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A general description of molecular genetic markers is provided in the present article. The classification of DNA markers used for identification of raw materials of plant origin is presented. The most appropriate method for identifying raw materials derived from fruit and berries is chosen using study reports. The use of PCR for determining the quantitative and qualitative composition of the raw materials is considered. DNA regions used for PCR diagnostics of raw material derived from fruit and berries are characterized. The significance of amplification for a PCR test is outlined. The optimal PCR conditions have been selected and the advantages of this method have been revealed in the present study. Amplification profiles of DNA from the samples have been analyzed using different primers. Experiments with different primers allowing for identification of the raw material were carried out. The possibility of using a complex including a common gene and a variable gene for the identification of raw materials derived from fruit and berries has been considered. The sequence of DNA regions has been analyzed. The possibility of using a ribosomal RNA gene for generic and interspecific differentiation of DNA samples has been demonstrated. The significance of oligonucleotide primers and PCR product length for the reliability of the whole genotyping system has been elucidated. A scheme of PCR-based DNA profiling has been developed. Two types of the procedure were compared and the most appropriate type was chosen according to cost efficiency.

Using polymerase chain reaction 316 strains of E. coli (strains with normal enzymatic activity, strains with weak enzymatic activity and strains with hemolytic activity) were examined for the presence of pathogenicity genes. They were isolatedfrom healthy children and children with functional disorders of the gastro-intestinal tract. The studies have shown that strains of Escherichia coli have pathogenic potential, as evidenced by the presence of genetic pathogenicity markers in them.

Primers are used to reliably initiate a secondary explosive in a wide range of industrial and defence applications. However, established primer technologies pose both direct and indirect risks to health and safety. This review analyses a new generation of primer materials and ignition control mechanisms that have been developed to address these risks in firearms. Electrically or optically initiated metal, oxide and semiconductor-based devices show promise as alternatives for heavy metal percussive primers. The prospects for wider use of low-cost, safe, reliable and non-toxic primers are discussed in view of these developments.

Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region ( ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate-specific primers for amplifying the whole ITS region ( ITS: 29F/1084R) and a part of it ( ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences ( STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole. [ABSTRACT FROM AUTHOR]

Saddle gall midge ( Haplodiplosis marginata ) is a cereal pest exhibiting sporadic outbreaks for which chemical control options are limited. Integrated Pest Management programs may offer a means of suppressing H. marginata outbreaks, reducing pesticide input. Many IPM programs benefit from the natural population suppression inflicted through predation and parasitism. The larval stage of H. marginata overwinters in the soil and may be preyed upon by ground-dwelling arthropods, however the natural enemies of H. marginata remain unrecognized. A PCR-based assay for detecting H. marginata in the guts of predators was designed using novel species-specific primers. Feeding trials involving H. marginata larvae showed a detectability half-life of 31.07 h post-feeding in Nebria brevicollis . The guts of field-caught Carabidae were screened for H. marginata DNA. Four species: Poecilus versicolor , Nebria brevicollis , Harpalus rufipes and Loricera pilicornis were identified as natural enemies of H. marginata for the first time. A higher proportion of positive results were obtained at the end of H. marginata emergence (July) compared to the beginning (May). The importance of understanding trophic interactions in the management of H. marginata is discussed in addition to the potential uses for the newly designed assay and primers. [ABSTRACT FROM AUTHOR]

Beetles (Coleoptera) are the most diverse and species-rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of 'traditional markers' (e.g. mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small, and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome-wide survey to search nuclear protein-coding ( NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community for NPC marker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95 NPC markers which can be PCR amplified from standard genomic DNA extracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support >95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the 'traditional markers', and show great potential to expedite resolution of many parts in the Beetle Tree of Life. [ABSTRACT FROM AUTHOR]

Background: The accurate tracking of Cryptosporidium in faecal, water and/or soil samples in water catchment areas is central to developing strategies to manage the potential risk of cryptosporidiosis transmission to humans. Various PCR assays are used for this purpose. Although some assays achieve specific amplification from Cryptosporidium DNA in animal faecal samples, some do not. Indeed, we have observed non-specificity of some oligonucleotide primers in the small subunit of nuclear ribosomal RNA gene (SSU), which has presented an obstacle to the identification and classification of Cryptosporidium species and genotypes (taxa) from faecal samples. Results: Using a novel bioinformatic approach, we explored all available Cryptosporidium genome sequences for new and diagnostically-informative, multi-copy regions to specifically design oligonucleotide primers in the large subunit of nuclear ribosomal RNA gene (LSU) as a basis for an effective nested PCR-based sequencing method for the identification and/or classification of Cryptosporidium taxa. Conclusion: This newly established PCR, which has high analytical specificity and sensitivity, is now in routine use in our laboratory, together with other assays developed by various colleagues. Although the present bioinformatic workflow used here was for the specific design of primers in nuclear DNA of Cryptosporidium, this approach should be broadly applicable to many other microorganisms. [ABSTRACT FROM AUTHOR]

Cellulose is basic structural part of cell wall of plant and cellulases digest cellulose into glucose and provide a useful utilization of this enzyme in food and feed industry. The purpose of this study was to investigate hyper production of cellulase complex from indigenous local strain of Aspergillus tubingensis IMMIS2 extracted from rotten tomato. Corn stover revealed maximum cellulase complex activity (81 ± 1.5 µg/mL/min) after screening six substrates. The conserve sequences of fungus were used to identify hyper cellulase producing fungus using primers. The optimum temperature, pH and incubation time were analyzed to be 40 °C, 4.8, 96 h with cellulase activity of 86.4 ± 2.1 µg/mL/min for Aspergillus tubingensis IMMIS2. Cellulase revealed maximum activity (112 µg/mL/min) with Response Surface Methodology (RSM) using 40 mesh size substrate, 8 g substrate, 80% moisture, 5 mL inoculum, 0.5 g urea, 0.1 g KCl, 0.1 g CaCl 2 and 0.06 g MgSO 4 using Aspergillus tubingensis -IMMIS2 (LT732556). Most of the factors had significant impact on cellulase yield while some factors did not have good effect on cellulase yield. Cellulases have wide spread application in fruit saccharification and saccharification value of mango was 59.54%. This optimization study paves the way for the scientists to utilize RSM for enzymes production. [ABSTRACT FROM AUTHOR]

A little attention has been given on molecular identification of thrips (Insecta: Thysanoptera) in Egypt. Thus, the primers ITS4A, 28S rRNA, 18S rRNA and the primer pairs COI-1 + COI-2 + COI-3 were used to identify the three dominant thrips species (Haplothrips cahirensis karny; Dendrothrips eremicola Priesener and Hydatothrips kassimanus Priesener). The samples were collected from a private olive grove during 2013 and 2014 at Ismailia governorate, Egypt. DNA sequence data for 28S rRNA gene showed a positive response to H. cahirensis and D. eremicola only, while 18S rRNA reacted with all species. ITS4A and COI-1 + COI-2 + COI-3 showed a negative response to the studied species. DNA sequences of the species based on 18S rRNA were recorded in the Gene Bank. The phylogenetic tree of the three thrips species was given also. [ABSTRACT FROM AUTHOR]

Since the discovery that anaerobic methanotrophic archaea (ANME) are involved in the anaerobic oxidation of methane coupled to sulfate reduction in marine sediments, different primers and probes specifically targeting the 16S rRNA gene of these archaea have been developed. Microbial investigation of the different ANME subtypes (ANME-1; ANME-2a, b, and c; and ANME-3) was mainly done in sediments where specific subtypes of ANME were highly enriched and methanogenic cell numbers were low. In different sediments with higher archaeal diversity and abundance, it is important that primers and probes targeting different ANME subtypes are very specific and do not detect other ANME subtypes or methanogens that are also present. In this study, primers and probes that were regularly used in AOM studies were tested in silico on coverage and specificity. Most of the previously developed primers and probes were not specific for the ANME subtypes, thereby not reflecting the actual ANME population in complex samples. Selected primers that showed good coverage and high specificity for the subclades ANME-1, ANME-2a/b, and ANME-2c were thoroughly validated using quantitative polymerase chain reaction (qPCR). From these qPCR tests, only certain combinations seemed suitable for selective amplification. After optimization of these primer sets, we obtained valid primer combinations for the selective detection and quantification of ANME-1, ANME-2a/b, and ANME-2c in samples where different ANME subtypes and possibly methanogens could be present. As a result of this work, we propose a standard workflow to facilitate selection of suitable primers for qPCR experiments on novel environmental samples. [ABSTRACT FROM AUTHOR]

Adhesion-promoting substances (primers) play an important role in the durability of UV-curable nail varnishes on human toe and finger nail plates. The efficacy of these substances regarding the adhesion that exists between the UV nail coating and the substratum depends on the type of primer and its method of application. In the current study, we used non-acid and acid-based primers as additives in the coating composition and as individual layers applied directly onto the substrate. Adhesion tests were performed using organoleptic, dynamic and “pull-off” methods and using different substrates. The application of adhesion promoters was found to increase the level of adhesion between the varnish formulation and substrate. The best adhesion was obtained when the primer was applied as a separate layer prior to application of the coating. To the best of our knowledge, this work is the first systematic study comparing the effect of using primers with UV-curable nail varnishes on the adhesion of the polymer to the nail plate. [ABSTRACT FROM AUTHOR]

The diamondback moth (DBM) (Plutella xylostella) is one of the main pests of brassicaceous crops worldwide and shows resistance against a wide range of synthetic insecticides incurring millions of dollars in control costs every year. The DBM is a prime example of the introduction of an exotic species as a consequence of globalization. In this study we analyzed the genetic population structure of the DBM and two of its parasitic wasps, Diadegma semiclausum and Diadegma fenestrale, based on mitochondrial DNA sequences. We analyzed DBM samples from 13 regions worldwide (n = 278), and samples of the two wasp species from six European and African countries (n = 131), in an attempt to reconstruct the geographic origin and phylogeography of the DBM and its two parasitic wasps. We found high variability in COI sequences in the diamondback moth. Haplotype analysis showed three distinct genetic clusters, one of which could represent a cryptic species. Mismatch analysis confirmed the hypothesized recent spread of diamondback moths in North America, Australia and New Zealand. The highest genetic variability was found in African DBM samples. Our data corroborate prior claims of Africa as the most probable origin of the species but cannot preclude Asia as an alternative. No genetic variability was found in the two Diadegma species. The lack of variability in both wasp species suggests a very recent spread of bottlenecked populations, possibly facilitated by their use as biocontrol agents. Our data thus also contain no signals of host-parasitoid co-evolution. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria play a very important role in food fermentation. For strain identification, characterization and protection, it is important to use highly discriminatory identification methods. In the present study, 37 strains isolated from vegetables and food products of Korea were identified using 16S rDNA gene sequencing and were found to be Leuconostoc mesenteroides . Further, molecular characterization of all the strains was performed using two RAPD primers, i.e. 239 and KAY3. All strains have shown RAPD profiles and the amplified products of the profiles ranged from 300 to 4000 bp with both the primers and only small differences in banding pattern were observed. Out of 37, maximum bands were observed in strain 11436 with 239 and strain 11260 with KAY3. With both the primers, the phylogenetic analysis revealed seven clades which could be further subdivided into groups. The dendrogram was constructed using the unweighted pair group method with arithmetic averages (UPGMA). The results showed that 16S rDNA sequencing and RAPD-PCR are suitable preliminary molecular tools for identification and characterization of bacteria. [ABSTRACT FROM AUTHOR]

Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities. IMPORTANCE: Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity. [ABSTRACT FROM AUTHOR]

The pattern of genetic diversity among 92 genotypes of soybean from 5 different origins/sources (Pakistan, the USA, Asian Vegetable Research Development Centre (AVRDC), Japan and North Korea) was analyzed using randomly amplified polymorphic DNA markers. Out of 20 random primers 6 tested, 10 were polymorphic among genotypes and they yielded 107 markers, with an average of 10.7 markers per primer. The proportion of polymorphic bands within genotypes ranged from 0.47 to 0.71 with an average of 0.59. Pakistani and US genotypes exhibited the highest number of polymorphic bands (95%), while North Korean genotypes revealed the lowest (60%). The mean band frequency of the primers among genotypes was 0.57 with a range of 0.08–0.99. The Shannon’s index and Nei’s genetic diversity index revealed that primer OPF-06 showed maximum genetic diversity among the genotypes. Dendrogram constructed using Unweighted Pair Group Mean Average (UPGMA) method divided the genotypes into 5 main groups consisting of 13 clusters. The results of cluster analysis indicated that the genetic diversity between Pakistani and US or AVRDC genotypes is much larger than that between Pakistani and North Korean or Japanese genotypes. The Pakistani genotypes had distinct bands from plant introductions. Therefore, the Pakistani genotypes may be useful to soybean breeders. [ABSTRACT FROM AUTHOR]

FIASCO magnetic beads method was utilized to develop polymophic SSR markers of Rhodiola alsia, a precious species endemic to the Qinghai-Xizang Plateau. Two SSR marker probes, (AG)15 and (AC)15, were used to construct enriched SSR library and 2 500 positive clones were obtained. Then 1 200 positive clones were randomly selected to check and within which 400 clones were found with polymorphism. Half of the polymorphic clones were randomly chosen for sequencing and 105 SSR loci were achieved. Subsequently, 105 pairs of primers were designed by online software, primer 3-2.3.4, for amplifying the SSR sequences. Among which, a total of 45 pairs of primers were positive for amplification and the sequences amplified by thirteen pairs showed high genetic polymorphism when detected in four far apart natural populations with 24 individuals. Afterwards, the whole of 80 individuals in the four populations were employed to check the thirteen SSR loci. The average number of alleles per locus (A) was around 9.192, the mean of observed heterozygosity (Ho) and the expected heterozygosity (He) were around 0.712 and around 0.734, respectively. Such an extraordinary polymorphism was enough to meet the needs of future research. However, several loci were significantly deviated from Weinberg-Hardy equilibrium (P<0.01) in some populations, which may be due to the fact that the population of the actual study could not reach the ideal state of Weinberg-Hardy's law. Combining SSR polymorphic loci developed previously based on EST (Expressed Sequence Tag)sequences, this study provides a set of serviceable tools for population genetic structure analysis on R. alsia and other researches based on SSR markers. [ABSTRACT FROM AUTHOR]

The paper presents selected aspects of the effect of primers on adhesive properties and strength of aluminium sheet adhesive joints, made using polyurethane adhesives. The strength of adhesive joints was determined based on two cure time variants: 15 and 64 h. It was found that the longer cure time at a humidity of 33% is more desired, as it leads to a substantial increase in strength of the tested adhesive joints. In addition, two variants of surface preparation were applied: degreasing and degreasing followed by the application of a primer (a pro-adhesive agent). It was observed that the primer application prior to the application of an adhesive leads to a significant increase in strength compared to the variant where the adhesive application is preceded only by degreasing. Moreover, the aluminium sheet surface that was subjected to cataphoretic painting and priming exhibits better adhesive properties. It has a higher value of both surface free energy and its dispersion and polar components compared to the surface that was only subjected to degreasing. [ABSTRACT FROM AUTHOR]

The article is a comparative analysis of the visual content of the contemporary Russian ABC book and primer for first graders and the analogous Soviet and Russian books of the past century. There is an update of content and form of the ABC book and primer of the new millennium. The electronic version of the printed ABC book and primer and applications for the books on the teaching of reading have appeared. Therefore, it is possible to classify these publications as new media. The content of the current Russian ABC book and primer reflects the trends of postmodern culture and manifests the postmodern worldview. The visual content of contemporary textbooks contributes to design of realities with a different ontological status (psychological, aesthetic, and others). By comparison, the primers of the twentieth century are dominated by the image of 'objective' reality. As a consequence, the visual content of the contemporary Russian primers is more complicated than that of the primers of the twentieth century. The increased cognitive complexity of visual texts of modern textbooks places greater demands on the cognitive abilities of students. The article puts forward the suggestion that the polyontic images (recognition of the multiple realities that exist in the mind) of reality in contemporary textbooks create cognitive prerequisites for the assimilation of virtual reality by students. [ABSTRACT FROM AUTHOR]

DNA sequences are prone to create secondary structures by folding back on non-specific hybridization among their nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and sequencing processes. In this paper, we study the primer design by using w -constacyclic codes over F 4. We have presented families of DNA codes with secondary structures of stem length at most three. The GC -balanced and almost GC -balanced code is studied by using w -constacyclic shift over F 4. We prove that almost GC -balanced code is (k + 2) -weakly mutually uncorrelated. Finally, we design the primers by utilizing an algorithm. [ABSTRACT FROM AUTHOR]

Calanoid copepod populations are being severely affected due to the effects of ocean acidification (OA) and ocean warming (OW). These marine organisms are the most abundant primary consumers contributing significantly in the marine food web. Any effect on the abundance and diversity of copepods due to climate change is likely to have serious implications on the marine ecosystem functioning. Molecular studies that play a vital role in assessing the genetic changes under the influence of environmental imbalances are completely lacking for this species. Here we report the genetic variations in three generations of copepods through transcriptome sequencing. RNA sequencing was performed on an Illumina HiSeq platform employing the 2 × 100 bp paired-end chemistry. Approximately, 10GB of data was obtained for all the samples. The raw sequences were assembled through Trinity 2.6.6 and mined for single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). MIcroSAtellite Identification Tool (MISA) was used for SSR detection and Primer 3 (v 3.0) was utilized to design short oligonucleotide primers (18-20 mers). A total of 15,222 SSRs were identified and 28,944 primer pairs were designed against these motifs. The transcriptome possessed 413,890 SNPs at a frequency of 2.8 per kb. The newly discovered SSRs and SNPs could act as genetic markers for future studies on genetic diversity and conservation for Parvocalanus crassirostris ., (© 2023 The Author(s).)

Universal genus-specific primers for comparative analysis of two aligned 16S rRNA gene nucleotide sequences of lactic acid bacteria were constructed. The method to identify lactic acid bacteria and a comprehensive plan for their genus and species identification may be used to characterize isolated strains of the Lactobacillus genus bacteria and in quality control of foodstuffs enriched with Lactobacillus .

Ribosomal DNA (rDNA) has become the primary target molecule for phylogenetic reconstruction and the cultivation-independent detection and quantification of microorganisms (barcoding). With the advent of high-throughput sequencing technologies (Next Generation Sequencing (NGS), PCR-based amplicon sequencing of rDNA fragments for diversity screening is now a routine technology, at least in environmental sciences. The resulting exponential increase of publicly available rDNA sequences demands specialized reference databases (Fig. 1). SILVA (from Latin silva, meaning forest) is designed to provide a comprehensive web resource for up-to-date, quality-controlled databases of aligned rDNA sequences from the Bacteria, Archaea and Eukaryota domains and the corresponding online services (Glöckner et al. 2017, Quast et al. 2012). The current SILVA database (release 132) contains 6,073,181 small subunit and 907,382 large subunit rRNA gene sequences. All sequences are checked for anomalies, carry a rich set of sequence-associated contextual information, multiple taxonomic classifications (EMB L-EBI/ENA, RDP and GTDB) and the latest validly-described nomenclature. SILVA maintains manually curated reference alignments of 75,000 ribosomal RNA genes, both 16S/18S (small subunit, SSU) and 23S/28S (large subunit, LSU). With every full release, a manually curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences where no validlydescribed cultivated representative is available (Yilmaz et al. 2014). SILVA incorporates other unique features, including a comprehensive 23S/28S database of aligned rDNA sequences and alignments that contain Eukaryota sequences. SILVA is an active partner of RNACentral. RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. The SILVA team is a member of the Bergey's Board of Trustees which provides the authoritative taxonomy for Bacteria and Archaea as well as the Protist Reference Taxonomy Project UniEuk funded by the Gordon and Betty Moore Foundation to create a unified taxonomic framework In 2018 SILVA became an ELIXIR Core Data Resource. ELIXIR Core Data Resources are a set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data. To facilitate classification tasks for high-throughput rDNA data the SILVAngs has been implemented and released in 2013. SILVAngs is a data analysis service for rDNA reads from high-throughput sequencing (NGS) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download. SILVAngs serves several thousands of registered users, which processes thousands of projects per year. The application spectrum of the SILVA databases ranges from environmental sciences, microbiology, agriculture, biochemistry, biotechnology to medicine in academia and industry. [ABSTRACT FROM AUTHOR]

This contribution sheds light on the interaction between print technology, social literacy and primary school pedagogy from the seventeenth to the twentieth century. The printing press opened up the possibility of a Christian education for all: psalters and catechisms became a vehicle for teaching both religious content and the writing system using the spelling method. To move beyond this limited Christian literacy combining reading and memorization, and enable learners to read any text directly, textbooks separated the process into two stages: training beginners first to decipher, using the spelling method, and then to read different kinds of texts (informative, moral, civic). As many beginners failed at decoding, all subsequent “innovations” (word method, sentence method, look-say method, phonics, etc.) aimed to bridge the gap produced by this separation. This article will show how this common objective has been realized to varying degrees in different countries, especially in France and the United States (based on education policy, national language, teacher training, textbook publishing, etc).

ABSTRACT Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.

Este artigo analisa as 19 cartilhas de alfabetização aprovadas pelo Ministério da Educação (MEC) para uso nas escolas públicas a partir de 2010. A análise tem por objetivo verificar em que medida foram cumpridos dois dos aspectos centrais do processo de alfabetização estabelecidos pelo Edital: o tratamento das relações fonema/grafema e o desenvolvimento da fluência de leitura. O artigo contrasta as bases conceituais usadas nas orientações gerais do MEC e nas bibliografias citadas pelos autores com o paradigma da Ciência Cognitiva da Leitura. A análise das atividades propostas nas cartilhas demonstra que menos de 1% das cartilhas ensina a decodificar e nenhuma delas promove a fluência de leitura. O artigo discute as razões pelas quais nem os autores seguiram as recomendações do Programa Nacional do Livro Didático (PNLD) nem as autoridades do MEC abriram mão do requisito pelo qual a não observância do Edital, segundo qualquer um dos critérios, resulta em exclusão. E sugere que as concepções de alfabetização subjacentes às propostas analisadas, contrastadas com o paradigma da ciência cognitiva da alfabetização, podem explicar o entendimento dos autores, mas não explicam o descumprimento ostensivo das recomendações do Edital.El presente artículo analiza las 19 cartillas de alfabetización aprobadas por el MEC/PNLD (Ministerio de Educación de Brasil /Programa Nacional del Libro Didáctico) para uso en las escuelas públicas a partir de 2010. El análisis tiene como objetivo verificar en qué medida dos de los aspectos centrales del proceso de alfabetización establecidos por el Edicto de Licitación se cumplieron: el tratamiento de las relaciones fonema/grafema y el desarrollo de la fluidez de la lectura. El artículo coteja las bases conceptuales usadas en las orientaciones generales del MEC y en las bibliografías citadas por los autores con el paradigma de la Ciencia Cognitiva de la Lectura. El análisis de las actividades propuestas en las cartillas demuestra que menos del 1% de las cartillas enseña a decodificar y ninguna de ellas promueve la fluidez de la lectura. El artículo discute las razones por las cuales ni los autores siguieron las recomendaciones del PNLD (Programa Nacional del Libro Didáctico) ni las autoridades del MEC desistieron del requisito por el cual la no observancia del Edicto según cualquier criterio resulta en exclusión. También sugiere que las concepciones de alfabetización subyacentes a las propuestas analizadas, cotejadas con el paradigma de la ciencia cognitiva de la alfabetización, pueden explicar la comprensión de los autores, pero no explican el no cumplimiento ostensivo de las recomendaciones del Edicto.This paper analyzes the 19 primers approved by MEC/PNLD for use in public schools from 2010 onwards. The purpose of the paper is to assess the extent to which the authors of the primers complied with two requirements established in the Terms of Reference concerning the central aspects of learning to read: decoding and reading fluency. The paper compares the conceptual basis proposed by MEC and the references used by the authors with the paradigm of the Cognitive Science of Reading. The analysis of the primers reveals that less than 1% of the activities are related to decoding and there are no activities to promote reading fluency. The paper suggests a hypothesis to explain why the authors did not comply with the requirements and why the MEC authorities did not enforce these requirements. The paper also suggests that the underlying ideas of teaching and reading in the books approved by MEC, when compared with the paradigm of the Cognitive Science of Reading may explain the author's interpretation of the Terms of Reference but does not explain the explicit violation of its requirements.

O objetivo deste trabalho foi caracterizar fenotípica e genotipicamente isolados de espécies de fungos micorrízicos arbusculares (FMA) mantidos em cultura pura e avaliar a aplicabilidade da técnica PCR-DGGE desenvolvida para Gigaspora, na identificação molecular de espécies de FMA pertencentes a outros gêneros. A caracterização fenotípica das espécies foi realizada de acordo com critérios morfológicos, descritos pela taxonomia, e com uso de descrições originais das espécies presentes na literatura especializada. A análise genotípica foi feita com base na discriminação específica da região V9 do 18S rDNA, que permitiu a diferenciação das espécies e não revelou qualquer diferença entre os isolados geográficos de Glomus clarum, e entre os de Glomus etunicatum. Isto indica a aplicabilidade da técnica para a avaliação da pureza genética e discriminação de espécies de FMA.The objective of this work was to characterize phenotypically and genotypically isolates of arbuscular mycorrhizal fungi (AMF) maintained in pure culture and to evaluate the applicability of PCR-DGGE analysis, developed for Gigaspora, for molecular identification of AMF species belonging to other genres. The species phenotypic characterization was done according to morphological criteria, as described by taxonomy, and according to original descriptions of species published in the specialized literature. The genotypic analysis was made through specific discrimination of the V9 region in the 18S rDNA, which allowed the distinction of species and showed no difference among geographical isolates of Glomus clarum, and among those of Glomus etunicatum. This indicates the applicability of this technique for assessment of genetic purity and discrimination of AMF species.

The RAM's technique (Random Amplified Microsatellites) was used to assess the genetic diversity of 43 accesions of Cape gooseberry collected in six regions of Colombia (Nariño, Valle del Cauca, Cauca, Caldas, Quindío and Cundinamarca), property of the National University of Colombia at Palmira's campus collection. This analysis was based on the data from 42 polymorphic loci generated with seven primers. The results showed high genetic distance among accessions from Valle del Cauca and low genetic distance among accessions from Nariño, Cauca, Quindío, Caldas and Cundinamarca departments.Key words: Solanaceae; Polymorphic loci; primers; RAM.La técnica RAM (Random Amplified Microsatellites) se usó para el análisis de diversidad genética de 43 accesiones de uchuva recolectadas en seis regiones de Colombia (Nariño, Valle del Cauca, Cauca, Caldas, Quindío y Cundinamarca), pertenecientes a la colección establecida en la Universidad Nacional de Colombia sede Palmira. El análisis se realizó sobre 42 loci polimórficos obtenidos con siete cebadores, encontrándose baja diversidad para las introducciones de Nariño, Cauca, Quindío, Caldas y Cundinamarca. La población del Valle del Cauca reunió la mayor diversidad de los materiales recolectados.Palabras claves: Solanaceae; loci polimórficos; cebadores; RAM.