Type Of Duplication Research Articles

Evaluation and Pathologic Classification of Choledochal Cysts: Clinicopathologic Analysis of 84 Cases From the West.

Choledochal cyst (CC) is believed to be a mostly Asian disorder. As a clinically defined entity, its pathologic correlates are poorly characterized. Eighty-four resected CCs from the West were reanalyzed. After applying established Japanese criteria, 9/66 with available imaging were disqualified and 10/39 with preoperative cyst typing had to be recategorized. None had been diagnosed with, or evaluated for, pancreatobiliary maljunction, but on retrospective analysis of radiologic images, 12/66 were found to have pancreatobiliary maljunction. The clinical findings were: F/M=5.7; mean age, 48; most (77%) presented with abdominal pain; mean size, 2.9 cm; choledocholithiasis 11%. Gross/histologic examination revealed 3 distinct pathology-based categories: (I) Cystic dilatation of native ducts (81%). (II) Double bile duct (13%), almost all of which were found in women (10/11); all were diagnosed by pathologic examination, and not preoperative diagnosis. (III) Gastrointestinal (GI) duplication type (6%). Microscopic findings of the entire cohort included mucosal-predominant lymphoplasmacytic inflammation (50%), follicular cholangitis (7%), mucosal hyperplasia (43%; 13% with papillae), intestinal metaplasia (10%), BilIN-like hyperplasia (17%), erosion/ulceration (13%), and severe dysplasia-mimicking atypia including "detachment atypia" and micropapillary degeneration (11%). Carcinomatous changes were seen in 14 cases (17%) (high-grade dysplasia/carcinoma in situ in 7, intraductal papillary neoplasm 1, and invasive carcinoma 6); and 13/14 of these occurred in pathologic category I, all with cyst size >1 cm. In conclusion, diagnostic imaging guidelines used in Asia are not routinely used (but should be adopted) in the West. Pathologically, cases designated as CC are classifiable in 3 groups: category 1 (dilated native duct type), more prone to carcinomatous change; category 2, double-duct phenomenon (all but 1 being female in this study); and category 3, GI-type duplication. Overall, 17% of CCs show carcinomatous change (50% of them invasive). CC specimens should be carefully examined with this classification and submitted entirely for assessment of at-risk mucosa and cancerous transformation.

Detection of exact and near duplicates in phased-array ultrasound weld scan

Finding duplicates in phased-array ultrasound weld scans is typically done by certified analysts. Due to the vast amount of data involved, this task is time-consuming and error-prone. Some automated analysis software exists but are still inefficient. In this paper, two types of duplicates are defined. A method to detect each type in a database of three-dimensional ultrasound weld scans is presented. The duplicate detection process is implemented in a cloud-computing service enabling near real-time processing in industrial applications. Experiments are performed to expose the detection accuracy of both methods.

Differential Complex-Valued Convolutional Neural Network-Based Individual Recognition of Communication Radiation Sources

Data assaults from unauthorized access to the Internet of Things will induce severe intrusion and hazard to the whole network. Employing only traditional application layer password authentication approaches cannot guarantee the security of the communication system. Therefore, it is critical to develop a capable and efficient radio frequency fingerprints based physical layer authentication system. To incorporate the domain knowledge in more capable feature extracting and reduce information loss caused by converting RF baseband I/Q signals, we propose a novel differential complex-valued convolutional neural network based individual recognition approach of communication radiation sources in the paper. The proposed method can fully capture the nonlinearity of the RF baseband I/Q signals while decreasing the unfavorable impact of phase rotation induced by carrier frequency offset, which also significantly reduces the required data length of the collected steady-state data transmission section. The recognition performance evaluation on 20 wireless network card devices with duplicate batch, type, and manufacturer shows that the proposed approach has the best recognition performance compared with two conventional approaches whose recognition accuracies are lower than 95%, achieving the total recognition accuracy of 99.7%. Moreover, compared with constellation based approaches, which require at least 5,000 to 10,000 data points as input parameters, the proposed method can reduce the required data length of the collected steady-state data transmission section effectively, which is easier to implement in practical applications.

Detection of presence of non-allelic interaction for yield and yield contributing characters in okra Abelmoschus esculentus L. Moench

The experimental material comprised of six generations (P1, P2, F1, F2, BC1 and BC2) through generation mean analysis of six crosses with different parents. The generations were analysed during kharif 2019 in Randomized Block Design with randomization of generations within each cross in two replications. The traits were studied number of ridges per pod, number of seeds per pod, weight of 10 seeds (g), weight of 100 seeds (g). The scaling test indicated the presence of non-allelic interaction in all the crosses. In all the crosses PBNOK-6 x Pusa Makhmali was observed superior in most of the characters. In the most of the crosses the dominance (h) component was observed to be important in the inheritance of characters like weight of 10 seeds, weight of 100 seeds and additive x dominance (j) interaction was showed importance in number of ridges per pod, number of seeds per pod. Most of the characters showed complementary type of gene action. Complementary type of gene action play role in transfer inheritance characters. Some characters showed duplicate type of epistasis. Its play important role for transgressive selection of the characters.

Generation mean analysis for important morpho-physiological traits in bread wheat (Triticum aestivum L.)

The present investigation consisted of six genetic populations i.e. P1, P2, F1, F2, BC1 and BC2 of six crosses which were evaluated during the rabi, 2015-16 season. The six populations (parents, F1, backcrosses and F2) of the two wheat crosses, (NIAW-34 X NIAW-343 and NIAW-917 X NIAW-2030) were grown under restricted irrigation at Post Graduate Institute Farm, Department of Botany, Mahatma Phule Krishi Vidyapeeth, Rahuri (MS). Mean performance of Parents, f1’s, f2’s, BC1 and BC2 for different morphological and physiological traits in wheat recorded significant differences among both the crosses. Analysis of variance showed significant variability for all the traits in both crosses. All the three individual scaling tests for viz., A, B and C were significant for four traits viz., Number of tillers per plant, Number of grains per spike, grain yield per plant and Chlorophyll stability index (CSI) in both the crosses indicating the inadequacy of additive-dominance model to explain inheritance. Additive as well as Dominant genetic effects were highly significant in both the crosses, for the Days for 50% flowering, Days to maturity, Number of tillers per plant, Number of grains per spike, grain yield per plant, Chlorophyll stability index (CSI) and Membrane injury index. The epistatic gene interactions (i, j and l) for Chlorophyll stability index (CSI) was highly significant. Additive x additive, additive x dominance and dominance x dominance was observed in both the crosses. Duplicate type of epistasis was observed in both the crosses for days to maturity, plant height, grain yield per plant, chlorophyll stability index (CSI) and membrane injury index.

New structural variations responsible for Charcot-Marie-Tooth disease: The first two large KIF5A deletions detected by CovCopCan software

Next-generation sequencing (NGS) allows the detection of mutations in inherited genetic diseases, like the Charcot-Marie-Tooth disease (CMT) which is the most common hereditary peripheral neuropathy. The majority of mutations detected by NGS are single nucleotide variants (SNVs) or small indels, while structural variants (SVs) are often underdiagnosed. PMP22 was the first gene described as being involved in CMT via a SV of duplication type. To date, more than 90 genes are known to be involved in CMT, with mainly SNVs and short indels described. Herein targeted NGS and the CovCopCan bioinformatic tool were used in two unrelated families, both presenting with typical CMT symptoms with pyramidal involvement. We have discovered two large SVs in KIF5A, a gene known to cause axonal forms of CMT (CMT2) in which no SVs have yet been described. In the first family, the patient presented with a large deletion of 12 kb in KIF5A from Chr12:57,956,278 to Chr12:57,968,335 including exons 2–15, that could lead to mutation c.(130-943_c.1717-533del), p.(Gly44_Leu572del). In the second family, two cases presented with a large deletion of 3 kb in KIF5A from Chr12:57,974,133 to Chr12:57,977,210 including exons 24–28, that could lead to mutation c.(2539-605_*36 + 211del), p.(Leu847_Ser1032delins33). In addition, bioinformatic sequence analysis revealed that a NAHR (Non-Allelic-Homologous-Recombination) mechanism, such as those in the PMP22 duplication, could be responsible for one of the KIF5A SVs and could potentially be present in a number of other patients. This study reveals that large KIF5A deletions can cause CMT2 and highlights the importance of analyzing not only the SNVs but also the SVs during diagnosis of neuropathies.

An unsupervised approach to detect review spam using duplicates of images, videos and Chinese texts

Intuitively, image- or video-based recommendations seem to be more reliable than those containing plain text, and these types of recommendations have recently become widely encouraged and commonly seen across opinion sharing platforms. Considering their potential for manipulation, graphs (e.g., images and videos) are more vulnerable to spam than scripts. However, most state-of-the-art solutions for opinion spam detection are exclusively devoted to natural language parsing, and less work has been done concerning photos or videos. After investigating the top two business-to-customer websites, i.e., JD.com and TMALL.com, we propose an unsupervised approach to label suspected spam based on different types of duplication across images, videos and Chinese texts. Experiments verified the effectiveness of this approach and obtained several conclusions: 1) the situation of image spam is more severe than that of video and text spam; 2) for manipulation, borrowing something from a marketing page is less attractive than stealing from other reviewers; 3) in addition to using identical texts, spammers also use fictitious rare incidents to influence customers; and 4) overlapping duplications of images, videos and texts are common.

The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean.

Regulatory changes include divergence in both cis-elements and trans-factors, which play roles in organismal evolution. Whole genome duplications (WGD) followed by diploidization are a recurrent feature in the evolutionary history of angiosperms. Prior studies have shown that duplicated genes have different evolutionary fates due to variable selection constraints and results in genomic compositions with hallmarks of paleopolyploidy. The recent sequential WGDs and post-WGD evolution in the common ancestor of cultivated soybean (Glycine max) and wild soybean (Glycine soja), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes in G. soja and G. max. We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance of G. max in their F1 hybrids. By classifying genes into different regulatory divergence types, we found the trans-regulatory changes played a predominant role in transcriptional divergence between wild and cultivated soybean. The same gene ontology (GO) and protein family (Pfam) terms were found to be over-represented in DEGs and genes of cis-only between JY47 and GS, suggesting the substantial contribution of cis-regulatory divergences to the evolution of wild and cultivated soybeans. By further dissecting genes into five different duplication modes, we found genes in different duplication modes tend to accumulate different types of regulatory differences. A relatively higher proportion of cis-only regulatory divergences was detected in singleton, dispersed, proximal, and tandem duplicates than WGD duplicates and genome-wide level, which is in line with the prediction of gene balance hypothesis for the differential fates of duplicated genes post-WGD. The numbers of cis-only and trans-only regulated genes were similar for singletons, whereas there were more genes of trans-only than cis-only in the rest duplication types, especially in WGD in which there were two times more trans-only genes than that in cis-only type. Tandem duplicates showed the highest proportion of trans-only genes probably due to some special features of this class. In summary, our results demonstrate that genes in different duplication modes have different fates in transcriptional evolution underpinned by cis- or trans-regulatory divergences in soybean and likely in other paleopolyploid higher organisms.

Genetics of Quality Attributes and Powdery Mildew Severity in Garden Pea (Pisum sativum Var. Hortense L.) under Sub Temperate Conditions of North-Western Himalayas

Background: The choice of appropriate breeding method for improvement of traits depends largely on gene action. Hence, an understanding of the inheritance of quantitative traits is essential to develop an efficient breeding strategy.Methods: Twelve generations of three inter-varietal crosses involving four diverse parents of garden pea were studied for biochemical traits and powdery mildew disease severity to analyze the nature of gene effects by using generation mean anaylsis.Result: Duplicate type of epistasis was observed for protein content in all or one or other crosses. In most cases, the presences of linkage among interacting genes or higher order interactions at several loci were involved. Non-fixable gene effects were many times higher than fixable one in all the crosses indicating a major role non-additive gene effects in the inheritance of these traits. The type of gene effects along with presence of non-allelic interactions suggested the adoption of population improvement methods to break undesirable linkages through recombination. The other alternative can be to defer selection in the later generations by advancing segregating populations through bulk pedigree or SSD methods with one or two inter-matings like recurrent selection. Based on pod characteristics and powdery mildew disease severity203 single plant progenies were isolated over the generations of three crosses along with bulk seed following SSD and bulk method to isolate transgressive segregants.

Generation mean analysis for seed yield and it’s contributing quantitative traits in chickpea (Cicer arietinum L.)

The present investigation was conducted in rabi seasons during 2015-16, 2016-17 and 2017-18 at G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand with the objectives to study gene effects for ten yield and yield attributing traits. The experimental material consisted of three families (GL 10006 X DCP 92-3, DKG 876 X H 208 & GL 10006 X H 208) developed from four parents, each family comprised of six generations as P1, P2, F1, F2, BC1 and BC2. Scaling test, three parameter model, six parameter model and joint scaling test were used for gene action studies. Predominant and significant role of non-additive gene action i.e. dominance (h) and dominance × dominance (l) components which are non-fixable. Duplicate type of epistasis was prevalent than complementary epistasis in almost all the crosses in different traits.

Epistasis and inheritance of yield contributing traits in Chilli (Capsicum annuum L.)

The generation mean analysis for yield contributing traits involving six generations (P1, P2, F1, F2, BC1P1 and BC1P2) was undertaken to study the nature and magnitude of gene effects in Chilli (Capsicum annuum L.). The significance of individual scaling test and three parameter genetic model revealed the existence of epistasis and indicated the importance of additive[d], dominance [h] and other three types of non-allelic gene interactions i.e. additive × additive [i], additive × dominance [j] and dominance × dominance [l] for five characters viz., plant height (cm), plant canopy width (cm), fruit length (cm), fruit width (cm) and fruit weight (g). The results suggested the presence of duplicate type of epistasis for most of the traits studied indicating that selection for improvement may be successful in later generations of segregating populations. In view of these results, the implementation of population improvement technique such as reciprocal recurrent selection will be more effective with high potential in Chilli.

A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment

IntroductionEnvironmental stress is both a major force of natural selection and a prime factor affecting crop qualities and yields. The impact of the GRAS [gibberellic acid-insensitive (GAI), repressor of GA1–3 mutant (RGA), and scarecrow (SCR)] family on plant development and the potential to resist environmental stress needs much emphasis. ObjectivesThis study aims to investigate the evolution, expansion, and adaptive mechanisms of GRASs of important representative plants during polyploidization. MethodsWe explored the evolutionary characteristics of GRASs in 15 representative plant species by systematic biological analysis of the genome, transcriptome, metabolite, protein complex map and phenotype. ResultsThe GRAS family was systematically identified from 15 representative plant species of scientific and agricultural importance. The detection of gene duplication types of GRASs in all species showed that the widespread expansion of GRASs in these species was mainly contributed by polyploidization events. Evolutionary analysis reveals that most species experience independent genome-wide duplication (WGD) events and that interspecies GRAS functions may be broadly conserved. Polyploidy-related Chenopodium quinoa GRASs (CqGRASs) and Arabidopsis thaliana GRASs (AtGRASs) formed robust networks with flavonoid pathways by crosstalk with auxin and photosynthetic pathways. Furthermore, Arabidopsis thaliana population transcriptomes and the 1000 Plants (OneKP) project confirmed that GRASs are components of flavonoid biosynthesis, which enables plants to adapt to the environment by promoting flavonoid accumulation. More importantly, the GRASs of important species that may potentially improve important agronomic traits were mapped through TAIR and RARGE-II publicly available phenotypic data. Determining protein interactions and target genes contributes to determining GRAS functions. ConclusionThe results of this study suggest that polyploidy-related GRASs in multiple species may be a target for improving plant growth, development, and environmental adaptation.

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

BackgroundThe recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome.ResultsHere we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains’ composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization.ConclusionCharacterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.

Genetics of lodging resistance related traits in bread wheat (Triticum aestivum L.)

To evaluate the genetic background of lodging traits, six populations of two wheat crosses were sown under different nitrogen levels by using split plot design. Generation mean analysis was used to estimate the gene action for lodging related traits. Results showed genetic variability and significant differences for all traits. Allelic and non-allelic gene actions were operative for different traits with different magnitude under both normal and lodging condition. Duplicate types of espistasis were observed for grain yield per plant, 1000- kernel weight, number of grains per spike and number of tillers. The stem diameter, height of basal nodes and basal inter-nodal distance depicted the additive, additive × dominance and dominance gene action. The aforementioned results showed that plant height, stem diameter, height of basal nodes and basal internodal distance were more prone traits for lodging and selection should be practiced in later generations with increasing homozygosity.

The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BackgroundProtein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized.ResultsHere, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection.ConclusionsThe findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

Development and validation of a custom panel including 183 Y‐SNPs for Chinese Y‐chromosomal haplogroups dissection using a MALDI‐TOF MS system

Y-chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y-chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high-resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y-SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case-type samples using a MALDI-TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI-TOF MS platform were fully consistent with those obtained from the next-generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10ng. However, if less DNA (≥156.25pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, blood stain on FTA card samples could be dissected by direct PCR amplification on the MALDI-TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost-effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.

Estimation of gene action for grain yield and its related traits in linseed (Linum Usitatissimum L.)

Genetic analysis of seed yield and its component traits were evaluatedin six crosses (Meera x T-397, Meera x KL-221, Meera x JLS-9, Shekhar x T-397, Shekhar x KL-221 and Shekhar x JLS-9) of linseed comprised of five diverse parents namely Meera, Shekhar, T-397, KL - 221 and JLS -9. Estimatesof additive, dominance andepistasis components were evaluated through generation mean analysis.Additive component was realized for number of primary branches per plant, number of capsules per plant, number of seeds per capsule, capsule diameter, seed yield per plant and test weight. Dominance component was found to play an important role in the expression of number of primary branches per plant, number of seeds per capsule, seed yield per plant, test weight, oil content and rust disease reaction. Among epistatic gene interactions, additive × additive ( ) gene effect has positive significant enhancing (+) effect were observed for almost all traits whereas reducing (-) effect was observed for plant height, days to maturity, wilt disease reaction and rust disease reaction in almost all the crosses. The role of additive × dominance ( ) gene interaction play an important role in expression of almost all the traits under study in most of the crosses. Dominance × dominance (l) gene effect was observed significant for days to 50 per cent flowering, plant height, number of capsules per plant, number of seeds per capsule in almost all the crosses. Duplicate type of gene action was observed in all the six crosses for all the characters under study whereas none of the cross showed complimentary type of gene action.

Properties of beta oscillations in Dup15q syndrome

BackgroundDuplications of 15q11.2-q13.1 (Dup15q syndrome) are highly penetrant for autism, intellectual disability, hypotonia, and epilepsy. The 15q region harbors genes critical for brain development, particularly UBE3A and a cluster of gamma-aminobutyric acid type A receptor (GABAAR) genes. We recently described an electrophysiological biomarker of the syndrome, characterized by excessive beta oscillations (12–30 Hz), resembling electroencephalogram (EEG) changes induced by allosteric modulation of GABAARs. In this follow-up study, we tested a larger cohort of children with Dup15q syndrome to comprehensively examine properties of this EEG biomarker that would inform its use in future clinical trials, specifically, its (1) relation to basic clinical features, such as age, duplication type, and epilepsy; (2) relation to behavioral characteristics, such as cognition and adaptive function; (3) stability over time; and (4) reproducibility of the signal in clinical EEG recordings.MethodsWe computed EEG power and beta peak frequency (BPF) in a cohort of children with Dup15q syndrome (N = 41, age range 9–189 months). To relate EEG parameters to clinical (study 1) and behavioral features (study 2), we examined age, duplication type, epilepsy, cognition, and daily living skills (DLS) as predictors of beta power and BPF. To evaluate stability over time (study 3), we derived the intraclass correlation coefficients (ICC) from beta power and BPF computed from children with multiple EEG recordings (N = 10, age range 18–161 months). To evaluate reproducibility in a clinical setting (study 4), we derived ICCs from beta power computed from children (N = 8, age range 19–96 months), who had undergone both research EEG and clinical EEG.ResultsThe most promising relationships between EEG and clinical traits were found using BPF. BPF was predicted both by epilepsy status (R2 = 0.11, p = 0.038) and the DLS component of the Vineland Adaptive Behavior Scale (R2 = 0.17, p = 0.01). Beta power and peak frequency showed high stability across repeated visits (beta power ICC = 0.93, BPF ICC = 0.92). A reproducibility analysis revealed that beta power estimates are comparable between research and clinical EEG (ICC = 0.94).ConclusionsIn this era of precision health, with pharmacological and neuromodulatory therapies being developed and tested for specific genetic etiologies of neurodevelopmental disorders, quantification and examination of mechanistic biomarkers can greatly improve clinical trials. To this end, the robust beta oscillations evident in Dup15q syndrome are clinically reproducible and stable over time. With future preclinical and computational studies that will help disentangle the underlying mechanism, it is possible that this biomarker could serve as a robust measure of drug target engagement or a proximal outcome measure in future disease modifying intervention trials.

Phylogenetic analysis of the Si7PPO gene in foxtail millet, Setaria italica, provides further evidence for multiple origins of the negative phenol color reaction phenotype.

To elucidate the diversity and evolution of the Si7PPO gene that controls phenol color reaction (Phr) in foxtail millet, Setaria italica, we analyzed sequence polymorphisms of the Si7PPO gene in 39 accessions consisting of foxtail millet landraces (32 accessions) and their wild ancestor ssp. viridis (seven accessions) collected from various regions in Europe and Asia. The accessions included wild type (positive Phr) and three different types of loss-of-function phenotype (negative Phr), "stop codon type", "TE1-insertion type" and "6-bp duplication type", found in our previous study. We constructed a phylogenetic tree of the gene and found that accessions with positive Phr showed higher genetic diversity at the nucleotide sequence level. We also found that the three different loss-of-function types formed different clusters, suggesting that landraces with negative Phr have multiple origins from three different lineages including both landrace and ssp. viridis accessions with positive Phr.

Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates

sBackgroundTc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood.ResultsHere, phylogenetic analysis show that pogo transposases, together with Tc1/mariner, DD34E/Gambol, and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover, and Fot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals—even mammals—and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix–turn–helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2–7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29–56D) were observed for pogo transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains.ConclusionsThis is the first report to systematically reveal the evolutionary profiles of the pogo transposons, suggesting that pogo and Tc1/Mariner are two separate superfamilies of ITm group, and demonstrating the repeated domestications of pogo in vertebrates. These data indicate that pogo transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of pogo transposons and updates the classification of ITm group.