggregability of platelets from normal pregnancy is mediated through thromboxane A2 and cyclic AMP pathways

There is substantial evidence of increased platelet reactivity in vivo and in vitro during pregnancy, with the risk of developing pre-eclampsia. In this study, platelet function was studied during 28-40 weeks of gestation in a group of women who remained normotensive and in a group of nonpregnant female controls. Platelet aggregation stimulated by thrombin and adenosine diphosphate was markedly enhanced in washed platelets from pregnant subjects. Thrombin (0.04 U/ml)-evoked increases in intracellular Ca+2 mobilization of Fura 2-AM-loaded platelets were also enhanced in pregnant subjects. The binding of fluorescein isothiocyanate (FITC)-triflavin (2 microg/ml) to the glycoprotein IIb/IIIa complex in thrombin-activated platelets did not differ significantly between the nonpregnant and pregnant groups. Thromboxane A2 (TXA2) formation in both resting and thrombin-activated platelets from pregnant subjects was significantly greater than from nonpregnant subjects. Levels of cyclic adenosine monophosphate (cAMP) in both resting and prostaglandin E1-treated platelets (10 micromol/l) from pregnant subjects were significantly lower than those from nonpregnant subjects. There were no significant differences between nonpregnant and pregnant subjects in platelet cAMP levels in the presence of imidazole (600 micromol/l) and indomethacin (500 micromol/l). Intracellular pH values in platelets were measured spectrofluorometrically using the fluorescent probe, BCECF-AM. The increase in intracellular pH stimulated by thrombin (0.04 U/ml) in pregnant subjects was markedly greater than that in observed nonpregnant subjects. We conclude that the agonist-induced hyperaggregability of platelets in normal pregnancy may be due, at least partly, to stimulation of the Na+/H+ exchanger and subsequently to elevated intracellular Ca+2 mobilization, and then to increased TXA2 formation and a lowered level of cAMP, which leads to further increases in intracellular Ca+2 mobilization, and finally to enhanced platelet aggregation.

Quantification of regional myocardial wall thickening on electrocardiogram-gated SPECT imaging

BACKGROUND

Current assessment of regional left ventricular function with electrocardiogram (ECG)-gated single photon emission computed tomography (SPECT) imaging is generally performed by visual inspection. The objective of this study was to develop and validate a new computer algorithm for quantifying regional left ventricular wall thickening on ECG-gated SPECT images.

METHODS

Regional wall thickening was measured from count density changes during the cardiac cycle observed in 24-sector circumferential count distribution profiles generated from each of 8 frames of an ECG-gated SPECT study. Wall thickening was expressed as the percent count increase during systole relative to end diastole. The program was tested in a phantom simulation and in patient studies consisting of a pilot study (n = 40) and a validation study (n = 33). In the phantom study varying degrees of wall thickening were simulated. The pilot study included 20 normal subjects with low likelihood (<3%) of coronary disease and 20 patients with prior myocardial infarction. Mean wall thickening - 2 standard deviations, measured in normal subjects, defined the lower limit of normal wall thickening. This criterion was tested in the validation study in 13 normal subjects and 20 patients with prior myocardial infarction. Abnormal wall thickening was characterized by extent (percent of circumferential profile) and severity (minimal thickening).

RESULTS

The phantom study showed excellent linear correlation between wall thickening computed by the new software and actual wall thickening (r = 0.98). Interobserver and intraobserver reproducibility of quantitative assessment of minimal wall thickening were excellent (r = 0.98 and 0.99, P < .001). Regional wall thickening varied considerably from apex to base in the same ventricle among normal subjects. The average lower limit of normal wall thickening was 25% to 30% at the apex, 19% to 24% in the mid-ventricle, and 13% to 20% at the base of the left ventricle. In the validation study 11 of 13 normal subjects had wall thickening profiles within the pre-defined normal range. All 20 patients with prior myocardial infarction had abnormal regional wall thickening. Minimal regional wall thickening in the infarct areas was 5.4% +/- 5.5%, compared with 30.1% +/- 9.1% wall thickening in comparable anatomic areas in normal subjects (P < .001).

CONCLUSION

Regional wall thickening can be quantified reliably from regional count density changes during the cardiac cycle on ECG-gated SPECT images. The new software measured the extent and severity of abnormal regional wall thickening relative to normal files. The method is highly reproducible. Clinical validation showed good differentiation between normal subjects and patients with prior infarction. Quantification of regional wall thickening may enhance diagnostic accuracy and reproducibility of interpretation of gated SPECT imaging.

Quantification of technetium 99m-labeled sestamibi single-photon emission computed tomography based on mean counts improves accuracy for assessment of relative regional myocardial blood flow: experimental validation in a canine model

BACKGROUND

Quantification of single-photon emission computed tomographic (SPECT) images is generally based on determination of maximal counts on radial sectors of short-axis slices. We hypothesized that analysis of mean counts may reduce estimation error.

METHODS AND RESULTS

We compared quantitative 99mTc-labeled sestamibi (MIBI) SPECT based on maximal myocardial counts with that based on mean myocardial counts for accuracy of quantifying relative regional myocardial perfusion in a canine model of permanent left anterior descending coronary artery occlusion. MIBI and radiolabeled microspheres were injected during left anterior descending coronary artery occlusion. Relative microsphere myocardial blood flow was expressed as a percentage of normal (left circumflex coronary artery territory) blood flow. SPECT imaging was performed in vivo and ex vivo. Relative MIBI uptake on SPECT short-axis slices was quantified with normalized circumferential profiles based on maximal and mean counts. In vivo and ex vivo SPECT relative myocardial count density was compared to relative myocardial blood flow in six dogs. In the comparisons, percent errors in estimating the relative blood flow and relative flow deficit with MIBI SPECT imaging were calculated. There was an excellent correlation between absolute myocardial tissue MIBI activity and regional myocardial blood flow for each of the six dogs (r = 0.90 to 0.98). The correlations between relative myocardial count density on SPECT and relative blood flow for individual sectors were similar for maximal and mean count profiles (maximal, 0.79 to 0.83; mean, 0.77 to 0.82). Comparing the nadirs of in vivo and ex vivo circumferential count profiles, the correlations were slightly better (maximal, 0.82 to 0.91; mean, 0.87 to 0.91). Average percent errors in assessing relative blood flow and relative flow deficit were decreased significantly by use of mean count profiles (p < 0.05).

CONCLUSIONS

Relative SPECT count density with either maximal or mean count profiles correlated well with relative myocardial blood flow. Compared with maximal count profiles, quantification with mean count profiles improved estimation of relative flow.

Vasoactive intestinal polypeptide and its receptor changes in human temporal lobe epilepsy

The distribution of the VIP receptor in the human hippocampus was studied by receptor autoradiography using [3-iodotyrosyl-125I]Vasoactive Intestinal Peptide (VIP) as a ligand, and the relationship of receptor distribution to the distribution of the peptide (visualized by immunocytochemistry) was examined in hippocampi surgically removed from patients with medically intractable temporal lobe epilepsy (TLE) and hippocampi obtained at autopsy from neurologically normal subjects. In the autopsy hippocampi and hippocampi from TLE patients with extrahippocampal temporal lobe lesions [125I]VIP binding was highest in the dentate molecular layer, with lower levels in the fields of Ammon's Horn (CA fields) and the subiculum. In hippocampi from patients with no temporal lobe lesions but considerable hippocampal neuronal loss there were significant elevations in the levels of ligand binding in all CA fields and the subiculum. Ligand binding densities in all CA fields of the patient hippocampi were strongly negatively correlated with neuronal numbers. Immunocytochemical localization of VIP shows no obvious change in the distribution patters of VIP immunoreactivity in the patient groups. This is the first demonstration of VIP and its receptor distribution in the human hippocampus. It is suggested that the elevated levels of receptor binding in the hippocampal seizure focus may indicate a mechanism for greater excitability of neurons and/or for their survivability in the face of the increased excitation and potential for injury in a seizure focus.

T cells induce terminal differentiation of transformed B cells to mature plasma cell tumors

Major interest in the analysis of mature plasma cell neoplasias of mice and humans has focused on identification of precursor cells that give rise to mature malignant plasma cells. Although several laboratories have recently suggested that such cells are present in the granulomas of pristane-treated mice and the bone marrow of some multiple myeloma patients, the in vivo cellular interactions required for their differentiation into mature plasma cell tumors remains unclear. Given the extensive interactions of peripheral T cells and normal B cells, we assessed the potential role of T cells in plasma-cell tumor development, by using a myc, raf-containing retrovirus, J3V1, to induce plasmacytomas in normal BALB/c mice, T-cell-deficient nude mice, and T-cell-reconstituted nude mice. The B-lineage tumors arising in normal BALB/c mice were uniformly mature plasmacytomas, most of which secreted immunoglobulin. In contrast, nude mice yielded predominantly non-immunoglobulin-secreting B-cell lymphomas with a phenotype characteristic of peripheral B cells. T-cell reconstitution of nude mice prior to tumor induction resulted in a shift from B-cell lymphomas to plasmacytomas. These results imply that transformation can occur prior to terminal differentiation of B cells and that such transformed cells can be driven to terminal differentiation by peripheral T cells. These findings further suggest that, in human multiple myeloma, the ability of T cells to influence the differentiation state of transformed B cells may provide a mechanism by which malignant plasma cells found in the bone marrow could arise from clonotypically related less-mature B cells found in both the bone marrow and periphery.

Immunophenotyping of 515 cases of acute lymphoblastic leukemia in China

Using cell surface markers and a panel of monoclonal antibodies, 515 cases of acute lymphoblastic leukemia (ALL) were immunophenotyped. T cell type ALL (T-ALL), non-T cell type ALL (Non-T-ALL) including common ALL (C-ALL), Null-ALL and B cell type ALL (B-ALL) were found. These major subtypes of ALL were further divided according to their phenotypes in detail. It was noticed that the phenotypes of these subtypes of ALL reflected basically the phenotypes of normal T or B cells at various differentiation stages or certain population of lymphocytes. The diagnosis of cell lineage was more precise when based on immunophenotyping than morphological description. The combination of morphological and immunological classification can improve the diagnosis of acute leukemias. In addition, it was observed that the immunophenotyping was relevant to clinicopathologic features, responses to therapy and prognosis of ALL patients. The incidences of major subtypes of ALL, the age distribution of ALL subsets and male sex bias with T-ALL in Chinese are discussed.

[Correlation of immunophenotype with clinical features in T-cell acute lymphoblastic leukemia]

The immunophenotype of leukemicblasts from 111 patients with T-ALL or T-NHL were further examined by using a panel of standardized McAbs of CD nomenclature to human leukocyte differentiation antigens. Four major subsets of T-ALL were defined: pre T-ALL, immature T-ALL (I), common T-ALL (II) and mature T-ALL (III), with the percentages 20.7%, 20.7%, 20.7% and 37.0% respectively. In addition there was a case with M-T acute hybrid leukemia. Some of the clinical features of the patients with T-ALL and T-NHL were compared. It was found that male predominance, older age, higher leukocyte count, lower platelet level, relative higher hemoglobin level and increased incidence of extramedullary involvement, including hepatomegaly, splenomegaly and lymphadenopathy were alike for all subsets of T-ALL cases. However, the average white cell level and incidence of lymphadenopathy in the pre T-ALL subset significantly differed from those in other subsets. The correlation of immunophenotype with morphologic characterization was also discussed in this paper.

Hippocampal neuronal density in temporal lobe epilepsy with and without gliomas

The majority of patients with temporal lobe epilepsy show hippocampal sclerosis, which pathologically represents neuronal loss and gliosis. We studied volumetric neuronal density on a representative mid to mid-posterior level slice of hippocampi surgically removed from intractable temporal lobe epilepsy cases, and compared the results between 25 non-tumor epilepsy (NTE) cases and 5 tumor-associated epilepsy (TAE) cases. Eleven age-matched non-epileptic autopsy cases were studied as controls. Cells were counted in the CA1 through CA4 fields and the stratum granulosum of the dentate fascia. In NTE every hippocampal field showed statistically significant loss of neurons, the neuronal density in each field ranging from 35% to 50% of that of control. The mean neuronal density between the TAE and NTE groups also showed statistically significant differences in all hippocampal fields. The neuronal density of hippocampal fields of NTE ranged from 43% to 58% of that of TAE. Tumor-associated epilepsy cases, however, failed to show any statistically significant deviation from the control in their neuronal density. The etiology of the difference in neuronal density between the TAE and NTE groups is discussed.

Distribution of juxtaglomerular cells and synthesis and release of renin granules in patients with renal artery stenosis

100 pieces of renal tissue from 4 patients with renal artery stenosis were studied histologically. Juxtaglomerular cells were found not only in the region close to the glomerulus but also in the proximal 2/3 of the afferent arteriole of the glomerulus, but not in the interlobular arterioles. In the cytoplasm of juxtaglomerular cells, three kinds of granules were found: crystalline granules (immature), the round or ovoid granules (mature), and the lobulated granules (fusion). Renin was synthesized in the rough endoplasmic reticulum and packaged in the Golgi complex. Electron microscopic findings suggested that the secretory microvesicles were produced on the surface of Golgi complex. They fused to form primary crystalline granules, which were enlarged by renin supplied by transportation vesicles and finally formed typical crystalline granules. The mature renin granules (round or ovoid) moved toward the periphery of the cytoplasma. Their limiting membranes on the side toward the basement membrane disintegrated and formed microvesicular bodies passing through the periplasm, and the basement membrane and were discharged into the interstitial matrix.

Antigenicity of sperm: immunization of rabbits with pig's sperm

The state of antibody production and the tissue and species specificities together with the sperm immobilizing action of various antibodies in rabbits were examined after immunization with pig's sperm. Before the immunization, the titers of various antibodies against pig's sperm seemed to be generally higher in male than in virgin female, but they became no obvious difference between the two sexes after the immunization. Precipitins of the sera obtained by immunizing rabbits with pig's spermatozoa extract reacted not only with pig's spermatozoa extract but also with heterologous spermatozoa extract to moderate degree, but no cross reaction with pig's serum or heterologous serum was visible, and it was not associated with the sperm immobilization. The sperm-microagglutinin obtained by immunization with pig's spermatozoa showed strong species specificity and moderate tissue specificity. The motility of the sperm was not obviously inhibited by sperm agglutinin. The titer of it was the highest among the immune antibodies, but there are problems in detecting the specific antibody because spontaneous sperm agglutination is common and it is difficult to determine whether the agglutination is due to antisperm antibody or to a nonspecific factor. The evidence that strong tissue and species specific sperm-immobilizing antibody could be produced by immunizing rabbits with heterologous pig's sperm in both sexes gives us the confidence that sperm immobilization by immunization of both sexes with homologous sperm could contribute to human population control in the future.