DNA hybridization Research Papers - Academia.edu (original) (raw)

2025, Polymer

Poly(tert-butyl acrylate) (PtBA) was grafted to the surface of poly(ethylene-co-acrylic acid) (EAA) film and the pendant groups of the tethered PtBA were modified to create chemically tailored surface modifying layers. The carboxylic acid groups in the copolymer film served as the grafting sites for the covalent tethering of end-functionalized PtBA. The progression of these reactions was monitored using attenuated total reflectance (ATR)-FTIR and X-ray photoelectron (XPS) spectroscopies along with static contact angle measurements. By controlling the reaction conditions, the chemical functionality of the grafted layer ranged from tert-butyl ester (EAA-g-PtBA) to carboxylic acid (EAA-g-PAA) and was demonstrated by corresponding changes in wettability. The choice of PtBA as the tethered polymer allows for the subsequent substitution of the tert-butyl ester groups. To demonstrate, a novel procedure was used to replace the tert-butyl ester with N,N-dimethylethylenediamine (DMEDA) to form EAA-g-PDMEDA. These reaction schemes can be used to create tunable surface-grafted layers with various pendant group chemistries.

2025, Biosensors and Bioelectronics

By coupling scattered light from DNA to excite fluorescence in a polymer, we describe a quantitative, label-free assay for DNA hybridization detection. Since light scattering is intrinsically proportional to number of molecules, the change in (scattering coupled) fluorescence is highly linear with respect to percent binding of single stranded DNA (ssDNA) target with the immobilized ssDNA probes. The coupling is achieved by immobilizing ssDNA on a fluorescent polymer film at optimum thickness in nanoscale. The fluorescence from the underlining polymer increases due to proportionate increase in scattering from double stranded DNA (dsDNA) (i.e., probe-target binding) compared to ssDNA (i.e., probe). Because the scattering is proportional to fourth power of refractive index, the detection of binding is an order of magnitude more sensitive compared to other label-free optical methods, such as, reflectivity, interference, ellipsometry and surface-plasmon resonance. Remarkably, polystyrene film of optimum thickness 30 nm is the best fluorescent agent since its excitation wavelength matches (within 5 nm) with wavelength for the maximum refractive index difference between ssDNA and dsDNA. A quantitative model (with no fitting parameters) explains the observations. Potential dynamic range is 1 in 10 4 at signal-to-noise ratio of 3:1.

2025, Analytical Chemistry

2025, International Journal of Systematic Bacteriology

Four yellow-pigmented group D enterococci of uncertain taxonomic position were isolated from several humans with severe infections. The results of DNA composition, DNA-DNA hybridization, fatty acid content, and biochemical property studies demonstrated that these organisms were slightly related to other previously described yellow-pigmented enterococcal species and constitute a new species, for which we propose the name Enterococcusjlavescens. The type strain of E. jlavescens is strain CCM 439.

2025

Domates oz nekrozuna neden olan bakteriyel etmenler Pseudomonas cichorii and Pseudomonas corrugata dunyada domates uretiminin yapildigi yerlerde onemli kayiplara sebep olabilmektedir. P. cichorii and P. corrugata Turkiye’de Akdeniz Bolgesi’nde uretimi yapilan domateslerde tespit edilmistir. Mersin ve Adana illerindeki sera domateslerinde, patojenlerin neden oldugu hastaligin simptomlari solgunluk, bitki govdesi uzerinde koyu renkte lekeler ve bitki ozunde koflasma ile karakterize edilmistir. Bu calismada, simptom gosteren bitkilerden elde edilen bakteriyel izolatlarin tanisi geleneksel ve ELISA (Enzyme-Linked ImmunoSorbent Assay)’ya dayali tani yontemleri kullanilarak yapilmistir. Test sonuclarina gore 15 adet izolat P. cichorii, 1 adet izolat P. corrugata olarak tanilanmistir. Her iki patojenin teshisinde, geleneksel tani testlerinin yani sira, saf bakteri kulturu kullanilarak yapilan indirekt-ELISA metodu hizli sonuc veren duyarli, guvenilir metot olarak degerlendirilmistir

2025

Pseudomonas cichorii and Pseudomonas corrugata, the causal bacterial agents of tomato pith necrosis, may cause severe losses on tomato worldwide. In Turkey, P. cichorii and P. corrugata were observed on tomato in the Mediterranean Region. The typical disease symptoms of pathogens were characterized as wilting, dark blotches on tomato stems, browning and hollowing of pith in greenhouse tomato plants in Adana and Mersin provinces. In this study, traditional and ELISA (Enzyme-Linked ImmunoSorbent Assay)-based methods were performed for identification of isolates obtained from symptoms showing plants. In total, 15 of P. cichorii isolates and 1 of P. corrugata isolate were identified according to the diagnostic tests. In addition to traditional diagnosis methods, Indirect-ELISA that was made with pure bacterial cultures was evaluated as capable and reliable diagnosis method of rapid resulting for both pathogenic bacteria.

2025, Journal of the Turkish Chemical Society, Section A: Chemistry

In various fields like health, environmental control, food security, and military defense, there is an increasing demand for on-site detection, fast identification, and urgent response which bring about the necessity to employ laboratory detection procedures on standalone automatic devices. In response to that, TUBITAK BILGEM's Bioelectronic Devices and Systems Group has been developing portable and fully automated biosensor devices using optical and electrochemical biosensor detection techniques. Here we describe a new integrated and fully automated lab-on-a-chip based biosensor device 'MiSens'. The key features of the MiSens include a new electrode array, an integrated microfluidic system, and real-time amperometric measurements during the flow of enzyme substrate. While simple protocols can be controlled from the LCD display on the device, other main device control procedures can be run wireless by a tablet/PC using the MiCont™ software developed by the team. For the device, a new plug and play type sensor chip docking station has been designed that with one move it enables the formation of a ~ 7-10 µL capacity flow cell on the electrode array with the necessary microfluidic and electronic connections. The MiSens device has been developed by our multi-disciplinary team by integrating and automatising the earlier developed sensing platform REP™ (Real-time Electrochemical Profiling). The performance of the MiSens device has been tested using cyclic voltammetry and amperometry tests and the results were compared with an of the shelf potentiostat.

2025, Tetrahedron Letters

Octaazaphthalocyanines with eight phenoxy groups in the peripheral sites are prepared for the first time using the simple synthetic procedure of heating their pyrazine-2,3-dicarbonitrile precursor in quinoline. This process avoids transetherification, which has hindered previous attempts at preparing metal-free octaazaphthalocyanines. Metal-containing derivatives were also prepared by adding the appropriate metal salt to the reaction mixture. Bulky iso-propyl or phenyl groups at the 2,6-positions of the phenoxy substituents prevent self-association of the octaazaphthalocyanine cores even in the solid state.

2025

This report was .prepared as an account of work sponsored by an agency of t h e United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, make any warranty, express or implied, or assumes a n y legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by t h e United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of t h e United States Government or any agency thereof.

2025, Nanoscale

Well-ordered, self-assembled monolayer films of 1,4-bis((4-ethynylphenyl)ethynyl)benzene on gold are shown to be nearly transparent to outer-sphere electron transfer processes.

2025, Electrochemistry Communications

Electrochemical DNA sensor has been fabricated by immobilizing thiolated single stranded oligonucleotide (ssDNA) probe onto gold (Au) coated glass electrode for meningitis detection using hybridization with complementary DNA (CtrA) in presence of methylene blue (MB). These electrodes (ssDNA/Au and dsDNA/Au) have been characterized using atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FT-IR), electrochemical impedance spectroscopy (EIS) and cyclic voltammetric (CV) technique. The DNA/Au electrode can detect the complementary DNA in the range of 7-42 ng/ll in 5 min (hybridization) with response time 60 s and electrode is stable for about 4 months when stored at 4 °C. The sensitivity of dsDNA/Au electrode is 115.8 lA/ng with 0.917 regression coefficient (R).

2025, International Journal of Systematic and Evolutionary Microbiology

A yellow-pigmented bacterial strain (CC-H3-2T), isolated from the rhizosphere of Lactuca sativa L. (garden lettuce) in Taiwan, was investigated using a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Chryseobacterium, with the highest sequence similarity to the type strains of Chryseobacterium indoltheticum (97·7 %), Chryseobacterium scophthalmum (97·5 %), Chryseobacterium joostei (97·2 %) and Chryseobacterium defluvii (97·2 %). The major whole-cell fatty acids were iso-C15 : 0 (52·2 %) and iso-C17 : 0 3-OH. DNA–DNA hybridization experiments revealed levels of only 27·4 % to C. scophthalmum, 27·1 % to C. indoltheticum, 14·1 % to C. joostei and 7·8 % to C. defluvii. DNA–DNA relatedness and biochemical and chemotaxonomic properties demonstrate that strain CC-H3-2 T represents a novel species, for which the name Chryseobac...

2025, Journal of Clinical Microbiology

During a 7-month period, we isolated 21 highly fluoroquinolone-resistant Enterobacter cloaecae strains in units from two hospitals in Marseille, France. Random amplification of polymorphic DNA showed clonal identity between isolates which, furthermore, presented the Enterobacter hormaechei genotype on DNA-DNA hybridization. The emergence of this clone was observed only in patients treated with fluoroquinolones.

2025, Journal of Clinical Microbiology

A procedure for preparing a DNA probe to be used in the specific detection of Legionella pneumophila by dot or colony hybridization has been devised. When total DNA from L. pneumophila was used as a radioactive probe, cross-hybridization occurred with DNA from many other species belonging to various families (including Legionellaceae, Enterobacteriaceae, Pseudomonadaceae, and Vibrionaceae). Cross-hybridizing restriction fragments in L. pneumophila ATCC 33152 DNA were identified on Southern blots. When unlabeled DNA from strain ATCC 33152 was cleaved by endonuclease BamHI, the DNA fragments cross-hybridizing with the labeled DNA from all of the other species and genera tested (or with Escherichia coli 16 + 23 S RNA) had a size of 21.4 and 16.2 kilobase pairs (major bands) and 28.0, 12.8, and 10.1 kilobase pairs (minor bands). BamHI restriction fragments of L. pneumophila DNA deprived of the cross-hybridizing fragments were pooled and used as a probe for the detection of L. pneumophil...

2025, Genomics

N-Oct 3 is a human POU domain transcription factor that binds to the octamer sequence ATGCAAAT. The protein is expressed in the central nervous system during development and in adult brain. We have isolated and characterized genomic clones encoding the human N-Oct 3 gene (HGMW-approved symbol POUF3). Comparison of the structure of these clones with the N-Oct 3 cDNA revealed that POUF3 is an intronless gene. Sequencing of 650 bp of the promoter region showed 84% sequence identity of POUF3 with its murine homologue, the brain-2 (designated brn-2) gene. Whereas both POUF3 and brn-2 lack a TATA box, consensus sequences for AP-2, GCF, and SP1 transcription factors were identified within the highly conserved 5'flanking region. These sequences may play a crucial role for the tissue-specific transcription activation of the POUF3 gene. Southern blotting and in situ hybridization localized the human POUF3 gene to chromosome 6q16.

2025, Independent Undergraduate Research Report – ICGEB Internship

Southern blotting is a widely used technique in genetic engineering to detect specific DNA sequences within a DNA sample. This experiment demonstrates the process of isolating DNA, digesting it using restriction enzymes, separating fragments via gel electrophoresis, and hybridizing them with labeled probes on a membrane. A positive result is indicated by a purple precipitate at the probe binding site, confirming the presence of the target gene. The experiment highlights core biotechnology skills including DNA extraction, electrophoresis, hybridization, and probe-based detection.

2025, American journal of human genetics

Protein 4.2 (P4.2), one of the major components of the red-blood-cell membrane, is located on the interior surface, where it binds with high affinity to the cytoplasmic domain of band 3. Individuals whose red blood cells are deficient in P4.2 have osmotically fragile, abnormally shaped cells and moderate hemolytic anemia. cDNA clones from both the 5' and the 3' coding regions of the P4.2 gene were used to map its chromosomal location by fluorescence in situ hybridization. The probes, individually or in combination, gave specific hybridization signals on chromosome 15. The hybridization locus was identified by combining fluorescence images of the probe signals with fluorescence banding patterns generated by Alu-PCR (R-like) probe and by DAPI staining (G-like). Our results demonstrate that the locus of the P4.2 gene is located within 15q15.

2025, PubMed

It has been demonstrated in animal studies that, in animals heterozygous for pericentric chromosomal inversions, loop formation is greatly reduced during meiosis. This results in absence of recombination within the inverted segment, with recombination seen only outside the inversion. A recent study in yeast has shown that telomeres, rather than centromeres, lead in chromosome movement just prior to meiosis and may be involved in promoting recombination. We studied by cytogenetic analysis and DNA polymorphisms the nature of meiotic recombination in a three-generation family with a large pericentric X chromosome inversion, inv(X)(p21.1q26), in which Duchenne muscular dystrophy (DMD) was cosegregating with the inversion. On DNA analysis there was no evidence of meiotic recombination between the inverted and normal X chromosomes in the inverted segment. Recombination was seen at the telomeric regions, Xp22 and Xq27-28. No deletion or point mutation was found on analysis of the DMD gene. On the basis of the FISH results, we believe that the X inversion is the mutation responsible for DMD in this family. Our results indicate that (1) pericentric X chromosome inversions result in reduction of recombination between the normal and inverted X chromosomes; (2) meiotic X chromosome pairing in these individuals is likely initiated at the telomeres; and (3) in this family DMD is caused by the pericentric inversion.

2025, Archives of Biological Sciences

Five bacteriocin-producing lactococci isolates from traditionally prepared kefir were determined as Lactococcus lactis subsp. lactis. The analyzed isolates showed different plasmid profiles and no cross inhibition between them was detected. Moreover, natural isolate BGKF26 was resistant to the antimicrobial activity of nisin producing strain NP45. Plasmid curing experiments revealed that the genes encoding bacteriocin and proteinase production are located on separate genetic elements, except in BGKF26. Production of the tested bacteriocins depends on the concentration of casitone or triptone in the medium. Higher concentrations of casitone or triptone induce bacteriocin activity. Our DNA-DNA hybridization analyses suggest that the analyzed antimicrobial compounds probably are lactococcin-like bacteriocins.

2025, Genomics

Members of the protein kinase C (PKC) family of serine/ threonine kinases play critical roles in the regulation of cellular differentiation and proliferation of diverse cell types (10). In an attempt to find PKC isoforms that are involved in growth control and/or activation of T lymphocytes, we have used a human peripheral blood lymphocyte-derived cDNA library to identify a novel PKC isoform, termed PKC-0 (1). The human PKC-0 cDNA (human gene symbol PRKCQ) was characterized and found to encode an ~80-kDa protein, expressed predominantly in lymphoid tissues and hematopoietic cell lines, in particular T cells (1, 2). A murine homolog gene derived from skin cDNA library was found to be expressed predominantly in skeletal muscle (11). Molecular cloning and biochemical studies identified PKC enzymes as members of a distinct family that constitutes, at the gene level, nine mammalian members, i.e., a,/~, T, 5, e, ~, ~, 0, and k (reviewed in Ref. 10), of which three have already been assigned to individual human chromosomes. Thus, PKC-a was mapped to H17q22-q24, PKC-f~ to H16pl2qll.1, and PKC-T to H19q13.4. The chromosomal location of other members is yet unknown (GDB Genome Data Bank,

2025, Journal of the American Chemical Society

We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.

2025, The FASEB Journal

Synthetic molecules that can bind with high sequence specificity to a chosen target in a gene sequence are of major interest in medicinal and biotechnological contexts. They show promise for the development of gene therapeutic agents, diagnostic devices for genetic analysis, and as molecular tools for nucleic acid manipulations. Peptide nucleic acid (PNA) is a nucleic acid analog in which the sugar phosphate backbone of natural nucleic acid has been replaced by a synthetic peptide backbone usually formed from N-(2-amino-ethyl)-glycine units, resulting in an achiral and uncharged mimic. It is chemically stable and resistant to hydrolytic (enzymatic) cleavage and thus not expected to be degraded inside a living cell. PNA is capable of sequencespecific recognition of DNA and RNA obeying the Watson-Crick hydrogen bonding scheme, and the hybrid complexes exhibit extraordinary thermal stability and unique ionic strength effects. It may also recognize duplex homopurine sequences of DNA to which it binds by strand invasion, forming a stable PNA-DNA-PNA triplex with a looped-out DNA strand. Since its discovery, PNA has attracted major attention at the interface of chemistry and biology because of its interesting chemical, physical, and biological properties and its potential to act as an active component for diagnostic as well as pharmaceutical applications. In vitro studies indicate that PNA could inhibit both transcription and translation of genes to which it has been targeted, which holds promise for its use for antigene and antisense therapy. However, as with other high molecular mass drugs, the delivery of PNA, involving passage through the cell membrane, appears to be a general problem.-Ray, A., Norde ´n, B. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future.

2025, The Biological Bulletin

2025, American Journal of Human Genetics

moters and enhancers of muscle-specific and growth-The MEF2 genes belong to the MADS box family of regulated genes ; Chamtranscription factors and encode proteins that bind as

2025, Journal of membrane science & technology

The pandemic caused by CoV-2 virus indicates that other unknown pandemic may occur in the future for which one must plan now. Full control of virus requires rapid diagnostics. We introduce a nanosensor system with specificity for fast detection of viruses. A novel Nanoporous Alumina Membrane Photonic Crystal (NAM-PC) is used that generates unique signature in the terahertz eigen spectrum. A terahertz eigen frequency analysis algorithm is deployed that measures the unique eigen frequencies of the NAM-PC by means of peaks in a terahertz eigen absorbance spectrum. This signature spectrum compared with the eigen absorbance spectrum of a given molecular entity (e.g., a virus), generates the signature of that virus with specificity. This principle was tested via a blank NAM-PC having 40 nm pore size and compared with that of a 25-mer Oligonucleotide Guanine (Oligo-G)'s eigen absorbance spectrum. Two prominent peaks were found in both spectra. The primary peak frequency of the Oligo-G was shifted by 0.2531 THz, while the secondary peak frequency of the same was shifted by 0.6169 THz, with respect to the blank NAM-PC. A criterion is formulated based on the combined aspects of the position of the respective peaks and the shift in the eigen frequency with respect to each other. This criterion, combined with the difference in loss factor calculated from the eigen spectra at saturation, provide unique detection technique for viruses and biomolecular entities with high specificity. The technology may provide a go/no-go protocol for the biological samples of a patient in a few minutes.

2025, Proceedings of the National Academy of Sciences

In vitro DNA amplification followed by oligonucleotide mismatch hybridization was used to study the frequency of HRAS mutations in the benign self-regressing skin tumors keratoacanthomas and in squamous cell carcinomas. We used freshly obtained keratoacanthomas as well as Formalin-fixed paraffin-embedded tissues from both types of tumors. DNA from 50 samples of each tumor type was analyzed for activating mutations involving codons 12 and 61. A relatively high percentage (30%) of HRAS mutations was found in the keratoacanthomas compared with 13% in the squamous cell carcinomas. The most frequent mutation identified is the A-T-to-T.A transversion in the second position of codon 61. The present findings demonstrate the involvement of the HRAS oncogene in human benign tumors. Moreover, they indicate that an activated HRAS oncogene is not sufficient to maintain a neoplastic phenotype and argue against a role of HRAS in the progression of skin tumorigenesis.

2025, Proceedings of the National Academy of Sciences of the United States of America

The expression of GTP-binding regulatory proteins (G proteins) in retinal pigment epithelial (RPE) cells was analyzed by RNA blot hybridization and cDNA amplification. Both adult and fetal human RPE cells contain mRNA for multiple G protein a subunits (Ga) including Gsa, G.1la, Gi.2a, Gi.3a, and Gza (or Gxa), where G, and G1 are proteins that stimulate or inhibit adenylyl cyclase, respectively, and Gz is a protein that may mediate pertussis toxin-insensitive events. Other Ga-related mRNA transcripts were detected in fetal RPE cells by low-stringency hybridization to Gi.2a and Gsa protein-coding cDNA probes. The diversity of G proteins in RPE cells was further studied by cDNA amplification with reverse transcriptase and the polymerase chain reaction. This approach revealed that, besides the above mentioned members of the Ga gene family, at least two other Ga subunits are expressed in RPE cells. Human retinal cDNA clones that encode one of the additional Gca subunits were isolated and characterized. The results indicate that this Ga subunit belongs to a separate subfamily of G proteins that may be insensitive to inhibition by pertussis toxin.

2025, Physics of Fluids

Numerical studies for two protocols of micromixing based on chaotic advection to improve DNA chip hybridization are presented. The first protocol uses syringes; the other one, pumps. For both protocols, numerical Poincaré sections and Lyapunov exponents of the three-dimensional, time-periodic flow are investigated as functions of the period. Model experiments also confirm numerical results. Homogeneity of the dispersion of particles inside the chamber is of primary importance to achieve best chip reliability: although global chaos was obtained for both protocols, we find that the one employing the pumps is more likely to achieve better and more rapid hybridization.

2025, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A thermophilic, strictly anaerobic, sulfur-reducing epsilonproteobacterium (strain AmH T ) isolated from deep-sea hydrothermal vents is described. Cells were motile, Gram-negative rods. Growth was observed at 30-55 6C, pH 6.0-9.0 and 2-5 % (w/v) NaCl. Chemolithoautotrophic growth occurred with molecular hydrogen or formate as the electron donor and elemental sulfur as the electron acceptor, producing hydrogen sulfide. Heterotrophic and mixotrophic growth occurred with formate as a source of carbon. The dominant phospholipid fatty acids were C 18 : 1 v7c (73.26 % of the total), C 16 : 1 v7c (12.70 %) and C 16 : 0 (12.27 %). The genomic DNA G+C content was 33.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain AmH T within the family Nautiliaceae of the Epsilonproteobacteria. DNA-DNA hybridization experiments between strain AmH T and Nautilia lithotrophica DSM 13520 T revealed a level of relatedness of 34.6 % between the two strains. Based on physiological and phylogenetic characteristics, strain AmH T is considered to represent a novel species of the genus Nautilia, for which the name Nautilia profundicola sp. nov. is proposed. The type strain is AmH T

2025, Genomics

in mammalian genomes . The We have previously reported , Gemechanisms and reasons, if any, for the presence of nomics 18: 223) the characterization of the human this high number of genes have not yet been elucidated, ZNF75 gene located on Xq26, which has only limited and, generally speaking, most of the zinc finger coding homology (less than 65%) to other ZF genes in the datagenes present in literature and databases are reprebases. Here, we describe three human zinc finger genes sented by incomplete sequences obtained by PCR with 86 to 95% homology to ZNF75 at the nucleotide whose genomic structure and transcriptional status are level, which represent all the members of the human unknown. A few of these genes have been analyzed in ZNF75 subfamily. One of these, ZNF75B, is a pseumore detail, mapped to specific human chromosomal dogene mapped to chromosome 12q13. The other two, regions, and shown, in some cases, to be present in ZNF75A and ZNF75C, maintain an ORF in the seclusters (

2025, Biosensors and Bioelectronics

A technique is demonstrated to detect DNA hybridization at low concentrations, based on Surface-Enhanced Raman Scattering (SERS) using silicon nanostructures coated with gold-silver as substrate. Standard silicon process technologies were employed to fabricate the SERS substrates featuring nanogaps with a characteristic distance of 15 ± 10 nm. Target DNA was hybridized with cysteine-modified Peptide Nucleic Acids (PNA), which was previously fixed into the nanogaps as the capture sites. After hybridization, the introduced phosphate groups from the backbone of the target DNA showed strong affinity to an inorganic linker, Zr 4+ , so that resulting in the assembly substrate-PNA-DNA-Zr. Since PNA does not possess phosphate groups, the linker is avoided when there is no hybridization from the complimentary DNA. Subsequently, the assembly of substrate-PNA-DNA-Zr was incubated with a Raman label, Rhodamine B (RB). The carboxylic acid group in RB reacted with the linker Zr 4+ allowing this Raman Label to be attached to the assembly substrate-PNA-DNA-Zr. The Raman peaks corresponding to RB were selected to detect the target DNA, with a detection limit of 1 × 10 -12 M.

2025

Citrus bacterial canker is an economically important disease in many tropical and subtropical countries and caused by Xanthomonas citri subsp. citri. Several pathotypes of this pathogen have been described that primarily distinguished by their geographical origin, host range and certain genotypic characteristics Leaves, fruits and twinges samples of 'Mexican 'lime, with bacterial canker symptoms were collected from Kohgiluyeh and Boyer-Ahmad province in 2012. The bacterial strains were isolated from infected tissues using classic methods and primary identification of bacterial isolates was performed based on phenotypic characterization. Pathogenicity of isolates was approved on leaves of Mexican lime. Based on the disease symptoms, phenotypic and pathogenicity tests, PCR test by using specific primers and sequencing data of histidine kinase gene, the isolates were identified as Xanthomonas citri subsp. citri. This is the first report of the disease and the causal bacterium in Kohgiluyeh and Boyer-Ahmad province.

2025, 2012 IEEE Sensors

We report for the first time the combination of a quartz-based photonic crystal (PC) with a detection instrument designed to perform label-free (LF) and enhanced fluorescence (EF) imaging for antibody microarray applications. Label-free detection is used to quantify binding density of immobilized capture antibodies. Angle-scanning approach is implemented to achieve more uniform fluorescence enhancement by reducing the coefficient of variation of replicate assays by 20-99% compared to ordinary fluorescence microscopy. I.

2025, IEEE Journal of Selected Topics in Quantum Electronics

There are a number of emerging optical biosensing techniques utilizing interferometric and resonant characteristics of light. We have recently demonstrated an interferometric technique, the spectral reflectance imaging biosensor (SRIB) that uses optical wave interference to detect changes in the optical path length as a result of capture of biological material on the microarray surface without the need for labels and secondary reagents. In this paper, we review the principles and performance of the SRIB technique in the context of label-free biosensors and demonstrate its high-throughput, quantitative and calibrated, versatile, and dynamic (kinetic) capabilities. A unique aspect of the SRIB system is that the measurement technique is independent of surface conformation and allows for utilization of novel polymeric coatings for surface binding, thus providing a versatile and high-density platform. We present experimental results on multiplexed antibody/antigen arrays and DNA hybridization in real time, as well as specific binding of whole virus particles. The simplicity of the overall system, its high sensitivity and compatibility with glass surface chemistries, and a linear dynamic range of nearly four orders of magnitude makes SRIB a promising platform for multiplexed detection of different biological analytes in a complex sample, with potential impact in research and clinical applications.

2025, Chemistry of Materials

Nanostructured palladium foams offer exciting potential for applications in diverse fields such as catalysts, fuel cells, and particularly hydrogen storage technologies. We have fabricated palladium nanowire foams using a cross-linking and freeze-drying technique. These foams have a tunable density down to 0.1% of the bulk, and a surface area-to-volume ratio of up to 1.54 × 10 6 :1 m -1 . They exhibit highly attractive characteristics for hydrogen storage, in terms of loading capacity, rate of absorption, and heat of absorption. The hydrogen absorption/desorption process is hysteretic in nature, accompanied by substantial lattice expansion/contraction as the foam converts between Pd and PdH x .

2025, Applied and Environmental Microbiology

The potential for biodegradation of aromatic hydrocarbons was evaluated in soil samples recovered along gradients of both contaminant levels and pH values existing downstream of a long-term coal pile storage basin. pH values for areas greatly impacted by runoff from the storage basin were 2.0. Even at such a reduced pH, the indigenous microbial community was metabolically active, showing the ability to oxidize more than 40% of the parent hydrocarbons, naphthalene and toluene, to carbon dioxide and water. Treatment of the soil samples with cycloheximide inhibited mineralization of the aromatic substrates. DNA hybridization analysis indicated that whole-community nucleic acids recovered from these samples did not hybridize with genes, such as nahA, nahG, nahH, todC1C2, and tomA, that encode common enzymes from neutrophilic bacteria. Since these data suggested that the degradation of aromatic compounds may involve a microbial consortium instead of individual acidophilic bacteria, experiments using microorganisms isolated from these samples were initiated. While no defined mixed cultures were able to evolve 14 CO 2 from labeled substrates in these mineralization experiments, an undefined mixed culture including a fungus, a yeast, and several bacteria successfully metabolized approximately 27% of supplied naphthalene after 1 week. This study shows that biodegradation of aromatic hydrocarbons can occur in environments with extremely low pH values.

2025, Analytical Biochemistry

2025

Objectives: In this study, extended-spectrum b-lactamases (ESBLs) were characterized from 30 selected multidrug-resistant Klebsiella pneumoniae strains isolated from patients with community-acquired urinary tract infections from Southwest Nigeria. Methods: The b-lactamases were phenotypically characterized using isoelectric focusing, genotypically characterized using PCR assays and hybridization of the PCR products. Two of the blaCTX-M genes were completely sequenced. The location of the CTX-M-type

2025, Journal of Antimicrobial Chemotherapy

Objectives: To determine antibiotic resistance genes associated with 17 Nigerian CTX-M-positive Klebsiella pneumoniae plasmids from patients with community-acquired urinary tract infections. The size and restriction patterns of the plasmids were determined, and antibiotic resistance genes were identified using DNA-DNA hybridization, PCR assays, hybridization of PCR products with internal probes, and sequencing. Results: All CTX-M plasmids were large (58-320 kb) and carried the following genes: aac(6 0 )-Ib (aminoglycoside resistance) which included aac(6 0 )-Ib-cr (aminoglycoside-fluoroquinolone resistance), aadA2 (aminoglycoside resistance), erm(B) (macrolide-lincosamide-streptogramin B resistance), bla TEM-1 (ampicillin resistance), tet(A) (tetracycline resistance), sul1 (sulphonamide resistance), dfr (trimethoprim resistance) and intI1, an integrase associated with class 1 integrons. Eleven (65%) plasmids carried an mph(A) gene (macrolide resistance), seven (41%) plasmids carried a qnrB1 gene (low-level quinolone resistance) and four (24%) plasmids carried multiple cat genes (chloramphenicol resistance). catA2, catA3 and qnrB1 genes and a 6 kb Pst I fragment, carrying the bla CTX-M gene, were sequenced. Conclusions: This is the first description of catA2 and catA3 genes in Klebsiella spp. and the first description of the erm(B) and floR genes associated with a CTX-M plasmid. This is also the first report of qnrB1 and aac(6 0 )-Ib-cr in isolates from Africa and the first report of these two genes on the same plasmid.

2025, Proceedings of the National Academy of Sciences

The genetic defect responsible for Huntington disease was originally localized near the tip of the short arm of chromosome 4 by genetic linkage to the locus D4S10. Several markers closer to Huntington disease have since been isolated, but these all appear to be proximal to the defect. A physical map that extends from the most distal of these loci, D4S90, to the telomere of chromosome 4 was constructed. This map identifies at least two CpG islands as markers for Huntington disease candidate genes and places the most likely location of the Huntington disease defect remarkably close (within 325 kilobases) to the telomere.

2025, Genomics

We have extended, in both directions, our recently published genetic map of markers for human chromosome 10 by the addition of 10 newly defined arbitrary loci. The map now covers 220 CM in males and 329 CM in femalea. In addition, three... more

2025, Molecular Genetics And Genomics

A procedure is described for the detection of specific DNA sequences in Saccharomyces cerevisiae. This method allows a rapid screening of a large number of yeast colonies. The yeast cells of each colony, grown on nitrocellulose filters, are converted, in situ, to protoplasts by snail enzyme, and are then lysed and their DNAs are denatured and fixed on the filter. The presence of the specific DNA sequence is detected directly on the filter by hybridization with a radioactive cRNA. We have used successfully this technique to detect the presence or the absence of specific mt DNA sequences, in p+, p-and p0 strains, and to detect the presence or the absence of the 2 gm DNA sequences in different strains.

2025, Molecular and General Genetics MGG

A detailed map of the 32 kb mitochondrial genome of Aspergillus nidulans has been obtained by locating the cleavage sites for restriction endonucleases Pst I, Barn H I, Hha I, Pvu II, Hpa II and Hae III relative to the previously determined sites for Eco R I, Hind II and Hind III. The genes for the small and large ribosomal subunit RNAs were mapped by gel transfer hybridization of in vitro labelled rRNA to restriction fragments of mitochondrial DNA and its cloned Eco R I fragment E3, and by electron microscopy of RNA/DNA hybrids. The gene for the large rRNA (2.9 kb) is interrupted by a 1.8 kb insert, and the main segment of this gene (2.4 kb) is separated from the small rRNA gene (1.4 kb) by a spacer sequence of 2.8 kb length. This rRNA gene organization is very similar to that of the two-times larger mitochondrial genome of Neurospora crassa, except that in A. nidulans the spacer and intervening sequences are considerably shorter.

2025, FEMS Microbiology Letters

A rosy-pigmented Gram-negative, thermophilic bacterium with an optimum growth temperature of about 55 ‡C was isolated from Tengchong hot springs in Yunnan province, China. Its growth scarcely occurred below 40 ‡C or above 70 ‡C. Phylogenetic and secondary structural analyses of 16S rRNA and DNA^DNA hybridization showed that the organism represented a new species of the genus Meiothermus. This new species could be distinguished easily from other species of the genus Meiothermus by the following phenotypic characteristics : rosy pigment, expanded body, sucrose and maltose were not utilized, gelatin and starch were not hydrolyzed. On the basis of the above data, the name Meiothermus rosaceus sp. nov. was proposed for the species represented by the strain RH9901 T (CCTCC-AB200291).

2025, BMC Research Notes

Background: From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions: Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas.

2025

Present study is to identify the halo tolerant strains and their toxic metal tolerance. A total of 126 isolates were isolated from solar salt pan sediment sample. Among them 96 isolates were identified as metal resistance. MIC values suggested that, the maximum concentration of Ni (200 ppm), Al (600 ppm), Cd (50 ppm), Zn (400 ppm), Hg (25 ppm) and As (200 ppm) inhibitory activity was identified 6 isolates. Maximum percentage of metal tolerant was identified with Ni (22%) and minimum percentage of tolerant was identified with the Hg (8%). None of the selected isolates were showed the presence of plasmids. It is concluded from the present findings that, the halobacterial strains which isolated from the solar salt pan showed wide range of metal tolerance.