Ambiguous Sequences Research Articles

Genome Galaxy Identified by the Circular Code Theory.

The genome galaxy identified in bacteria is studied by expressing the reading frame retrieval (RFR) function according to the YZ-content (GC-, AG- and GT-content) of bacterial codons. We have developed a simple probabilistic model for ambiguous sequences in order to show that the RFR function is a measure of the gene reading frame retrieval. Indeed, the RFR function increases with the ratio of ambiguous sequences and the ratio of ambiguous sequences decreases when the codon usage dispersion increases. The classical GC-content is the best parameter for characterizing the upper arm, which is related to bacterial genes with a lowGC-content, and the lower arm, which is related to bacterial genes with a highGC-content. The galaxy center has aGC-content around 0.5. Then, these results are confirmed by expressing the GC-content of bacterial codons as a function of the codon usage dispersion. Finally, the bacterial genome galaxy is better described with the GC3-content in the 3rd codon site compared to the GC1-content and GC2-content in the 1st and 2nd codons sites, respectively. Whereas the codon usage is used extensively by biologists, its dispersion, which is an important parameter to reveal this genome galaxy, is surprisingly little known and unused. Therefore, we have developed a mathematical theory of codon usage dispersion by deriving several formulæ. It shows three important parameters in codon usage: the minimum and maximum codon probabilities and the number of codons with high frequency, i.e. with a probability at least1/64. By applying this theory to the evolution of the genetic code, we see that bacteria have optimised the number of codons with high frequency to maximise the codon dispersion, thus maximising the capacity to retrieve the reading frame in genes. The derived formulæ of dispersion can be easily extended to any weighted code over a finite alphabet.

Environmental niche models improve species identification in DNA barcoding

Abstract Recent advances in DNA barcoding have immeasurably advanced global biodiversity research in the last two decades. However, inherent limitations in barcode sequences, such as hybridization, introgression or incomplete lineage sorting can lead to misidentifications when relying solely on barcode sequences. Here, we propose a new Niche‐model‐Based Species Identification (NBSI) method based on the idea that species distribution information is a potential complement to DNA barcoding species identifications. NBSI performs species membership inference by incorporating niche modelling predictions and traditional DNA barcoding identifications. Systematic tests across diverse scenarios show significant improvements in species identification success rates under the newly proposed NBSI framework, where the largest increase is from 4.7% (95% CI: 3.51%–6.25%) to 94.8% (95% CI: 93.19%–96.06%). Additionally, obvious improvements were observed when using NBSI on potentially ambiguous sequences whose genetic nearest neighbours belongs to another species or more than two species, which occurs commonly with species represented by single or short DNA barcodes. These results support our assertion that environmental factors/variables are valuable complements to DNA sequence data for species identification by avoiding potential misidentifications inferred from genetic information alone. The NBSI framework is currently implemented as a new R package, ‘NicheBarcoding’, that is open source under GNU General Public Licence and freely available from https://CRAN.R‐project.org/package=NicheBarcoding.

Privileged proteins with a second residence: dual targeting and conditional re‐routing of mitochondrial proteins

Almost all mitochondrial proteins are encoded by nuclear genes and synthesized in the cytosol as precursor proteins. Signals in the amino acid sequence of these precursors ensure their targeting and translocation into mitochondria. However, in many cases, only a certain fraction of a specific protein is transported into mitochondria, while the rest either remains in the cytosol or undergoes reverse translocation to the cytosol, and can populate other cellular compartments. This phenomenon is called dual localization which can be instigated by different mechanisms. These include alternative start or stop codons, differential transcripts, and ambiguous or competing targeting sequences. In many cases, dual localization might serve as an economic strategy to reduce the number of required genes; for example, when the same groups of enzymes are required both in mitochondria and chloroplasts or both in mitochondria and the nucleus/cytoplasm. Such cases frequently employ ambiguous targeting sequences to distribute proteins between both organelles. However, alternative localizations can also be used for signaling, for example when non‐imported precursors serve as mitophagy signals or when they represent transcription factors in the nucleus to induce the mitochondrial unfolded stress response. This review provides an overview regarding the mechanisms and the physiological consequences of dual targeting.

Algorithm for the Weak Target Joint Detection and Ambiguity Resolution Based on Ambiguity Matrix

The looking-down mode of space airship bistatic radars faces complex sea–land clutter, and the mode of wide-range surveillance and the over-sight detection of the satellite platform generates a low SNR and range–Doppler ambiguity. The method traditionally used involves the transmission of multiple Pulse Repetition Frequencies (PRFs) and correlating them to solve the ambiguity. However, with a low SNR, the traditional disambiguation fails due to the large number of false alarms and target omissions. In order to solve this problem, a new algorithm for multi-target joint detection and range–Doppler disambiguation based on an ambiguity matrix is presented. Firstly, all possible state values corresponding to the ambiguous sequence are filled into the ambiguity matrix one by one. Secondly, the state values in the matrix cell are divided into several groups of subsequences according to the PRF. By disambiguating multiple sets of subsequences, performing subsequence fusion, and then undertaking point aggregation, the targets can be effectively detected in scenarios with a strong clutter rate, the false alarms can be suppressed, and the disambiguation of the range and Doppler is completed. The simulation shows that the proposed algorithm has the strong ability to detect targets and perform ambiguity resolution in the scenario of a multi-target and multi-false alarm.

Abstract 3557: A pancancer gamma delta T cell repertoire atlas

Abstract While representing only a small portion of T cell population, Gamma delta (γδ) T cells have unique contributions to both innate and adaptive immunity. Compared to αβ T, γδ T cells have a more diverse TCR repertoire, allowing them to recognize a broader range of tumor antigens. Recent breakthrough discoveries indicate that the antitumor efficacy of γδ T cells can be potentiated or rescued through targeted therapeutic approaches. Despite their functional and translational significance, a comprehensive understanding of the γδ T cell repertoire within tumor tissues has yet to be fully achieved.In this work, we generated a pan-cancer γδ T cell repertoire Atlas through reanalyzing RNA-seq data from more than 11,000 tumors in TCGA utilizing TRUST4, an advanced computational method for reconstruction of TCR repertoires. This allowed us to offer the most accurate and comprehensive examination of the γδ TCR landscape spanning 33 cancer types, marking it the largest collection of γδ clones on human cancer to date. We processed 660 billion RNAseq reads, identified ~3 million CDR3 reads, applied a series of stringent filtering criteria to remove biologically implausible, ambiguous sequences, and out-of-frame TCRs, which resulted in 22,205 unique γδ TCR clones from 6,751 tumors. TCR gene enrichment scores were calculated to represent overall expression of γδ in each tumor. The γδ enrichment is highly variable between and within cancer types. As expected, tumors traditionally classified as immune-cold (UVM and GBM) show the lowest scores. Cancers intrinsically related to lymphatic system (LAML, THYM and DLBC), exhibit the highest scores. Beyond THYM, the top five solid-tumor cancers carrying the highest enrichment are PRAD, KIRC, TGCT, LUAD and KICH. We further profiled the clone counts, spectrum of clone sizes, CDR3 length, V-J pair usage, and clonality in 33 cancers. Overall, a dominant presence of large clone segment is not observed in most cancers. The most prevalent V-J pairs are TRGV10/9/2-TRGJ1 for γ, and TRDV1-TRDJ1 for δ chain. Cancers including LAML, KIRC, LUAD, SKCM, CESC, LUSC, STAD, display a relatively higher proportion of intermediate to larger clones. THYM exists the highest γδ diversity, with the lowest clonality and most diverse V-J pairs. In addition, we evaluated the prognostics value of γδ genes by multivariate Cox regression, adjusting for age, sex, stage, and tumor purity, and identified 38 γδ genes associated with patient survival with p<0.05 in 25 cancer types. Finally, within HNSC, we observed higher γδ gene enrichment (p=1.6e-9) and clone diversity (p=0.014) in HPV+ vs. HPV- tumors. The γδ gene enrichment is also found associated with patients’ survival (p=0.002) in HPV+, but not in HPV- HNSC. Similarly, COAD tumors with high Microsatellite Instability (MSI) shows higher γδ gene enrichment and clone diversity compared to MSI low COAD. Collectively, our findings serve as a foundational resource for γδ T cell research in oncology. . Citation Format: Xiaoqing Yu, Song Li, Ling Cen, Xuefeng Wang. A pancancer gamma delta T cell repertoire atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3557.

A cluster-based disambiguation method using pose consistency verification for structure from motion

Structure from motion (SfM) recovers scene structures and camera poses based on feature matching, and faces challenges from ambiguous scenes. There are a large number of ambiguous scenes in real environment, which contain many duplicate structures and textures. The ambiguity leads to incorrect feature matches between images with similar appearance, and makes geometric misalignment in SfM. To address this problem, recent methods have focused on investigating the inconsistencies in feature topology among multi-view images. However, the feature topology is directly derived from 2D images. Thus, it is susceptible to feature occlusion caused by changes in perspective. Therefore, we propose a new method that disambiguates scenes using pose consistency rather than feature consistency. The pose consistency is conducted in 3D geometric space which is less sensitive to feature occlusion. Thus, the pose consistency is more robust than feature consistency. Our core motivation lies that the incorrect matches between ambiguous images will cause pose deviation from the global poses generated by correct matches. To detect this pose deviation, we first combine local and global information of the scene to generate the global reliable camera poses. The local information of each image is obtained by image clustering, and it strengthens the global information that is represented as the verified maximum spanning tree of clusters. Then, the global poses serve as the reference for further pose consistency verification. The global poses also enable us to perform both rotation and translation consistency verification for uncertain matches. During the pose consistency verification, the pose deviation calculated on image-level may be too small to be noticed. Thus, we propose to perform pose consistency verification at cluster-level instead of image-level to amplify the pose deviation. In the experiments, we compared our approach with several state-of-the-art methods, including COLMAP, Geodesic-SfM and TC-SfM, on both ambiguous and regular datasets. The results demonstrate that our approach achieves the best robustness, only our approach succeeds on all ambiguous image sequences (14/14). The quantitative evaluation results on image sequences with ground truth also show that our approach achieves the best accuracy (average RMSE of translation = 0.109, average RMSE of rotation = 0.827) among all methods. The source code of our approach is publicly available at https://github.com/gongyeted/MA-SfM.

Scalable neighbour search and alignment with uvaia.

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.

Neural alpha oscillations index context-driven perception of ambiguous vowel sequences

Perception of bistable stimuli is influenced by prior context. In some cases, the interpretation matches with how the preceding stimulus was perceived; in others, it tends to be the opposite of the previous stimulus percept. We measured high-density electroencephalography (EEG) while participants were presented with a sequence of vowels that varied in formant transition, promoting the perception of one or two auditory streams followed by an ambiguous bistable sequence. For the bistable sequence, participants were more likely to report hearing the opposite percept of the one heard immediately before. This auditory contrast effect coincided with changes in alpha power localized in the left angular gyrus and left sensorimotor and right sensorimotor/supramarginal areas. The latter correlated with participants' perception. These results suggest that the contrast effect for a bistable sequence of vowels may be related to neural adaptation in posterior auditory areas, which influences participants' perceptual construal level of ambiguous stimuli.

Development and Validation of a High-Throughput Sequencing Test for Mitogenome and rDNA Assembly and Annotation, and Its Use in Support of Nematode Identification of Regulatory Concern

Nematoda is a diverse phylum, and representatives are found in most habitats, including in and on animals and plants. Nematodes are regarded as the most abundant group in terms of individuals in marine and terrestrial sediments. Plant-parasitic nematodes are globally responsible for an annual yield loss of $125 billion. Reliable species identification is essential to take appropriate phytosanitary measures. The introduction of validated Sanger sequencing of 18S, 28S, and cox1 barcode loci represented a powerful tool in support of nematode identification. However, technical challenges associated with PCR and Sanger sequencing and the need for additional loci for identification hamper the efficient use of sequence data. To overcome these challenges, we developed an automated bioinformatic pipeline for the assembly and annotation of mitochondrial genomes and ribosomal DNAs, and we defined and validated a standardized test protocol including controls for routine diagnostics (i.e., high-throughput sequencing [HTS] test). The HTS test can be performed on single nematode specimens and outperforms the Sanger-based sequencing by producing less ambiguous consensus sequences and by yielding additional sequence data offering additional diagnostic resolution when needed. Compared with Sanger sequencing, the HTS test represents a reduction in hands-on time. The HTS test is regarded as fit for the purpose of the molecular identification of single nematode specimens in support of nematode diagnostics of regulatory concern. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Traitement de l’ambiguïté syntaxique et sémantique en TA neuronale : analyse de la traduction de l’anglais vers le français, l’espagnol et l’italien

Syntactic and Semantic Ambiguity Processing in Neural MT from English to French, Spanish and Italian
 Despite recent advances in artificial intelligence, human translators outperform MT for at least three types of tasks: identifying referents in anaphora (especially of the interphrastic kind), resolving semantic ambiguity (which is mainly due to polysemy or homonymy), and resolving syntactic ambiguity (especially with poorly inflected source languages such as English). Using the results obtained by two freely available online machine translation programs, Google Translate and DeepL, we examine how these two types of ambiguity are processed in translation from English into French, Spanish and Italian. Our results show that the two programs perform well overall in resolving the simplest cases of syntactic ambiguity, with difficulties arising more frequently for noun phrases featuring atypical syntactic divisions and rarely used collocations. MT output for ambiguous structures involving verb roots followed by the –ING morpheme (flying planes, growing pains) is studied, as well as syntactic structures in which two or more nouns are preceded by one or more adjectives. MT handles relatively well the longest of those structures (ADJ ADJ N N N N), probably because their subsets are part of the bilingual or target language monolingual corpora that underlie MT systems. Structures involving head modification and coordination (ADJ N AND N) are also known to pose problems for MT and human translators alike. But since many of the most frequent N AND N structures involve cohyponyms (men and women, brothers and sisters), antonyms (rights and duties, costs and benefits) or near- synonyms (aid and advice), their translation as a whole unit generally triggers the choice of correct syntact dependencies in translation. Structures in which the adjective only modifies the first noun (fresh air and exercise, social sciences and humanities) are much less frequent and are also probably translated as a whole unit. Structures involving premodification, coordination and post-modification may give rise to four distinct types of structures depending on whether long-range dependencies apply (detailed [knowledge and understanding] of the IT industry, [ethnic group] and [place of birth], invaluable [context and [source of information], [close friend] and confidant] of Mr Jones. Structures in which both long-range dependencies apply (integrated prevention and control of pollution) are the ones which most frequently cause errors for MT. Semantic ambiguity cases have been processed with increasing success by MT, especially when collocates vary widely for the main two meanings of homonyms (a well-known example is the word pen). Processing polysemy (for instance the medical use of conditions in pre-existing conditions) is a bit more of a challenge for MT. Other cases involving concentration of several polysemic terms in the same sentence (Changing the placement of beams relative to the staff involves changing the direction of the stems in the beam) also create difficulties for MT when the polysemic terms are used without any of their usual collocates (here in the specialised field of musical edition). Homonymy cases involving grammatical category changes (N-to-V or V-to-N conversion) seem to continue to pose the most difficulties to neural MT, despite increasing consideration of intra- and extraphrastic context. Potentially ambiguous word sequences (treatment increase in as the daily dose and duration of treatment increase), which were processed incorrectly before neuronal MT, are now correctly translated. But word sequences in which one word belongs to a part of speech which is not the most commonly used one (e.g. the noun remains in what remains can be considered) may cause occasional errors. Several examples that involve the verb founder are studied, and they frequently trigger translation of the noun in all three Romance languages (or translations of the verbs find or found due to incorrect segmentation).

A simple approach for random genomic insertion-deletions using ambiguous sequences in Escherichia coli.

Escherichia coliK-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction(PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt. Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletionmutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics.

Exploring the potential of mRNA for taxonomic delineation of marine benthic eukaryotes.

Direct sequencing of mRNA isolated from environmental samples has been commonly used to analyze the functional activity of ambient communities and, occasionally used for taxonomic identification. Here we assess the viability of using mRNA for investigating the species composition of marine benthic eukaryotes. Total RNA was extracted from sediments sampled close to fish farms and mRNA was sequenced after poly-A enrichment on an Illumina MiSeq sequencer. We investigated the origin of both raw reads and assembled contigs by aligning them to the NCBI non-redundant (nr/nt) nucleotide database. Although sequences were predominantly of eukaryotic origin, the analyses were complicated both by experimental and database artefacts. These issues were addressed by applying filtering procedures that removed the majority of ambiguous sequences from downstream analyses. These processes resulted in a set of 436 high-confidence contigs, the vast majority of which mapped to benthic organisms. Our alignments were dominated by annelids, consistent with burrowing groups found in a parallel morphological analysis. This study shows that it is possible to obtain adequate taxonomic information from the RNA of an eukaryotic community from a limited sample at a moderate cost, demonstrates how both laboratory and in silico artefacts can be overcome through appropriate bioinformatic procedures, and finally highlights some of the drawbacks and caveats of using NCBI as a reference database for such a dataset.

Trinucleotide [formula omitted]-circular codes II: Biology

A code X is (⩾k)-circular if every concatenation of words from X that admits, when read on a circle, more than one partition into words from X, must contain at least k+1 words. In other words, the reading frame retrieval is guaranteed for any concatenation of up to k words from X. A code that is (⩾k)-circular for all integers k is said to be circular. Any code is (⩾0)-circular and it turns out that a code of trinucleotides is circular as soon as it is (⩾4)-circular. A code is k-circular if it is (⩾k)-circular and not (⩾k+1)-circular. The theoretical aspects of trinucleotide k-circular codes have been developed in a companion article (Michel et al., 2022).Trinucleotide circular codes always retrieve the reading frame, leaving no ambiguous sequences. On the contrary, trinucleotide k-circular codes, for k∈{0,1,2,3} all have ambiguous sequences, for which the reading frame cannot always be retrieved. However, such a trinucleotide k-circular code is still able to retrieve the reading frame for a number of sequences, thereby exhibiting a partial circularity property. We describe this combinatorial property for each class of trinucleotide k-circular codes with k∈{0,1,2,3}. The circularity, i.e. the reading frame retrieval, is an ordinary property in genes. In order to consider the different cases of ambiguous sequences, we derive a new and general formula to measure the reading frame loss, whatever the trinucleotide k-circular code. This formula allows us to study the evolution of any trinucleotide k-circular code of (maximal) cardinality 20 to the genetic code, based on the reading frame retrieval property. We apply this approach to analyse the evolution of the trinucleotide circular code X observed in genes to the genetic code.The (⩾1)-circular codes of maximal size 20 necessarily have the same number of each nucleotide, specifically 15=3⋅20/4. This balanceness property can also be achieved by trinucleotide codes of cardinality 4,8,12 and 16. We call such trinucleotide codes balanced. We develop a general mathematical method to compute the number of balanced trinucleotide codes of each size, which also applies to self-complementary trinucleotide codes. We establish and quantify a relation between this balanceness property and the self-complementarity property.The combinatorial hierarchy of trinucleotide k-circular codes is updated with the growth function results. The numbers of amino acids coded by the trinucleotide k-circular codes are given for the cases maximal, minimal, self-complementary k-, (k,k,k)- and self-complementary (k,k,k)-circular.

SangeR: the high-throughput Sanger sequencing analysis pipeline.

In the era of next generation sequencing and beyond, the Sanger technique is still widely used for variant verification of inconclusive or ambiguous high-throughput sequencing results or as a low-cost molecular genetical analysis tool for single targets in many fields of study. Many analysis steps need time-consuming manual intervention. Therefore, we present here a pipeline-capable high-throughput solution with an optional Shiny web interface, that provides a binary mutation decision of hotspots together with plotted chromatograms including annotations via flat files. SangeR is freely available at https://github.com/Neuropathology-Giessen/SangeR and https://hub.docker.com/repository/docker/kaischmid/sange_r. Kai.Schmid@patho.med.uni-giessen.de or Daniel.Amsel@patho.med.uni-giessen.de. Supplementary data are available at Bioinformatics online.

Phylogenetic relationships of the commercial red snapper (Lutjanidae sp.) from three marine regions

Unambiguous and precise identifications of a species are crucial for managing and conserving the species across their dispersal regions. This study analyzed the molecular signatures and phylogenetic relationship of 84 specimens of lutjanids obtained from Malaysia, which covers three marine regions; Straits of Malacca (SM), west South China Sea (west SCS), and east South China Sea (east SCS). The assessment of 613 bp mtDNA COI has markedly classified the samples into five distinct species namely Lutjanus malabaricus, L. argentimaculatus, L. erythtropterus, L. sebae and L. bohar. The intraspecific and interspecific genetic distance ranged between 0.1% − 0.7% and 8.2% − 19.6%, respectively. While genetic homogeneity occurred among population and species across SM and west SCS, significant genetic structuring was detected among species between west and east SCS as evidenced by the occurrence of a single species, L. bohar that can be found only in Sabah (east SCS). The divulged potential loss of gene flow among the regions and was probably caused by oceanic currents. This study detected an ambiguous sequence (from Genbank) probably due to hybridization between species or simply because of an unidentified node. This study proposed that COI is the valid and reliable genetic marker for identifying lutjanids distributed across Malaysian waters. Future revision in distribution pattern and diversity exploration on a large scale with a higher number of samples and different genetic markers is needed to fill this current study's gaps.

Postdiction: When Temporal Regularity Drives Space Perception through Prestimulus Alpha Oscillations.

In postdiction, the last stimulus of a sequence changes the perception of the preceding stimuli. Postdiction has been reported in all sensory modalities, but its neural underpinnings remain poorly understood. In the rabbit illusion, a sequence of nonequidistant stimuli presented isochronously is perceived as equidistantly spaced. This illusion might be driven by an internal prior favoring a constant-speed motion. Here, we hypothesized that prestimulus alpha oscillations (8–12 Hz), known to correlate with perceptual expectations and biases, would reflect the degree to which perceptual reports are influenced by a constant-speed prior. Human participants were presented with ambiguous visual sequences while being recorded simultaneously with MEG and EEG: the same sequences yielded an illusory perception in about half the trials, allowing contrasting brain responses elicited by identical sequences causing distinct percepts. As a proxy of an individual’s prior, we used the percentage of perceived illusion and the detection criterion, assuming that a strong constant-speed prior would result in a higher rate of illusory percepts. We found that high frontoparietal alpha power was associated with perceiving the sequence according to the individual’s prior: participants with high susceptibility to the illusion would report the illusion, while participants with low susceptibility would report the veridical sequence. Additionally, we found that prestimulus alpha phase in occipitoparietal regions dissociated illusion from no-illusion trials. We interpret our results as suggesting that alpha power reflects an individual’s constant-speed prior, whereas alpha phase modulates sensory uncertainty.

MtDNA D-loop sequence analysis of Kalang, Krayan, and Thale Noi buffaloes (Bubalus bubalis) in Indonesia and Thailand reveal genetic diversity

Kalang (KBuf), Krayan (KrBuf), and Thale Noi buffaloes (TBuf) are swamp buffalo genetic resources in Indonesia and Thailand. The maternally inherited mitochondrial DNA (mtDNA), particularly D-loop region is an important material for phylogenetic inference and analyzing genetic diversity. Therefore, the objectives of the present study were to evaluate genetic diversity and to reconstruct the phylogenetic tree within buffalo breeds in Kalimantan, Indonesia, and Phatthalung, Thailand using mtDNA D-loop sequences. A total of one hundred forty buffaloes (70 males and 70 females) were observed including 40 buffaloes from North (NK), 40 from East (EK), and 40 from South Kalimantan (SK) provinces Indonesia and 20 from Phatthalung (PT) province, Thailand. DNA samples were isolated from buffalo tail hairs. DNA sequences were manually assembled using BioEdit program with consideration of gaps and ambiguous sequences. The phylogenetic tree of buffalo was generated by PHYLIP software. The observed variables included haplotype diversity, genetic distance, and genetic tree. The 956 bp of amplified mtDNA D-loop fragment presented a total of 24 haplotypes with several mutations that included transitions (293), transversions (60), deletions (15), and insertions (20). The neighbor-joining tree using the Kimura 2 parameter model demonstrated two local buffalo clusters among buffalo from Kalimantan and Thailand with four buffalo relationship patterns observed from buffaloes in Kalimantan Island (KBuf and KrBuf), Indonesia. The Results of the present study demonstrated that the buffaloes sequence analysis revealed relatively high diversity and is a good basis to perform selection and modern buffalo breeding development.

Duality Between the Local Score of One Sequence and Constrained Hidden Markov Model

We are interested here in a theoretical and practical approach for detecting atypical segments in a multi-state sequence. We prove in this article that the segmentation approach through an underlying constrained Hidden Markov Model (HMM) is equivalent to using the maximum scoring subsequence (also called local score), when the latter uses an appropriate rescaled scoring function. This equivalence allows results from both HMM or local score to be transposed into each other. We propose an adaptation of the standard forward-backward algorithm which provides exact estimates of posterior probabilities in a linear time. Additionally it can provide posterior probabilities on the segment length and starting/ending indexes. We explain how this equivalence allows one to manage ambiguous or uncertain sequence letters and to construct relevant scoring functions. We illustrate our approach by considering the TM-tendency scoring function.

Molecular and Alkaloid Characterization of Claviceps purpurea Sensu Lato From Grass Seed Production Areas of the U.S. Pacific Northwest.

Ergot, caused by Claviceps purpurea sensu lato, is an economically important seed replacement disease of Kentucky bluegrass (Poa pratensis) and perennial ryegrass (Lolium perenne) seed crops. C. purpurea sensu stricto is considered the primary Claviceps species responsible, but genetic diversity and cryptic species within C. purpurea sensu lato have previously been reported. Fifty-six C. purpurea sensu lato isolates collected from P. pratensis (n = 21) and L. perenne (n = 35) in Oregon and Washington between 2010 and 2014 were characterized via random amplified polymorphic DNA (RAPD), partial internal transcribed spacer (ITS), β-tubulin and elongation factor-1α (EF-1α) sequences, conidial size, and ergot alkaloid chemotype. Based on RAPD analysis, seven isolates from P. pratensis and 33 isolates from L. perenne collected in Oregon corresponded to C. purpurea sensu stricto, and 13 isolates collected from P. pratensis in Washington and Oregon were identified as C. humidiphila. Partial ITS, β-tubulin, and EF-1α sequences identified 10 isolates from P. pratensis as C. humidiphila, and seven isolates from P. pratensis and 33 isolates from L. perenne were identified as C. purpurea sensu stricto. Several isolates generated ambiguous RAPD bands or sequences that prevented identification. Ergot alkaloid chemotype profiling found that ergocornine and its epimer were predominant in sclerotia from P. pratensis, whereas ergotamine and its epimer were most abundant in sclerotia from L. perenne. This study confirms the presence of the C. purpurea sensu lato species complex in the U.S. Pacific Northwest and suggests that more research is needed to characterize and mitigate Claviceps spp. infection of grass seed crops in North America.

Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India.

Mutational status of SARS-CoV-2 genomes from India along with their impact on proteins was ascertained through multiple tools including MEGA, Genome Detective, SIFT, PROVEAN and ws-SNPs&GO. Excluding gaps and ambiguous sequences, 493 variable sites (152 parsimony informative and 341 singleton) were observed. NSP3 had the highest incidence of 101 sites followed by S protein (74), NSP12b (43) and ORF3a (31). Average mutations per sample for males and females was 2.56 and 2.88 respectively. Non-uniform geographical distribution of mutations suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 Neutral and 83 Disease) affecting amino acid sequence. NSP13 has a maximum of 14 Disease variants followed by S protein and ORF3a with 13 each. Disease mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2.