Specific DNA Fragments Research Articles

Multiplex polymerase chain reaction (mPCR) assay for detection and differentiation of Campylobacter jejuni and Campylobacter coli in carcasses of chicken

Introduction: Campylobacter is a major cause of gastroenteritis in developed countries. In Brazil, the incidence of this disease and consequently those that may occur after the infection is unknown. The prevalence of Campylobacter in raw poultry products varies widely. Although Brazil is the largest world exporter of chicken there is little information on the contamination of this product by Campylobacter. Objective: develop a multiplex PCR for the detection and differentiation between C. jejuni and C coli. Methods: The PCR was developed using mapA primers specific for detection of C. jejuni and ceuE primers specific for detection of C. coli which produce specific DNA fragments of 202-bp and 889-pb, respectively. The standardized PCR was tested on 11 different isolates of Campylobacter and on 22 non-Campylobacter species and the specificity was 100%. Results: Campylobacter was detected from chicken skin artificially contaminated with approximately 50 colony forming unit (CFU) of Campylobacter per 10-g, after 48 h of selective enrichment. Campylobacter spp. was detected in thirteen (46.4%) of 28 analyzed chicken carcasses purchased from local retail market. Specific DNA fragments of the PCR confirmed the presence of C. jejuni and C. coli. Conclusion: The standardized multiplex PCR was found to be sensitive and specific on the detection and simultaneously differentiation of C. jejuni and C. coli after 48h of analysis.

Disposable amperometric biotool for peanut detection in processed foods by targeting a chloroplast DNA marker

This work reports the development and application of a disposable amperometric sensor built on magnetic microcarriers coupled to an Express PCR strategy to amplify a specific DNA fragment of the chloroplast trnH-psbA. The procedure involves the selective capture of a 68-mer synthetic target DNA (or unmodified PCR products) through sandwich hybridization with RNA capture probe-modified streptavidin MBs and RNA signaling probes, labeled using antibodies specific to the heteroduplexes and secondary antibodies tagged with horseradish peroxidase. Amperometric measurements were performed on screen-printed electrodes using the H2O2/hydroquinone system. Achieving a LOD of 3 pM for the synthetic target, it was possible to detect 2.5 pg of peanut DNA and around 10 mg kg−1 of peanut in binary mixtures (defatted peanut flours prepared in spelt wheat). However, the detectability decreased between 10 and 1000 times in processed samples depending on the treatment. The Express PCR-bioplatform was applied to the detection of peanut traces in foodstuff.

Exploring Gut Microbiome Composition and Circulating Microbial DNA Fragments in Patients with Stage II/III Colorectal Cancer: A Comprehensive Analysis.

Colorectal cancer (CRC) significantly contributes to cancer-related mortality, necessitating the exploration of prognostic factors beyond TNM staging. This study investigates the composition of the gut microbiome and microbial DNA fragments in stage II/III CRC. A cohort of 142 patients with stage II/III CRC and 91 healthy controls underwent comprehensive microbiome analysis. Fecal samples were collected for 16S rRNA sequencing, and blood samples were tested for the presence of microbial DNA fragments. De novo clustering analysis categorized individuals based on their microbial profiles. Alpha and beta diversity metrics were calculated, and taxonomic profiling was conducted. Patients with CRC exhibited distinct microbial composition compared to controls. Beta diversity analysis confirmed CRC-specific microbial profiles. Taxonomic profiling revealed unique taxonomies in the patient cohort. De novo clustering separated individuals into distinct groups, with specific microbial DNA fragment detection associated with certain patient clusters. The gut microbiota can differentiate patients with CRC from healthy individuals. Detecting microbial DNA fragments in the bloodstream may be linked to CRC prognosis. These findings suggest that the gut microbiome could serve as a prognostic factor in stage II/III CRC. Identifying specific microbial markers associated with CRC prognosis has potential clinical implications, including personalized treatment strategies and reduced healthcare costs. Further research is needed to validate these findings and uncover underlying mechanisms.

Biologically produced and metal-organic framework delivered dual-cut CRISPR/Cas9 system for efficient gene editing and sensitized cancer therapy

Manipulation of the lactate metabolism is an efficient way for cancer treatment given its involvement in cancer development, metastasis, and immune escape. However, most of the inhibitors of lactate transport carriers suffer from poor specificity. Herein, we use the CRISPR/Cas9 system to precisely downregulate the monocarboxylate carrier 1 (MCT1) expression. To avoid the self-repairing during the gene editing process, a dual-Cas9 ribonucleoproteins (duRNPs) system is generated using the biological fermentation method and delivered into cells by the zeolitic imidazolate framework-8 (ZIF-8) nanoparticles, enabling precise removal of a specific DNA fragment from the genome. For efficient cancer therapy, a specific glucose transporter 1 inhibitor (BAY-876) is co-delivered with the duRNPs, forming BAY/duRNPs@ZIF-8 nanoparticle. ZIF-8 nanoparticles can deliver the duRNPs into cells within 1 h, which efficiently downregulates the MCT1 expression, and prohibits lactate influx. Through simultaneous inhibition of the lactate and glucose influx, BAY/duRNPs@ZIF-8 prohibits ATP generation, arrests cell cycle, inhibits cell proliferation, and finally induces cellular apoptosis both in vitro and in vivo. Consequently, we demonstrate that the biologically produced duRNPs delivered into cells by the nonviral ZIF-8 carrier have expanded the CRISPR/Cas gene editing toolbox and elevated the gene editing efficiency, which will promote biological studies and clinical applications. Statement of significanceThe CRISPR/Cas9 system, widely used as an efficient gene editing tool, faces a challenge due to cells’ ability to self-repair. To address this issue, a strategy involving dual-cutting of the genome DNA has been designed and implemented. This strategy utilizes biologically produced dual-ribonucleoproteins delivered by a metal-organic framework. The effectiveness of this dual-cut CRISPR-Cas9 system has been demonstrated through a therapeutic approach targeting the simultaneous inhibition of lactate and glucose influx in cancer cells. The utilization of the dual-cut gene editing strategy has provided valuable insights into gene editing and expanded the toolbox of the CRISPR/Cas-based gene editing system. It has the potential to enable more efficient and precise manipulation of specific protein expression in the future.

Survey of bacterial and protozoan microorganisms in ticks collected from birds in the Atlantic Forest biome in Piraí municipality, Rio de Janeiro, Brazil</p >

This study aimed to verify the diversity of ticks in wild birds of remnant fragments of the Atlantic Forest biome in the municipality of Piraí, Rio de Janeiro state, and to detect pathogenic agents in the ticks collected. Birds were captured between June 2016 and April 2017. The collected ticks were identified using a specific dichotomous key. Tick DNA was tested using polymerase chain reaction (PCR) for Borrelia spp., Rickettsia spp., Ehrlichia spp., Anaplasma spp., and Babesia spp. In total, 150 birds were captured, including 64 species, 18 families, and 5 orders. Of these, 22 (14.67%) of 18 different species were parasitized by Amblyomma spp. (n=7), Amblyomma longirostre (n=10), Amblyomma sculptum (n=1), and Amblyomma parkeri (n=21). Only one Amblyomma sp. amplified specific DNA fragments for Rickettsia amblyommatis, whereas the others were negative for Borrelia spp., Ehrlichia spp., Anaplasma spp., and Babesia spp. The avifauna play an important role in maintaining the life cycle of ticks, in addition to contributing to the dispersion of arthropods and the microorganisms transmitted by them.

Universal photoelectrochemical aptasensing platform for antibiotic based on CuInS2/rGO and triplex DNA

In this work, a universal and convenient photoelectrochemical (PEC) biosensor was proposed to detect antibiotic on the basis of CuInS2/rGO and triplex DNA molecular switch. High performance photoactive structure was formed via p-type CuInS2 nanosphere complexed with rGO, which was employed to enhance the cathode photocurrent. Capture probe (CP) was conjugated onto the photoactive interface through covalent bonding. In the absence of target, the triplex DNA (THMS) was in a closed state. After introducing a target, the interaction between the target and the specific ring part DNA fragment leaded to the dissociation of the THMS and thereby liberated the single strand DNA (SP). The above identification process was completed in the homogeneous solution. Then, SP was captured to the electrode by CP and hybridized to form dsDNA. The steric effect of dsDNA hindered the interfacial charge transfer, resulting in signal-off photocurrent output. By only altering the specific loop section sequence of THMS, different targets can release the same SP, and can be detected on the same sensing platform under the same testing conditions. As proof of principle, three kinds of antibiotics amoxicillin (AMOX), ampicillin (AMP) and tobramycin (TOB) was detected, achieving limit of detection values of 3.17 pM, 0.63 nM and 2.81 fM, respectively. This approach was also used to detect antibiotic residues in food and environmental samples, which provides a promising paradigm for developing universal, high-performance and convenient PEC biosensing platform.

Investigation of potentially pathogenic Vibrionaceae in Saint-Louis city, Senegal.

as cholera, due to toxigenic bacteria Vibrio cholera (serogroups O1 and O139), is a major public health threat in Africa, the aim of this work was to investigate potentially pathogenic Vibrionaceae bacteria firstly from human stool samples, and secondly from various environmental water points of Saint-Louis city in Senegal. a hospital-based study was conducted between 2013 and 2015. Stool samples were taken and cultured from daily incoming patients or hospitalized for acute diarrhea at Saint-Louis´ regional hospital. For environment, a monthly longitudinal sampling from January to October 2016 was carried out at 10 sites in the city. We used total DNA extracted from APW (alkaline peptone water) broth solutions and on suspect bacterial colonies to run PCR Multiplex targeting specific DNA fragments to detect Vibrio genus and specific species. In case of positivity, a simplex PCR was performed to test for cholera toxins Ctx, and V. parahaemolyticus TRH and TDH. for 43 patients screened, bacterial culture was positive in 6% of cases but no strain of V. cholerae or other Vibrio sp. was isolated. PCR on 90 APW solutions were positive for Vibrio sp.(n = 43), V. cholera(n = 27), V. mimicus(n = 16), V. parahaemolyticus(8), V. alginolyticus(n = 4), and V. vulnificus(n = 2). Unlike for those on suspected colonies which were positive for a majority of V. parahaemolyticus (n = 40) and V. cholerae non-O1 / O139 (n = 35). Six strains of V. parahaemolyticus carried TRH gene, 3 of which expressed simultaneously virulence TRH and TDH genes. For physicochemical parameters, all temperatures varied similarly according to a unimodal seasonality, as well as salinity. despite the presence of natural populations of Vibrionaceae, even toxigenic ones, was noted in water environment, along with favorable habitat conditions that could play a role in transmission of Vibriosis in the Saint Louis population, we did not isolate any of them from patients screened at the hospital.

Study on Drug Resistance to Treatment for Ureaplasma Urealyticum Infections in the Female Genital Tract.

Ureaplasma urealyticum (U. urealyticum) commonly occurs in female genitourinary infections, and its different biovars and serotypes have varying degrees of resistance to different antibiotics. This study aimed to ex-plore the characteristics of U. urealyticum infection and drug-resistant profiles in Chinese females. We included 1,045 females with genital tract infections who visited Tangshan Workers' Hospital and Tangshan Maternal and Child Health Center from September 2017 to December 2018. The bacteria were selectively cultured, and drug sensitivity experiments were conducted. Eight pairs of oligonucleotide primers were designed, and polymerase chain reaction (PCR) was performed to amplify specific DNA fragments to perform bacterial strain typing. Among the 1,045 participants included, 566 (54.11%) participants were positive for mycoplasma infection. There were 432 (41.34%) participants with U. urealyticum infection, accounting for 76.33% of the positive participants. The infection rate of U. urealyticum was the highest in females who were 21 - 30 years old, followed by those who were 31 - 40 years old. Ureaplasma urealyticum showed the highest sensitivity to tetracyclines and the greatest resistance to quinolones. The biovar 1 of U. urealyticum with the highest detection rate of serotype 4, accounted for 66.88%. The biovar 2 of U. urealyticum mainly showed mixed subtypes 2 and 3. Biovar 2 showed higher resistance to sparfloxacin, clarithromycin, josamycin, and doxycycline than biovar 1. Women might be more susceptible to U. urealyticum, especially if they are of childbearing age. Urea-plasma urealyticum is mainly caused by a single serotype 6 infection. The resistance of U. urealyticum to quinolone (e.g., norfloxacin) is a great concern. Sparfloxacin, clarithromycin, ciprofloxacin, and doxycycline might be more suitable for people with biovar 1 infection. Biotyping may facilitate clinical drug use and help avoid the emergence of drug-resistant strains.

SARS-CoV-2 Spike Protein-Expressing Enterococcus for Oral Vaccination: Immunogenicity and Protection.

The declaration of the conclusion of the COVID-19 pandemic notwithstanding, coronavirus remains prevalent in circulation, and the potential emergence of novel variants of concern introduces the possibility of new outbreaks. Moreover, it is not clear how quickly and to what extent the effectiveness of vaccination will decline as the virus continues to mutate. One possible solution to combat the rapidly mutating coronavirus is the creation of safe vaccine platforms that can be rapidly adapted to deliver new, specific antigens in response to viral mutations. Recombinant probiotic microorganisms that can produce viral antigens by inserting specific viral DNA fragments into their genome show promise as a platform and vector for mucosal vaccine antigen delivery. The authors of this study have developed a convenient and universal technique for inserting the DNA sequences of pathogenic bacteria and viruses into the gene that encodes the pili protein of the probiotic strain E. faecium L3. The paper presents data on the immunogenic properties of two E. faecium L3 vaccine strains, which produce two different fragments of the coronavirus S1 protein, and provides an assessment of the protective efficacy of these oral vaccines against coronavirus infection in Syrian hamsters.

Assessment of the capacity of Whatman filter papers as support to store stools for the molecular diagnostic testing of soil-transmitted helminthiasis

Storage of stools for the detection of soil-transmitted helminths (STH) remains challenging for the molecular diagnostic testing of STH infections. This study aimed to overcome this challenge by assessing the capacity of Whatman filter papers to store stools for the molecular detection of STHs. Stool samples were collected from school-aged children of soil-transmitted helminthiasis endemic areas of Cameroon and then, analysed using Kato Katz technique. For this study, 128 and 40 stool samples respectively with and without STH eggs were analysed. From each sample, 10, 20, 40 and 80 mg of stool were weighted and spread on 6 grades of Whatman filter papers that were stored at room temperature from one to ten weeks. DNA was extracted from spread stool using CTAB based-method. The amount of stool to spread on filter papers and the grade of filter paper offering good storage were determined by amplifying specific DNA fragments of Ascaris lumbricoides. The capacity of filter papers to store stool samples for several weeks before the molecular detection of STH species was assessed by amplifying specific DNA fragments of different STHs. The amplification rates of A. lumbricoides were significantly higher (P < 0.0001) for 10 and 20 mg of stored stools. Stools spread on Whatman paper grade 2 yielded the highest amplification rate of 100% for A. lumbricoides, T. trichiura and hookworm. PCR revealed STH infections in all the 128 spread stools carrying STH eggs. It also revealed Necator americanus and Ancylostoma duodenale respectively in 10 and 13 of 15 spread stools contained hookworm eggs. PCR confirmed the co-infections of these hookworm species as well as that of A. lumbricoides and Trichuris trichiura in 7 spread stools. Out of 40 stools without STH eggs, PCR revealed that 5 (12.5%) and 9 (22.5%) had respectively A. lumbricoides and T. trichiura infections. The amplification rate of each STH species was 100% from one to 8 weeks and decreased to 86.7% after 10 weeks of storage. This study highlighted the capacity of filter papers to store stools for the molecular detection of STHs. Storing stools on these papers will enable to monitor and evaluate control programs and ensure post-elimination surveillance.

Method for creating a recombinant strain of enterococcus L3-SARS based on biologically active strain Enterococcus faecium L3

The current pandemic caused by the SARS-Cov-2 virus has significantly influenced the emergence of new injectable vaccines that provide a predominantly specific IgG response. However, it is generally accepted that protection against pathogens at the mucosal surface, which is the first barrier to viral entry, is predominantly dependent on the IgA response. It is now widely accepted that the use of genetically modified microorganisms, including probiotics, allows the oral or nasal mucosal delivery of therapeutic molecules, inducing an immune response in the mucous membranes. Probiotic strains are well studied for safety for the organism and are able to remain viable after passing through the gastric barrier, improve intraepithelial connections, and can generate a number of surface expressed molecules that enhance the effectiveness of vaccination.Recombinant probiotic microorganisms capable of producing vaccine antigens by inserting specific DNA fragments into their genome are one of the potential platforms that can be used to develop an appropriate vaccine containing a specific antigen for rapid response to viral mutations. Here, we demonstrate the construction of a novel SARS-Cov-2 vaccine candidate employing the gene fragment of S1 SARS-Cov-2 gene. According to the available data on new variants of SARS-Cov-2 mutations, three amino acid substitutions were made in the chosen sequence. This DNA fragment was inserted in frame into major pili protein gene within d2 domain of enterococcal operon encoding for pili.

Identification of Pituitary-Specific Transcription Factor-1 (PIT-1) Genotype in Bali Cattle

This study aimed to identify the genotype of the gene Pituitary-specific transcription factor 1 (Pit-1) in Bali cattle (Bos sondaicus). A total of 20 cows Bali (13 males and 7 females) were used in this study. DNA samples isolated from blood samples using phenol-chloroform extraction method (Sambrook et al., 1989). This study using PCR-RFLP method. Amplification of specific DNA fragments (size 451 bp, intron regions stretching from 4 to exon 6) of the Pit-1 gene Bali cattle samples was performed using a pair of specific primers (forward: 5'-AAA-CCA-TCA-TCT-CCC-TTC-TT -3 ', and reverse: 5'-AAT-GTA-CAA-TGT-GCC-TTC-TGA-G-3'). Based on the results of RFLP analysis/HinfI was found that all of Bali cattle research resulted banding pattern uniform (monomorphic), the band size 244 bp and 207 bp, and the band patterns thus identified as genotype BB, so it is known that the frequency of A and B alleles at 0 and 1. The frequency of A allele was not found in Bali cattle (Bos sondaicus) showed a significant difference with other cattle breeds (Bos taurus and Bos indicus).

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

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. 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 (757bp) was then confirmed against the indicated brewer's yeast type. The development of SRAP-SCAR marker is more economical, simple, and fast compared to morphological markers.

Fluorescence In Situ Hybridization of DNA Probes on Mitotic Chromosomes of the Mexican Axolotl.

Fluorescence in situ hybridization (FISH) is used extensively for visual localization of specific DNA fragments (and RNA fragments) in broad applications on chromosomes or nuclei at any stage of the cell cycle: metaphase, anaphase, or interphase. The cytogenetic slides that serve as a target for the labeled DNA probe might be prepared using any approach suitable for obtaining cells with appropriate morphology for imaging and analysis. In this chapter, we focus on the application of molecular cytogenetic methods such as DNA labeling, slide preparation, and in situ hybridization related to cells from Mexican axolotl.

Thyroid tuberculosis: rare location or rarely diagnosed? Literature review

Objective — to study of the frequency, clinical picture, diagnosis and treatment of tuberculosis of thyroid gland.&#x0D; Materials and methods. Analyses the date of the world experience and own observations.&#x0D; Results and discussion. Thyroid tuberculosis is a less frequent localization of this disease. Currently, most authors believe that thyroid tuberculosis is diagnosed in 0.1–1 % of all known cases of tuberculosis. Clinical observations have found that the thyroid gland is more often involved in the tuberculous process with a generalized miliary process, and, as previously thought, in this case there are no clinical signs of damage to the thyroid gland. A variable clinical presentation of thyroid tuberculosis was demonstrated. It is usually presented with local symptoms associated with diffuse enlargement of the thyroid gland. It is difficult to estimate the quantity of diagnosed cases due to insufficient knowledge of the doctors about this pathology and difficulties of tuberculosis etiology diagnosis. Tuberculous etiology must be ruled out in all lesions on the median surface of the neck. Fine-needle biopsy can help to confirm the diagnosis of thyroid tuberculosis, but the final diagnosis is possible only with histological or cytological studies. The diagnosis of thyroid tuberculo­sis requires the use of most of all the methods used in the diagnosis of tuberculosis: from the simplest (such as X-ray or Mantoux test (with 2 international units of tuberculin) methods to modern rapid molecule-genetic tests XpertMTB/Rif that detect specific fragments of MTB DNA in serum or plasma). Ultrasound and computer tomography also help the clearing of the diagnosis. Surgical treatment in combination with antimycobacterial chemotherapy is effective. &#x0D; Conclusions. Further investigations are needed to understand the definition, diagnosis and treatment of tuberculosis among other diseases of thyroid.

Identifying Transcription Factors That Prefer Binding to Methylated DNA Using Reduced G-Gap Dipeptide Composition.

Transcription factors (TFs) play an important role in gene expression and regulation of 3D genome conformation. TFs have ability to bind to specific DNA fragments called enhancers and promoters. Some TFs bind to promoter DNA fragments which are near the transcription initiation site and form complexes that allow polymerase enzymes to bind to initiate transcription. Previous studies showed that methylated DNAs had ability to inhibit and prevent TFs from binding to DNA fragments. However, recent studies have found that there were TFs that could bind to methylated DNA fragments. The identification of these TFs is an important steppingstone to a better understanding of cellular gene expression mechanisms. However, as experimental methods are often time-consuming and labor-intensive, developing computational methods is essential. In this study, we propose two machine learning methods for two problems: (1) identifying TFs and (2) identifying TFs that prefer binding to methylated DNA targets (TFPMs). For the TF identification problem, the proposed method uses the position-specific scoring matrix for data representation and a deep convolutional neural network for modeling. This method achieved 90.56% sensitivity, 83.96% specificity, and an area under the receiver operating characteristic curve (AUC) of 0.9596 on an independent test set. For the TFPM identification problem, we propose to use the reduced g-gap dipeptide composition for data representation and the support vector machine algorithm for modeling. This method achieved 82.61% sensitivity, 64.86% specificity, and an AUC of 0.8486 on another independent test set. These results are higher than those of other studies on the same problems.

New insights into the pathogenesis and molecular understanding of cutaneous T-cell lymphomas

The pathogenesis of cutaneous T‑cell lymphomas (CTCL) is still an enigma. Therefore, extensive translational research efforts have been undertaken in recent years to gain further clinical and molecular insights. There is increasing evidence that the different clinical appearance of the CTCL subtypes derives from the assumption that they develop from different skin subpopulations of Tcells. Detection and quantification of the malignant T‑cell clones is crucial for the diagnosis and prognosis of CTCL. Numerous recurrent mutant cellular signalling pathways have been found in recent years. This includes the JAK-STAT, NFκB, T‑cell receptor and MAP kinase signalling pathways, as well as cell cycle control and epigenetics. The most recent analyses imply atumour evolution model with initial copy number variation, like amplification or deletions of specific DNA fragments (CNVs) and only subsequent later single nucleotide variations (SNVs). The crucial question, however, is which CNVs are sufficient to initiate general tumourigenesis? The challenge is to identify possible driver genes. Increasing molecular understanding in CTCL will include new breakthrough therapeutic options in the near future.

Investigating a putative transcriptional regulatory protein encoded by Rv1719 gene of Mycobacterium tuberculosis.

Mycobacterium tuberculosis, the causative agent of tuberculosis, demonstrates immense plasticity with which it adapts to a highly dynamic and hostile host environment. This is facilitated by a web of signalling pathways constantly modulated by a multitude of proteins that regulate the flow of genetic information inside the pathogen. Transcription factors (TFs) belongs to one such family of proteins that modulate the signalling by regulating the abundance of proteins at the transcript level. In the current study, we have characterized the putative transcriptional regulatory protein encoded by the Rv1719 gene of Mycobacterium tuberculosis. This TF belongs to the IclR family of proteins with orthologs found in both bacterial and archaeal species. We cloned the Rv1719 gene into the pET28a expression vector and performed heterologous expression of the recombinant protein with E coli as the host. Further, optimization of the purification protocol by affinity chromatography and characterization of proteins for their functional viability has been demonstrated using various biochemical and/or biophysical approaches. Scale-up of purification yielded approximately 30mg of ~ 28kDa protein per litre of culture. In-silico protein domain analysis of Rv1719 protein predicted the presence of the helix-turn-helix (HTH) domain suggesting its ability to bind DNA sequence and modulate transcription; a hallmark of a transcriptional regulatory protein. Further, by performing electrophoretic mobility shift assay (EMSA) we demonstrated that the protein binds to a specific DNA fragment harboring the probable binding site of one of the predicted promoters.

Distribution and Identification of Pepper yellow leaf curl Indonesia virus Infecting Chili Pepper in Bali Island

Yellow leaf curl disease in chili pepper has been reported in Bali Island since the early 2012. Research was conducted to identify the virus causing this disease and disease distribution in Bali. Field survey was carried out to observe disease intensity and to collect field samples from several chili pepper growing areas in Bali (Karangasem, Bangli, Tabanan, and Gianyar). Begomovirus identification from field samples was then conducted by polymerase chain reaction method using universal primers SPG1/SPG2, followed by an analysis of the amplified target DNA sequences. The incidence of pepper yellow leaf curl disease reached 100% at all sites and disease severity reached 18%−87%. Begomovirus specific DNA fragment measuring 912 bp was successfully amplified from 12 field samples. Sequence analysis of DNA fragments showed the highest homology with Pepper yellow leaf curl Indonesia virus (PYLCIV). Further phylogenetic analysis confirmed the relationship between PYLCIV isolates from Bali and various PYLCIV isolates from Indonesia.

Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding.

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain—the motif—may be seen as the generator of a finitely generated group on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structures close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated with the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs, such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such DNA syntactical rules and their functional roles. This includes the TATA box in the promoter region of some genes, the single-nucleotide markers (SNP) and the motifs of some genes of ubiquitous roles in transcription and regulation.