Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple ...Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum).
•A novel method using moments of cumulative Fourier power spectrum (CPS) in clustering the DNA sequences.•Each sequence is translated into a vector and the distances between vectors represent the relationships between sequences.•The mapping between the spectra and moment vector is one-to-one, thus much information is kept in this way.•CPS outperforms the traditional MSA and another alignment-free method on both the accuracy and the calculation speed.•We upload the code for CPS on GitHub to help people apply and analyze our method in practice.
Anaplasmosis is a rickettsial infection with significant effects on human and animal health, and the discovery of new species or genotypes with zoonotic potential in recent years has increased this ...importance. The aim of this study was to provide the first assessment of the molecular etiology and prevalence of bovine anaplasmosis in Kyrgyzstan (specifically in the Chuy, Talas, Djalal-Abad, Naryn, and Issyk-Kul regions). The prevalence of bovine anaplasmosis was determined as 1.7% (6/358). PCR and partial DNA sequencing results of the 16S ribosomal RNA (rRNA) gene revealed that Anaplasma centrale, A. phagocytophilum like-1, and the human pathogenic novel genotype A. capra are circulating in cattle herds in Kyrgyzstan. Six DNA nucleotide sequences obtained in this study were deposited in GenBank under the following accession numbers: A. centrale (MW672117, MW672118, MW672119, MW672120), A. phagocytophilum (MW672121), and A. capra (MW672115).
Here, to facilitate the solid-phase purification of synthetic DNA sequences, a riboside phosphoramidite, carrying a 5-O-capture linker and a 2-O-silyl ether protecting group, is incorporated into a ...DNA sequence during its last solid-phase synthesis cycle. After deprotection and release of the DNA sequence from the synthesis support, the sequence is then covalently linked to a capture support to enable the removal of shorter unbound DNA sequences by simply washing these off the support. The solid-phase purified DNA sequence is then released from the capture support, through an innovative intramolecular cyclodeesterification of its terminal riboside ethyl phosphate triester entity and is isolated in a yield of 94% while displaying an exquisite purity of 97%.
The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to ...treat names 'validly published' under that code in the
(IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only 'validly published' under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since 'validly published under the SeqCode' is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as
names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.
Plant and soil microbial diversities are linked through a range of interactions, including the exchange of carbon and nutrients but also herbivory and pathogenic effects. Over time, associations ...between plant communities and their soil microbiota may strengthen and become more specific, resulting in stronger associations between plant and soil microbial diversity.
We tested this hypothesis at the end of a 4‐year field experiment in 48 plots with different plant species compositions established 13 years earlier in a biodiversity experiment in Jena, Germany. We factorially crossed plant community history (old vs. new plant communities) and soil legacy (old vs. new soil) with plant diversity (species richness levels 1, 2, 4 and 8, each with 12 different species compositions). We use the term ‘plant community history’ to refer to the co‐occurrence history of plants in different species compositions in the Jena Experiment. We determined soil bacterial and fungal community composition in terms of operational taxonomic units (OTUs) using 16S rRNA gene and ITS DNA sequencing.
Plant community history (old plants) did not affect overall soil community composition but differentially affected bacterial richness and abundances of specific bacterial taxa in association with specific plant species compositions. Soil legacy (old soil) markedly increased soil bacterial richness and evenness and decreased fungal evenness. Soil fungal richness increased with plant species richness, regardless of plant community history or soil legacy, with the strongest difference between plant monocultures and mixtures. Specific plant species compositions and functional groups were associated with specific bacterial and fungal community compositions. Grasses increased fungal richness and evenness and legumes decreased fungal evenness, but bacterial diversity was not affected.
Synthesis. Our findings indicate that as experimental ecosystems varying in plant diversity develop over time (2002–2010), plant species associate with specific soil microbial taxa. This can have long‐lasting effects on below‐ground community composition in re‐assembled plant communities, as reflected in strong soil legacy signals still visible after 4 years (2011–2015). Effects of plant community history on soil communities are subtle and may take longer to fully develop.
The results of our study indicate that as experimental ecosystems varying in plant diversity develop over time, plant species associate with specific soil bacterial and fungal taxa. This can have long‐lasting effects on belowground community composition in newly assembled plant communities. Effects of plant community history on soil bacterial and fungal communities are more subtle and may take longer to develop.
DNA built from modular repeats presents a challenge for gene synthesis. We present a solid surface-based sequential ligation approach, which we refer to as iterative capped assembly (ICA), that adds ...DNA repeat monomers individually to a growing chain while using hairpin 'capping' oligonucleotides to block incompletely extended chains, greatly increasing the frequency of full-length final products. Applying ICA to a model problem, construction of custom transcription activator-like effector nucleases (TALENs) for genome engineering, we demonstrate efficient synthesis of TALE DNA-binding domains up to 21 monomers long and their ligation into a nuclease-carrying backbone vector all within 3 h. We used ICA to synthesize 20 TALENs of varying DNA target site length and tested their ability to stimulate gene editing by a donor oligonucleotide in human cells. All the TALENS show activity, with the ones >15 monomers long tending to work best. Since ICA builds full-length constructs from individual monomers rather than large exhaustive libraries of pre-fabricated oligomers, it will be trivial to incorporate future modified TALE monomers with improved or expanded function or to synthesize other types of repeat-modular DNA where the diversity of possible monomers makes exhaustive oligomer libraries impractical.
Infections with the tapeworm Taenia solium (taeniosis and cysticercosis) are Neglected Tropical Diseases (NTD) highly endemic in Madagascar. These infections are however underdiagnosed, underreported ...and their burden at the community level remains unknown especially in rural remote settings. This study aims at assessing the prevalence of T. solium infections and associated risk factors in twelve remote villages surrounding Ranomafana National Park (RNP), Ifanadiana District, Madagascar.
A community based cross-sectional survey was conducted in June 2016. Stool and serum samples were collected from participants. Tapeworm carriers were identified by stool examination. Taenia species and T. solium genotypes were characterised by PCR and sequencing of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Detection of specific anti-cysticercal antibodies (IgG) or circulating cysticercal antigens was performed by ELISA or EITB/Western blot assays.
Of the 459 participants with paired stool and blood samples included ten participants from seven distinct villages harbored Taenia spp. eggs in their stools samples DNA sequencing of the cox1 gene revealed a majority of T. solium Asian genotype (9/10) carriage. The overall seroprevalences of anti-cysticercal IgGs detected by ELISA and EITB were quite similar (27.5% and 29.8% respectively). A prevalence rate of 12.4% of circulating cysticercal antigens was observed reflecting cysticercosis with viable cysts. Open defecation (Odds Ratio, OR = 1.5, 95% CI: 1.0-2.3) and promiscuity with households of more than 4 people (OR = 1.9, 95% CI: 1.1-3.1) seem to be the main risk factors associated with anticysticercal antibodies detection. Being over 15 years of age would be a risk factor associated with an active cysticercosis (OR = 1.6, 95% CI: 1.0-2.7). Females (OR = 0.5, 95% CI: 0.3-0.9) and use of river as house water source (OR = 0.3, 95% CI: 0.1-1.5) were less likely to have cysticercosis with viable cysts.
This study indicates a high exposure of the investigated population to T. solium infections with a high prevalence of cysticercosis with viable cysts. These data can be useful to strengthen public health interventions in these remote settings.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Ensuring faithful homologous recombination in allopolyploids is essential to maintain optimal fertility of the species. Variation in the ability to control aberrant pairing between ...homoeologous chromosomes in Brassica napus has been identified. The current study exploited the extremes of such variation to identify genetic factors that differentiate newly resynthesised B. napus, which is inherently unstable, and established B. napus, which has adapted to largely control homoeologous recombination.
A segregating B. napus mapping population was analysed utilising both cytogenetic observations and high‐throughput genotyping to quantify the levels of homoeologous recombination.
Three quantitative trait loci (QTL) were identified that contributed to the control of homoeologous recombination in the important oilseed crop B. napus. One major QTL on BnaA9 contributed between 32 and 58% of the observed variation. This study is the first to assess homoeologous recombination and map associated QTLs resulting from deviations in normal pairing in allotetraploid B. napus.
The identified QTL regions suggest candidate meiotic genes that could be manipulated in order to control this important trait and further allow the development of molecular markers to utilise this trait to exploit homoeologous recombination in a crop.
See also the Commentary on this article by Sourdille & Jenczewski, 229: 3041–3043.
PDF
