A Fluorescent Reporter Mouse for In Vivo Assessment of Genome Editing with Diverse Cas Nucleases and Prime Editors

CRISPR-based genome-editing technologies, including nuclease editing, base editing, and prime editing, have recently revolutionized the development of therapeutics targeting disease-causing mutations. To advance the assessment and development of genome editing tools, a robust mouse model is valuable, particularly for evaluating in vivo activity and delivery strategies. In this study, we successfully generated a knock-in mouse line carrying the Traffic Light Reporter design known as TLR-multi-Cas variant 1 (TLR-MCV1). We comprehensively validated the functionality of this mouse model for both in vitro and in vivo nuclease and prime editing. The TLR-MCV1 reporter mouse represents a versatile and powerful tool for expediting the development of editing technologies and their therapeutic applications.

Efficient Homology-Directed Repair with Circular Single-Stranded DNA Donors

While genome editing has been revolutionized by the advent of CRISPR-based nucleases, difficulties in achieving efficient, nuclease-mediated, homology-directed repair (HDR) still limit many applications. Commonly used DNA donors such as plasmids suffer from low HDR efficiencies in many cell types, as well as integration at unintended sites. In contrast, single-stranded DNA (ssDNA) donors can produce efficient HDR with minimal off-target integration. In this study, we describe the use of ssDNA phage to efficiently and inexpensively produce long circular ssDNA (cssDNA) donors. These cssDNA donors serve as efficient HDR templates when used with Cas9 or Cas12a, with integration frequencies superior to linear ssDNA (lssDNA) donors. To evaluate the relative efficiencies of imprecise and precise repair for a suite of different Cas9 or Cas12a nucleases, we have developed a modified traffic light reporter (TLR) system (TLR-multi-Cas variant 1 [MCV1]) that permits side-by-side comparisons of different nuclease systems. We used this system to assess editing and HDR efficiencies of different nuclease platforms with distinct DNA donor types. We then extended the analysis of DNA donor types to evaluate efficiencies of fluorescent tag knockins at endogenous sites in HEK293T and K562 cells. Our results show that cssDNA templates produce efficient and robust insertion of reporter tags. Targeting efficiency is high, allowing production of biallelic integrants using cssDNA donors. cssDNA donors also outcompete lssDNA donors in template-driven repair at the target site. These data demonstrate that circular donors provide an efficient, cost-effective method to achieve knockins in mammalian cell lines.

5'-Modifications improve potency and efficacy of DNA donors for precision genome editing

Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach to correct mutations that cause disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA-repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit HDR efficacy. Here, we explore chemical modifications to both double-stranded and single-stranded DNA-repair templates. We describe 5'-terminal modifications, including in its simplest form the incorporation of triethylene glycol (TEG) moieties, that consistently increase the frequency of precision editing in the germlines of three animal models (Caenorhabditis elegans, zebrafish, mice) and in cultured human cells.

Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice

Prime editors (PEs) mediate genome modification without utilizing double-stranded DNA breaks or exogenous donor DNA as a template. PEs facilitate nucleotide substitutions or local insertions or deletions within the genome based on the template sequence encoded within the prime editing guide RNA (pegRNA). However, the efficacy of prime editing in adult mice has not been established. Here we report an NLS-optimized SpCas9-based prime editor that improves genome editing efficiency in both fluorescent reporter cells and at endogenous loci in cultured cell lines. Using this genome modification system, we could also seed tumor formation through somatic cell editing in the adult mouse. Finally, we successfully utilize dual adeno-associated virus (AAVs) for the delivery of a split-intein prime editor and demonstrate that this system enables the correction of a pathogenic mutation in the mouse liver. Our findings further establish the broad potential of this genome editing technology for the directed installation of sequence modifications in vivo, with important implications for disease modeling and correction.

68 A Full Audit Cycle: Documentation of Discharge Summaries and Functional Status in Electronic Discharge Letters

Introduction

Electronic discharge letter is the most effective way to handover to General Practitioners for the continuity of care by providing the information about what happened during hospitalisation and what needs to happen after discharge. Well written discharge letters prevent miscommunication, missing information and medications errors as well as reduction of hospital workload. It also provides timely follow up to decrease the risk of re-hospitalisation.

The aim of this project is to analyse the documentation of discharge summaries and functional status after hospital admission in discharge letters. Discharge summary template was introduced and made compulsory in all Geriatric wards following first cycle of audit. We then compared data after introduction of discharge summary template.

Methods

Electronic discharge letters were reviewed for all patients discharged from Geriatric Department in July 2019 and results were compared with data from January 2019.

Results

162 patients were discharged in the second cycle of audit. Among these, 18 patients were deceased, and 4 patients had no discharge letters available. Therefore, total number of discharge letters analysed was 140. Please see Table 1 for comparative results on documentation of discharge summaries in discharge letters.

Conclusions

Introduction of the discharge summary template improved the documentation of summaries in discharge letters. Well-written discharge letter ensures the smooth transition for when patients leave the hospital. Therefore, it should be accurate, precise and relevant.

Healthcare workers' knowledge and attitudes towards COVID-19 in Saudi Arabia

OBJECTIVE

The world is facing a devastating challenge in the COVID-19 (coronavirus disease 19) outbreak.  Healthcare workers (HCWs) provide the first line of defense against any disease outbreak. Thus, the present study is designed to assess HCWs' attitudes towards, knowledge of, and awareness of COVID-19.

MATERIALS AND METHODS

A cross-sectional observational study was conducted using an online survey on social media; the participants were 597 adults. The study was conducted from March to April 2020. The questionnaire was randomly administered on Arabic-language social media applications; the 26-item survey assessed knowledge levels, attitudes, and practices.

RESULTS

The analysis includes 597 complete responses from HCWs; participants included physicians, nurses, medical students, and pharmacists. Most participants were females aged 18 to 25 years. Most participants agreed that the virus can spread via direct and indirect contact. Most participants indicated that they wash their hands; avoid touching their eyes, nose, or mouth; and avoid crowded places to protect themselves against infection. Most indicated that a bat was the original source of the virus. Most participating HCWs indicated that the symptoms of COVID-19 include fever, cough, and shortness of breath. Most of the participants also indicated that there is no specific treatment for patients infected with COVID-19.

CONCLUSIONS

The findings of this work can support the design of effective measures to prevent and control COVID-19 infections during the pandemic. The results also highlight where improvement is needed to HCWs' knowledge of and attitudes towards COVID-19; the findings also highlight the best healthcare practices regarding this illness.

Anti-CRISPR AcrIIA5 Potently Inhibits All Cas9 Homologs Used for Genome Editing

CRISPR-Cas9 systems provide powerful tools for genome editing. However, optimal employment of this technology will require control of Cas9 activity so that the timing, tissue specificity, and accuracy of editing may be precisely modulated. Anti-CRISPR proteins, which are small, naturally occurring inhibitors of CRISPR-Cas systems, are well suited for this purpose. A number of anti-CRISPR proteins have been shown to potently inhibit subgroups of CRISPR-Cas9 systems, but their maximal inhibitory activity is generally restricted to specific Cas9 homologs. Since Cas9 homologs vary in important properties, differing Cas9s may be optimal for particular genome-editing applications. To facilitate the practical exploitation of multiple Cas9 homologs, here we identify one anti-CRISPR, called AcrIIA5, that potently inhibits nine diverse type II-A and type II-C Cas9 homologs, including those currently used for genome editing. We show that the activity of AcrIIA5 results in partial in vivo cleavage of a single-guide RNA (sgRNA), suggesting that its mechanism involves RNA interaction.

A novel fusion based on the evolutionary features for protein fold recognition using support vector machines

Protein fold recognition plays a crucial role in discovering three-dimensional structure of proteins and protein functions. Several approaches have been employed for the prediction of protein folds. Some of these approaches are based on extracting features from protein sequences and using a strong classifier. Feature extraction techniques generally utilize syntactical-based information, evolutionary-based information and physicochemical-based information to extract features. In recent years, finding an efficient technique for integrating discriminate features have been received advancing attention. In this study, we integrate Auto-Cross-Covariance and Separated dimer evolutionary feature extraction methods. The results’ features are scored by Information gain to define and select several discriminated features. According to three benchmark datasets, DD, RDD ,and EDD, the results of the support vector machine show more than 6\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\%$$\end{document}% improvement in accuracy on these benchmark datasets.

Skin disease profile of Syrian refugees in Jordan: a field-mission assessment

BACKGROUND

Since the beginning of the Syrian war in 2011, the world has faced the most severe refugee crisis in history and 5.6 million Syrians have sought asylum in neighbouring countries or in Europe. According to recent estimates, more than 650 000 Syrian refugees are displaced in Jordan.

OBJECTIVES

This article aims to assess the demographic characteristics and skin disease profile of Syrian displaced people residing in Al Za'atari camp and in communities in Jordan. Furthermore, the authors discuss the barriers to healthcare provision experienced during field missions.

METHODS

This is a retrospective analysis of medical records collected during three medical missions in Jordan by an international dermatological team. Data on patient age, gender, country of origin and skin disease diagnoses were recorded both in Al Za'atari camp and Jordanian towns near the Syrian border.

RESULTS

A total of 1197 patients were assessed during the field missions, with 67.7% female and 37.1% under the age of 14 years. Dermatitis was the leading dermatological condition in both refugee camp and community healthcare clinics. Infectious diseases were the second most common; however, fungal presentations were more common in the community as opposed to viral in Al Za'atari.

CONCLUSIONS

High dermatitis presentations were likely secondary to the environment, living conditions and lack of access to emollients. Infectious diseases were postulated secondary to poor hygiene and sharing of overcrowded spaces. Barriers to health care included limited pharmacological formulary, difficulty in continuity of care and case referrals due to lack of specialized services. Better access to health care, improvement of living conditions and hygiene, and increased availability of medications including emollients and sunscreens are all interventions that should be carried out to reduce skin disease burden. Our findings should further urge the international community to uphold their commitments and uptake engagement in improving health care for Syrian displaced people.

A Compact, High-Accuracy Cas9 with a Dinucleotide PAM for In Vivo Genome Editing

CRISPR-Cas9 genome editing has transformed biotechnology and therapeutics. However, in vivo applications of some Cas9s are hindered by large size (limiting delivery by adeno-associated virus [AAV] vectors), off-target editing, or complex protospacer-adjacent motifs (PAMs) that restrict the density of recognition sequences in target DNA. Here, we exploited natural variation in the PAM-interacting domains (PIDs) of closely related Cas9s to identify a compact ortholog from Neisseria meningitidis-Nme2Cas9-that recognizes a simple dinucleotide PAM (N4CC) that provides for high target site density. All-in-one AAV delivery of Nme2Cas9 with a guide RNA targeting Pcsk9 in adult mouse liver produces efficient genome editing and reduced serum cholesterol with exceptionally high specificity. We further expand our single-AAV platform to pre-implanted zygotes for streamlined generation of genome-edited mice. Nme2Cas9 combines all-in-one AAV compatibility, exceptional editing accuracy within cells, and high target site density for in vivo genome editing applications.

NmeCas9 is an intrinsically high-fidelity genome-editing platform

BACKGROUND

The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wildtype SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively large open reading frame, limiting its utility in applications that require size-restricted delivery strategies such as adeno-associated virus vectors. In contrast, some genome-editing-validated Cas9 orthologs are considerably smaller and therefore better suited for viral delivery.

RESULTS

Here we show that wildtype NmeCas9, when programmed with guide sequences of the natural length of 24 nucleotides, exhibits a nearly complete absence of unintended editing in human cells, even when targeting sites that are prone to off-target activity with wildtype SpyCas9. We also validate at least six variant protospacer adjacent motifs (PAMs), in addition to the preferred consensus PAM (5'-N4GATT-3'), for NmeCas9 genome editing in human cells.

CONCLUSIONS

Our results show that NmeCas9 is a naturally high-fidelity genome-editing enzyme and suggest that additional Cas9 orthologs may prove to exhibit similarly high accuracy, even without extensive engineering.

All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo

BACKGROUND

Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) has been extensively used for genome editing. Currently, three Cas9 orthologs have been adapted for in vivo genome engineering applications: Streptococcus pyogenes Cas9 (SpyCas9), Staphylococcus aureus Cas9 (SauCas9), and Campylobacter jejuni (CjeCas9). However, additional in vivo editing platforms are needed, in part to enable a greater range of sequences to be accessed via viral vectors, especially those in which Cas9 and sgRNA are combined into a single vector genome.

RESULTS

Here, we present in vivo editing using Neisseria meningitidis Cas9 (NmeCas9). NmeCas9 is compact, edits with high accuracy, and possesses a distinct protospacer adjacent motif (PAM), making it an excellent candidate for safe gene therapy applications. We find that NmeCas9 can be used to target the Pcsk9 and Hpd genes in mice. Using tail-vein hydrodynamic-based delivery of NmeCas9 plasmid to target the Hpd gene, we successfully reprogram the tyrosine degradation pathway in Hereditary Tyrosinemia Type I mice. More importantly, we deliver NmeCas9 with its sgRNA in a single recombinant adeno-associated vector (rAAV) to target Pcsk9, resulting in lower cholesterol levels in mice. This all-in-one vector yielded > 35% gene modification after two weeks of vector administration, with minimal off-target cleavage in vivo.

CONCLUSIONS

Our findings indicate that NmeCas9 can enable the editing of disease-causing loci in vivo, expanding the targeting scope of RNA-guided nucleases.

Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing

RNA-based drugs depend on chemical modifications to increase potency and to decrease immunogenicity in vivo. Chemical modification will likely improve the guide RNAs involved in CRISPR-Cas9-based therapeutics as well. Cas9 orthologs are RNA-guided microbial effectors that cleave DNA. Here, we explore chemical modifications at all positions of the crRNA guide and tracrRNA cofactor. We identify several heavily modified versions of crRNA and tracrRNA that are more potent than their unmodified counterparts. In addition, we describe fully chemically modified crRNAs and tracrRNAs (containing no 2'-OH groups) that are functional in human cells. These designs will contribute to Cas9-based therapeutics since heavily modified RNAs tend to be more stable in vivo (thus increasing potency). We anticipate that our designs will improve the use of Cas9 via RNP and mRNA delivery for in vivo and ex vivo purposes.

Type II-C CRISPR-Cas9 Biology, Mechanism, and Application

Genome editing technologies have been revolutionized by the discovery of prokaryotic RNA-guided defense system called CRISPR-Cas. Cas9, a single effector protein found in type II CRISPR systems, has been at the heart of this genome editing revolution. Nearly half of the Cas9s discovered so far belong to the type II-C subtype but have not been explored extensively. Type II-C CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins. Cas9s are central players in type II-C systems since they function in multiple steps of the CRISPR pathway, including adaptation and interference. Type II-C CRISPR systems are found in bacteria and archaea from very diverse environments, resulting in Cas9s with unique and potentially useful properties. Certain type II-C Cas9s possess unusually long PAMs, function in unique conditions (e.g., elevated temperature), and tend to be smaller in size. Here, we review the biology, mechanism, and applications of the type II-C CRISPR systems with particular emphasis on their Cas9s.

Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction

The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn(2+) specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH-rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction.

Rubisco catalytic properties optimized for present and future climatic conditions

Because of its catalytic inefficiencies, Rubisco is the most obvious target for improvement to enhance the photosynthetic capacity of plants. Two hypotheses are tested in the present work: (1) existing Rubiscos have optimal kinetic properties to maximize photosynthetic carbon assimilation in existing higher plants; (2) current knowledge allows proposal of changes to kinetic properties to make Rubiscos more suited to changed conditions in chloroplasts that are likely to occur with climate change. The catalytic mechanism of Rubisco results in higher catalytic rates of carboxylation being associated with decreased affinity for CO2, so that selection for different environments involves a trade-off between these two properties. The simulations performed in this study confirm that the optimality of Rubisco kinetics depends on the species and the environmental conditions. In particular, environmental drivers affecting the CO2 availability for carboxylation (Cc) or directly shifting the photosynthetic limitations between Rubisco and RuBP regeneration determine to what extend Rubisco kinetics are optimally suited to maximize CO2 assimilation rate. In general, modeled values for optimal kinetic reflect the predominant environmental conditions currently encountered by the species in the field. Under future climatic conditions, photosynthetic CO2 assimilation will be limited by RuBP-regeneration, especially in the absence of water stress, the largest rise in [CO2] and the lowest increases in temperature. Under these conditions, the model predicts that optimal Rubisco should have high Sc/o and low kcat(c).

A Novel Familial BBS12 Mutation Associated with a Mild Phenotype: Implications for Clinical and Molecular Diagnostic Strategies

Bardet-Biedl syndrome (BBS) is an autosomal recessively inherited ciliopathy mainly characterized by rod-cone dystrophy, postaxial polydactyly, obesity, renal tract anomalies, and hypogonadism. To date, 14 BBS genes, BBS1 to BBS14, have been identified, accounting for over 75% of mutations in BBS families. In this study, we present a consanguineous family from Pakistan with postaxial polydactyly and late-onset retinal dysfunction. Adult affected individuals did not show any renal or genital anomalies, obesity, mental retardation or learning difficulties and did thus not fulfill the proposed clinical diagnostic criteria for BBS. We mapped the disease in this family to the BBS12 locus on chromosome 4q27 and identified the novel homozygous p.S701X nonsense mutation in BBS12 in all three affected individuals of this family. We conclude that BBS12 mutations might cause a very mild phenotype, which is clinically not diagnosed by the current diagnostic criteria for BBS. Consequently, we suggest the use of less strict diagnostic criteria in familial BBS families with mild phenotypic expression.

Effects of inhaled nitric oxide on primary graft dysfunction in lung transplantation

INTRODUCTION AND OBJECTIVES

Inhaled nitric oxide (iNO) is a gaseous drug with known properties of specific pulmonary vasodilation and improved oxygenation. In some clinical trials on lung transplantation (LT) in animals, it has been demonstrated to reduce primary graft dysfunction (PGD) by limiting neutrophil adhesion and the inflammatory cascade. Our objective was to assess whether iNO showed this immunomodulatory effect by determining interleukin (IL)-6, -8, and -10 levels in blood and bronchoalveolar lavage (BAL) in LT patients, and its relationship with PGD incidence.

MATERIALS AND METHODS

Forty-nine LT patients were recruited and included in the iNO or in the control group. Patients in the first group were given iNO (10 ppm) from the start of LT to 48 hours afterward. BAL and blood samples were taken preimplantation and at 12, 24, and 48 hours after graft reperfusion.

RESULTS

The iNO group displayed a significantly lower incidence (P < .035) of PGD (17.2%) than the control group (45%). Significant differences (P < .05) were also observed in the iNO group with lower levels of IL-6 (in blood at 12 hours), IL-8 (in blood and BAL at 12 and 24 hours), and IL-10 (in blood at 12 and 24 hours and BAL at 24 hours).

CONCLUSIONS

PGD is associated with the development of an inflammatory process that is reduced by giving iNO to lung recipients. In our series, the iNO group displayed significantly lower content of IL-6, IL-8, and IL-10 in the majority of samples at 12 and 24 hours compared with the control group.

Characterization of white matter damage in animal models of multiple sclerosis by magnetization transfer ratio and quantitative mapping of the apparent bound proton fraction f*

Quantitative magnetization transfer magnetic resonance imaging (qMT-MRI) can be used to improve detection of white matter tissue damage in multiple sclerosis (MS) and animal models thereof. To study the correlation between MT parameters and tissue damage, the magnetization transfer ratio (MTR), the parameter f* (closely related to the bound proton fraction) and the bound proton transverse relaxation time T2B of lesions in a model of focal experimental autoimmune encephalomyelitis (EAE) were measured on a 7T animal scanner and data were compared with histological markers indicative for demyelination, axonal density, and tissue damage. A clear spatial correspondence was observed between reduced values of MTR and demyelination in this animal model. We observed two different levels of MTR and f* reduction for these lesions. One was characterized by a pronounced demyelination and the other corresponded to a more severe loss of the cellular matrix. Changes in f* were generally more pronounced than those of MTR in areas of demyelination. Moreover, a reduction of f* was already observed for tissue where MTR was virtually normal. No changes in T2B were observed for the lesions. We conclude that MTR and qMT mapping are efficient and reliable readouts for studying demyelination in animal models of MS, and that the analysis of regional f* might be even superior to the analysis of MTR values. Therefore, quantitative mapping of f* from human brains might also improve the detection of white matter damage in MS.

Contribution of BRCA1 germline mutation in patients with sporadic breast cancer

Hereditary artifacts in BRCA1 gene have a significant contributory role in familial cases of breast cancer. However, its germline mutational penetrance in sporadic breast cancer cases with respect to Pakistani population has not yet been very well defined. This study was designed to assess the contributory role of germline mutations of this gene in sporadic cases of breast cancer. 150 cases of unilateral breast cancer patients, with no prior family history of breast cancer and no other disorders or diseases in general with age range 35–75 yrs, were included in this study.

Mutational analysis for hot spots on Exon 2, 3 and 13 of BRCA1 was done by using Single Strand Conformational Polymorphism (SSCP). Sequence analysis revealed five variants (missense) and one novel splice site mutation at exon 13. No germline mutation was observed on the remaining exons with respect sporadic breast cancer cases in Pakistani population. A vast majority of breast cancer cases are sporadic; the present study may be helpful for designing a better genetic screening tool for germline BRCA mutations in sporadic breast cancer patients of Pakistani population. Further studies involving a screening of entire coding region of BRCA1 is required to explore the merits of genetic diagnosis and counseling in breast cancer patients.

Axonal loss is progressive and partly dissociated from lesion load in early multiple sclerosis

OBJECTIVE

To assess the relationship between the spectroscopically measured axonal damage in the normal-appearing white matter of the brainstem, the total brain T2-hyperintense lesion volume (T2LV), and disability in patients with early relapsing-remitting multiple sclerosis (RRMS).

METHODS

Forty-three RRMS patients and 10 sex- and age-matched healthy controls were prospectively studied for 2 years. T2-weighted magnetic resonance (MR) images and proton MR spectroscopy were acquired at the time of recruitment and at year 2. Brainstem was considered, where large tracts join together, as a suitable region to detect early axonal damage. The T2LV was calculated with a semiautomatic program; N-acetylaspartate (NAA), creatine (Cr), and choline (Cho) resonances areas were integrated with the jMRUI program, and the ratios were calculated for the sum of the volume elements represented at brainstem.

RESULTS

The basal NAA/Cho ratio was significantly decreased in patients compared with controls. After 2-year follow-up, there was a decrease in the NAA/Cho (-9%; p = 0.002) and NAA/Cr (-13%; p = 0.001) ratios, and an increase in the T2LV (19%; p = 0.043) in multiple sclerosis patients, whereas control subjects had no significant metabolic changes. Significant NAA/Cr ratio decreases were observed in both patients, with and without relapses, whereas T2LV only increased in patients with relapses. The final Expanded Disability Status Scale (EDSS) score correlated with T2LV at baseline, but no significant correlations were found between metabolic values, T2LV change, or EDSS score over the study period.

CONCLUSIONS

Our data reveal an early and progressive axonal damage in relapsing-remitting multiple sclerosis. Axonal loss and T2 lesion volume seem to be at least partly dissociated processes in early stages of the disease.

Eosinophil-selective mediators in human strongyloidiasis

Strongyloides stercoralis infection is characterized by the production of IgE and eosinophils in peripheral blood. Experimental studies have demonstrated that eosinophils play an important role in protection against Strongyloides stercoralis, but the mechanisms regulating eosinophils are not known. In this study we have focused on analysing the molecules that selectively regulate eosinophil migration, namely eotaxin and interleukin-5 (IL-5), using an enzyme-linked immunosorbent assay in patients with strongyloidiasis. Serum expression of eotaxin and IL-5 were significantly increased in patients compared with the control group. This rise suggests that selective mediators of the eosinophil can have a role in immunity against S. stercoralis in human infection.

A sensitive monoclonal antibody-based enzyme-linked immunosorbent assay to quantify Parietaria judaica major allergens, Par j 1 and Par j 2

BACKGROUND

Parietaria pollen is one of the most important causes of pollinosis in Mediterranean countries. Parietaria judaica pollen extract presents two major allergens, Par j 1 and Par j 2, that belong to the lipid transfer protein family.

OBJECTIVE

To develop an ELISA for quantification of both major allergens of P. judaica pollen extracts, and to assert correlation of these allergens content with the allergenic activity of extracts.

METHODS

Natural Par j 1-Par j 2 allergens were purified by gel filtration, ion exchange, and affinity chromatography and identified by mass spectrometry. Rabbit antisera were obtained using this protein preparation as antigen and used for immunoaffinity purification of nPar j 1-Par j 2. BALB/c mice were immunized with the immunopurified nPar j 1-Par j 2 and after fusion and screening by direct ELISA, 5D4 monoclonal antibody was selected as capture antibody to develop a quantitative two-site ELISA. Bound proteins were detected by a biotinylated Par j 1-Par j 2-specific polyclonal antibody.

RESULTS

The optimized ELISA was developed from 25 to 8000 pg/mL of purified Par j 1-Par j 2, and a linear portion of 200-1000 pg/mL. The intraassay and interassay coefficients of variation were lower than 7% and 14% respectively. The assay was very sensitive and specific as it had a detection limit of 25 pg/mL and did not detect reactivity with the same family plants, as Urtica. Par j 1-Par j 2 allergens content was measured in 14 P. judaica and two P. officinalis pollen extracts showing a significant correlation with their allergenic activity measured by enzyme allergosorbent test inhibition.

CONCLUSIONS

The results proved the usefulness of the two-sandwich ELISA for the standardization of Parietaria pollen extracts intended for clinical use, because of its good correlation with allergenic potency.

Development of a Sandwich-Type ELISA for Measuring Pla a 1, the Major Allergen of Platanus acerifolia Pollen

BACKGROUND

Platanus acerifolia is an important cause of pollinosis in Western European cities. Pla a 1, a nonglycosylated 18-kDa protein with a prevalence of 80%, is a major allergen in P. acerifolia pollen extracts. Our aim was to develop a Pla a 1-specific ELISA to quantify this protein in allergenic extracts and preparations for clinical use.

METHODS

Pla a 1 was purified by cation exchange at pH 7.0, gel filtration, and anion exchange chromatography at pH 10.0. Monoclonal (mAb) and polyclonal antibodies were obtained by immunizing mice and rabbits with nPla a 1. One (5C1) of the 13 mAb obtained was used as capture antibody at 5 mug/ml and biotin-labeled specific polyclonal antiserum at 0.63 microg/ml served for detection.

RESULTS

The prevalence of Pla a 1-specific IgE to purified Pla a 1 among 47 P. acerifolia-allergic patients was 79%. The Pla a 1-ELISA developed has a linear range of 3-25 ng/ml, high sensitivity with a detection limit of 0.5 ng/ml and is highly specific as none of the 24 pollen, mite, mold, and plant food extracts tested gave positive results. The assay could quantify Pla a 1-like proteins in other planetree pollen extracts. A good correlation was obtained between Pla a 1 content of 11 P. acerifolia pollen extracts (average content 0.69% of the total protein) and their IgE-binding activity.

CONCLUSIONS

The described two-site sandwich ELISA to measure Pla a 1 is useful for standardization of planetree pollen extracts intended for clinical use.

Biological characterization of glutaraldehyde-modified Parietaria judaica pollen extracts

BACKGROUND

Allergoids are widely used in specific immunotherapy (SIT) for the treatment of IgE-mediated allergic diseases, but all techniques for standardization of conventional allergic extracts may not be appropriate for standardization of a glutaraldehyde (GA)-modified extract because of the unique characteristics of these extracts.

OBJECTIVE

To assess an accurate methodology for standardization of chemically modified extracts.

METHODS

GA-modified extracts from Parietaria judaica pollen were purified by diafiltration. Biochemical properties were investigated by determination of amino groups, chromatography, and SDS-PAGE. The IgE-binding activity was determined by skin prick test, enzyme allergosorbent test inhibition, basophil activation, and histamine release tests. Peripheral blood mononuclear cells (PBMCs) from P. judaica pollen-allergic subjects were stimulated with either native or allergoid extracts, and proliferation was measured.

RESULTS

Biochemical data indicated a high degree of allergen polymerization resulting in extract components higher than 100 kDa. IgE-binding activity, both in vivo and in vitro, was reduced by more than 99.8%. Both allergen and allergoid induced PBMC proliferation and synthesis of blocking IgG antibodies at similar rates. Moreover, no evidence of introduction of new determinants by chemical modification was found.

CONCLUSIONS

The preparation of GA-modified extracts by diafiltration is faster and more reliable than previous chromatographic methods. These modified extracts have drastically reduced their allergenicity while maintaining their immunogenicity, and therefore they can be used in safer and shortened schedules of SIT.

Esterification of fatty acids using nylon-immobilized lipase in n-hexane: kinetic parameters and chain-length effects

The esterification of long-chain fatty acids in n-hexane catalyzed by nylon-immobilized lipase from Candida rugosa has been investigated. Butyl oleate (22 carbon atoms), oleyl butyrate (22 carbon atoms) and oleyl oleate (36 carbon atoms) were produced at maximum reaction rates of approximately equal to 60 mmol h(-1) g(-1) immobilized enzyme when the substrates were present in equimolar proportions at an initial concentration of 0.6 mol l(-1). The observed kinetic behavior of all the esterification reactions is found to follow a ping-pong bi-bi mechanism with competitive inhibition by both substrates. The effect of the chain-length of the fatty acids and the alcohols could be correlated to some mechanistic models, in accordance with the calculated kinetic parameters.

Extra-virgin olive oil increases the resistance of LDL to oxidation more than refined olive oil in free-living men with peripheral vascular disease

Patients with peripheral vascular disease (Fontaine stage II) are characterized by ischemia of the lower extremities, atherosclerosis and alteration of blood coagulation and fibrinolysis. A randomized, two-period, crossover design was used to compare the effects of extra-virgin (VO) and refined olive (RO) oils on plasma lipids and lipoprotein composition and LDL oxidation susceptibility in free-living men with peripheral vascular disease. The oils differed in their antioxidant profile (alpha-tocopherol: 300 vs. 200 mg/kg; phenolic compounds 800 vs. 60) and concentration but not in their fatty acid composition. Subjects were randomly assigned to two groups. The first group (n = 12) received VO with which to freely cook all meals for 3 mo, followed by a 3-mo wash-out period; they then received RO for the final 3 mo. The second group (n = 12) consumed the oils in the opposite order. Energy, fat, polyunsaturated fatty acids (PUFA) and alpha-tocopherol intakes were not different when patients consumed the two oils. Profiles of the major fatty acids in plasma and LDL were not different after consumption of VO and RO. The slope of the line for LDL oxidation vs. the line for copper concentration was significantly higher after the intake of RO than after the intake of VO. Total LDL taken up by macrophages was significantly greater when the men consumed RO rather than VO. We suggest that antioxidants present in VO may protect LDL against oxidation more than does RO in men with peripheral vascular disease.

Phenotypic analysis of peripheral lymphocyte subpopulations in hydatid patients

Peripheral T-lymphocytes were analyzed in three groups of people: (1) individuals with current liver hydatid disease (hydatid patients, n = 20), (2) persons who had undergone surgical cyst removal at least 2 years previously (recovered patients, n = 9), and (3) a control group of healthy volunteers (uninfected controls, n = 13). Group 1 was subdivided according to cyst status, relapse of disease, and the presence or absence of symptoms. Percentages of lymphocytes expressing CD3, CD4, CD8, CD56, CD25, CD45RA, CD45RO, and HLA-DR were determined. Symptomatic patients had proportionally fewer CD3+ CD8 + lymphocytes than the control group (P=0.038). Hydatid patients with active cysts had proportionally more natural killer cells (CD56 + CD8-) than the control group (P = 0.028).

Lifestyle changes in free-living patients with peripheral vascular disease (Fontaine stage II) related to plasma and LDL lipid composition: a 15 month follow-up study

Peripheral vascular disease (PVD) is characterized by arteriosclerosis and lower extremity ischemia which cause intermittent claudication. Patients grouped in the Fontaine stage II have more than 75% organic stenosis in their large coronary arteries and exhibit a number of alterations in blood coagulation and plasma lipids. The aim of this study was to evaluate an intervention program of lifestyle habits including dietary recommendations, moderate exercise and decreased smoking in a population of patients with PVD for a period of 15 months, with respect to plasma-lipid and lipoprotein composition as well as LDL susceptibility to peroxidation. These parameters are well known risk indicators of arteriosclerosis and coronary heart disease. A total 13 subjects diagnosed with PVD (Fontaine stage II) were selected, while a healthy age-matched group (n=20) was used as a reference. This study design was an uncontrolled trial of lifestyle interventions. The group of patients was examined at 0, 3, 6, 9, 12 and 15 months. Patients smoking one or more packets of cigarettes per day at the beginning of the study (54.2%) decreased smoking by as much as 7.7% 15 months later. In addition, physical activity intensified significantly (walking > 1 km: 13.1-77%) and treadmill running increased over the study period while the energy intake decreased by 10%. The percentage of saturated fat in the diet decreased by 10% while the intake of polyunsaturated fat rose, and monounsaturated-fat intake showed a parallel trend to increase; the average intake of cholesterol also fell by 10% and plasma triglycerides and HDL-cholesterol showed a trend to decrease and increase, respectively. No permanent changes in LDL lipid fractions for patients were detected during the follow-up period and no differences between patients and the age-matched reference group were found. The macrophage uptake of plasma-oxidized LDL was significantly higher in patients than in the reference group and no differences due to the intervention period were detected. In conclusion, the education in lifestyle and nutritional habits of patients with PVD led to reduced energy intake parallel with augmented physical activity as well to a fall in plasma triglycerides and a rise in HDL-cholesterol, which are good indicators of a reduced risk of vascular and myocardial complications.

Effect of extra-virgin olive oil and fish-oil supplementation on plasma lipids and susceptibility of low-density lipoprotein to oxidative alteration in free-living spanish male patients with peripheral vascular disease

The aim of this study was to analyse the in vivo effect of a diet rich in extra-virgin olive oil and a fish-oil supplement on plasma and lipoprotein fatty-acid composition and on LDL susceptibility to oxidative modification in free-living Spanish male patients with peripheral vascular disease. A total of 12 patients were included in the experimental group which received extra virgin olive oil and a fish oil supplement (group OF). On the other hand, 13 patients which had refined olive oil as the main visible fat were considered as Control group. Plasma triglycerides decreased significantly after three months of dietary intervention. The LDL and plasma fatty-acid pattern in the group OF was characterized by a significant increase in n-3 polyunsaturated fatty acids, mainly 20:5 n-3 and 22:6 n-3. The slopes of LDL oxidative susceptibility were similar between baseline and endpoint values in both groups. However, the uptake of oxidized LDL by macrophages was significantly reduced in OF patients in comparison with the Control group. In conclusion, the daily intake of about 40 g/d of extra-virgin olive oil in combination with a daily supplement of 16 g of fish oil for 3 months in patients with peripheral vascular disease leads to a plasma-lipid profile less atherogenic than in patients having refined olive oil as the main visible food fat. The simultaneous consumption of alpha-tocopherol and natural antioxidants provided by extra-virgin olive oil seems to have a protective effect on the LDL susceptibility to oxidative modifications in spite of a higher proportion of n-3 polyunsaturated fatty acids.

Soluble-protein and antigenic heterogeneity in axenic Blastocystis hominis isolates: pathogenic implications

The protein profile and the antigenic cross-reactivity of 18 axenic isolates of Blastocystis hominis obtained from symptomatic patients with chronic diarrhea (14 isolates) showing no evidence of parasitic etiology and from patients with acute diarrhea attributable in 2 cases to Salmonella spp. were analyzed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of soluble proteins showed the existence of a common profile composed of 31 bands, with molecular weights ranging between 24 and >200 kDa, and minor differences in the proteins of 149, 118, 106, 50, 48, 47, and 30 kDa. These differences allowed us to classify the strains into three related patterns (I-III). In an indirect immunofluorescence assay, all strains were serologically identical, but two related antigenic groups (1 and 2) were found in double-immunodiffusion and Western-blot studies. The isolates of protein patterns I and II belonging to antigenic group 1 were isolated from patients with chronic diarrhea, whereas the four isolates from patients with acute diarrhea were clustered in protein pattern III and in antigenic group 2. These results confirm the protein and antigenic heterogeneity of B. hominis and the existence of demes with different pathogenic roles.