Amplification Of Specific Sequences Research Articles

The association of the killer cell immunoglobulin-like receptor (KIR) genotype distribution and HLA-C ligands in colorectal cancer in the eastern region of Saudi Arabia

Colorectal cancer (CRC) is the most common cause of cancer-related mortality globally. It ranks as the most common cancer among men and the third most prevalent among women in Saudi Arabia, especially in the eastern region. The immune system's response to cancer is significantly influenced by natural killer cells through their killer-cell immunoglobulin-like receptors (KIRs) interaction with human leukocyte antigen (HLA) molecules. Our research aimed to target a homogeneous ethnic group in the eastern region of Saudi Arabia, analyzing the distribution of 16 KIR genes and HLA-C1/C2 allotypes in 50 CRC patients and 63 healthy controls using the sequence-specific PCR amplification method. Findings revealed significantly lower frequencies of the 2DL2 and 3DL1 genes in CRC patients compared to controls (OR = 2.21; P = 0.04) and (OR = 7.46; P = 0.00009), respectively. Additionally, a higher prevalence of HLA-C2 was noted in CRC patients (84 %) versus controls (66.7 %) (OR = 2.26; P = 0.04). Conversely, the HLA-C1C2 combination showed a protective effect against CRC (OR = 0.38; P = 0.04). Our combinatorial analysis further identified specific gene combinations correlating with CRC risk or protection. Notably, the absence of KIR2DL2 combined with the presence of KIR2DS2 emerged as a significant risk factor, while various combinations involving KIR2DL2 and/or KIR2DS1 with HLA-C ligands were associated with either increased susceptibility or protection. The study underscores the protective role of KIR2DL2 against CRC in Saudi Arabia's eastern region and suggests that the absence of KIR2DL2, especially when KIR2DS2 is present, might increase CRC risk. This research contributes to understanding genetic influences on CRC susceptibility, emphasizing the potential of KIR and HLA interactions as biomarkers for CRC risk assessment.

HOW THE PAST SHAPES CURRENT STORIES: (EPI)GENETIC EPIDEMIOLOGICAL PROFILES OF METABOLIC SYNDROME IN BRAZILIAN MENNONITES

Mennonites present cc. 500 years genetic isolation and three bottleneck events that reducedtheir genetic diversity. In order to identify (epi)genetic markers for metabolic syndrome (MS),we used a modified version of the Brazilian National Health Survey to interview 762Mennonites from three settlements, between 2016-2023. We compared 63 vs. 127 exomes(Illumina HiSeq) from Mennonites with/without metabolic syndrome (MS) and genotypedcandidate variants in regulatory regions with mass spectrometry (iPLEX) and sequence-specific amplification (PCR-SSP). We also evaluated DNA methylation of the NR3C1 andFKBP5 genes in peripheral blood mononuclear cells (PBMCs) of up to 66 and 141 individualswith/without MS. MS prevalence was 14.02%, less than half the one reported forNeobrazilians (34.8%, P<0.00001), being paralleled by a three times lower prevalence ofacute myocardial infarction (AMI). Among independent MS risk factors, we found lowermaternal warmth in infancy (OR=1.59, P=0.019) and a higher susceptibility to AMI with theharshest migratory route to Brazil (OR=1.57, P=0.001). Thirty-nine variants of 34 genes wereassociated with MS (p<0.02), 41% create/disrupt CpG sites and 12 were associated withvisceral adipose and/or cardiovascular tissue expression. There were no methylationdifferences between individuals with and without MS in PBMCs with the NR3C1 and FKBP5genes, pointing to other epigenetic causal effects. In conclusion, Mennonites have a peculiarepidemiological profile marked by (epi)genetic founder effects that also affect theirmetabolism, calling for urgent action for prevention and to alleviate the burden ofcomorbidities due to late diagnosis.

Detection of Soybean-Derived Components in Dairy Products Using Proofreading Enzyme-Mediated Probe Cleavage Coupled with Ladder-Shape Melting Temperature Isothermal Amplification (Proofman–LMTIA)

Food adulteration is a serious problem all over the world. Establishing an accurate, sensitive and fast detection method is an important part of identifying food adulteration. Herein, a sequence-specific ladder-shape melting temperature isothermal amplification (LMTIA) assay was reported to detect soybean-derived components using proofreading enzyme-mediated probe cleavage (named Proofman), which could realize real-time and visual detection without uncapping. The results showed that, under the optimal temperature of 57 °C, the established Proofman-LMTIA method for the detection of soybean-derived components in dairy products was sensitive to 1 pg/μL, with strong specificity, and could distinguish soybean genes from those of beef, mutton, sunflower, corn, walnut, etc. The established Proofman-LMTIA detection method was applied to the detection of actual samples of cow milk and goat milk. The results showed that the method was accurate, stable and reliable, and the detection results were not affected by a complex matrix without false positives or false negatives. It was proved that the method could be used for the detection and identification of soybean-derived components in actual dairy products samples.

Key methodological challenges in detecting circulating miRNAs in different biofluids.

The technological advancement in diagnostic techniques has immensely improved the capability of predicting disease progression. Yet, there is a great interest in developing newer biomarkers that can enhance disease risk prediction thereby minimising the associated morbidity and mortality. Circulating miRNAs, a non-coding RNA molecule, are critical regulators in the pathophysiology of various complex multifactorial diseases. In recent years, circulating miRNAs have been enormously studied and are considered as an emerging biomarker due to their easy accessibility, stability, and detection by sequence-specific amplification methods. However, there is a distinct lack of consensus regarding the preanalytical factors such as preferred sample selection, methodological aspects, etc that may independently or together influence the detection of circulating miRNAs resulting in erroneous expression profiles. Therefore, the present review makes an attempt to highlight the various pre-analytical and analytical factors that can potentially influence the circulating miRNA levels. Literature on circulating miRNA's stability, processing and quantitation in different biofluids along with the effect of various controllable and uncontrollable factors influencing circulating miRNA expression have been summarised in the current review.

Isothermal amplification using sequence-specific fluorescence detection of SARS coronavirus 2 and variants in nasal swabs.

Coronavirus disease 2019 is a public health challenge requiring rapid testing for the detection of infections and transmission. Nucleic acid amplification tests targeting SARS coronavirus 2 (CoV2) are used to detect CoV2 in clinical samples. Real-time reverse transcription quantitative PCR is the standard nucleic acid amplification test for CoV2, although reverse transcription loop-mediated isothermal amplification is used in diagnostics. The authors demonstrate a sequence-specific reverse transcription loop-mediated isothermal amplification-based nucleic acid amplification assay that is finished within 30 min using minimally processed clinical nasal swab samples and describe a fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay using labeled primers and a quencher oligonucleotide. This assay can achieve rapid (30 min) and sensitive (1000 plaque-forming units/ml) fluorescence detection of CoV2 (WA1/2020), B.1.1.7 (Alpha) and variants of concern Delta (B.1.617.2) and Omicron (B.1.1.529) in nasal samples.

Killer immunoglobulin-like receptor (KIR) genes are associated with the risk of episodes of high-level and detectable viremia among HIV controllers

Background: HIV controllers (HICs) constitute a heterogeneous group of HIV-1 individuals able to suppress plasma viremia to low or undetectable levels in the absence of antiretroviral therapy. Host genetic factors may be involved in the sustained control of viral replication observed. We investigated the distribution and the potential impact of human leukocyte antigens (HLA)-B and -C alleles, killer immunoglobulin-like receptor (KIR) genes, single nucleotide polymorphisms (SNPs) of the NLRP3, CARD8 and IL-1β inflammasome genes, and CCR5Δ32 mutation on the viral control among HICs. Methods: In total, 28 HICs were categorized as persistent elite controllers (PECs, n = 7), ebbing elite controllers (EECs, n = 7), and viremic controllers (VCs, n = 14) according to the level of natural suppression of viremia. HLA alleles were assigned by sequencing-based typing, KIR alleles by polymerase chain reaction (PCR) sequence-specific amplification, SNPs by real-time PCR, and the CCR5Δ32 mutation by PCR. Results: Significant differences were observed in the pairwise comparisons of protective HLA-B alleles, KIR Bx genotype, KIR2DL3 + C1 pair, KIR2DL5, and KIR2DS5 allelic carrier frequencies among the HIC groups. Multivariate models showed that HICs without the KIR2DL3 allele or without KIR2DL3 + C1/C2 pair, with the HLA-C*08 allele or with the NLRP3 rs10754558-G SNP had a higher mean hazard of a viral load above 2,000 copies/mL, while a lower mean hazard of this event was observed for HICs with KIR2DL5, KIR2DS1, KIR2DS5, and KIR3DS1 alleles. Moreover, HICs with the KIR2DS5 allele had less risk of undergoing viral load (VL) blips within the same normalized period than those participants without this allele, while HICs without the KIR2DL3 allele had a mean higher risk of experiencing VL blips. Conclusions: These results indicate that innate immune mechanisms may play an essential role in modulating the sustained control of viral replication in HICs.

A1B and BB blood group genotypes are risk factors for pulmonary embolism.

Pulmonary embolism (PE) is apotentially life-threatening condition that mainly affects the people of advanced age. While certain blood group phenotypes (non‑O blood group) are known risk factors for the development of venous thromboembolism (VTE), there is no research which investigated the association of blood group genotypes with severity of PE. The aim of this study was to investigate the frequency of ABO blood group genotypes among the population of patients with PE and to investigate the correlation of the pulmonary embolism severity index (PESI) score to specific ABO blood group genotypes. In this cross-sectional study 74patients with PE diagnosed using CT pulmonary angiography were included and 303 blood donors without VTE or congenital thrombophilia participated as acontrol group. After isolation of genomic DNA ABO blood group genotype was determined using the polymerase chain reaction sequence-specific amplification (PCR-SSP) method. We observed asignificantly higher frequency of A1B and BB genotypes in patients with PE compared to healthy individuals (A1B 14.9% vs. 4.3%, P < 0.001; BB 5.4% vs. 0.7%, P = 0.004), while the O1O1 genotype was significantly less frequent in patients (24.3% vs. 37.3%, P = 0.036). Analyzing the severity of the clinical presentation according to the PESI score, we did not find acorrelation between the severity of the clinical presentation and acertain blood type genotype. Patients with A1B and BB blood type genotype were at increased risk for developing pulmonary embolism, while patients with O1O1 genotype had asignificantly lower risk of developing PE.

Molecular Characteristics of the Serological Weak D Phenotype in Koreans.

Serological weak D is a reaction of 2+ or less to anti-D reagent and includes weak D and partial D phenotypes. Although identifying the RhD subtype is important for transfusion safety, serological tests are insufficient for defining the RhD subtype, and molecular tests are needed. To analyze the molecular characteristics of D variants in Koreans to facilitate the formulation of individualized transfusion strategies, molecular tests such as RhD genotyping using real-time polymerase chain reaction (PCR) and partial-D and/or weak-D sequence-specific amplification (SSP) were performed on 105 Korean Rare Blood Program (KRBP) patients exhibiting serological weak D. In total, 58 out of 68 serologically determined weak D KRBP patients were typed as having weak D or partial D phenotypes via RhD genotyping. In detail, eight (13.8%) were typed as partial DVa or DBS, nine (15.5%) as weak D type 15, and four others (6.8%) as partial DVI, partial DVII, weak D type 2, or weak D type 41 or 45, whereas the rest (n = 37, 63.8%) was typed as having either weak D or partial D. This suggests that serological weak D Koreans who require transfusion should be treated as D-negative.

Using single cell/filament PCR method for study non-cultured cyanobacteria

Cyanobacteria are photosynthetic prokaryotic organisms, and they are believed to be the Earth’s oldest life form. They were responsible for forming the oxygen on the Earth and from then they have been able to adapt to a multitude of environmental conditions, which allowing to be present in a wide range of habitats. When it comes to perform ecological and/or taxonomic studies one of problems which we must confront is the fact of some cyanobacteria are present in the nature in a few amounts, going unnoticed. Moreover, some of them show large mucilaginous sheaths, which making difficulted its isolation and growth later in culture. All these aspects have hindered the molecular assessment of a large portion of traditional cyanobacterial taxa, as Rivularia and Stigonema, especially necessary evaluation in the taxonomic studies. Rivularia genus grows on submerged stones, rocks, and damp soils near riverbanks, often on calcareous substrates and in clear, unpolluted, and streaming or stagnant waters, but also there are several species known from marine littoral. However, Stigonema genus grows aerophytically or subaerophytically on bark of trees or wet rocks, from lowland to the alpine zone of high mountains, but also several species are known from pools, swamps and moors. In this study, several Rivularia colonies collected in the Croatian Adriatic coast and several Stigonema species from Spanish alpine terrestrial environments are being analysed. The used methodology consists of a number of stages. In the first step, the samples are washed in EDTA disodium salt solution for dissolving the associated of calcium carbonate deposits (STEP 1). For the isolation of single cells and filaments, we are using a modified single filament isolation technique for planktonic cyanobacteria applying a glass capillary under sterile conditions (Zapomělová et al. 2008) described by Mareš et al. 2015 (STEP 2). Then, an optimized protocol we are utilized for amplification of the 16S rRNA gene, the associated 16S–23S internal transcribed spacer (ITS) region and the partially the 23S rRNA gene (2,000-2,500 bp) (Berrendero et al. 2016) (STEP 3). Finally, sequences analysis will carry out to determine the phylogenetic position of the different genotypes found inside a same Rivularia colony to be able to relation them with the morphotypes observed by the microscope. In the case of the Stigonema samples, we have successfully gotten the isolation of several filaments and, at the present, we are working on the amplification the studied region. This methodology, based on a glass capillary isolation technique and a PCR protocol for amplification of specific sequences, has been applied with success in the Rivularia and Stigonema samples without the need to cultivate them. Our future research will focus on the amplification of several taxonomic marker genes at the same time.

ROLE OF miRNAs IN CORONARY ARTERY DISEASE: A MINI REVIEW

While coronary artery disease (CAD) has become a major threat worldwide, early diagnosis of CAD, based on timely biomarkers, remains a major unmet clinical challenge. Micro-RNAs (miRNAs) play a pivotal role in development of the cardiovascularsystem while they are associated with multiple cardiovascular diseases. Several cardiac miRNAs (circulating miRNAs) are observable in circulation and function as biomarkers for CVDs diagnosis and therapy. C-miRNAs display various critical features as biomarkers although their distribution is incredibly stable in circulation; their expression is tissue-/diseasespecific and can be easily identified using sequence-specific amplification methods. Such circulating-miRNAs features are useful in designing non-invasive assays to track the development of CVDs. Given substantial success in serum and plasma identification of c-miRNAs. There are several conflicting studies on the alterations of circulating miRNAs concentration in circulation system. Measurements of microRNA (miRNA, miR) in patients with coronary heart disease are impeded by the confoundingeffects of medication commonly used in cardiovascularpatients.

Application of fungal laccase for heavy metals precipitation using tannin as a natural mediator

Nowadays, natural compounds have generated innovative attention for metal removal and precipitation; here, a fungus was isolated from soil samples in tannin media for metal removal. The isolate was identified as ‘Albifimbria viridisʼ by morphology and amplification of specific sequence. The isolate produced high activities of laccase when induced with tannin. The cell-free supernatant with 50 U/ml laccase activities could remove nickel, cobalt, cadmium, and copper nitrate salts by 59.69%, 59.75%, 46.97%, and 66.79%, respectively, while the precipitation of crude enzyme and metal salts by Fourier transform infrared spectroscopy analyses showed that only 2 metal salts (Cobalt and Copper nitrate) are precipitated in oxide form. Tannin was used as a mediator for metal removal, and the data were supported using a zymogram with partially purified laccase and metal precipitation on polyacrylamide gel electrophoresis. A 66 KDa laccase can remove metals and tannin. The metal interaction by this isolated compared with Phanerochaete chrysosporium and Aspergillus niger. All studied fungi could biodegrade the tannin as sole carbon source; however, for maximum activities, the new isolate Albifimbria viridis was selected in further study. The purified fungus in this study is a herbicide and has a high activity of laccase. The precipitation of metals by the enzyme of grown fungus in tannic acid is reported for the first time, which promoted the functional importance of this fungus.

Real-time loop-mediated isothermal amplification assay for rapid detection of Fusarium circinatum.

Fusarium circinatum is the causal agent of pitch canker, a lethal disease of pine and other conifers. Since F. circinatum is a quarantine organism, its timely detection could efficiently prevent its introduction into new areas or facilitate spread management in already infected sites. In this study, we developed a sequence-specific probe loop-mediated isothermal amplification (LAMP) assay for F. circinatum using a field-deployable portable instrument. The assay was able to recognize the pathogen in host tissues in just 30min, and the sensitivity of the assay made it possible to detect even small amounts of F. circinatum DNA (as low as 0.5pg/μl). The high efficiency of this method suggests its use as a standard diagnostic tool during phytosanitary controls.

HLA-G14bp ins/del polymorphism and post-transplant weight gain in kidney transplantation: potential implications beyond tolerance

BackgroundHuman leukocyte antigen (HLA)-G is a non-classical HLA molecule with immunomodulant and immunosuppressive functions, involved in transplantation tolerance. HLA-G14bp ins/del polymorphism in exon 8 has been associated with allograft rejection and kidney transplant outcome, with controversial results. We investigated associations of HLA-G14bp ins/del polymorphism on onset of some of the main post-transplant risk factors, like excess body weight, lipid abnormalities, increased fasting plasma glucose. Polymorphisms of cytokines with both immunosuppressive and metabolic effects were also assessed for comparisons and associated analysis.MethodsThe present study involved kidney transplant recipients (n = 173) in which body mass index, cholesterol, triglycerides, fasting plasma glucose were registered in the first years after transplantation and analyzed in association with genotypes. Presence of hypertension and smoking habits, demographic, transplant-related and therapeutic data of patients were also recorded. Polymerase chain reaction, sequence-specific primer amplification and Taqman allelic discrimination techniques were used for genotyping of HLA-G14bp ins/del, interleukin (IL)-10(−1082G > A,-819 T > C,–592A > C), transforming growth factor-β(+ 869 T > C,+915C > G), IL-6(−174G > C), tumor necrosis factor-α(−308G > A) and IL-18(−137G > C,-607C > A). Effects of genotypes on clinical markers at each time point (pre-transplant and 1 to 5 years after transplant) were analyzed using a repeated-measures general linear model analysis; adjustment for potential confounders was performed.ResultsResults showed that HLA-G14bp ins/ins was significantly associated with obesity, in particular after transplantation (3 years, p = 0.002, OR = 4.48, 95% CI:1.76–11.41). Post-transplant body mass index was significantly increased in HLA-G14bp ins/ins carriers (3 and 4 years, p = 0.033 and p = 0.044); effects of HLA-G14bp genotypes on post-transplant BMI were confirmed by using repeated-measures analysis and after controlling for confounding variables. Cytokine genotypes did not associate with the examined factors.ConclusionsThe study of transplanted patients allowed to evidence a potential relationship between post-transplant weight gain and HLA-G14bp ins/del polymorphism, previously involved in rejection for its immunosuppressive/tolerogenic activity. This novel association could widen the knowledge of the role and functions of HLA-G molecules in diseases and transplantation.

Challenges in Using Circulating Micro-RNAs as Biomarkers for Cardiovascular Diseases.

Micro-RNAs (miRNAs) play a pivotal role in the development and physiology of the cardiovascular system while they have been associated with multiple cardiovascular diseases (CVDs). Several cardiac miRNAs are detectable in circulation (circulating miRNAs; c-miRNAs) and are emerging as diagnostic and therapeutic biomarkers for CVDs. c-miRNAs exhibit numerous essential characteristics of biomarkers while they are extremely stable in circulation, their expression is tissue-/disease-specific, and they can be easily detected using sequence-specific amplification methods. These features of c-miRNAs are helpful in the development of non-invasive assays to monitor the progress of CVDs. Despite significant progress in the detection of c-miRNAs in serum and plasma, there are many contradictory publications on the alterations of cardiac c-miRNAs concentration in circulation. The aim of this review is to examine the pre-analytical and analytical factors affecting the quantification of c-miRNAs and provide general guidelines to increase the accuracy of the diagnostic tests in order to improve future research on cardiac c-miRNAs.

A sequence-specific plasmonic loop-mediated isothermal amplification assay with orthogonal color readouts enabled by CRISPR Cas12a

Herein, we introduce a sequence-specific plasmonic loop-mediated isothermal amplification (LAMP) assay with dual, complementary color readouts enabled by CRISPR Cas12a. Using this assay, any double-stranded LAMP amplicon containing a 5'-TTN PAM sequence can be recognized by Cas12a through a specific CRISPR RNA. The signal transduction is achieved using two orthogonal plasmonic systems mediated by Cas12a.

Identification through Culture and Molecular Methods of Campylobacter jejuni, Campylobacter coli and Campylobacter fetus in Surface Waters in Rasht

Backgrounds: As zoonotic infectious agents, Campylobacter spp. are important factors causing gastroenteritis in humans. Surveys show that the three strains; Campylobacter jejuni, Campylobacter coli and Campylobacter fetus play a major role in human infections. Identification of these infectious agents is valuable for sanitary control of disease transmission through water resources.&#x0D; Objectives: The aim of this study was identification and molecular diagnosis of Campylobacter jejuni, Campylobacter coli and Campylobacter fetus in surface waters in Rasht.&#x0D; Materials and Methods: This cross-sectional study was conducted on 45 samples of surface water in Rasht collected according to water health guidelines. After culture and biochemical tests on collected samples, detection and identification of Campylobacter jejuni, Campylobacter coli and Campylobacter fetus was done using sequence-specific amplification by Multiplex PCR. The results were subjected to statistical analysis using SPSS software.&#x0D; Results: Out of 45 samples tested, 6 were positive in culture, four of which were identified as Campylobacter jejuni after biochemical tests. Using Multiplex PCR, 8 samples were positive, from which 3 were Campylobacter jejuni, 1 Campylobacter coli and 4 were positive for both Campylobacter jejuni and Campylobacter coli. All the samples did not yield C. fetus.&#x0D; Conclusions: Multiplex PCR is regarded a diagnostic method with higher sensitivity and specificity than compared to methods for Campylobacter. The prevalence of Campylobacter jejuni and Campylobacter coli in surface waters in Rasht is considerable. Therefore, public health measures for the control of these organisms are recommended.

Precise definition of starting time by capillary-based chemical initiation of digital isothermal DNA amplification

Digital polymerase chain reaction is a sensitive and reproducible method to assess the presence or absence of the amplification of individual target molecules confined in isolated compartments; this is used for the quantification of nucleic acids. In this paper, the precise definition of the start time of recombinase polymerase amplification (RPA) is proposed to achieve the digital quantification of nucleic acids at the single molecule level. RPA is a sequence-specific isothermal amplification method. Since the reaction will start immediately albeit slowly at room temperature following the addition of the chemical initiator (magnesium acetate), the number of false positives in digital RPA is increased if all reagents are mixed prior to compartmentalization. A capillary-based setup is described here to control the initiation of RPA reactions by encapsulating the chemical initiator to each reaction compartment using shear force when passed through a cross connector. Thousands of independent compartments are generated. The performance of digital droplet RPA (ddRPA) was validated by counting the positive application results of target molecules (Avian virus DNA) confined in the partitions. The ddPRA capillary-based setup provides a simple nucleic acid quantification method without thermal cycling. Potential applications in clinical and academic research under resource-limited settings can be envisaged. The ability to initiate chemical reaction compartments by the encapsulation of a chemical initiator using similar capillaries can be applied to a broader range of applications.

Sickening or Healing the Heart? The Association of Ficolin-1 and Rheumatic Fever.

Rheumatic fever (RF) and its subsequent progression to rheumatic heart disease (RHD) are chronic inflammatory disorders prevalent in children and adolescents in underdeveloped countries, and a contributing factor for high morbidity and mortality rates worldwide. Their primary cause is oropharynx infection by Streptococcus pyogenes, whose acetylated residues are recognized by ficolin-1. This is the only membrane-bound, as well as soluble activator molecule of the complement lectin pathway (LP). Although LP genetic polymorphisms are associated with RF, FCN1 gene's role remains unknown. To understand this role, we haplotyped five FCN1 promoter polymorphisms by sequence-specific amplification in 193 patients (138 with RHD and 55, RF only) and 193 controls, measuring ficolin-1 serum concentrations in 78 patients and 86 controls, using enzyme-linked immunosorbent assay (ELISA). Patients presented lower ficolin-1 serum levels (p < 0.0001), but did not differ according to cardiac commitment. Control's genotype distribution was in the Hardy-Weinberg equilibrium. Four alleles (rs2989727: c.−1981A, rs10120023: c.−542A, rs10117466: c.−144A, and rs10858293: c.33T), all associated with increased FCN1 gene expression in whole blood or adipose subcutaneous tissue (p = 0.000001), were also associated with increased protection against the disease. They occur within the *3C2 haplotype, associated with an increased protection against RF (OR = 0.41, p < 0.0001) and with higher ficolin-1 levels in patient serum (p = 0.03). In addition, major alleles of these same polymorphisms comprehend the most primitive *1 haplotype, associated with increased susceptibility to RF (OR = 1.76, p < 0.0001). Nevertheless, instead of having a clear-cut protective role, the minor c.−1981A and c.−144A alleles were also associated with additive susceptibility to valvar stenosis and mitral insufficiency (OR = 3.75, p = 0.009 and OR = 3.37, p = 0.027, respectively). All associations were independent of age, sex or ethnicity. Thus, minor FCN1 promoter variants may play a protective role against RF, by encouraging bacteria elimination as well as increasing gene expression and protein levels. On the other hand, they may also predispose the patients to RHD symptoms, by probably contributing to chronic inflammation and tissue injury, thus emphasizing the dual importance of ficolin-1 in both conditions.

Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity.

In this review, we explore progress on DNA aptamers (evolved DNA), DNA circuits (designed DNA), and the newest projects that integrate both. Designed DNA nanotechnology includes static nanostructures, dynamic nanodevices, and reaction networks (sometimes called DNA circuits). DNA circuits are dynamic DNA reactions that perform computations and sequence-specific amplification. Directed evolution can be used to produce DNA that can recognize specific targets. Aptamers are evolved nucleic acids; they are produced artificially with an in vitro selection process. DNA aptamers are molecular recognition elements made of single-stranded DNA (ssDNA) with the potential to interact with proteins, small molecules, viruses, and even cells. Designed molecular structures can incorporate aptamers for applications with immediate practical impact.

Verification of taxonomic relationships within the genus Secale (Poaceae: Pooideae: Triticeae) based on multiple molecular methods

This study aimed to verify the taxonomic relationships within the genus Secale. The plant material included 16 wild rye accessions from four species. Two approaches were applied: 1) whole genome scanning using three molecular marker systems: diversity arrays technology sequencing, simple sequence repeats and sequence-specific amplification polymorphism; and 2) characterisation based on polymorphisms within the sequences of two genes involved in benzoxazinoid biosynthesis: ScBx1 and ScBx5. Bayesian and neighbour-joining clustering and principal coordinate analysis were applied to illustrate relationships among species and accessions of Secale based on genetic distance (GD) matrices. Pearson’s correlation analysis between GD matrices was conducted. Clustering of Secale accessions revealed that S. sylvestre samples were the most divergent. The remaining accessions formed two clusters. One of them comprised S. strictum accessions while the second cluster consisted of subspecies of S. cereale, the species S. vavilovii and S. strictum subsp. ciliatoglume.