Target Fragments Research Articles

Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding.

Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase that exists in monomeric, dimeric, and tetrameric forms. It is activated by GTP binding to an A1 allosteric site on each monomer subunit, which induces dimerization, a prerequisite for dNTP-induced tetramerization. SAMHD1 is a validated drug target stemming from its inactivation of many anticancer nucleoside drugs leading to drug resistance. The enzyme also possesses a single-strand nucleic acid binding function that promotes RNA and DNA homeostasis by several mechanisms. To discover small molecule inhibitors of SAMHD1, we screened a custom ∼69 000-compound library for dNTPase inhibitors. Surprisingly, this effort yielded no viable hits and indicated that exceptional barriers for discovery of small molecule inhibitors existed. We then took a rational fragment-based inhibitor design approach using a deoxyguanosine (dG) A1 site targeting fragment. A targeted chemical library was synthesized by coupling a 5'-phosphoryl propylamine dG fragment (dGpC3NH2) to 376 carboxylic acids (RCOOH). Direct screening of the products (dGpC3NHCO-R) yielded nine initial hits, one of which (R = 3-(3'-bromo-[1,1'-biphenyl]), 5a) was investigated extensively. Amide 5a is a competitive inhibitor against GTP binding to the A1 site and induces inactive dimers that are deficient in tetramerization. Surprisingly, 5a also prevented ssDNA and ssRNA binding, demonstrating that the dNTPase and nucleic acid binding functions of SAMHD1 can be disrupted by a single small molecule. A structure of the SAMHD1-5a complex indicates that the biphenyl fragment impedes a conformational change in the C-terminal lobe that is required for tetramerization.

Molecular characterization of Brazilian FeLV strains in São Luis, Maranhão Brazil.

The feline leukemia virus (FeLV) belongs to the Retroviridae family and Gammaretrovirus genus, and causes a variety of neoplastic and non-neoplastic diseases in domestic cats (Felis catus), such as thymic and multicentric lymphomas, myelodysplastic syndromes, acute myeloid leukemia, aplastic anemia, and immunodeficiency. The aim of the present study was to carry out the molecular characterization of FeLV-positive samples and determine the circulating viral subtype in the city of São Luís, Maranhão, Brazil, as well as identify its phylogenetic relationship and genetic diversity. The FIV Ac/FeLV Ag Test Kit (Alere™) and the commercial immunoenzymatic assay kit (Alere™) were used to detect the positive samples, which were subsequently confirmed by ELISA (ELISA - SNAP® Combo FeLV/FIV). To confirm the presence of proviral DNA, a polymerase chain reaction (PCR) was performed to amplify the target fragments of 450, 235, and 166bp of the FeLV gag gene. For the detection of FeLV subtypes, nested PCR was performed for FeLV-A, B, and C, with amplification of 2350-, 1072-, 866-, and 1755-bp fragments for the FeLV env gene. The results obtained by nested PCR showed that the four positive samples amplified the A and B subtypes. The C subtype was not amplified. There was an AB combination but no ABC combination. Phylogenetic analysis revealed similarities (78% bootstrap) between the subtype circulating in Brazil and FeLV-AB and with the subtypes of Eastern Asia (Japan) and Southeast Asia (Malaysia), demonstrating that this subtype possesses high genetic variability and a differentiated genotype.

Quantification of cefaclor in human plasma using SIL-IS LC-ESI-MS/MS for pharmacokinetics study in healthy Chinese volunteers.

A steady, high-efficiency, and precise liquid chromatography-electrospray ionization-tandem mass spectrometry method was established and validated using cefaclor-d5 as the stable isotope-labeled internal standard for quantification of cefaclor in human plasma. One-step protein precipitation was applied to extract human plasma samples using methanol as precipitant. An Ultimate XB C18 column (2.1 × 50.0mm, 5.0μm) was used to achieve chromatographic separation. Mobile phases of gradient elution were an aqueous solution containing 0.1% formic acid (mobile phase A) and an acetonitrile solution containing 0.1% formic acid (mobile phase B). Electrospray ionization in positive-ion mode was applied to detect under multiple reaction monitoring mode. Target fragment ion pairs of cefaclor and stable isotope-labeled internal standard, respectively, were m/z 368.2 → 191.1 and m/z 373.2 → 196.1. Linear range of this method was between 20.0 and 10,000.0ng/ml, with coefficient of determination (R2 ) >0.9900. Seven concentrations of quality control samples were used: 20.0ng/ml (lower limit of quantitation), 60.0ng/ml (low quality control), 650 ng/ml (middle quality control), 5000 ng/ml (arithmetic average middle quality control [AMQC]), 7500 ng/ml (high quality control), 10,000 ng/ml (upper limit of quantification), and 40,000 ng/ml (dilution quality control [DQC]). The method was validated for selectivity, lower limit of quantitation, linearity, accuracy, precision, recovery, matrix effect, dilution reliability, stability, carryover, and incurred sample reanalysis. This stable isotope-labeled internal standard liquid chromatography-electrospray ionization-tandem mass spectrometry approach has been successfully applied to study the pharmacokinetics of cefaclor dry suspension among healthy Chinese volunteers.

Gut microbiota in chronic liver diseases in children

The impact of gut microbiota on the development of various diseases is of great interest to researchers. However, data on the taxonomic diversity of the intestinal microbiota in chronic liver diseases in children are lacking.Purpose. To study the taxonomic diversity of the fecal microbiota in children with chronic liver diseases in comparison with healthy patients.Material and methods. A metagenomic analysis of the intestinal microbiota of 24 children with chronic liver diseases (mean age 10.3 ± 4.7 years) was carried out with the isolation of the target fragment of the 16S rRNA gene. The group included 18 children with autoimmune liver diseases and 6 children with non-autoimmune liver diseases. The comparison group consisted of fecal samples of 34 apparently healthy children.Results. The conducted study revealed 684 types of microorganisms in the studied samples of patients’ feces. An analysis of the conducted studies showed that fecal samples of healthy children and patients with chronic liver diseases differ in bacterial diversity. The dominant taxa in healthy children were Neisseria flavescens, in patients with chronic liver diseases, the dominant taxa were Bifidobacterium longum, Bifidobacterium adolescentis, Blautia massiliensis. At the same time, Bifidobacterium longum, Bifidobacterium adolescentis, Blautia massiliensis in fecal samples of patients with chronic liver diseases was 8 times as high.Conclusion. Studies have shown differences in the composition of the intestinal microbiota in healthy children and children with chronic liver diseases.

Association of ventricular septal defect with rare variations of the HAND2 gene

To study the association of ventricular septal defect (VSD) with rare variations in the promoter region of HAND2 gene, as well as related molecular mechanisms. Blood samples were collected from 349 children with VSD and 345 healthy controls. The target fragments were amplified by polymerase chain reaction and sequenced to identify the rare variation sites in the promoter region of the HAND2 gene. Dual-luciferase reporter assay was used to perform a functional analysis of the variation sites. Electrophoretic mobility shift assay (EMSA) was used to investigate related molecular mechanisms. TRANSFAC and JASPAR databases were used to predict transcription factors. Sequencing revealed that three variation sites (g.173530852A>G, g.173531173A>G, and g.173531213C>G) were only observed in the promoter region of the HAND2 gene in 10 children with VSD, among whom 4 children had only one variation site. The dual-luciferase reporter assay revealed that g.173531213C>G reduced the transcriptional activity of the HAND2 gene promoter. EMSA and transcription factor prediction revealed that g.173531213C>G created a binding site for transcription factor. The rare variation, g.173531213C>G, in the promoter region of the HAND2 gene participates in the development and progression of VSD possibly by affecting the binding of transcription factors.

Prediction of superantigen active sites and clonal expression of staphylococcal enterotoxin-like W

Objective: The docking and superantigen activity sites of staphylococcal enterotoxin-like W (SElW) and T cell receptor (TCR) were predicted, and its SElW was cloned, expressed and purified. Methods: AlphaFold was used to predict the 3D structure of SElW protein monomers, and the protein models were evaluated with the help of the SAVES online server from ERRAT, Ramachandran plot, and Verify_3D. The ZDOCK server simulates the docking conformation of SElW and TCR, and the amino acid sequences of SElW and other serotype enterotoxins were aligned. The primers were designed to amplify selw, and the fragment was recombined into the pMD18-T vector and sequenced. Then recombinant plasmid pMD18-T was digested with BamHⅠand Hind Ⅲ. The target fragment was recombined into the expression plasmid pET-28a(+). After identification of the recombinant plasmid, the protein expression was induced by isopropyl-beta-D- thiogalactopyranoside. The SElW expressed in the supernatant was purified by affinity chromatography and quantified by the BCA method. Results: The predicted three-dimensional structure showed that the SElW protein was composed of two domains, the amino-terminal and the carboxy-terminal. The amino-terminal domain was composed of 3 α-helices and 6 β-sheets, and the carboxy-terminal domain included 2 α-helices and 7 antiparallel β-sheets composition. The overall quality factor score of the SElW protein model was 98.08, with 93.24% of the amino acids having a Verify_3D score ≥0.2 and no amino acids located in disallowed regions. The docking conformation with the highest score (1 521.328) was selected as the analysis object, and the 19 hydrogen bonds between the corresponding amino acid residues of SElW and TCR were analyzed by PyMOL. Combined with sequence alignment and the published data, this study predicted and found five important superantigen active sites, namely Y18, N19, W55, C88, and C98. The highly purified soluble recombinant protein SElW was obtained with cloning, expression, and protein purification. Conclusions: The study found five superantigen active sites in SElW protein that need special attention and successfully constructed and expressed the SElW protein, which laid the foundation for further exploration of the immune recognition mechanism of SElW.

Development of a Real-Time TaqMan RT-PCR Assay for the Detection of NADC34-like Porcine Reproductive and Respiratory Syndrome Virus

NADC34-like porcine reproductive and respiratory syndrome virus first appeared in 2017 in a herd of pigs in Liaoning Province, China. The virus was subsequently found in other provinces. Given the potential for this virus to cause an epidemic, rapid, sensitive, and specific detection of NADC34-like PRRSV is required. The virus' ORF5 gene was artificially synthesized based on a Chinese reference strain, and specific primers/probes for the ORF5 gene were designed. Then, the amplified target fragment was cloned into the pMD19-T vector, and a series of diluted recombinant plasmids were used to generate a standard curve. An optimized real-time TaqMan RT-PCR method was established. The method was highly specific for NADC34-like PRRSV, without cross-reactions with other non-targeted pig viruses. The detection limit of this assay was 101 copies/μL. The method had an efficiency of 98.8%, a squared regression value (R2) of 0.999, and showed a linear range of 103-108 copies/μL of DNA per reaction. This method was shown to be analytically specific and sensitive with a low intra- and inter-assay coefficient of variation (<1.40%). A total of 321 clinical samples were tested using the established method, and four were shown to be positive (1.24%). This study confirmed the existence of NADC34-like PRRSV and HP-PRRSV co-infection in Sichuan and provided a promising alternative tool for the rapid detection of NADC34-like PRRSV.

First Measurement of Λ Electroproduction off Nuclei in the Current and Target Fragmentation Regions.

We report results of Λ hyperon production in semi-inclusive deep-inelastic scattering off deuterium, carbon, iron, and lead targets obtained with the CLAS detector and the Continuous Electron Beam Accelerator Facility 5.014GeV electron beam. These results represent the first measurements of the Λ multiplicity ratio and transverse momentum broadening as a function of the energy fraction (z) in the current and target fragmentation regions. The multiplicity ratio exhibits a strong suppression at high z and an enhancement at low z. The measured transverse momentum broadening is an order of magnitude greater than that seen for light mesons. This indicates that the propagating entity interacts very strongly with the nuclear medium, which suggests that propagation of diquark configurations in the nuclear medium takes place at least part of the time, even at high z. The trends of these results are qualitatively described by the Giessen Boltzmann-Uehling-Uhlenbeck transport model, particularly for the multiplicity ratios. These observations will potentially open a new era of studies of the structure of the nucleon as well as of strange baryons.

A CRISPR/Cas12a-Mediated Sensitive DNA Detection System for Gene-Edited Rice.

In recent years, genome editing technology represented byclustered regularly interspaced short palindromic repeat/CRISPR-associated nuclease 9 （CRISPR/Cas9） has been developed and applied in transgenic research and development, and transgenic products have been developed for a variety of applications. Gene editing products, unlike traditional genetically modified crops, which are generally obtained by target gene deletion, insertion, base mutation, etc., may not differ significantly at the gene level from conventional crops, which increases the complexity of testing. We established a specific and sensitive CRISPR/Cas12a-mediated gene editing system to detect target fragments in a variety of transgenic rice lines and commercial rice-based processing products. In this study, the CRISPR/Cas12a visible detection system was optimized for the visualization of nucleic acid detection in gene-edited rice. The fluorescence signals were detected by both gel electrophoresis and fluorescence-based methods. The detection limit of the CRISPR/Cas12a detection system established in this study was more precise, especiallyfor low-concentration samples. In addition to achieving single-base detection in gene-edited rice, we showed that different base mutations in the target sequence have different detection efficiencies by sitewise variant compact analysis. The CRISPR/Cas12a system was verified via a common transgenic rice strain and commercial rice sources. The results proved that the detection method could not only be tested in samples with multiple mutation types but could also effectively detect target fragments in commercial rice products. We have developed a set of efficient detection methods with CRISPR/Cas12a for gene-edited rice detection to provide a new technical basis for rapid field detection of gene-edited rice. The CRISPR/Cas12a-mediated visual detection method used to detect gene-edited rice was evaluated for its specificity, sensitivity, and robustness.

Polymorphism of the Full-Length mRNA Sequences of MNS blood group-related genes GYPA, GYPB and GYPE

The characteristics of the full-length mRNA sequences of MNS blood group-related genes GYPA, GYPB and GYPE were analyzed to understand the polymorphism of MNS blood group genes. Anticoagulated blood within 24 h from 500 unpaid blood donors (8 ml each) were randomly selected, and MN, Ss and Mia blood types were identified by serological methods. 5 samples with different combinations of MNS and Mia blood types were randomly selected from 500 samples, and peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation, then total mRNA was extracted. cDNA was prepared by using the reverse transcription kit. The target fragments were amplified by nested PCR, and the full-length mRNA sequences of GYPA, GYPB and GYPE were sequenced after gel cutting and recycling, and the base sequences were analyzed by Oligo 6.0 software. The MN, Ss and Mia phenotypes were detected by serological methods, and there were differences in agglutination intensity of red blood cells (RBC) and anti-Mia serum between different individuals. The full-length mRNA sequences of GYPA, GYPB and GYPE genes in 5 samples of different phenotype combinations were detected. The exon-6 was completely deleted from the GYPA mRNA in 1 sample, and the full-length of GYPA mRNA in the other 4 samples were complete. The exon-2 was completely deleted from the GYPB mRNA in 2 samples, with Mia blood type negative. 2 samples showed complete full-length of GYPB mRNA, with Mia blood type positive. There was base substitution in exon-5 of GYPB mRNA in 1 sample. The full-length of GYPE mRNA was intact in 5 samples. MNS blood group related-genes have obvious polymorphism, and the detection of full-length mRNA sequence lays a foundation for the analysis of GYPA, GYPB and GYPE gene structure and in-depth study of MNS blood group antigen expression.

First report of Dickeya dadantii causing bacterial soft rot of Thaumatophyllum bipinnatifidum in Taiwan.

Philodendrons are important foliage ornamentals planted worldwide (Chen et al. 2010). In November 2021, soft rot symptoms were observed on Philodendron selloum (now known as Thaumatophyllum bipinnatifidum; Sakuragui et al. 2018) grown in a nursery in Taichung, Taiwan. On symptomatic plants, the petioles were macerated; leaf lesions were also found on some plants (Figure S1). About 60% of the plants on site were symptomatic; these plants tended to cluster together. Four plants were sampled. Infected tissues were soaked and cut into pieces in 10 mM MgCl2 (using scalpels); undiluted samples were streak-plated onto nutrient agar (NA) and grown for 24 h at 28°C. Translucent, creamy-white colonies were isolated from all of the tissues examined, and 4 isolates, PHIL1 to PHIL4, were obtained (each from a different plant). All isolates exhibited typical phenotypes of bacteria belonging to Dickeya; they could cause maceration symptoms on potato slices, ferment glucose and produce phosphatase (Schaad et al. 2001); they could also produce indigoidine on NGM medium (NA added with glycerol and MnCl2; Lee and Yu. 2006). Polymerase chain reactions using Dickeya-specific primers 5A and 5B (Chao et al. 2006) amplified the expected amplicon in all 4 isolates. The 16S rDNA of PHIL1 to PHIL4 were amplified using primer pair 27f/1492r (Lane 1991) and the amplicons were sequenced; all 4 isolates shared the same 1,395-bp sequence (accession nos. ON203122, ON479664-ON479666). Among the strains belonging to known species (in GenBank), PHIL1 to PHIL4 shared the highest sequence identity (99.93%) with D. dadantii 3937; they also shared 98.78% sequence identity with D. dadantii CFBP 1269T. Multilocus sequence analysis (MLSA) targeting fragments of PHIL1 to PHIL4's dnaA (720 bp), dnaJ (672 bp), dnaX (450 bp), gyrB (822 bp), and recN (762 bp) genes (Marrero et al. 2013) were conducted. The five-gene concatenated sequences (3,426 bp) of the 4 isolates (accession nos. ON227444-ON227448, ON494509-ON494523) were identical. A maximum-likelihood phylogenetic analysis including these sequences and those of type strains of other known Dickeya species revealed that PHIL1 to PHIL4 clustered with strains belonging to D. dadantii (Figure S2). Koch's postulates were fulfilled with an inoculation test conducted on T. bipinnatifidum (17 cm in aboveground height; 7-months-old). Stab inoculation using sterile toothpicks was conducted on petioles. Three plants were tested for each isolate and 2 petioles were inoculated for each plant; all 4 isolates were included in the assay. The pathogen loads inoculated were quantified by the spread plate method and were 3.22 - 4.81 x 107 colony forming units. Three plants were stabbed with bacteria-free toothpicks, serving as controls. All plants were bagged post inoculation and kept in a growth chamber (28°C; 14 h light). After 72 h, all of the inoculated petioles exhibited symptoms resembling those observed in the nursery. Bacteria were re-isolated from the symptomatic tissues (one isolate from each treatment), and all of their five-gene concatenated sequences were the same as those of PHIL1 to PHIL4. This is the first formal report of the occurrence of D. dadantii infecting T. bipinnatifidum in Taiwan. Studies have shown that D. dadantii could affect other Araceae plants in Taiwan (Lee and Chen 2021). Since different Araceae ornamentals are often planted together in gardens and nurseries, growers should be aware of potential transmission of D. dadantii among them.

Simple visualization method for the c.577del of erythropoietin variant: CRISPR/dCas9-based single nucleotide polymorphism diagnosis.

One of the single nucleotide polymorphisms (SNPs) in human erythropoietin (hEPO), the c.577del variant, can produces 26 amino acids longer than the wild-type hEPO, posing a risk of misinterpretation in routine doping analysis. To prevent this, the World Anti-Doping Agency (WADA) included a procedure for reporting the sequencing results regarding the presence or absence of SNPs for suspected cases in the new version of the technical document for recombinant EPO in 2022. However, it is very expensive for anti-doping laboratories to purchase a gene sequencing analyzer, which costs hundreds of thousands of dollars, and only a few companies provide specific gene sequencing services with accredited certification. Therefore, in this study, we developed a simple visualization method for the c.577del of the EPO variant at the gene level. The gene fragment of the EPO gene, including c.577del, was amplified using a fast polymerase chain reaction (PCR), and the PCR products were incubated with the clustered regularly interspaced short palindromic repeats (CRISPR)/deadCas9 system using variant-specific single-guide RNA (sgRNA). This ribonucleoprotein complex binds specifically to the EPO variant gene fragment, causing a band shift on native-PAGE. We designed 4 sgRNAs that can bind only to the EPO variant or wild-type gene. In addition, an electrophoretic mobility shift assay on a gel demonstrated that one of the sgRNAs had a high level of specificity. Consequently, the c.577del variant was selectively detected by visualizing the target fragment of the gene on the gel within 3h using only 3μl of the whole blood.

Nuclear fragmentation cross section measurements with the FOOT experiment

Different fields can profit by nuclear fragmentation cross section measurements: among them hadrontherapy and space radioprotection are of particular interest. Hadrontherapy employs high-energy beams of charged particles (protons and heavier ions) to treat deep-seated tumours. In these treatments nuclear interactions have to be considered: beam particles can fragment in the human body releasing a non-zero dose beyond the tumour while fragments of human body nuclei can modify the dose released in healthy tissues. On the radioprotection side, the interest in long-term manned space missions beyond Low Earth Orbit is growing in these years but it has to cope with significant health concerns from radiation in space, necessitating an accurate cross section data description. The FOOT (FragmentatiOn Of Target) experiment was proposed to cover these gaps in data. It was designed to detect, track and identify nuclear fragments and aims to measure double differential cross sections both in angle and kinetic energy which is the most complete information to address existing questions. The FOOT experimental setups, the experimental program and a first cross section analysis of 400 MeV/u 16O beam on Carbon target data acquired in July 2021 at GSI (Darmstadt, Germany) will be presented.

Nuclear fragmentation cross section measurements with the FOOT experiment

FOOT (FragmentatiOn Of Target) is an applied nuclear physics experiment that aims at a full characterization of the nuclear fragmentation processes of interest for Particle Therapy and Radiation Protection in Space. The physics program foresees a set of measurements in direct and inverse kinematics using particle beams and targets with composition similar to human tissues and spacecraft shielding materials. The final goal of the experiment is the measurement of double differential cross sections with respect to angle and fragment energy in the 100-800 MeV/u range with a precision better than 5%. The FOOT Collaboration is currently completing the development of the apparatus and data acquisition campaigns with partial setups have already started. In this paper, an overview of the current status of the experiment is given, together with a summary of the preliminary results obtained from the first measurements with 16O beams.

Clonagem, expressão e efeito antifúngico da quitinase recombinante de Streptomyces sampsonii KJ40

ABSTRACT: Streptomyces sampsonii is a kind of biocontrol bacterium with antifungal effects, and chitinase is one of the main antifungal substances. To improve and further study the structure and function of the chitinase gene of S. sampsonii, we amplified the target fragment by PCR, ligated the fragment to the expression vector pET-32a, introduced the resulting plasmid into Escherichia coli BL21 (DE3) and induced expression of the chitinase. Then, the recombinant chitinase was purified by is-labelled protein micro purification kit. A chitinase gene, Sschi61, was cloned from the genome and expressed in a prokaryote. The antifungal effect of the recombinant protein was also studied. Finally, the chitinase gene Sschi61 with a length of 1755 bp was obtained, and the expression of the 82 kDa recombinant chitinase was induced in E. coli by IPTG. The recombinant chitinase could inhibit the black spot pathogen of Eucommia ulmoides (Pestalotiopsis trachicarpicola). After the hyphae of the pathogen of black spot of Eucommia ulmoides (Pestalotiopsis trachicarpicola) were soaked with recombinant chitinase, the hyphae cells expanded, broke, and dissolved.

Carica papaya Represents a New Host of 16SrI-B Subgroup Phytoplasma Associated with Yellow Symptoms in China.

Carica papaya Linn, belonging to the Caricaceae family, is an economic and medicinal plant, which is widely cultivated in tropical and subtropical countries (Soib et al., 2020). Beginning in 2021, abnormal symptoms of Carica papaya exhibiting leaf yellow, crinkle and leaflet were found in Wanning city of Hainan Province, China. The diseased symptoms of the plant, with about 20 % incidence in the sampling regions, were suspected to be induced by phytoplasma, a phloem-limited and could not be cultured in vitro prokaryotic pathogen. Total DNAs were extracted from 0.10 g fresh leaves of symptomatic or asymptomatic Carica papaya using CTAB DNA extraction method (Doyle and Doyle, 1990). PCR reactions were performed using primers R16mF2/R16mR1 (Gundersen and Lee, 1996), secAfor1/secArev3 (Hodgetts et al., 2008) and AYgroelF/AYgroelR (Mitrović et al., 2011) specific for phytoplasma 16S rRNA, secA and groEL gene fragments. PCR products of the 16S rRNA, secA and groEL gene target fragments of phytoplasma were obtained from the DNA of eight diseased Carica papaya samples whereas not from the DNA of the asymptomatic plant samples. The PCR amplicons of the three genes were cloned and sequenced by Biotechnology (Shanghai) Co., Ltd. (Shanghai, China) and the sequences data were deposited in GenBank. The 16S rRNA, secAgroEL gene of phytoplasma was in length of 1326 (GenBank accession: OL625608), 716 (OL630087) and 1300 (OL630088) bp separately, putatively encoding 238 (secA) and 432 (groEL) amino acids sequence. The phytoplasma strain was named as Carica papaya yellow phytoplasma (CpY), CpY-hnwn strain. A blast search based on 16Sr RNA gene of CpY-hnwn showed 100 % sequence identity with that of 16SrI aster yellows group members (16SrI-B subgroup), such as Onion yellows phytoplasma strain OY-M (AP006628), Chinaberry witches'-broom phytoplasma (CWB) strain CWB-hnsy1 (KP662119) and CWB-hnsy2 (KP662120), Rapeseed phyllody phytoplasma isolate RP166 (CP055264). RFLP analysis based on the 16S rRNA gene fragment of CpY-hnwn was performed by the interactive online phytoplasma classification tool iPhyClassifier (Zhao et al., 2009) indicated that the phytoplasma strain is a member of 16SrI-B subgroup. Blast search based on secA gene of CpY-hnwn showed 100 % sequence identity with that of CWB strains CWB-gdgz (KP662182), CWB-jxnc (KP662180) and CWB-fjya (KP662178) belonging to 16SrI-B subgroup. Blast search based on groEL gene of CpY-hnwn showed 99.77 % sequence identity with that of mulberry dwarf phytoplasma (AB124809) and 99.69 % sequence identity with that of Onion yellows phytoplasma strain OY-M (AP006628) and Rapeseed phyllody phytoplasma isolate RP166 (CP055264). Phylogenetic analysis based on the 16S rRNA gene fragments performed by MEGA 7.0 employing neighbor-joining (NJ) method with 1000 bootstrap value (Kumar et al., 2016; Felsenstein, 1985) indicated that the CpY-hnwn phytoplasma strain was clustered into one clade with the phytoplasma strains of OY-M (AP006628), RP166 (CP055264), CWB-hnsy1 (KP662119), CWB-hnsy2 (KP662120) and areca palm yellow leaf (KF728948), with 100 % bootstrap value. To our knowledge, this is the first report that a 16SrI-B subgroup phytoplasma infects Carica papaya in Hainan Province, a tropical island of China. Carica papaya was previously reported to be infected by 16SrXII-O subgroup phytoplasmas in Nigeria (Kazeem et al., 2021), 16SrII-U subgroup in Hainan Province of China (Yang et al., 2016). The findings in this study indicated that one plant couldthe phytoplasmas belonging to different 16Sr groups, which would be beneficial to the specific detection of the pathogens and the epidemic monitoring of the related diseases.

Forensic analysis of raw meat adulteration using mtDNA

Meat species identification has become essential with the increasing events of frauds like the illegal slaughter of cows, meat adulteration, and substitution. Food scam directly influences public well-being, trade, and wildlife. In Pakistan, donkey meat is used as adulterants for cow meat and is considered Haram in Islamic concepts. In this study PCR, based detection methods are used for identification purposes. The mitochondrial gene cytochrome b has been used in this study to identify the origin of meat specie. Specie-specific primers of cyt b of cow and donkey were used for identification. DNA from different binary ratios of cow and donkey meat was extracted by the phenol-chloroform method. Ratios were made from 1-10 and extracted DNA was subjected to PCR to amplify the target fragment of the cyt b gene. Primers were sensitive to identifying species origin in all meat ratios. Multiplex PCR was designed to identify both species and the results were analyzed by gel electrophoresis. Fragment size of 309bp for cow and 475bp for donkey was observed. Results of the current study conclude that PCR assays, including multiplex PCR, is efficient and has a high sensitivity for even small amount of meat. It is concluded that multiplex PCR is useful and reliable for adulterated meat detection.

A metabarcoding framework for wild bee assessment in Luxembourg

Wild bees are crucial organisms for terrestrial environments. Their ongoing decline could cause irreparable damage to ecosystem services vital to plant reproduction and human food production. The importance of taking swift action to prevent further declines is widely acknowledged, but the current deficit of reliable taxonomic information complicates the development of efficient conservation strategies targeting wild bees. DNA metabarcoding can help to improve this situation by providing rapid and standardized mass identification. This technique allows the analysis of large numbers of specimens without the need for specialized taxonomic knowledge by matching high-throughput sequencing reads against public DNA barcode reference libraries. However, the validation of this approach for wild bees requires the evaluation of potential error sources on a regional scale. Here we analyzed the effects of three potential error sources on a metabarcoding pipeline customized for the wild bee fauna of Luxembourg. In an in silico study, we checked the completeness of the BOLD reference library for 349 species found in the country, the correspondence between molecular and morphological species delimitation for these taxa, and the amplification efficiency of three commonly used metabarcoding primer pairs (mlCOlintF/HCO2198, LepF1/MLepF1-Rev and BF2/BR2). The detection power of the pipeline was evaluated based on the species recovery rates from mock communities of known composition under variable DNA concentration treatments. The reference barcode library evaluation results show that 97% of the species have at least a single barcode in BOLD Systems (minimal length 196 bp) and that 85% of species have ≥ 5 barcodes in the public domain. The mlCOlintF/HCO2198 target fragment presented the highest coverage (77.94% of the species with full barcode sequences), followed by the target fragments of LepF1/MLepF1-Rev (77.65%) and BF2/BR2 (68.48%). Only 60% of the morphospecies presented a complete coverage of the prominent Folmer region (658 bp). The in silico amplification efficiency analysis shows that the BF2/BR2 primer pair has the best-predicted amplification performance, but none of the primer combinations evaluated can be expected to efficiently amplify all local wild bee genera. Finally, all species detection rates in the mock communities, except for the sample with the most discrepant DNA concentrations, were above 97%, with no significant differences found among treatments. These results indicate that the detection capacity of the pipeline is robust enough to be used for the reliable assessment of local wild bee biodiversity, even if species from various size categories are pooled together. Primer bias has a major effect on species detection, which can be acknowledged with a preliminary assessment of primer-template mismatch and sophisticated methodological designs (e.g. mock community controls, replicates). Overall, the metabarcoding pipeline here described provides a suitable tool for quick and reliable taxonomic identification of the regional wild bee fauna to aid conservation initiatives in Luxembourg – and beyond.

Functional analysis of the long-range regulatory element of BMP2 gene.

Recently, several pedigree-based studies have shown that abnormal replication of an enhancer element regulatory region in the downstream of the bone morphogenetic protein 2 (BMP2) gene is the cause of brachydactyly type A2 (BDA2). However, the exact molecular function of this regulatory region is unclear, and even conflicting results have emerged. In this study, based on bioinformatics analysis, we amplified target fragments of different lengths in this regulatory region by PCR technology, including a highly conserved 2.1 kb core sequence and 3 fragments that can completely cover the core 2.1 kb fragment. Then, the gene recombination vectors were constructed, and the biological function of these fragments was analyzed by the dual-luciferase reporter gene technology system. We found that the highly conserved 2.1 kb fragment did not have enhancer activity, while all of three truncated fragments showed strong enhancer activity. The results suggest that the expression regulation mode of the BMP2 gene is very complex. For the downstream regulatory region, selecting fragments of different lengths may have different effects on the regulation of BMP2 expression, which may due to the fragments with different lengths carrying different regulatory elements in the number of types. In summary, this study revealed the complexity of BMP2 gene regulatory elements, and provided new clues and directions for the subsequent in-depth exploration of the molecular pathogenic mechanism of BDA2.

Precision of the PET activity range during irradiation with 10C, 11C, and 12C beams

Objective. Beams of stable ions have been a well-established tool for radiotherapy for many decades. In the case of ion beam therapy with stable 12C ions, the positron emitters 10,11C are produced via projectile and target fragmentation, and their decays enable visualization of the beam via positron emission tomography (PET). However, the PET activity peak matches the Bragg peak only roughly and PET counting statistics is low. These issues can be mitigated by using a short-lived positron emitter as a therapeutic beam. Approach. An experiment studying the precision of the measurement of ranges of positron-emitting carbon isotopes by means of PET has been performed at the FRS fragment-separator facility of GSI Helmholtzzentrum für Schwerionenforschung GmbH, Germany. The PET scanner used in the experiment is a dual-panel version of a Siemens Biograph mCT PET scanner. Main results. High-quality in-beam PET images and activity distributions have been measured from the in-flight produced positron emitting isotopes 11C and 10C implanted into homogeneous PMMA phantoms. Taking advantage of the high statistics obtained in this experiment, we investigated the time evolution of the uncertainty of the range determined by means of PET during the course of irradiation, and show that the uncertainty improves with the inverse square root of the number of PET counts. The uncertainty is thus fully determined by the PET counting statistics. During the delivery of 1.6 × 107 ions in 4 spills for a total duration of 19.2 s, the PET activity range uncertainty for 10C, 11C and 12C is 0.04 mm, 0.7 mm and 1.3 mm, respectively. The gain in precision related to the PET counting statistics is thus much larger when going from 11C to 10C than when going from 12C to 11C. The much better precision for 10C is due to its much shorter half-life, which, contrary to the case of 11C, also enables to include the in-spill data in the image formation. Significance. Our results can be used to estimate the contribution from PET counting statistics to the precision of range determination in a particular carbon therapy situation, taking into account the irradiation scenario, the required dose and the PET scanner characteristics.