Amplification Profiles Research Articles

Development of a Multiplex PCR Assay to Detect Neofusicoccum parvum and Botryosphaeria dothidea in Walnut.

In walnut orchards, frequent symptoms of cankers and dieback (fruit blight, twig and branch cankers up to tree death) are caused by different agents, in particular by Botryosphaeriaceae, primarily Neofusicoccum parvum and Botryosphaeria dothidea. This study aimed at developing a sensitive, rapid, specific and internally controlled multiplex PCR assay for the detection of these species. The ability of the multiplex PCR, with an internal inhibition control (i.e. E. coli DNA), to specifically and successfully detect members of the two targeted species was validated using 11 different isolates for each fungal target (inclusivity) and 20 tree-associated fungal species different from B. dothidea or N. parvum (exclusivity). Applicability to plant materials was further investigated and showed an absence of amplification for asymptomatic husk or twig samples while the amplification profiles of symptomatic tissues ranged from no amplification to amplification of both species, in correlation with the observed fungal contamination level. In conclusion, we developed a rapid diagnostic tool for simultaneous detection of two major fungal pathogens of walnut. Although this protocol was tailored for walnut husks and twigs, applicability to any plant sample contaminated by these pathogens can be considered.

Somatic amplification and addiction profile as risk factors for medication overuse headache with chronic migraine

IntroductionOveruse of analgesics can lead to medication-overuse headache (MOH) in chronic migraine (CM) patients, and is often linked to addiction. This study explores the addiction-related characteristics and somatic amplification in patients with, CM with medication overuse headache (CM+MOH), CM, and healthy controls.Methods73 CM patients and 70 CM+MOH, along with 63 healthy controls, participated in the study. Assessments included a Sociodemographic Form, Migraine Disability Assessment Scale (MIDAS), Addiction Profile Index (API), Addiction Profile Index-Clinical Version (API-C), and the Somatosensory Amplification Scale (SSAS).ResultsSubstance use characteristics, craving, motivation for use, and addiction severity scores were higher in the CM+MOH group than in both the CM and the control group. Specifically, the SSAS scores within the CM+MOH group surpassed those of both the CM and control groups. In the CM+MOH group, SSAS scores were a strong predictor of the amount of analgesic usage. Besides, craving and motivation for substance use scores significantly predicted the number of days analgesic taken per month in the CM+MOH groupConclusionCM patients with MOH exhibit a pronounced association with addiction, and a heightened manifestation of somatic symptoms. Addressing addiction characteristics and psychosomatic amplification is important to ensure comprehensive management.

EGFR, HER2, and MET gene amplification and protein expression profiles in biliary tract cancer and their prognostic significance.

There are limited conventional chemotherapy options for biliary tract cancers (BTCs), a heterogenous group of lethal, rare malignancies. The receptor tyrosine kinase (RTK) is closely associated with the progression of human malignancies through the regulation of cell cycle. Overexpression or amplification of RTKs has been investigated as a potential biomarker and therapeutic target in BTC; herein, we investigate the value of such interventions. Overexpression of RTK proteins was examined by immunohistochemistry in 193 BTC samples, of which 137 were gallbladder carcinoma, 29 were perihilar cholangiocarcinoma, and 27 were intrahepatic cholangiocarcinoma. Silver in situ hybridization of MET and HER2 was performed to assess gene amplification. In the entire cancer group, gallbladder, perihilar, and intrahepatic, MET amplification rates were 15.7%, 19.0%, 3.4%, and 14.8%, respectively, and of HER2 amplification rates were 22.4%, 27.2%, 17.2%, and 3.7%, respectively. MET and HER2 protein expressions were significantly correlated with their gene amplification status. RTKs were significantly associated with adverse clinicopathologic features such as advanced pT category and lymph node metastasis. Overall survival was significantly shorter in MET-amplified (P = .024) and EGFR-overexpressed cases (P = .045). Recurrence-free survival was significantly correlated with HER2-amplified (P = .038) and EGFR-overexpressed cases (P = .046) in all patient groups. Overall and recurrence-free survival were significantly shorter in patients who were double positive for HER2 and EGFR. Our data suggested that MET, HER2, and EGFR might be potential therapeutic targets and that their co-expression is a strong prognostic factor for BTCs.

A smartphone-controllable molecular diagnostic platform for SARS-CoV-2 detection by reverse-transcription recombinase polymerase amplification

We constructed a portable molecular diagnostic microsystem, enabling the whole processes of genetic analysis for SARS-CoV-2. The proposed platform was a miniaturized size and was comprised of three main parts: a microfluidic device with a 3D-printed solution loading cartridge, an operating system including a tailor-made heater board, a syringe pump and an optical fluorescence detector, and a smartphone with a customized app for the remote and automatic control. The microfluidic device was designed to control the complicated fluidic flow through only the passive valves, and could perform the RNA extraction from the viral lysate via glass membranes and the target gene amplification by reverse-transcription recombinase polymerase amplification (RT-RPA). The 3D-printed cartridge allowed the facile chemical solution storage and loaded a designated solution into the microfluidic device. A smartphone with a browser-based app could control the on-and-off status of solenoid valves, the workflow of a syringe pump to automatically introduce solutions on a chip, the heater board to supply the constant temperature for RT-RPA, and the periodic activation of the Pi camera and a 488 nm laser to measure the fluorescence signal in the reaction chambers that showed the amplification profiles on the smartphone display in real-time. Using the proposed smartphone-controllable diagnostic platform, the N gene and S gene of SARS-CoV-2 were successfully detected at a limit-of-detection (LOD) of 10 copies/μL within 1 hr in a sample-to-answer-out format. Ten out of 22 clinical samples were successfully analyzed for SARS-CoV-2, demonstrating the practical applications for the on-site diagnostics of patient samples.

Exploring the effect of sound scene on self-directed hearing-aid gain adjustment

Self-directed gain adjustments may present a plausible solution for fitting a hearing-aid (HA) without the requirement of audiometric tests. In the current experiment, users interacted with their hearing aids using a touchscreen-enabled mobile device while a continuous speech stimulus with background noise was played in the sound field, simulating real-world sound scenes. They explored different settings by dragging a cursor on the touchscreen, experiencing real-time audio changes, and identifying their preferred amplification level. Thirteen older adults with self-identified hearing difficulties participated in the study (RHHI score ≥6). The self-fitting procedure was conducted in two sound scenes: Restaurant and Traffic. The speech level was set at 60 dB-A in both sound scenes, and the signal-to-noise ratios were 5 and 10 dB for the Restaurant and Traffic scenes, respectively. Following the self-fitting procedure, real-ear aided responses were measured for the amplification profiles obtained using the two sound scenes. The real-ear aided responses for the two scenes resembled each other, with a median correlation coefficient across participants of 0.81. Nevertheless, a marginally significant difference was found between them, mostly driven by higher or lower frequency regions. This suggests that scene-specific adjustments of hearing-aid fitting may be beneficial for some users.

Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism.

A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.

Optimization of the CuBr＋Ne＋HBr brightness amplifier operating mode for high-speed imaging

The paper presents the research and development of a low-volume brightness amplifier for imaging laser active optical systems (laser monitors) with a pulse repetition frequency (PRF) of up to 100 kHz. A small-sized active element and pumping source based on tasitron have been developed. The effect of the brightness amplifier’s operating features (concentration of CuBr and HBr) on the numerical characteristics of images obtained in the laser monitor has been studied. The optimal concentrations were determined, and it was proven for the first time that they should be 30% lower than what is needed for obtaining maximum laser power. It was shown that increasing the CuBr concentration leads to a decrease in the field of view. The effect of the one-pass amplification profile on the quality of LOAS-based images was experimentally determined. A small-sized active element (40 cm3) excited with a specific pulse energy input of 238 μJ/cm3 can be used to obtain images with a time resolution of up to 10 μs.

Pharmacogenetic Practice of Anticancer Drugs: Multiple Approaches for an Accurate and Comprehensive Genotyping.

The application of pharmacogenetics in oncology is part of the routine clinical practice. In particular, genotyping of dihydropyrimidine dehydrogenase (DPYD) and UDP-glucuronosyltransferase (UGT1A1) is crucial to manage the treatment of patients taking fluoropyrimidines and irinotecan. The unique approach of our laboratory to the pharmacogenetic diagnostic service in oncology is to combine two real-time PCR methods, LightSNiP assay (TIB MOLBIOL), and more recently FRET (Fluorescent Resonance Energy Transfer) probes technology (Nuclear Laser Medicine), plus TaqMan assay (Thermo Fisher) for the confirmation of the presence of variant alleles on DNA from a second extraction. We found that both the FRET and LightSNiP assays, where detection occurs by melting curve analysis, offer an advantage over the competing TaqMan technology. Whereas unexpected genetic variants may be missed using a mutation-specific TaqMan assay, the information thus obtained can be useful to adjust the therapy in case of unexpected post-treatment toxicity. The combination of TaqMan and FRET assays helped us to achieve more accurate genotyping and a correct result for the patient. The added value of the DPYD FRET assay is the possibility of detecting, with the same amplification profile of the polymorphisms detailed in the guidelines, also the c.2194G>A (*6 rs1801160), cited in the recommendations as a variant to be investigated in case of severe toxicity. Regarding the UGT1A1 (TA)n promoter polymorphism (rs3064744), the distinctive and positive feature of the FRET assay is to allow clearly identifying all those potential variant alleles, including the (TA)5 and (TA)8 alleles, that are frequent in African Americans. Our clinical practice emphasizes the importance of not only rapid and easy-to-use assays, such as the new FRET ones, but also of accurate and comprehensive genotyping for good pharmacogenetic diagnostic activity.

Clinical characterization of MYC family proto-oncogene amplification in solid tumors from Chinese patients.

e15140 Background: The dysregulation of the MYC family oncogenes ( c-MYC, MYCN and MYCL) play critical roles in tumorigenesis, prognosis and immune escape. MYC inactivation can result in sustained tumour regression and many therapeutic agents that directly target MYC are under development. MYC signaling is associated with tumor cell PD-L1, overall immune cell infiltration. Herein, we explore MYC family proto-oncogene amplification profiles and clinical characterization in chinese solid tumors. Methods: This research comprehensively characterized gene mutations by next-generation sequencing (NGS) in 23990 chinese solid tumors tissues to reveal the prevalence of MYC family proto-oncogene amplification(MYC AMP) and the association with Tumor mutational burden(TMB) and microsatellite instability(MSI). Results: The prevalence of MYC AMP (copy number, CN≥5) in the cohort was 2.1% (504/23,990), in which ovarian cancer (7.6%, 22/289) showed the highest prevalence, followed by breast cancer (6.1%, 26/429), esophagus cancer (5.9%, 17/287). Only one glioma patient(pt) carried co-amplification of MYCN and c-MYC. In 504 MYC AMP pts, c-MYC AMP accounted for 93.7%(472/504), MYCN and MYCL AMP accounted for 6.5%(33/504) in total. The CN was significantly higher in MYCN and MYCL AMP pts than c-MYC AMP pts (22.9 vs 7.6, p < 0.0001). MSI-H showed a lower detection rate in MYC AMP pts other than Non-MYC AMP pts (0% vs 1.2%, p < 0.05). The proportion of TMB-L in MYC AMP pts was similar to Non-MYC AMP pts (90.9% vs. 90.1%, p > 0.05). Conclusions: In totally, 2.1% of chinese solid tumor pts had MYC high level AMP, mainly c-MYC Amp. The CN was higer in MYCN/ MYCL AMP pts than c-MYC AMP pts. In addition, MYC AMP pts tended to have MSS and TMB-L, suggesting that MYC may be a novel target for tumor immunotherapy. MYC inhibitor combines with immunotherapy may be an important direction for the treatment of MYC AMP pts.

Small cardamom genome: development and utilization of microsatellite markers from a draft genome sequence of Elettaria cardamomum Maton.

Small cardamom (Elettaria cardamomum Maton), the queen of spices, is the third most expensive spice in the world after saffron and vanilla, valued highly for its aroma and taste. This perennial herbaceous plant is a native of coastal parts of Southern India and displays a significant amount of morphological diversity. Its genetic potential has not been exploited due to lack of genomic resources limiting our understanding of the genome and important metabolic pathways which give it the economic advantage in the spice industry. Here, we report upon the de novo assembled, draft whole genome sequence of cardamom variety, Njallani Green Gold. We used a hybrid assembly strategy using the reads from the Oxford Nanopore, Illumina and 10x Genomics GemCode sequencing chemistries. The assembled genome length was 1.06 Gb (gigabases) which is close to the estimated genome size of cardamom. More than 75% of the genome was captured in 8000 scaffolds with a N50 of 0.15 Mb. The genome appears to have a high repeat content and 68055 gene models were predicted. The genome is close to Musa species and displays an expansion and contraction in different gene families. The draft assembly was used for in silico mining of simple sequence repeats (SSRs). A total of 2,50,571 SSRs were identified of which 2,18,270 were perfect SSRs and 32,301 were compound SSRs. Among the perfect SSRs, trinucleotides were most abundant (1,25,329) and hexanucleotide repeats appear least (2,380). From the 2,50,571 SSRs mined, 2,27,808 primer pairs were designed based on flanking sequence information. Wet lab validation was performed for 246 SSR loci and based on their amplification profiles, 60 SSR markers were used for diversity analysis of a set of 60 diverse cardamom accessions. The average number of alleles detected per locus were 14.57 with a minimum of 4 and maximum of 30 alleles. Population structure analysis revealed the presence of high degree of admixtures which could primarily be due to cross-pollination prevalent in this species. The SSR markers identified would help in the development of gene or trait-linked markers which can be subsequently used for marker-assisted breeding for crop improvement in cardamom. The information on utilization of the SSR loci for generation of markers has been developed into a public database, 'cardamomSSRdb' that is freely available for use by the cardamom community.

Histological and molecular insights in to in vitro regeneration pattern of Xanthosoma sagittifolium

A study on the effect of various phytohormonal combinations on in vitro propagation of Cocoyam [Xanthosoma sagittifolium (L.) Schott] was conducted to develop an improved and efficient in vitro regeneration protocol for its mass multiplication. Histological analysis to understand the in vitro regeneration pattern and genetic fidelity assessment of regenerated plants were also carried out. Single shoots excised from in vitro established cultures of X. sagittifolium were used as explants. Among the 32 different phytohormonal combinations tested, indirect organogenesis with intervening callus phase was observed on majority of the media combinations. Meristematic clump formation was optimally achieved on all the tested media combinations with maximum 43.54 ± 0.51 shoot primordia on MS medium containing 0.2 mg/L BAP + 0.1 mg/L NAA followed by 36.44 ± 0.76 shoot primordia on MS medium having 2.5 mg/L TDZ. Micro-morphological analysis of different morphogenetic structures revealed that the regeneration of cocoyam is well executed via meristematic nodules, shoot primordia formation that may evolve in to proper shoots. Adventitious shoots (> 2 cm) were successfully (100.00 ± 0.00%) rooted on the half-strength MS medium containing IBA (0.05–1.0 mg/L) and IAA (0.05–0.5 mg/L). The number of roots ranged from 0.78 ± 0.31 on the control half-strength MS medium to 13.94 ± 0.46 on half-strength MS supplemented with 1.0 mg/L IBA. Considering somaclonal variations as a potential restriction to in vitro multiplication of plants, genetic stability was assessed using 40 ISSR primers. The PCR amplification profiles obtained from all the tested propagules (calli, meristematic clumps, regenerated plantlets) were similar to the mother plants indicating the homogeneity of the individuals raised through the regeneration protocol reported here.

Histopathological and molecular methods as complementary diagnostic in case of lymphadenopathies suggestive of bovine tuberculosis.

Bovine tuberculosis (TB) is a chronically evolving zoonotic infectious disease caused by Mycobacterium bovis. Anatomopathological examination during post mortem inspection in bovines is the main resource engaged in sanitary slaughter; however, it is very troublesome since many granulomatous inflammatory processes have similar morphological characteristics. Thus, this study aims to use complementary diagnosis methods (histopathological and polymerase chain reaction - PCR assays) to confirm the macroscopic assessment of lymphadenopathies indicative of tuberculosis in bovines slaughtered in a refrigerated slaughterhouse in Tailândia city, PA, Brazil. Fifty‑one samples were collected from lesions indicative of tuberculosis in pre‑scapular and pre‑pectoral lymph nodes (or different lymphadenitis) in condemned carcasses. Histological processing employed routine techniques carried out at the Laboratory of Animal Pathology of the Federal Rural University of the Amazon, while the PCR assay was performed at the Bacteriology Laboratory of the Evandro Chagas Institute. Results showed that 1.96% of the histopathology samples corresponded to inflammatory processes typical of TB and that, in PCR, 4.25% of the samples had the amplification profile of the M. bovis species. These results indicate the importance of adding complementary methods to assist the sanitary inspection line and make inspection more efficient in its decisions.

Abstract P4-09-12: Baseline and End-of-Treatment Biomarkers in Patients With PIK3CA-Mutated, Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Advanced Breast Cancer From BYLieve Study Cohorts A and B

Abstract Introduction: Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is mutated in ~40% of patients (pts) with hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2−) advanced breast cancer (ABC). PIK3CA mutations are associated with resistance to endocrine therapy (ET) and worse overall survival. Alpelisib (ALP), an α-selective PI3K inhibitor and degrader, is indicated in combination with fulvestrant (FUL) for pts with PIK3CA-mutated (mut) HR+, HER2− ABC following progression on/after ET-based treatments. In the Phase 2, open-label, 3-cohort, noncomparative BYLieve study, clinical benefit of ALP in combination with ET was observed in the post-cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) setting in pts with PIK3CA-mut, HR+, HER2− ABC. Here we report the results of a biomarker analysis using paired baseline (Cycle 1 Day 1) and end-of-treatment (EOT) circulating tumor DNA (ctDNA) samples from pts in BYLieve Cohorts A and B. Methods: In the BYLieve study, pts with PIK3CA-mut, HR+, HER2− ABC had CDK4/6i + aromatase inhibitor (Cohort A; N=127) or CDK4/6i + FUL (Cohort B; N=126) as treatment immediately prior to receiving ALP + FUL and ALP + letrozole, respectively. In this biomarker analysis, gene alterations were detected in ctDNA at baseline and EOT using next-generation sequencing (PanCancer V2 panel). Pts included in this interim analysis had confirmed PIK3CA mutations and matched baseline/EOT samples with enough sequencing coverage and ctDNA fraction to detect mutations at both time points. ctDNA fractions, tumor mutation burden (TMB) distributions, genomic landscapes, gain/loss of PIK3CA and estrogen receptor 1 (ESR1), chromosome 8/11 amplification profiles, and alterations in PI3K pathway and potential CDK4/6i resistance markers were assessed across time points. Sample sizes were small; results should thus be interpreted with caution. Results: Forty-three pts were included in the Cohort A biomarker population and 40 pts were included in Cohort B. ctDNA fraction was numerically higher at EOT compared with baseline in both cohorts; further analyses will be presented. In Cohort A, no significant differences were observed in TMB at EOT compared with baseline (P=0.21). In Cohort B, TMB was higher at EOT compared with baseline (P=0.053). Chromosome 8/11 amplifications were consistent between baseline and EOT for both cohorts. Small variations were observed in ESR1/PIK3CA mutations between baseline and EOT on both cohorts (Table). The status of potential CDK4/6i resistance markers was relatively unchanged at EOT (Table). Loss-of-function mutations in PTEN, a known PI3K inhibitor resistance marker, increased from 9% at baseline to 14% at EOT in Cohort A and from 12% at baseline to 22% at EOT in Cohort B. Conclusions: Between baseline and EOT, only small variations in gene alterations in PIK3CA-mutated HR+, HER2– ABC were observed in the post-CDK4/6i setting. As the disease progressed, increases in loss-of-function mutations in PTEN at EOT in both Cohorts A and B suggested loss of PTEN in PI3K pathway may drive resistance to ALP. Early intervention with ALP, when the tumor is particularly driven by PIK3CA oncogenic mutations and before it develops more genomic complexity, may potentially provide better clinical outcomes. Table. Gene Alteration Gain/Loss at Baseline/EOT Across Cohorts A and B Citation Format: Dejan Juric, Nicholas Turner, Sherene Loi, Fabrice Andre, Stephen K. Chia, Komal Jhaveri, Patrick Neven, Rebecca Dent, Eva Ciruelos, Mukta Joshi, Estelle Roux, Heather Patino, Murat Akdere, Hope Rugo. Baseline and End-of-Treatment Biomarkers in Patients With PIK3CA-Mutated, Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Advanced Breast Cancer From BYLieve Study Cohorts A and B [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-09-12.

DETECCIÓN CLONAL DE CEPAS PARENTALES DE Streptococcus agalactiae Lehmann y Neumann POR AMPLIFICACIÓN ALEATORIA DE ADN POLIMÓRFICO

Streptococcus agalactiae (GBS) causes invasive infections in newborns, being the most frequent the maternal transmission. Epidemiological studies use molecular techniques that assess genetic diversity, including random amplification of polymorphic DNA (RAPD) that is found to be accessible, sensitive and uses arbitrary primers to amplify polymorphic segments of DNA by PCR. The objective was to determine the clonal relationship between GBS strains recovered from mothers and their respective newborns. Four pairs of GBS isolates obtained from vaginal-rectal swabs of mothers and blood cultures of their newborns were studied with RAPD. Primers OPS11, OPB17 and OPB18 were used to select one with the ability to discriminate between non-genetically related strains. The Hunter-Gaston formula that establishes the discrimination index (D) was used; when D>0.90, it is considered that the isolates belong to different clones. The amplification profiles for the eight isolates, using each primer independently, allowed to calculate a D=1 for OPS11, and D=0.84 for OPB17 and OPB18. Therefore, OPS11 was selected for the study of the clonal relationship of the isolates, and similar amplification profiles were found by RAPD for each mother-newborn pair of GBS isolates. Different amplification profiles were observed between pairs of mother-newborn strains, which reveals the discrimination between unrelated strains, confirmed by pulsating field electrophoresis (PFGE). These results indicated vertical transmission for each studied case and robustness of the OPS11 primer. Appropriate conditions of the RAPD trial were found, which is useful for epidemiological studies. Key words: Streptococcus agalactiae, neonatal disease, molecular epidemiology, RAPD technique, vertical transmission

PERFIL DE AMPLIFICAÇÃO E SELEÇÃO DE MARCADORES ISSR PARA ESTUDOS GENÉTICOS EM Calotropis procera

ABSTRACT Sodom apple is a plant species adapted to various ecosystems and has stood out for its economic and ecological importance. We evaluated the amplification profile of 23 ISSR primers and selected polymorphic loci for genetic studies of a natural population of Calotropis procera by collecting and extracting genomic DNA from 33 individuals. Genomic DNA was extracted using the sorbitol protocol and 2% CTAB and the ISSR amplification products were resolved by electrophoresis. Based on the amplification profile, the 23 primers were classified as suitable, moderate, and unsuitable. We described the quality of primers considering the total number of bands, mean bands per primer, percentage of polymorphism, Nei’s genetic diversity (expected heterozygosity – He), assuming Hardy-Weinberg equilibrium and the polymorphic information content (PIC). All ISSR primers showed an amplification profile, which generated 173 bands with an average of 7.5 loci per primer. However, only 18 out of the 23 tested primers allowed visible and high-quality amplification, which were classified as suitable and polymorphic. We also observed a mean of 0.30 and 0.24 for PIC and He estimates, respectively. The DiCA3`RG, TriAGA3`RC, and TriCGC3`RC primers were highly transferable to C. procera (they presented quality for amplification with good reproducibility), with PIC values higher than 0.40, He higher than 0.30, and polymorphism higher than 86%.

Development and diagnostic validation of a one-step multiplex RT-PCR assay as a rapid method to detect and identify Nervous Necrosis Virus (NNV) and its variants circulating in the Mediterranean.

Nervous Necrosis Virus (NNV) represents one of the most threatening pathogens for Mediterranean aquaculture. Several NNV strains are currently co-circulating in the Mediterranean Basin with a high prevalence of the RGNNV genotype and the RGNNV/SJNNV reassortant strain and a more limited diffusion of the SJNNV genotype and the SJNNV/RGNNV reassortant. In the present study, a one-step multiplex RT-PCR (mRT-PCR) assay was developed as an easy, cost-effective and rapid diagnostic technique to detect RGNNV and the reassortant RGNNV/SJNNV strain and to distinguish them from SJNNV and the reassortant SJNNV/RGNNV strain in a single RT-PCR reaction. A unique amplification profile was obtained for each genotype/reassortant enabling their rapid identification from cell culture lysates or directly from brain tissues of suspected fish. The method’s detection limit varied between 102.3 and 103.4 TCID50 ml-1 depending on viral strains. No cross-reacitivty with viruses and bacteria frequently associated with gilthead seabream, European seabass and marine environment was observed. The mRT-PCR was shown to be an accurate, rapid and affordable method to support traditional diagnostic techniques in the diagnosis of VNN, being able to reduce considerably the time to identify the viral genotype or the involvement of reassortant strains.

AmPyfier: Test amplification in Python

AbstractTest amplification aims to automatically improve a test suite. One technique generates new test methods through transformations of the original tests. These test amplification tools heavily rely on analysis techniques that benefit a lot from type declarations present in the source code of projects written in statically typed languages. In dynamically typed languages, such type declarations are not available, and therefore, research regarding test amplification for those languages is sparse. Recent work has brought test amplification to the dynamically typed language Pharo Smalltalk by introducing the concept of dynamic type profiling. The technique is dependent on Pharo‐specific frameworks and has not yet been generalized to other languages. Another significant downside in test amplification tools based on the mutation score of a test suite is their high time cost. In this paper, we present AmPyfier, a tool that brings test amplification and type profiling to the dynamically typed language Python. AmPyfier introduces multi‐metric selection in order to increase the time efficiency of test amplification. We evaluated AmPyfier on 11 open‐source projects and found that AmPyfier could strengthen 37 out of 54 test classes. Multi‐metric selection decreased the time cost ranging from 17% to 98% as opposed to selection based on the full mutation score.

Characterization and selection of inter simple sequence repeat markers for genetic studies of mesquite

Since characterization and selection of molecular markers are crucial steps in genetic research for plant conservation and/or (pre) breeding, this study aimed to describe the amplification profile of Inter Simple Sequence Repeat (ISSR) markers in Prosopis juliflora (Sw.) DC. so that the most suitable ones could be selected. To do so, the genomic DNA of 16 individuals collected at the Federal Institute - Campus Itapetinga, Bahia State, were extracted at the Applied Molecular Genetics Laboratory of the State University of Southwest Bahia, in Itapetinga-BA (Brazil). The amplification profile was obtained using 23 ISSR primers, visualized after electrophoresis in 2% agarose gels, and photo-documented under ultraviolet light; then, genotyping was performed. In total, amplification of 206 markers was observed, with an average of nine tags per primer, a polymorphic percentage equivalent to 90% of the markers generated; and mean polymorphic information content of 0.63. Expected and observed heterozygosity means were similar (0.28 and 0.29, respectively). Our findings confirm that ISSR primers are suitable for molecular-genetic studies of P. juliflora. Among the 23 analyzed primers, 13 can be prioritized (DiGA3’G, DiCA 3'RG, DiCA 3'YG, DiGA 3'C, DiGA 3'RC, DiGA 3'T, TriCAG 3'RC, TriTGT 3'YC, TriAAC 3'RC, TriAAG 3'RC, TriCGC 3'RC, TriGAC 3'RC, and TriGGA 3'RC) for genetic studies of P. juliflora.

CCND1 Amplification Profiling Identifies a Subtype of Melanoma Associated With Poor Survival and an Immunosuppressive Tumor Microenvironment.

BackgroundAlthough melanoma is generally regarded as an immunogenic cancer that will respond to immune checkpoint inhibitors (ICIs), melanomas with CCND1 amplification respond poorly to these therapies. Further understanding how CCND1 amplification impacts the effectiveness of ICI therapy is important for the design of future clinical trials.MethodsWe used data from tumor samples taken from Chinese patients with melanoma analyzed at the Geneplus Institute (n=302), as well as data from the Cancer Genome Atlas (TCGA) database (n=367) and the Memorial Sloan Kettering Cancer Center (MSKCC) database (n=350) to estimate the prevalence of CCND1 amplification in melanoma, interrogate the relationship between CCND1 amplification and survival in patients with melanoma, and explore the molecular mechanisms of CCND1 amplification. We also established a murine model of melanoma harboring CCND1 amplification and utilized RNA-seq to verify the findings from human tissue samples.ResultsData from all three sources revealed a low frequency of CCND1 amplification co-occurring with BRAF V600, NRAS, NF1, and KIT mutations. Data from TCGA did not show a statistically significant correlation between CCND1 amplification and prognosis, irrespective of ICI use. In contrast, the MSKCC cohort showed that CCND1 amplification was an unfavorable prognostic factor for patients with melanoma, especially for patients who received ICIs and had a high tumor mutation burden (TMB). The TCGA data showed that CCND1 amplification was associated with a higher proportion of immunosuppressive cells (Treg cells and M2 macrophages) and a lower proportion of immune boosting cells (follicular helper T cells naïve B cells, CD8+ T cells). Murine models supported the association between a suppressive immune microenvironment and CCND1 amplification; tumors with CCND1 amplification had reduced mRNA expression of CD8, Gzm, B2m and Tap1, significantly higher proportions of resting CD4 memory T cells and significantly lower proportions of plasma cells, CD8 T cells, and T follicular helper cells. Furthermore, a Gene Set Enrichment Analysis (GSEA) analysis of data from the TCGA database suggested that signaling pathways involved in oxidative phosphorylation, reactive oxygen species, adipogenesis, fatty acid metabolism, DNA repair, and Myc targets were differentially enriched in melanoma tumors with CCND1 amplification. Finally, we observed a notable reduction in levels of angiogenesis-related molecules (encoded by HIF1A, VEGFA, VEGFR1, FGF2, FGFR1, FGFR4, HGF, PDGFA, PDGFRA, ANGPT1, and ANGPT2) in a high CCND1 amplification group from the TCGA database.ConclusionsMelanoma with CCND1 amplification is an independent genomic subtype associated with a poor prognosis, an immunosuppressive TME, activated oxidative and lipid metabolism, and down-regulated angiogenesis. Therefore, avoiding ICIs and antiangiogenic agents, while employing CDK4/6 inhibitors alone or in combination with ICIs, and targeting oxidative and lipid metabolism pathways, may be effective therapeutic strategies for melanoma patients harboring CCND1 amplification.

A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile.

Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragments varies widely among different sequences and, after a few rounds of phage display panning, the output repertoire often includes rapidly amplified sequences with low or no binding activity, significantly diminishing the efficiency of antibody isolation. In this work, a novel synthetic single-chain variable fragment (scFv) library with complementarity-determining region (CDR) diversities aimed at improved amplification efficiency was designed and constructed. A previously reported synthetic scFv library with low, non-combinatorial CDR diversities was panned against protein A superantigen, and the library repertoires before and after the panning were analyzed by next generation sequencing. The enrichment or depletion patterns of CDR sequences after panning served as the basis for the design of the new library. Especially for CDR-H3 with a higher and more random diversity, a machine learning method was applied to predict potential fast-amplified sequences among a simulated sequence repertoire. In a direct comparison with the previous generation library, the new library performed better against a panel of antigens in terms of the number of binders isolated, the number of unique sequences, and/or the speed of binder enrichment. Our results suggest that the amplification-centric design of sequence diversity is a valid strategy for the construction of highly functional phage display antibody libraries.