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sults demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost.

American shad (Alosa sapidissima) is an important migratory fish under Alosinae and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no published genetic resources prevailing yet. Here, we reported the first de novo assembled and annotated transcriptome of A. sapidissima using blood and brain tissues.

We generated 160,481 and 129,040 non-redundant transcripts from brain and blood tissues. The entire work strategy involved RNA extraction, library preparation, sequencing, de novo assembly, filtering, annotation and validation. Both coding and non-coding transcripts were annotated against Swissprot and Pfam datasets. Nearly, 83% coding transcripts were functionally assigned. Protein clustering with clupeiform and non-clupeiform taxa revealed ~ 82% coding transcripts retained the orthologue relationship which improved confidence over annotation procedure. This study will serve as a useful resource in future for the research community to elucidate molecular mechanisms for several key traits like migration which is fascinating in clupeiform shads.

We generated 160,481 and 129,040 non-redundant transcripts from brain and blood tissues. The entire work strategy involved RNA extraction, library preparation, sequencing, de novo assembly, filtering, annotation and validation. Both coding and non-coding transcripts were annotated against Swissprot and Pfam datasets. Nearly, 83% coding transcripts were functionally assigned. Protein clustering with clupeiform and non-clupeiform taxa revealed ~ 82% coding transcripts retained the orthologue relationship which improved confidence over annotation procedure. This study will serve as a useful resource in future for the research community to elucidate molecular mechanisms for several key traits like migration which is fascinating in clupeiform shads.

Divergence in the evolutionary interests of males and females leads to sexual conflict. Traditionally, sexual conflict has been classified into two types inter-locus sexual conflict (IeSC) and intra-locus sexual conflict (IaSC). IeSC is modeled as a conflict over outcomes of intersexual reproductive interactions mediated by loci that are sex-limited in their effects. IaSC is thought to be a product of selection acting in opposite directions in males and females on traits with a common underlying genetic basis. While in their canonical formalisms IaSC and IeSC are mutually exclusive, there is growing support for the idea that the two may interact. Empirical evidence for such interactions, however, is limited.

Here, we investigated the interaction between IeSC and IaSC in Drosophila melanogaster. Using hemiclonal analysis, we sampled 39 hemigenomes from a laboratory-adapted population of D. melanogaster. We measured the contribution of each hemigenome to adult male and female fitness at three different intensities of IeSC, obtained by varying the operational sexratio. Subsequently, we estimated the intensity of IaSC at each sexratio by calculating the intersexual genetic correlation (r

) for fitness and the proportion of sexually antagonistic fitness-variation. We found that the intersexual genetic correlation for fitness was positive at all three sex ratios. Additionally, at male biased and equal sex ratios the r

was higher, and the proportion of sexually antagonistic fitness variation lower, relative to the female biased sex ratio, although this trend was not statistically significant.

Our results indicate a statistically non-significant trend suggesting that increasing the strength of IeSC ameliorates IaSC in the population.

Our results indicate a statistically non-significant trend suggesting that increasing the strength of IeSC ameliorates IaSC in the population.

Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are additional complications in the data deconvolution steps required to assign each cell to their originating samples.

To meet computational needs for efficient sample deconvolution, we developed the tools BarCounter and BarMixer that compute barcode counts and deconvolute mixed single-cell data into sample-specific files, respectively. Together, these tools are implemented as the BarWare pipeline to support demultiplexing from large sequencing projects with many wells of hashed 10x Genomics scRNA-seq data.

BarWare is a modular set of tools linked by shell scripting BarCounter, a computationally efficient barcode sequence quantification tool implemented in C; and BarMixer, an R package for identification of barcoded populations, merging barcoded data from multiple wells, and quality-control reporting related to scRNA-seq data. These tools and a self-contained implementation of the pipeline are freely available for non-commercial use at https//github.com/AllenInstitute/BarWare-pipeline .

BarWare is a modular set of tools linked by shell scripting BarCounter, a computationally efficient barcode sequence quantification tool implemented in C; and BarMixer, an R package for identification of barcoded populations, merging barcoded data from multiple wells, and quality-control reporting related to scRNA-seq data. These tools and a self-contained implementation of the pipeline are freely available for non-commercial use at https//github.com/AllenInstitute/BarWare-pipeline .

Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles.

We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision.

The isolate's genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences.

This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.

This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.

A birth-death process of which the births follow a hypoexponential distribution with L phases and are controlled by an on/off mechanism, is a population process which we call the on/off-seq-L process. buy 5-Ethynyl-2'-deoxyuridine It is a suitable model for the dynamics of a population of RNA molecules in a single living cell. Motivated by this biological application, our aim is to develop a statistical method to estimate the model parameters of the on/off-seq-L process, based on observations of the population size at discrete time points, and to apply this method to real RNA data.

It is shown that the on/off-seq-L process can be seen as a quasi birth-death process, and an Erlangization technique can be used to approximate the corresponding likelihood function. An extensive simulation-based numerical study is carried out to investigate the performance of the resulting estimation method.

A statistical method is presented to find maximum likelihood estimates of the model parameters for the on/off-seq-L process. Numerical complications related to the likelihood maximization are identified and analyzed, and solutions are presented. The proposed estimation method is a highly accurate method to find the parameter estimates. Based on real RNA data, the on/off-seq-3 process emerges as the best model to describe RNA transcription.

A statistical method is presented to find maximum likelihood estimates of the model parameters for the on/off-seq-L process. Numerical complications related to the likelihood maximization are identified and analyzed, and solutions are presented. The proposed estimation method is a highly accurate method to find the parameter estimates. Based on real RNA data, the on/off-seq-3 process emerges as the best model to describe RNA transcription.

The emerging epitranscriptome plays an essential role in female fertility. As the most prevalent internal mRNA modification, N6-methyladenine (m

A) methylation regulate mRNA fate and translational efficiency. However, whether m

A methylation was involved in the aging-related ovarian reserve decline has not been investigated. Herein, we performed m

A transcriptome-wide profiling in the ovarian granulosa cells of younger women (younger group) and older women (older group).

m

A methylation distribution was highly conserved and enriched in the CDS and 3'UTR region. Besides, an increased number of m

A methylated genes were identified in the older group. Bioinformatics analysis indicated that m

A methylated genes were enriched in the FoxO signaling pathway, adherens junction, and regulation of actin cytoskeleton. A total of 435 genes were differently expressed in the older group, moreover, 58 of them were modified by m

A. Several specific genes, including BUB1B, PHC2, TOP2A, DDR2, KLF13, and RYR2 which were differently expressed and modified by m

A, were validated using qRT-PCR and might be involved in the decreased ovarian functions in the aging ovary.

Hence, our finding revealed the transcriptional significance of m

A modifications and provide potential therapeutic targets to promote fertility reservation for aging women.

Hence, our finding revealed the transcriptional significance of m6A modifications and provide potential therapeutic targets to promote fertility reservation for aging women.

To achieve a target-based drug delivery with minimal side effects, novel drug delivery systems are being continuously explored. Vesicular systems are one such system that can ameliorate the bioavailability of the encapsulated drug by delivering the drug at the targeted site and can minimize the side effect.

The objective of this review is to provide a vivid description of glycerosomes and their applications. Glycerosomes are sphere-shaped versatile vesicles consisting of one or more phospholipid bilayers similar to liposomes but contain a high concentration of glycerol, which modifies the liposome bilayer fluidity. Glycerosomes can encapsulate both hydrophobic and hydrophilic drugs, which makes them the promising vehicle in the field of drug delivery.

Most of the glycerosome formulations prepared were targeted for topical delivery and in particular, a cutaneous route where they have shown promising results. These vesicles are biocompatible and due to the high glycerol concentration, they have improved spreadability and penetrability.