Plant-derived EpCAM-Fc fusion proteins induce in vivo immune response to produce IgGs inhibiting invasion and migration of colorectal cancer cells.

Transgenic tobacco plant expressed EpCAM-Fc fusion proteins to induce in vivo immune responses producing anti-EpCAM antibodies inhibiting human colorectal cancer cell invasion and migration. Plant is emerging as a promising alternative to produce valuable immunotherapeutic vaccines. In this study, we examined the in vivo anti-cancer efficacy of epidermal cell adhesion molecule (EpCAM)-Fc and EpCAM-FcK fusion proteins produced in transgenic plants as colorectal cancer vaccine candidates.

General Treatments Promoting Independent Living in Parkinson's Patients and Physical Therapy Approaches for Improving Gait-A Comprehensive Review.

This study delves into the multifaceted approaches to treating Parkinson's disease (PD), a neurodegenerative disorder primarily affecting motor function but also manifesting in a variety of symptoms that vary greatly among individuals. The complexity of PD symptoms necessitates a comprehensive treatment strategy that integrates surgical interventions, pharmacotherapy, and physical therapy to tailor to the unique needs of each patient. Surgical options, such as deep brain stimulation (DBS), have been pivotal for patients not responding adequately to medication, offering significant symptom relief.

ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulation.

Recent studies have highlighted the effectiveness of using antisense oligonucleotides (ASOs) for cellular RNA regulation, including targets that are considered undruggable; however, manually designing optimal ASO sequences can be labor intensive and time consuming, which potentially limits their broader application. To address this challenge, we introduce a platform, the ASOptimizer, a deep-learning-based framework that efficiently designs ASOs at a low cost. This platform not only selects the most efficient mRNA target sites but also optimizes the chemical modifications for enhanced performance.

A Comprehensive Review: Robot-Assisted Treatments for Gait Rehabilitation in Stroke Patients.

Robot-assisted gait training (RAGT) is at the cutting edge of stroke rehabilitation, offering a groundbreaking method to improve motor recovery and enhance the quality of life for stroke survivors. This review investigates the effectiveness and application of various RAGT systems, including both end-effector and exoskeleton robots, in facilitating gait enhancements. The selection process for this comprehensive analysis involved a meticulous review of the literature from databases such as PubMed, the Cochrane Library, and EMBASE, focusing on studies published between 2018 and 2023.

Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies.

Background: Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities.

A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa).

As plentiful high-quality genome assemblies have been accumulated, reference-guided genome assembly can be a good approach to reconstruct a high-quality assembly. Here, we present a chromosome-level genome assembly of the Korean crossbred pig called Nanchukmacdon (the NCMD assembly) using the reference-guided assembly approach with short and long reads. The NCMD assembly contains 20 chromosome-level scaffolds with a total size of 2.

A comparative study on the overlapping effects of clinically applicable therapeutic interventions in patients with central nervous system damage.

This study was conducted to investigate the effects of anti-gravity treadmill (AGT) training, which provides visual feedback and Biorescue training on proprioception, muscle strength, balance, and gait, in stroke patients. A total of 45 people diagnosed with post-stroke were included as study subjects; they were randomized to an AGT training group provided with visual feedback (Group A), a Biorescue training group provided with visual feedback (Group B), and an AGT/Biorescue group that subsequently received AGT training and Biorescue training (Group C). A muscle strength-measuring device was used to evaluate muscle strength.

Reference-based read clustering improves the genome assembly of microbial strains.

Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in microbial genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present a new read-clustering algorithm, called RBRC, for improving microbial genome assembly, by accurately estimating read proximity using multiple reference genomes.

Generation and application of pseudo-long reads for metagenome assembly.

Background: Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon.

Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop "Nanchukmacdon" a pig breeds with an enhanced variety of meat and high fertility rate.

Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms.

Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds.

Population analysis of the Korean native duck using whole-genome sequencing data.

Background: Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data.

TAMA: improved metagenomic sequence classification through meta-analysis.

Background: Microorganisms are important occupants of many different environments. Identifying the composition of microbes and estimating their abundance promote understanding of interactions of microbes in environmental samples. To understand their environments more deeply, the composition of microorganisms in environmental samples has been studied using metagenomes, which are the collections of genomes of the microorganisms.

Using INTERSPIA to Explore the Dynamics of Protein-Protein Interactions Among Multiple Species.

INTER-Species Protein Interaction Analysis (INTERSPIA) is a web application for identifying diverse patterns of protein-protein interactions (PPIs) in different species. Given a set of proteins of interest to the user, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins as well as different or common patterns of PPIs among the proteins in multiple species through a server-side pipeline. Second, it visualizes the dynamics of PPIs in multiple species via an easy-to-use web interface.

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.

Background: Genomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional and evolutionary genetic studies, including human diseases, such as cancers. Recently, a large number of whole genomes of evolving populations of yeast (Saccharomyces cerevisiae W303 strain) were sequenced in a time-dependent manner to identify temporal evolutionary patterns. For this type of study, a chromosome-level sequence assembly of the strain or population at time zero is required to compare with the genomes derived later.

Analysis of the ratios of medial-lateral and proximal-distal muscle activities surrounding the hip joint in the step-up and step-down positions.

Background: Many practitioners recommend step-up and step-down exercises to increase muscle strength in the lower extremities. However, decreased stability of the hip joint and imbalanced muscle activities can alter limb biomechanics during these movements.

Objective: This study investigated muscle imbalance between the medial and lateral muscle components and between the proximal and distal muscle components by expressing the proportions of muscle activation in the step-up and step-down positions.

Study on the design development of a multi joint ankle foot orthosis.

[Purpose] The purpose of this study was to investigate the effects of a newly designed multi joint ankle-foot orthosis on the gait and dynamic balance of stroke patients having foot drop. [Participants and Methods] This study was investigated 10 participants who were diagnosed with stroke. Patients were evaluated based on a 10-meter walk test, timed up and go test and Berg balance scale after each participant wore a plastic ankle-foot orthosis and a multi joint ankle-foot orthosis (AFO) that consisted of orthosis joints (having poster-stop joint and Klenzak joint functions).

mySyntenyPortal: an application package to construct websites for synteny block analysis.

Background: Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills.

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.

Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions.

The genome of the marine medaka Oryzias melastigma.

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma.

Functional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data.

Rapid and cost effective production of large-scale genome data through next-generation sequencing has enabled population-level studies of various organisms to identify their genotypic differences and phenotypic consequences. This is also used to study indigenous animals with historical and economical values, although they are less studied than model organisms. The objective of this study was to perform functional and evolutionary analysis of Korean bob-tailed native dog Donggyeong with distinct tail and agility phenotype using whole-genome sequencing data by using population and comparative genomics approaches.

Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population.

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species.

Synteny Portal: a web-based application portal for synteny block analysis.

Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes.

Comparison of alpha-synuclein immunoreactivity in the spinal cord between the adult and aged beagle dog.

Alpha-synuclein (α-syn) is a presynaptic protein that is richly expressed in the central and peripheral nervous systems of mammals, and it is related to the pathogenesis of Parkinson's disease and other neurodegenerative disorders. In the present study, we compared the distribution of the immunoreactivity of α-syn and its related gliosis in the spinal cord of young adult (2-3 years) and aged (10-12 years) beagle dogs. We discovered that α-syn immunoreactivity was present in many neurons in the thoracic level of the aged spinal cord, however, its protein level was not distinct inform that of the adult spinal cord.