Drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms. Part II diagnosis and management

Drug-induced hypersensitivity syndrome, also known as drug reaction with eosinophilia and systemic symptoms, is a severe cutaneous adverse reaction characterized by an exanthem, fever, and hematologic and visceral organ involvement. The differential diagnosis includes other cutaneous adverse reactions, infections, inflammatory and autoimmune diseases, and neoplastic disorders. Three sets of diagnostic criteria have been proposed; however, consensus is lacking. The cornerstone of management is immediate discontinuation of the suspected drug culprit. Systemic corticosteroids remain first-line therapy, but the literature on steroid-sparing agents is expanding. Longitudinal evaluation for sequelae is recommended. Adjunctive tests for risk stratification and drug culprit identification remain under investigation. Part II of this continuing medical education activity begins by exploring the differential diagnosis and diagnosis of drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms and concludes with an evidence-based overview of evaluation and treatment.

Drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms. Part I. Epidemiology, pathogenesis, clinicopathological features, and prognosis

Drug-induced hypersensitivity syndrome (DiHS), also known as drug reaction with eosinophilia and systemic symptoms (DRESS), is a severe cutaneous adverse reaction (SCAR) characterized by an exanthem, fever, and hematologic and visceral organ involvement. Anticonvulsants, antibiotics, and allopurinol are the most common triggers. The pathogenesis involves a complex interplay between drugs, viruses, and the immune system primarily mediated by T-cells. DiHS/DRESS typically presents with a morbilliform eruption 2-6 weeks after drug exposure, and is associated with significant morbidity, mortality, and risk of relapse. Long-term sequelae primarily relate to organ dysfunction and autoimmune diseases. Part I of this continuing medical education activity on DiHS/DRESS provides an update on epidemiology, novel insights into pathogenesis, and a description of clinicopathological features and prognosis.

Development of SCAR Markers for Genetic Authentication of Metarhizium acridum

In this study, molecular typing using Randomly Amplified Polymorphic DNA (RAPD-PCR) was conducted on 16 original isolates of Metarhizium acridum obtained from locusts (Schistocerca piceifrons ssp. piceifrons.) in Mexico (MX). The analysis included reference strains of the genus Metarhizium sourced from various geographical regions. The isolates were identified by phenotypic (macro and micromorphology) and genotypic methods (RAPD-PCR and Amplified Fragment Length Polymorphisms (AFLP), through a multidimensional analysis of principal coordinates (PCoA) and a minimum spanning network (MST). Subsequently, Sequences-Characterized Amplified Region (SCAR) markers were developed for the molecular detection of M. acridum, these markers were chosen from polymorphic patterns obtained with 14 primers via RAPD-PCR. Phenotypic and genotypic characterization identified the MX isolates as M. acridum. Of all the polymorphic patterns obtained, only OPA04 and OPA05 were chosen, which presented species-specific bands for M. acridum, and further utilized to create SCAR markers through cloning and sequencing of the specific bands. The specificity of these two markers was confirmed via Southern hybridization. The SCAR markers (Ma-160OPA-05 and Ma-151OPA-04) exhibit remarkable sensitivity, detecting down to less than 0.1 ng, as well as high specificity, as evidenced by their inability to cross-amplify or generate amplification with DNAs from other strains of Metarhizium (as Metarhizium anisopliae) or different genera of entomopathogenic fungi (Cordyceps fumosorosea and Akanthomyces lecanii). These SCAR markers yield readily detectable results, showcasing high reproducibility. They serve as a valuable tool, especially in field applications.

Development of a novel SRAP-SCAR marker for rapid identification of lager and ale types in brewer's yeast

BACKGROUND

Beer is a globally consumed and universally popular beverage. According to the fermentation conditions of brewer's yeast, ale yeast and lager yeast are the two major varieties. Normal phenotypic and genotypic approaches are insufficient and time-consuming for identifying these two forms of yeast. Therefore, a method for the rapid and cost-effective identification of lager and ale-type brewer's yeasts is necessary.

METHODS AND RESULTS

In this study, we analysed the genetic diversity of 23 industrial brewer's yeasts from around the world using sequence-related amplified polymorphism (SRAP) markers and produced stable sequence characteristic amplification region (SCAR) markers. The specific DNA fragments identified by the SRAP marker were sequenced and primers were constructed; the resultant SCAR marker (757 bp) was then confirmed against the indicated brewer's yeast type.

CONCLUSION

The development of SRAP-SCAR marker is more economical, simple, and fast compared to morphological markers.

Updates on the immunopathology and genomics of severe cutaneous adverse drug reactions

Severe cutaneous adverse reactions (SCARs) such as Stevens-Johnson syndrome, toxic epidermal necrolysis (SJS/TEN), and drug reaction with eosinophilia and systemic symptoms (DRESS)/drug-induced hypersensitivity syndrome (DIHS) cause significant morbidity and mortality and impede new drug development. HLA class I associations with SJS/TEN and drug reaction with eosinophilia and systemic symptoms/drug-induced hypersensitivity syndrome have aided preventive efforts and provided insights into immunopathogenesis. In SJS/TEN, HLA class I-restricted oligoclonal CD8+ T-cell responses occur at the tissue level. However, specific HLA risk allele(s) and antigens driving this response have not been identified for most drugs. HLA risk alleles also have incomplete positive and negative predictive values, making truly comprehensive screening currently challenging. Although, there have been key paradigm shifts in knowledge regarding drug hypersensitivity, there are still many open and unanswered questions about SCAR immunopathogenesis, as well as genetic and environmental risk. In addition to understanding the cellular and molecular basis of SCAR at the single-cell level, identification of the MHC-restricted drug-reactive self- or viral peptides driving the hypersensitivity reaction will also be critical to advancing premarketing strategies to predict risk at an individual and drug level. This will also enable identification of biologic markers for earlier diagnosis and accurate prognosis, as well as drug causality and targeted therapeutics.

Cannabidiol and Δ8-Tetrahydrocannabinol: Cannabinoids of Rising Interest and Concern

Although much is known about Δ9-tetrahydrocannabinol and its inactive open ring isomer, cannabidiol, far less is known about the effects, metabolism, and pharmacodynamics of Δ9-tetrahydrocannabinol's double-bond isomer, Δ8-tetrahydrocannabinol. With the passage of the so-called United States "Farm Bill," which was made law in order to allow legal hemp cultivation in the United States, more needs to be known about the effects of Δ8-tetrahydrocannabinol, a double-bond isomer of Δ9-tetrahydrocannabinol, and cannabidiol (CBD), which is an open-ring isomer of Δ8-tetrahydrocannabinol. It is the aim of the review to summarize current knowledge of Δ8-tetrahydrocannabinol and CBD, including the pharmacodynamics and pharmacokinetics of CBD. Also, plant genetics, the effect of cannabinoids on the current topic of viral entry into mammalian cells, and the current practice of vaping, dabbing, and dripping are covered.

Placental stem cells-derived exosomes stimulate cutaneous wound regeneration via engrailed-1 inhibition

Introduction: Skin wounds generally heal by scarring, a fibrotic process mediated by the Engrailed-1 (EN1) fibroblast lineage. Scar is detrimental to tissue structure and function, but perfect healing in clinical settings remains to be explored. Recent studies have shown that mesenchymal stem cell (MSC) transplantation can reduce scarring Methods: Here, we investigated the effects of placental MSCs (pMSCs) and exosomes derived from pMSCs (pMSC-exos) on wound healing using a full-thickness rat model. Results: The results showed that placental MSCs significantly accelerated the wound healing rate. Moreover, placental MSCs improved the quality of wound healing, including regenerating cutaneous appendages (hair follicles and sebaceous glands), decreasing collagen I and increasing collagen III, and improving collagen pattern (basket-wave-like) in the healed skin. placental MSCs treatment also increased the regeneration of blood vessels. Importantly, all these listed effects of placental MSCs were comparable to those of exosomes derived from pMSCs, but significantly stronger than those of adipose MSC-derived exosomes (aMSC-exos). Further studies showed that the effects of placental MSCs and exosomes derived from pMSCs on wound regeneration may be mainly achieved via the down-regulation of the Yes-associated protein signaling pathway, thus inhibiting the activation of EN1. Discussion: In summary, placental MSCs could effectively stimulate wound regeneration, and their effect could be achieved through their exosomes. This suggests that exosomes derived from pMSCs treatment could be used as a novel cell-free approach to induce wound regeneration in clinical settings.

Screening a collection of local and foreign varieties of Solanum lycopersicum L. in Kazakhstan for genetic markers of resistance against three tomato viruses

The tomato is one of the most important vegetable crops. The successful development of tomato cultures in Kazakhstan depends on the implementation of intensive agricultural methods, including breeding and selecting for new tomato varieties resistant to plant pathogens. Common tomato viruses, although not detected in our country to date, may potentially have a deleterious impact on agriculture if allowed to spread. The implementation of tomato breeding programs based on molecular markers of resistance is therefore an important preventive measure for protecting the agriculture and food safety of Kazakhstan. In the present work, we used nine molecular markers associated with resistance to three tomato viruses, i.e., tomato mosaic virus (ToMV), tomato spot wilt virus (TSWV), and tomato yellow leaf curl virus (TYLCV), to test the local breeding collection for the presence of genetic resistance factors. Two tomato varieties, 'Zhiraf' (Russia) and 'Sunnik' (Armenia), were revealed to possess the resistant allele marker PrRuG86-151 against ToMV; three hybrid forms had the same allele in the heterozygous state. One hybrid, based on the 'Mirsini' F1 variety from the Netherlands, had resistance to TSWV, which was confirmed by four markers: NCSw003, NCSw007, NCSw011, and NCSw012. Two cultivars, 'Nicola' and 'Malinovyi Slon' (Russia), and the local hybrid based on 'Yarkiy Rumyanets' had two to three resistant alleles of markers based on locus Tm-3 of resistance to TYLCV. The obtained results have demonstrated that the collection of tomato varieties involved in breeding programs in Kazakhstan lacks well-known genetic resistance factors to the considered tomato viruses. Thus, the prospective breeding programs require introduction of known resistant genetic resources to establish resistance to viruses using marker-assisted selection.

WASP family proteins: Molecular mechanisms and implications in human disease

Proteins of the Wiskott-Aldrich syndrome protein (WASP) family play a central role in regulating actin cytoskeletal dynamics in a wide range of cellular processes. Genetic mutations or misregulation of these proteins are tightly associated with many diseases. The WASP-family proteins act by transmitting various upstream signals to their conserved WH2-Central-Acidic (WCA) peptide sequence at the C-terminus, which in turn binds to the Arp2/3 complex to stimulate the formation of branched actin networks at membranes. Despite this common feature, the regulatory mechanisms and cellular functions of distinct WASP-family proteins are very different. Here, we summarize and clarify our current understanding of WASP-family proteins and how disruption of their functions is related to human disease.

Cardiac Magnetic Resonance for Ventricular Tachycardia Ablation and Risk Stratification

Ventricular tachycardia is the most frequent cause of sudden cardiovascular death in patients with structural heart disease. Radiofrequency ablation is the treatment cornerstone in this population. Main mechanism for structural heart disease-related ventricular tachycardia is re-entry due to presence of slow conduction area within the scar tissue. Electroanatomical mapping with high density catheters can elucidate the presence of both scar (voltage maps) and slow conduction (activation maps). Despite the technological improvements recurrence rate after ventricular tachycardia ablation is high. Cardiac magnetic resonance has demonstrated to be useful to define the location of the scar tissue in endocardium, midmyocardium and/or epicardial region. Furthermore, recent studies have shown that cardiac magnetic resonance can analyse in detail the ventricular tachycardia substrate in terms of core scar and border zone tissue. This detailed tissue analysis has been proved to have good correlation with slow conduction areas and ventricular tachycardia isthmuses in electroanatomical maps. This review will provide a summary of the current role of cardiac magnetic resonance in different scenarios related with ventricular tachycardia in patients with structural heart disease, its limitations and the future perspectives.

Immediate and Delayed Hypersensitivity Reactions to Beta-Lactam Antibiotics

Beta-lactam antibiotics are the most commonly reported drug allergy in adults and children. More than 95% of those with reported allergy labels to beta lactams are not confirmed when subjected to allergy testing. Beta lactam antibiotics are associated with a wide spectrum of immediate and delayed drug hypersensitivity reactions. The latency period to symptoms and clinical presentation aids in the causality assessment. Risk stratification based on diagnosis and timing then allows for appropriate management and evaluation. Skin prick testing, intradermal testing and oral challenge are well established for evaluation of immediate reactions. Delayed intradermal testing, patch testing and oral challenge can also be considered for evaluation of mild to moderate delayed reactions. Cross-reactivity between beta-lactams appears to be driven most commonly by a shared R1 side-chain. Standardized algorithms, protocols and pathways are needed for widespread implementation of a pragmatic and effective approach to patients reporting beta lactam allergy.

Expanding the phenotype of AFG3L2 mutations: Late-onset autosomal recessive spinocerebellar ataxia

The AFG3L2 gene encodes AFG3-like protein 2, which is a subunit of human mitochondrial ATPases associated with various cellular protease activities (m-AAA). The clinical spectrum of AFG3L2 mutations is broad. Dominant AFG3L2 mutations can cause autosomal dominant spinocerebellar ataxia type 28 (SCA28), whereas biallelic AFG3L2 mutations may lead to spastic ataxia 5 (SPAX5). However, the role of AFG3L2 mutations in autosomal recessive spinocerebellar ataxia (SCAR) remains elusive. The aim of this study is to delineate the clinical features and spectrum of AFG3L2 mutations in a Taiwanese cohort with cerebellar ataxia. Mutational analyses of AFG3L2 were carried out by targeted resequencing in a cohort of 133 unrelated patients with molecularly undetermined cerebellar ataxia. We identified one single patient carrying compound heterozygous mutations in AFG3L2, p.[R632*];[V723M] (c.[1894C > T];[2167G > A]). The patient has suffered from apparently sporadic and slowly progressive cerebellar ataxia, ptosis, and ophthalmoparesis since age 55 years. These findings expand the clinical spectrum of AFG3L2 mutations and suggest a new subtype of late-onset SCAR caused by biallelic AFG3L2 mutations.

Recognition and Management of Severe Cutaneous Adverse Drug Reactions (Including Drug Reaction with Eosinophilia and Systemic Symptoms, Stevens-Johnson Syndrome, and Toxic Epidermal Necrolysis)

Severe cutaneous adverse reactions to medications (SCARs) include drug reaction with eosinophilia and systemic symptoms, Stevens-Johnson syndrome, toxic epidermal necrolysis, and acute generalized exanthematous pustulosis. They are all non-immunoglobulin E mediated hypersensitivity reaction patterns, distinguished from simple cutaneous drug eruptions by immunologic pathogenesis and internal organ involvement. Herein the clinical features, diagnostic workup, and management considerations are presented for each of these major SCARs.

Role of Multiple Comorbidities and Therapies in Conditioning the Clinical Severity of DRESS: A Mono-Center Retrospective Study of 25 Cases

DRESS/DiHS is a complex and potentially fatal drug reaction. Little is known about risk factors and elements that can help to identify patients with a severe reaction early. The aim of the study was to investigate those factors favoring the disease and its severity by analyzing the clinical conditions and therapies preceding the reaction. We conducted a retrospective analysis on patients admitted to our center between 2010 and 2020 who were discharged with a diagnosis of DRESS. We used the RegiSCAR diagnostic criteria. We defined the severity of DRESS using the criteria of Mizukawa et al. We included 25 patients (15 females) with a median age of 66 years. Skin involvement, eosinophilia, and liver injury were the most important aspects. Allopurinol was found to be the most involved drug. Reaction severity was significantly associated with the number of daily medications (p = 0.0067) and an age of at least 68 years (p = 0.013). In addition, 75% of severe cases had at least three comorbidities in history, and most of the severe cases were female. In our study the advanced age, the high number of comorbidities and home therapies, and the inflammatory state were found to be predisposing elements to the development of the disease and its severity.

Punch Incision with Secondary Healing (PISH) Technique for Benign Facial Lesions: An Institutional Experience in 307 Patients

Background  Multiple or solitary facial lesions pose a unique challenge to the attending surgeon in terms of delivering the best cosmetic outcome. There are various methods in dealing with them and the preference of using them is based on the surgeon’s experience, patient expectations, and availability of instruments. One such tool, skin-punch, primarily designed for a biopsy can play a very important therapeutic role in this era of keyhole surgery. In this paper, we assess the technique of punch incision with its combination of secondary healing for various facial lesion.

Methods  This observational study, a total of 307 patients with solitary or multiple benign facial lesions were treated with punch incision technique using 2 to 6 mm sterile, disposable skin biopsy punches. Subsequently, the wounds were managed with healing with secondary intention.

Results  In our series all superficial wounds epithelized by 7 to 14 days while the deeper lesions epithelized by 14 to 28 days. We had three recurrences which were managed by fusiform excision and one patient had surgical site infection which was managed conservatively. On application of our self-devised facial scar scoring system (SCAR or Scar Cosmesis Assessment and Rating) ³ on all the scars, the mean score was 6 at 1 year followup.

Conclusion  Punch incision with healing by secondary intention is a relatively easy, effective, single-stage office procedure. This method can be considered as an alternative method for the removal of various skin lesions, especially on face, thus providing a simple solution to complex problems.

Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD

Background

Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. More analytic methods and data are still needed. Random amplified polymorphic DNA (RAPD) technology can sensitively identify slight intraspecific differences, and it is a powerful tool to seek species-specific markers. This work attempted to identify Chinese Leishmania isolates from diverse geographic regions at the genomic level. Meanwhile, specific markers of the L. donovani complex were also developed by RAPD.

Methods

RAPD was applied to 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into a data matrix, based on which genetic similarity was calculated, and a UPGMA dendrogram was constructed to analyse the genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of the L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified region (SCAR) markers, which were validated preliminarily in 17 available Leishmania strains in this study and analysed by bioinformatics.

Results

The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, the strains of the L. donovani complex clearly divided into two clades, and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of the L. donovani complex, i.e., 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on 17 available Leishmania strains in this study. Through bioinformatic analyses, Marker 1-AD17 may have more specificity for PCR detection of VL, and Marker 3-O13 has the potential to encode a protein.

Conclusions

The RAPD results verified that the undescribed Leishmania species causing visceral leishmaniasis (VL) in China was a unique clade distinguished from L. donovani and revealed that there was genetic differentiation among Chinese L. donovani. The identification of L. donovani-specific markers may help to provide a foundation for future research attempting to develop new specific diagnostic markers of VL and identify specific gene functions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06163-y.

Genetic Determinants in HLA and Cytochrome P450 Genes in the Risk of Aromatic Antiepileptic-Induced Severe Cutaneous Adverse Reactions

Adverse drug reaction (ADR) is a pressing health problem, and one of the main reasons for treatment failure with antiepileptic drugs. This has become apparent in the event of severe cutaneous adverse reactions (SCARs), which can be life-threatening. In this review, four hypotheses were identified to describe how the immune system is triggered in the development of SCARs, which predominantly involve the human leukocyte antigen (HLA) proteins. Several genetic variations in HLA genes have been shown to be strongly associated with the susceptibility to developing SCARs when prescribed carbamazepine or phenytoin. These genetic variations were also shown to be prevalent in certain populations. Apart from the HLA genes, other genes proposed to affect the risk of SCARs are genes encoding for CYP450 drug-metabolising enzymes, which are involved in the pharmacokinetics of offending drugs. Genetic variants in CYP2C9 and CYPC19 enzymes were also suggested to modulate the risk of SCARs in some populations. This review summarizes the literature on the manifestation and aetiology of antiepileptic-induced SCARs, updates on pharmacogenetic markers associated with this reaction and the implementation of pre-emptive testing as a preventive strategy for SCARs.

Genetic Variation between Triploid and Diploid Clarias gariepinus (Burchell, 1822) Using RAPD Markers

This study was designed to examine the use of RAPD markers in discriminating triploid and diploid African catfish Clarias gariepinus (Burchell, 1822). Following a routine technique, triploidy was induced by cold shock and confirm by erythrocyte measurement in C. gariepinus. Thereafter, 80 RAPD markers were screened; out of which, three showed the highest percentage of polymorphism (i.e., OPB 16 = 71.43%; OPC 14 = 61.9%; OPD 12 = 75%). The results obtained showed genotype differences between triploid and diploid without overlapping. However, the development of a Sequence Characterized Amplified Region (SCAR) marker was not achievable because progenies of triploid and diploid C. gariepinus could not be differentiated based on a specific fragment. Consequently, the genetic distance showed high similarities for both treatments and the UPGMA-generated dendrogram could not separate the treatments into two distinct clusters. It was concluded that RAPD makers cannot be used to separate the ploidy status of fishes.

Long Term Outcome After Open Abdomen Treatment: Function and Quality of Life

Background: Open abdomen treatment (OAT) is widely accepted to manage severe abdominal conditions such as peritonitis and abdominal compartment syndrome but can be associated with high morbidity and mortality. The main risks in OAT are (1) entero-atmospheric fistula (EAF), (2) failure of primary fascial closure, and (3) incisional hernias. In this study, we assessed the long-term functional outcome after OAT to understand which factors impacted most on quality of life (QoL)/daily living activities and the natural course after OAT. Materials and Methods: After a retrospective analysis of 165 consecutive OAT patients over a period of 10 years (2002-2012) with over 65 clinical parameters that had been performed at our center (1), we initiated a prospective structured follow-up approach. All survivors were invited for a clinical follow-up. Forty complete datasets including clinical and social follow-up with SF-36 scores were available for full analysis. Results: The patients were dominantly male (75%) with a median age of 52 years. Primary fascial closure (PC) was achieved in 9/40 (23%), while in 77% a planned ventral hernia (PVH) approach was followed. A total of 3/4 of the PVH patients underwent a secondary-stage abdominal wall reconstruction (SSR), but 2/3 of these reconstructed patients developed recurrent hernias. Fifty-five percent of the patients with PC developed an incisional hernia, while 20% of all patients developed significant scarring (Vancouver Scar Score >8). Scar pain was described by 15% of the patients as "moderate" [Visual Analog Scale (VAS) 4-6] and by 10% as "severe" (VAS > 7). While hernia presence, PC or PVH, and scarring showed no impact on QoL, male sex and especially EAF formation significantly reduced QoL. Discussion: Despite many advantages, OAT was associated with relevant mortality and morbidity, especially in the early era before the implementation of a structured concept at our center. Follow-up revealed that hernia incidence after OAT and secondary reconstruction were high and that 25% of patients qualifying for a secondary reconstruction either did not want surgery or were unfit. Sex and EAF formation impacted significantly on QoL, which was lower than in the general population. With regard to hernia incidence, new strategies such as prophylactic mesh implantation upon fascial closure should be discussed analogous to other major abdominal procedures.

Development of species-specific SCAR markers for identification and authentication of three rare Peninsular Malaysian endemic Coelogyne (Orchidaceae) orchids

Background: Coelogyne kaliana, Coelogyne stenochila and Coelogyne tiomanensis are three valuable rare orchid species endemic to Peninsular Malaysia, currently rampantly traded illegally via the internet and through local nurseries, which label them as hybrids to avoid enforcement detection. Drastic measures to ensure the continued existence of their populations in the wild should be introduced as they are rapidly diminishing into extinction, including the development of rapid and accurate species-specific identification tools. These three orchid species are highly similar morphologically and currently it is impossible to distinguish among them without their reproductive structures.

Methods:  RAPD-based species-specific SCAR markers were developed to distinguish and authenticate the identity of these three endemic Peninsular Malaysian Coelogyne species.

Results: Three SCAR markers were successfully developed in this study. SCAR marker primer pair , CKL_f / CKL_r was specific to C. kaliana as it produced a unique single band of 271 bp but not in C. stenochila and C. tiomanensis.  SCAR marker primer pair CST_f / CST_r amplified a single band of 854 bp in C. stenochila and two bands of different sizes (372 bp and 858 bp) in C. tiomanensis, but no amplification in C. kaliana. The third SCAR marker primer pair, CTI_f / CTI_r produced a single band (about 500 bp) for both C. stenochila and C. tiomanensis, but showed no amplification in C. kaliana.

Conclusions: Although not all these SCAR markers were species amplification specific, they could be used to discriminate among the three Coelogyne species effectively.  Accurate species identification is one of the most important steps to allow a proper management plan to be established in the effort to conserve these three endangered orchid species of Peninsular Malaysia. Besides, it could effectively put a stop to the illegal trading of these rare endangered orchid species worldwide.

Random Amplified Polymorphic DNA (RAPD) and Derived Techniques

Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selection of core collections, determination of genetic distances, genome analysis, development of molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest, is cost-effective, and can be performed in a moderate laboratory for most of its applications. In addition, RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like arbitrarily primed polymerase chain reaction (AP-PCR), sequence characterized amplified region (SCAR), DNA amplification fingerprinting (DAF), sequence-related amplified polymorphism (SRAP), cleaved amplified polymorphic sequences (CAPS), random amplified microsatellite polymorphism (RAMPO), and random amplified hybridization microsatellites (RAHM) can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented along with the applications of RAPD in genetic diversity analysis, mapping, varietal identification, genetic fidelity testing, etc.

Basal cell carcinoma secondary to trauma: A 3-year experience of the single center

BACKGROUND

Basal cell carcinoma (BCC) is the most frequent cancer worldwide in humans. The risk factors reported in the literature encompass excessive sun exposure, genetic predisposition, irradiation, exposure to arsenic, and trauma. The exact role of trauma in the etiology of BCC remains unexplained.

OBJECTIVES

To analyze patients with BCC treated surgically in the Dermatosurgery Unit, looking for possible cases of BCC secondary to trauma.

MATERIAL AND METHODS

We performed a retrospective review all of treated BCCs in the Dermatosurgery Unit between January 2017 and June 2020.

RESULTS

Among 1,832 patients with BCC, 5 (0.27%) tumors had a positive history of previous trauma. Many different types of injuries have been associated with oncogenesis in the area of the scar. The clinical presentations of lesions varied between the patients.

CONCLUSIONS

It is worth to underline that BCC may be located in the area of post-traumatic scar; however, the incidence seems to be lower comparing to reported previously (7.3-13%). This article illustrates the importance of exclusion malignancy in every non-healing lesion. A neoplasm may be difficult to differentiate from infection or local ischemia in the area of the scar. Prudent management of all clinically unclear lesions should include a biopsy.

Further observations on Meloidogyne enterolobii (Nematoda: Meloidogynidae) infecting guava (Psidium guajava) in India

Root-knot nematodes (Meloidogyne spp.) infect a large number of crops including guava. We investigated a population of Meloidogyne sp. infecting guava in the Coimbatore region of Tamil Nadu, India for identification and species confirmation. Detailed morphological and morphometric observations based on second-stage juveniles, males, females, and perineal patterns showed resemblance of the isolated population with the original and subsequent descriptions of M. enterolobii. Isozyme analysis of the young egg-laying females displayed the characteristic esterase phenotype pattern similar to that of M. enterolobii. Additionally, the identity of the nematode population was further validated by M. enterolobii specific SCAR marker and ITS rDNA. Recently published reports on the occurrence and morphological descriptions of M. enterolobii from India are largely incongruent with the original and subsequent redescriptions of the species. Here, we present the most comprehensive morphology and morphometrics of an Indian population of M. enterolobii for its authentic identification.

The development of species-specific AFLP-derived SCAR and SSCP markers to identify mantis shrimp species

Mantis shrimp has become commercially valuable in many countries, while the commercially aquaculture still unsuccessful. The stable supply of the species-specific markers for precise identification can play a key role of foods authentication as well as restoring/enhancing mantis shrimp stocks in future. The aim of this research was to identify species-specific markers for Squillid and Harpiosquillid mantis shrimp taxa using Amplified fragment length polymorphism-Single strand conformation polymorphism (AFLP-SSCP) approaches. Selective amplification would be substituted as a total of 40 primer combinations was performed using either three-base (i.e., EcoRI+3 and MseI+3 in 20 primer combinations) or two-base (i.e., EcoRI+2 and MseI+2 in 20 primer combinations) selective primers. These had been size-fractionated via 6% denaturing polyacrylamide gel electrophoresis, ten AFLP fragments exhibiting species or genus-specific characteristics were cloned, sequenced, and GenBank interrogated. A primer pair was designed and their specificity was tested versus the genomic DNA of various species. Results show that the primer E₊₂-13/M₊₂-13Hr₁₅₈ generated PCR products for just H. harpax, while E₊₃-14/M₊₃-2HhHr₁₅₁ and E₊₂-13/M₊₂-13Hh₁₅₀ generated PCR products for both H. harpax and H. raphidea and not others (i.e., M. nepa, O. oratoria, and E. woodmasoni). SSCP was then applied in order to differentiate between H. harpax and H. raphidea. These SSCP results indicate that species can be differentiated based on polymorphic fragment nucleotides. Indeed, primers E₊₂-13/M₊₂-13Hr₁₅₈, E₊₃-14/M₊₃-2HhHr_151, and E₊₂-13/M₊₂-13Hh₁₅₀ were all successfully confirmed as present in processed mantis shrimp samples (i.e., saline-preserved and heat-dried). These results provide new species-specific markers for mantis shrimp identification.

Mid-term follow-up after all-size acetabular revision and proposal for a stability classification system

BACKGROUND

There is a trend for using jumbo cups/oblong devices for acetabular reconstruction as alternative to biological solutions. We report about a spectrum of reconstruction methods and their mid-term results.

METHODS

Inclusion of 214 consecutive patients undergoing total hip arthroplasty revision surgery. Patients were examined using the Harris Hip Score (HHS). Based on the intraoperative acetabular defect situation, cases were classified into 1 of 5 possible categories of a stability classification for acetabular replacement (SCAR).

RESULTS

Mean HHS improved from 42 preoperatively (range 12-62) to 77 (range 54-90; p < 0.05) 6 months after operation. There were significant differences of the pre-and postoperative HHS between SCAR subgroups (p < 0.05). Inter-observer reliability of the SCAR was high (kappa 0.94 (95% CI, 0.90-0.98)). Re-revision was performed in 15 cases (7%).

CONCLUSION

The SCAR classification is a practicable tool for intraoperative decision-making as it provides standardised treatment recommendations.

Role of in vivo and in vitro Tests in the Diagnosis of Severe Cutaneous Adverse Reactions (SCAR) to Drug

Severe cutaneous adverse reactions (SCAR) are life-threatening conditions including acute generalized exanthematous pustulosis (AGEP), Stevens-Johnson Syndrome (SJS), toxic epidermal necrolysis (TEN) and drug reaction with eosinophilia and systemic symptoms (DRESS). Diagnosis of causative underlying drug hypersensitivity (DH) is mandatory due to the high morbidity and mortality upon re-exposure with the incriminated drug. If an underlying DH is suspected, in vivo test, including patch tests (PTs), delayed-reading intradermal tests (IDTs) and in vitro tests can be performed in selected patients for which the suspected culprit drug is mandatory, or in order to find a safe alternative treatment. Positivity of in vivo and in vitro tests in SCAR to drug varies depending on the type of reaction and the incriminated drugs. Due to the severe nature of these reactions, drug provocation test (DPT) is highly contraindicated in patients who experienced SCAR. Thus, sensitivity is based on positive test results in patients with a suggestive clinical history. Patch tests still remain the first-line diagnostic tests in the majority of patients with SCAR, followed, in case of negative results, by delayed-reading IDTs, with the exception of patients with bullous diseases where IDTs are still contra-indicated. In vitro tests have shown promising results in the diagnosis of SCAR to drug. Positivity is particularly high when the lymphocyte transformation test (LTT) is combined with cytokines and cytotoxic markers measurement (cyto-LTT), but this still has to be confirmed with larger studies. Due to the rarity of SCAR, large multi-center collaborative studies are needed to better study the sensitivity and specificity of in vivo and in vitro tests.

The WWOX Gene Influences Cellular Pathways in the Neuronal Differentiation of Human Neural Progenitor Cells

The brain is the most functionally organized structure of all organs. It manages behavior, perception and higher cognitive functions. The WWOX gene is non-classical tumor suppressor gene, which has been shown to have an impact on proliferation, apoptosis and migration processes. Moreover, genetic aberrations in WWOX induce severe neuropathological phenotypes in humans and rodents. The aim of the present study was to investigate in detail the impact of WWOX on human neural progenitor cell (hNPC) maintenance and how depletion of WWOX disturbs signaling pathways playing a pivotal role in neuronal differentiation and central nervous system (CNS) organogenesis. hNPC with a silenced WWOX gene exhibited lowered mitochondrial redox potential, enhanced adhesion to fibronectin and extracellular matrix protein mixture, downregulation of MMP2/9 expression and impaired 3D growth. Global transcriptome analysis using cap analysis of gene expression (CAGE) found that WWOX downregulation significantly changes the expression of multiple genes engaged in cytoskeleton organization, adhesion, cell signaling and chromatin remodeling. The massive changes in gene expression caused by WWOX silencing may strongly affect the differentiation and migration of neurons in organogenesis, brain injury, cancerogenesis or neurodifferentiation. WWOX gene appears to be an important regulator of neural tissue architecture and function.

nicotianae and Candidatus Liberibacter asiaticus in citrus

AIMS

This study aimed to develop a random amplified polymorphic DNA (RAPD)-based sequence characterized amplified region (SCAR) marker for species-specific detection of Phytophthora nicotianae, a global plant pathogen. Another objective was to develop a multiplex PCR assay for simultaneous detection of P. nicotianae and huanglongbing-causing bacterium, Candidatus Liberibacter asiaticus (CaLas) in citrus roots using the developed SCAR marker and a previously published 16SrDNA-based CaLas-specific primer set.

METHODS AND RESULTS

The RAPD primer, OPA4, amplified a specific fragment of c. 400 bp only in P. nicotianae isolates. The fragment was eluted, purified, cloned and sequenced. One set of SCAR primers (SCAR4F/SCAR4R1), developed from the sequence information of the fragment, was found specific to P. nicotianae and produced an amplicon of 330 bp size, and was found non-specific to the five Phytophthora species (P. citrophthora, P. palmivora, P. lacustris, P. boehmeriae and P. insolita) and five other pathogens (Mycosphaerella citri, Alternaria alternata, Septobasidium pseudopedicillatum, Phytopythium vexans and Colletotrichum gloeosporioides) isolated from the citrus agroecosystem. The sensitivity of the primer pair was 5 pg µl^-1 of mycelial DNA. Furthermore, the specific SCAR primers coupled with a previously reported CaLas-specific primer set were used effectively in developing a multiplex PCR assay to detect P. nicotianae and CaLas simultaneously in root tissues of citrus plants.

CONCLUSIONS

A rapid method using a RAPD-based SCAR marker for the detection of P. nicotianae was developed. Furthermore, a multiplex PCR assay was established for simultaneous detection of P. nicotianae and CaLas in citrus roots.

SIGNIFICANCE AND IMPACT OF THE STUDY

A RAPD-SCAR marker-based detection system and the one-step multiplex PCR method developed in this study can be applied to index citrus trees infected (individually or conjointly) with P. nicotianae and CaLas. The present technique developed would also be useful in monitoring disease epidemiology and phytosanitary surveillance.

Analysis of differential gene expression by SRAP-cDNA in mantle tissue of Meretrix petechialis with different external shell color

Gene expression of two shell colors in Meretrix petechialis were analyzed by sequence related amplified polymorphism-cDNA to screen the associated molecular markers. The two shell color genomes of M. petechialis were amplified using combinations of 30 primers; 11 pairs of primers showed differential fragments, and by recovery, cloning and sequencing, 18 different differential sequences were obtained. The sequencing results were analyzed by BlastX. Only one fragment shared high homology with memory-related protein-2 and TonB-dependent receptor was found that related to shell color. Sequence characterized amplified region primers were designed according to the difference sequences, and PCR amplification was performed in both 'yellow' and 'red' M. petechialis. Four pairs of differential primers were obtained. Using the population to verify the four markers (Me1-Em2, Me2-Em3, Me4-The Em11 and Me4-Em12), it was found that Me1-Em2 and Me2-Em3 were positive in the 'yellow' and Me4-The Em11 and Me4-Em12 were positive in the 'red' M. petechialis populations. All four markers can, therefore, be used as M. petechialis shell color related markers. This provides a theoretical basis for studying shell color regulation in M. petechialis, which may help to reveal the underlying molecular mechanisms more comprehensively.

[Development of sequence characterized amplified region markers for identification of Azospirillum brasilense Az39]

Azospirillum brasilense Az39 has been used since more than 30 years by several companies in South America for biofertilizers production. This strain may promote plants growth and development, as well as the ability of inoculated plants to tolerate environmental stresses, which determines an increase in the productivity under field conditions. At present, there are no protocols in Argentina to confirm the identity of Az39 in commercial products; however, such biofertilizers are formulated almost exclusively with this strain. Therefore, the objective of this paper was to develop a molecular methodology that allows the accurate identification of A. brasilense Az39. Using the complete genome sequence and several bioinformatics tools, fragments of DNA present only in the Az39 genome were recognized. A set of PCR primers to amplify these sequences were designed, and the specific products were observed only in the strain of our interest. The sensitivity of the methodology was evaluated, where the strain could be detected up to a titer of 10⁵ CFU/ml (4.5 ng/μl ADN) or 10² CFU/ml (0.88 ng/μl DNA) or in a minimal concentration of 0.098 ng/μl DNA, depending on the DNA extraction methodology used. Primers were tested against direct samples of commercial inoculants and cultures, in both cases there were specifics products, both in direct samples and in confirmatory tests from isolated colonies from those products. The procedure presented in this paper allows the accurate identification of A. brasilense Az39 in pure cultures, mixtures of microorganisms, and commercial biofertilizers.

saccharinum)

Red maple (Acer rubrum) and silver maple (A. saccharinum) are sister species that readily hybridize in nature. No genetic or barcoding markers have been tested in these species. The main objective of the present study is to develop and characterize molecular markers for distinguishing A. rubrum and A. saccharinum and to validate the hybridity of A. freemanii derived from their crossings using the ISSR marker system. Thirteen A. rubrum and seven A. saccharinum populations were used. Four ISSR primers including ISSR 5, ISSR 8, ISSR 10, and ISSR UBC 825 were selected to amplify genomic DNA from the two species and their hybrids. Each primer generated at least one species-diagnostic ISSR marker for a total of six. Analysis of A. freemanii collected from North Dakota (USA) confirmed that the genotypes screened were true hybrids between A. rubrum and A. saccharinum. These markers were cloned and sequenced. Successful sequences were converted to SCAR markers using specifically designed primers. Overall, the developed diagnostic and specific ISSR and SCAR markers are useful in the certification of these two maple species and their hybrids. They can be used in tracking the introgression of A. rubrum and A. saccharinum DNA in other hybrid trees or populations.

Epidemiology of Severe Cutaneous Adverse Drug Reaction and Its HLA Association among Pediatrics

Severe cutaneous adverse drug reaction (SCAR) is considered to be a multifactorial drug side effect. This study was designed to investigate the epidemiology and human leukocyte antigen (HLA)-A and -B gene polymorphisms in pediatric patients with SCAR admitted in tertiary referral center, southwestern of Iran from 2013 to 2017. Demographic data, past allergy and autoimmune history, clinical presentations, drugs confirmed to be the cause of SCAR as well as its therapy were reviewed for each patient. HLA-A and -B allele frequencies were determined in 40 of the patients using polymerase chain reaction based on sequence specific primers (PCR-SSP) and compared with 40 healthy individuals as control group. Sixty-one patients with mean age of 6 years old and boy to girl ratio was 1.2/1 in this study. The most common type of SCAR in our patients was Steven Johnson Syndrome (SJS)/Toxic Epidermal Necrosis (TEN) mainly caused by beta-lactam antibiotics. Carbamazepine was the second cause of drug-induced SCAR. Moreover, HLA-A*02:01 and A*51:01 were related to the increased risk of SCAR while A*11:01 seemed to be protective against SCAR. HLA-A*02:01, HLA-A*24:02, and HLA-B*51:01 showed associations to the increased risk of SJS. Based on our results, beta-lactam antibiotics and antiepileptic drugs are the most common causes of severe adverse drug reaction in southwestern Iranian pediatric patients. Moreover, some HLA-A alleles can influence risk of SCAR.

Quick and accurate detection of Fusarium oxysporum f. sp. carthami in host tissue and soil using conventional and real-time PCR assay

Safflower wilt, caused by Fusarium oxysporum f. sp. carthami (Foc) is a major limiting factor for safflower (Carthamus tinctorius) production worldwide. In India alone, about 40-80% disease incidence has been reported. A rapid, efficient, specific, and sensitive diagnostic technique for Foc is therefore crucial to manage Fusarium wilt of safflower. Twenty-five isolates of F. oxysporum formae speciales infecting other crops, 17 isolates of Fusarium spp. and seven isolates of other fungal pathogens of safflower along with 75 Foc isolates were used for identification of band specific to Foc using inter-simple sequence repeat (ISSR) analysis. Out of 70 ISSR primers, the one that specifically amplified a 490 bp fragment from all the Foc isolates was selected. Sequence of the amplified fragment was utilized to design sequence characterized amplified region (SCAR) primers (FocScF/FocScR). The primer pair unambiguously and exclusively amplified a DNA fragment of approximately 213 bp in all the 75 Foc isolates. The primer set was able to detect as low as 10 pg of Foc genomic DNA using conventional PCR, while the SCAR primers when coupled with real-time qPCR demonstrated detection limits of 1 pg for Foc genomic DNA and 1000 conidia/g for soil. The assay enabled reliable diagnosis of Foc DNA in contaminated safflower fields and expedited Foc detection at 72 h post inoculation in asymptomatic seedlings. This method facilitates quick and precise detection of Foc in plant and soil samples and can be exploited for timely surveillance and sustainable management of the disease.

Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers

Safflower (Carthamus tinctorius L.) is considered as an oil crop that is rich in medicinal and industrial properties. In this study, the genetic diversity of safflower was assessed using 12 polymorphic sequence-related amplified polymorphism (SRAPs) and 11 polymorphic start codon targeted (SCoT) markers in 100 genotypes of safflower gathered from different geographical regions of the world. The 23 primers generated a total of 227 polymorphism fragments with a mean of 68.2% within the range of 3 (SCoT 31 and SCoT 35) to 13 (SCoT 35) bands per primer. Polymorphism per primer ranged between 100% (in Me4-Em1) and 18.1% (in SCoT19), with an average of 36.76%. The polymorphism information contents of the SRAP and SCoT markers were 0.35 and 0.30, respectively, indicating that SRAP markers were more effective than SCoT markers for assessing the degree of genetic diversity of the safflower. The results of the analysis of molecular variance showed a significant difference across cultivated safflower genotypes possessing a high intra-population variation. The examined accessions were categorized into five clusters based on similarity centers: the Middle East containing Iran, Iraq, Turkey, and Tajikistan; the Far East, including India, Pakistan, and Korea; Europe; the American continent; and Africa, including Egypt, Sudan and Libya. The present study shows the effectiveness of employing the mixture of SRAP and SCoT markers in the identification of safflower genetic diversity that would be useful for conservation and population genetics of safflower improvement in further studies.

Non-specificity of sequence characterised amplified region as an alternative molecular epidemiology marker for the identification of Salmonella enterica subspecies enterica serovar Typhi

Objective

Identification of Salmonella Typhi by conventional culture techniques is labour-intensive, time consuming, and lack sensitivity and specificity unlike high-throughput epidemiological markers that are highly specific but are not affordable for low-resource settings. SCAR, obtained from RAPD technique, is an affordable, reliable and reproducible method for developing genetic markers. Hence, this study investigated the use of SCAR as an alternative molecular epidemiological marker for easy identification of S. Typhi in low-resource settings.

Results

One hundred and twenty RAPD primers were screened through RAPD-PCR against a panel of common enterobacteriaceae for the best RAPD band pattern discrimination to develop SCAR primers that were used to develop a RAPD-SCAR PCR. Of this number, 10 were selected based on their calculated indices of discrimination. Four RAPD primers, SBSA02, SBSA03, SBSD08 and SBSD11 produced suitable bands ranging from 900 to 2500 bp. However, only SBSD11 was found to be specific for S. Typhi, and was cloned, sequenced and used to design new SCAR primers. The primers were used to amplify a panel of organisms to evaluate its specificity. However, the amplified regions were similar to other non-Typhi genomes denoting a lack of specificity of the primers as a marker for S. Typhi.

Incidence of Stevens-Johnson syndrome/toxic epidermal necrolysis among new users of different individual drugs in a European population: a case-population study

PURPOSE

To estimate the specific incidences of Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) among new users of drugs frequently reported to be associated with this serious event.

METHODS

We performed a case-population approach, which combined data from a registry of SJS/TEN cases from the Madrid region (numerator) during the study period 2005-2015 and a primary healthcare database from the same catchment population. The proportion of new users of drugs estimated in the primary healthcare database was stratified by calendar year, sex and age (5-year bands), and then applied to the same strata of Madrid's population census to compute the number of new users (denominator). Incidences were re-estimated using only cases in which the concerned drug had a probable or very probable causal relationship.

RESULTS

A total of 44 SJS/TEN cases aged > 14 years were registered during the study period. The highest SJS/TEN incidence was found for phenytoin with 68.9 per 100,000 new users (95% CI 27.7-141.9), followed by dexamethasone (5.48; 1.49-14.03), allopurinol (3.29; 1.07-7.67) and cotrimoxazole (3.19; 0.87-8.16). Considering only probable and very probable cases, the incidences hardly changed, except for dexamethasone, which was left without cases. Pantoprazole, levofloxacin and lorazepam showed incidences between 1 per 100,000 and 1 per 1,000,000 new users. Ibuprofen, amoxicillin-clavulanic acid, metamizole, amoxicillin, paracetamol and omeprazole showed incidences around 1 per one million new users.

CONCLUSIONS

Phenytoin was the drug with the highest incidence of SJS/TEN, followed by allopurinol and cotrimoxazole. For the rest of the drugs, the estimated incidences were below 1 in 100,000 new users.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in maize using DNA transposon-based markers

Transposable elements (TEs), are a rich source for molecular marker development as they constitute a significant fraction of the eukaryotic genome and impact the overall genome structure. Here, we utilize Mutator-based transposon display (Mu-TD), and CACTA-derived sequence-characterized amplified regions (SCAR) anchored by simple sequence repeats and single nucleotide polymorphisms to locate quantitative trait loci (QTLs) linked to agriculturally important traits on a genetic map. Specifically, we studied recombinant inbred line populations derived from a cross between dent corn and waxy corn. The resulting linkage map included 259 Mu-anchored fragments, 34 SCARs, and 614 SSR markers distributed throughout the ten maize chromosomes. Linkage analysis revealed three SNP loci associated with kernel starch synthesis genes (sh2, su1, wx1) linked to either Mu-TD loci or SSR markers, which may be useful for maize breeding programs. In addition, we used QTL analysis to determine the chromosomal location of traits related to grain yield and kernel quality. We identified 24 QTLs associated with nine traits located on nine out of ten maize chromosomes. Among these, 13 QTLs involved Mu loci and two involved SCARs. This study demonstrates the potential use of DNA transposon-based markers to construct linkage maps and identify QTLs linked to agronomic traits.

Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis

Transposable elements are highly abundant elements that are present in all eukaryotic species. Here, we present a molecular description of abalone retrotransposon (Abret) elements. The genome of Haliotis discus hannai contains 130 Abret elements which were all Ty3/Gypsy retrotransposons. The Ty1/Copia elements were absent in the H. discus hannai genome. Most of the elements were not complete due to sequence truncation or coding region decay. However, three elements Abret-296, Abret-935, and Abret-3259 had most of the canonical features of LTR (long terminal repeat)-retrotransposons. There were several reading frame shifts in Abret-935 and Abret-3259 elements. Surprisingly, phylogenetic analysis indicated that all of the elements belonged to the Osvaldo lineage. The sequence divergence between LTRs revealed that the Abret elements were mostly active within 2 million years ago. Abret elements were used as molecular markers in SSAP analyses, which allowed clear distinction of different species in the genus Haliotis. The polymorphic markers were converted into SCAR markers for use in species identification by simple PCR in the Haliotis genus.

via RAPD and SCAR Markers

The dioecious property of the sea buckthorn (Hippophae rhamnoides L.) prevents sex recognition via traditional observation at the juvenile stage, thus impeding breeding and economic cropping; A random amplified polymorphic DNA (RAPD) and a sequence characterized amplified region (SCAR) markers were used to identify the sexes. A total of 45 random decamer primers were used to screen genomic DNA pools of staminate and pistillate genotypes for genetic polymorphisms. One female sex-linked marker was identified. D15 (5′-CATCCGTGCT-3′) amplified a particular band of 885 bp, which showed polymorphism among staminate and pistillate genotype plants. The SCAR marker Hrcx-15 was obtained by sequencing the fragment. The alleles of 140 pistillate genotypes were examined but not of the 140 staminate genotypes discerned via taxonomy. Staminate and pistillate genotypes of sea buckthorn plants can be distinguished, using Hrcx-15 as a genetic marker for sex identification and for expediting cultivation for commercial applications.

The WAVE Regulatory Complex and Branched F-Actin Counterbalance Contractile Force to Control Cell Shape and Packing in the Drosophila Eye

Contractile forces eliminate cell contacts in many morphogenetic processes. However, mechanisms that balance contractile forces to promote subtler remodeling remain unknown. To address this gap, we investigated remodeling of Drosophila eye lattice cells (LCs), which preserve cell contacts as they narrow to form the edges of a multicellular hexagonal lattice. We found that during narrowing, LC-LC contacts dynamically constrict and expand. Similar to other systems, actomyosin-based contractile forces promote pulses of constriction. Conversely, we found that WAVE-dependent branched F-actin accumulates at LC-LC contacts during expansion and functions to expand the cell apical area, promote shape changes, and prevent elimination of LC-LC contacts. Finally, we found that small Rho GTPases regulate the balance of contractile and protrusive dynamics. These data suggest a mechanism by which WAVE regulatory complex-based F-actin dynamics antagonize contractile forces to regulate cell shape and tissue topology during remodeling and thus contribute to the robustness and precision of the process.

Whole-Genome Re-Alignment Facilitates Development of Specific Molecular Markers for Races 1 and 4 of Xanthomonas campestris pv. campestris, the Cause of Black Rot Disease in Brassica oleracea

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4 are the two most frequent races found in Brassica oleracea crops. In this study, a PCR molecular diagnostic tool was developed for the identification of Xcc races 1 and 4 of this pathogen. Whole genomic sequences of races 1, 3, 4 and 9 and sequences of three other Xanthomonas pathovars/species (X. campestris pv. incanae (Xci), X. campestris pv. raphani (Xcr) and X.euvesicatoria (Xev) were aligned to identify variable regions among races. To develop specific markers for races 1 and 4, primers were developed from a region where sequences were dissimilar in other races. Sequence-characterized amplified regions (SCAR) and insertion or deletion of bases (InDel) were used to develop each specific set of primers. The specificity of the selected primers was confirmed by PCR tests using genomic DNA of seven different Xcc races, two strains of X. campestris pathovars and other species of bacteria. Bacterial samples of the races 1 and 4 isolates were collected from artificially inoculated cabbage leaves to conduct bio-PCR. Bio-PCR successfully detected the two Xcc isolates. By using our race-specific markers, a potential race 1 strain from the existing Korean Xcc collection was identified. The Xcc race 1 and 4-specific markers developed in this study are novel and can potentially be used for rapid detection of Xcc races through PCR.

Gender Identification in Date Palm Using Molecular Markers

Breeding of date palm is complicated because of its long life cycle and heterozygous nature. Sexual propagation of date palm does not produce true-to-type plants. Sex of date palms cannot be identified until the first flowering stage. Molecular markers such as random amplified polymorphic DNA (RAPD), sequence-characterized amplified regions (SCAR), and simple sequence repeats (SSR) have successfully been used to identify the sex-linked loci in the plant genome and to isolate the corresponding genes. This chapter highlights the use of three molecular markers including RAPD, SCAR, and SSR to identify the gender of date palm seedlings.

Identification of male-specific AFLP and SCAR markers in the dioecious plant Humulus scandens

In this study, 17 male-specific amplified fragment length polymorphism (AFLP) markers were identified between male and female Humulus scandens plants. BLAST analysis revealed that 7 of the 17 sex-linked sequences were highly similar to retrotransposons. Two stable male-specific sequence-characterized amplified regions (SCAR) markers were developed. These AFLP and SCAR markers are novel molecular probes that can be used efficiently to identify the genetic gender of H. scandens and may provide a basis for further investigations on the evolution of sex chromosomes.

Cost-effectiveness Analysis for Genotyping before Allopurinol Treatment to Prevent Severe Cutaneous Adverse Drug Reactions

OBJECTIVE

Patients with an HLA-B*58:01 allele have an increased risk of developing severe cutaneous adverse drug reactions (SCAR) when treated with allopurinol. Although one-off pharmacogenetic testing may prevent life-threatening adverse drug reactions, testing prior to allopurinol initiation incurs additional costs. The study objective was to evaluate the cost-effectiveness of HLA-B*58:01 screening compared with using other available urate-lowering agents (ULA).

METHODS

A decision-analytical model was used to compare direct medical costs and effectiveness [including lifetime saved, quality-adjusted life-yrs (QALY) gained] in treating new patients with the following options: (1) genetic screening followed by allopurinol prescribing for noncarriers of HLA-B*58:01, (2) prescribing benzbromarone without screening, (3) prescribing febuxostat without screening, and (4) prescribing allopurinol without screening. A 1-year time frame and third-party payer perspective were modeled for both the entire cohort (base-case) and for the subgroup of patients with chronic kidney disease (CKD).

RESULTS

The incremental cost-effectiveness ratio of genetic screening prior to ULA therapy was estimated as New Taiwan (NT) $234,610 (US$7508) per QALY gained in the base-case cohort. For patients with CKD, it was estimated as NT$230,925 (US$7390) per QALY. The study results were sensitive to the probability of benzbromarone/febuxostat-related hypersensitivity, and a negative predicted value of genotyping.

CONCLUSION

HLA-B*58:01 screening gave good value for money in preventing allopurinol-induced SCAR in patients indicated for ULA therapy. In addition to the costs of genotyping, it is important to monitor ULA safety closely in adopting HLA-B*58:01 screening in practice.

ISSR markers for gender identification and genetic diagnosis of Hippophae rhamnoides ssp. turkestanica growing at high altitudes in Ladakh region (Jammu and Kashmir)

Hippophae rhamnoides L. ssp. turkestanica (Elaeagnaceae) is a predominantly dioecious and wind-pollinated medicinal plant species. The mature fruits of the species possess antioxidative, anti-inflammatory, antimicrobial, anticancerous, and antistimulatory properties that are believed to improve the immune system. The identification of male and female plants in H. rhamnoides ssp. turkestanica is quite difficult until flowering which usually takes 3-4 years or more. A sex-linked marker can be helpful in establishing the orchards through identification of genders at an early stage of development. Therefore, we studied the genetic diversity of populations in Ladakh with the aim to identify a gender-specific marker using ISSR markers. Fifty-eight ISSR primers were used to characterize the genome of H. rhamnoides ssp. turkestanica, of which eight primers generated 12 sex-specific fragments specific to one or more populations. The ISSR primer (P-45) produced a fragment which faithfully segregates all the males from the female plants across all the three valleys surveyed. This male-specific locus was converted into a SCAR. Forward and reverse primers designed from this fragment amplified a 750-bp sequence in males only, thus specifying it as an informative male-specific sex-linked marker. This SCAR marker was further validated for its capability to differentiate gender on an additional collection of plants, representing three geographically isolated valleys (Nubra, Suru, and Indus) from Ladakh region of India. The results confirmed sex-linked specificity of the marker suggesting that this conserved sequence at the Y chromosome is well preserved through the populations in Ladakh region. At present, there are no reliable markers which can differentiate male from female plants across all the three valleys of Ladakh region at an early stage of plant development. It is therefore envisaged that the developed SCAR marker shall provide a reliable molecular tool for early identification of the sex in this commercial crop. The genetic diversity of populations as surveyed by ISSR primers revealed 85.71 % polymorphism at the population level. The dendrogram obtained divided the genotypes into three different clusters, and the distribution of male and female genotypes in all the clusters was random. The Nei's genetic similarity index was in the range of 0.63-0.96.

RAPD/SCAR Approaches for Identification of Adulterant Breeds' Milk in Dairy Products

Food safety and quality are nowadays a major consumers' concern. In the dairy industry the fraudulent addition of cheaper/lower-quality milks from nonlegitimate species/breeds compromises the quality and value of the final product. Despite the already existing approaches for identification of the species origin of milk, there is little information regarding differentiation at an intra-species level. In this protocol we describe a low-cost, sensitive, fast, and reliable analytical technique-Random Amplified Polymorphic DNA/Sequence Characterized Amplified Region (RAPD/SCAR)-capable of an efficient detection of adulterant breeds in milk mixtures used for fraudulent manufacturing of dairy products and suitable for the detection of milk adulteration in processed dairy foods.

Genetic Characterization of Green Bean (Phaseolus vulgaris L.) Accessions from Turkey with SCAR and SSR Markers

Characterization, conservation, and utilization of genetic resources is essential for the sustainability in agriculture. Plant genetic resources are important for breeding efforts designed for the generation of new cultivars or for the improvement of existing ones. Green bean has been cultivated extensively in Turkey giving rise to local accessions through selection over time and adaptation to various environmental conditions. The objective of the present study was to determine the genetic relationships of green bean accessions collected from Kırşehir Province of Turkey, located at the central Anatolia. Within a population of 275 green bean accessions, 50 accessions were selected on the basis of morphological observations for further evaluation with SSR and STS/SCAR markers together with 4 reference cultivars of Andean and Mesoamerican origin. SSR markers selected on the basis of high polymorphism information content revealed the genetic relatedness of selected green bean accessions. STS/SCAR markers associated with bean anthracnose, common bacterial blight, white mold, halo blight, and phaseolin protein demonstrated the inheritance of resistance traits of local accessions at the selected loci. These findings may help better utilize genetic resources and furthermore are expected to facilitate forthcoming breeding studies for the generation of novel cultivars well adapted to the region.