Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. ...Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at http://vntr.csie.ntu.edu.tw/.
Infection by Toxocara spp. is known to be significantly associated with partial epilepsy. It has become popular for people to raise dogs/cats as pets and consume roasted meat/viscera, and the status ...of Toxocara spp. infection, epilepsy awareness, and associated risk factors among the general population are currently unknown in Taiwan.
A seroepidemiological investigation among 203 college students (CSs), consisting of 110 males and 93 females with an average age of 21.5 ± 1.2 years, was conducted in 2009 in Taipei City. A Western blot analysis based on excretory-secretory antigens derived from Toxocara canis larvae (TcESs) was applied to determine the positivity of serum immunoglobulin G antibodies. A self-administered questionnaire was also given to obtain information about demographic characteristics, epilepsy awareness, and risk factors. A logistic regression model was applied for the statistical analysis using SPSS software.
The overall seropositive rate of Toxocara spp. infection was 8.4% (17/203). As to epilepsy awareness, a non-significantly higher seroprevalence was found in CSs who claimed to "know" about epilepsy compared to those who did not know (P > 0.05).
It appears that appropriate educational programs are urgently needed to provide correct knowledge related to the prevention and control measures against Toxocara spp. infections to avoid potential threats by this parasite to the general population in Taiwan.
The mitotic spindle is an essential molecular machine for chromosome segregation during mitosis. Achieving a better understanding of its organization at the topological level remains a daunting task. ...To determine the functional connections among 137 mitotic spindle proteins, a protein-protein interaction network among queries was constructed. Many hub proteins, which connect more than one query and serve as highly plausible candidates for expanding the mitotic spindle proteome, are ranked by conventional degree centrality and a new subnetwork specificity score. Evaluation of the ranking results by literature reviews and empirical verification of SEPT6, a novel top-ranked hub, suggests that the subnetwork specificity score could enrich for putative spindle-related proteins. Topological analysis of this expanded network shows the presence of 30 3-cliques and six 4-cliques (fully connected subgraphs) that, respectively, reside in eight kinetochore-associated complexes, of which seven are evolution conserved. Notably, these complexes strikingly form dependence pathways for the assembly of the kinetochore complex. These analyses indicate the feasibility of using network topology, i.e. cliques, to uncover novel pathways to accelerate our understanding of potential biological processes.
Regarding the issue of role-playing games (RPG) and the experiential learning cycle (ELC), the integration of RPG use as a pedagogical and simulation tool for practice and ELC as a learning ...theoretical foundation is essential for promoting students’ effective learning. However, few studies have applied RPG to simulate the practice with the ELC stages, namely, concrete experience (CE), reflective observation (RO), abstract conceptualization, (AC) and active experimentation (AE), to examine the learning process and further enhance the effective learning outcomes for learners. This study integrates the RPG development and use for practice derived from the ELC’s four stages based on practising the project assessment of software development in a software engineering course. The results show a significant improvement in students’ learning outcomes after RPG use. More importantly, this study provides the major activities and findings of each ELC stage via RPG use and the mapping of RPG activities with ELC stages. The insightful implications and suggestions of this study are discussed.
•This study examined the effectiveness of the role-playing game.•This study revealed the existence of an experiential learning cycle in the RPG.•This study provided some findings and its implications for RPG issue.
A genome-wide association study Kao, Pei-Ying; Chen, Ming-Hui; Chang, Wei-An ...
PloS one,
02/2023, Letnik:
18, Številka:
2
Journal Article
Recenzirano
Here in this study we adopted genome-wide association studies (GWAS) to investigate the genetic components of the personality constructs in the Chinese Personality Assessment Inventory 2 (CPAI-2) in ...Taiwanese Hakka populations, who are likely the descendants of a recent admixture between a group of Chinese immigrants with high emigration intention and a group of the Taiwanese aboriginal population generally without it. A total of 279 qualified participants were examined and genotyped by an Illumina array with 547,644 SNPs to perform the GWAS. Although our sample size is small and that unavoidably limits our statistical power (Type 2 error but not Type 1 error), we still found three genomic regions showing strong association with Enterprise, Diversity, and Logical vs. Affective Orientation, respectively. Multiple genes around the identified regions were reported to be nervous system related, which suggests that genetic variants underlying the certain personalities should indeed exist in the nearby areas. It is likely that the recent immigration and admixture history of the Taiwanese Hakka people created strong linkage disequilibrium between the emigration intention-related genetic variants and their neighboring genetic markers, so that we could identify them despite with only limited statistical power.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Multiclass classification methods that combine a genetic algorithm with support vector machine have been shown to have superior performance in digital biomedical data analyses. However, they usually ...require a lot of computing resources. Cloud computing has recently played a more important role in this area, as it provides large computing power, storage space, and network bandwidth. The present study proposes a high-performance multiclass classification framework that adopts cloud computing technology to speed up analysis and enhance performance. The MapReduce parallel programming paradigm supported in the Apache Hadoop environment is adopted. A benchmark mRNA dataset of 14 tumor types was used to evaluate the classification framework. Accurate tumor classification based on gene expression profiles (GEP) has great promise for early diagnosis and clinical prognosis of cancers. However, GEP samples are usually very highly dimensional and statistically differentially expressed genes are not always tumor-related. In the experiment, when the number of servers increased from 1 to 10, the training time of the classifier was significantly reduced from 22.06 to 2.33 days. The classification accuracy reached to 94 %, a significant improvement over previous studies (78 and 90 %). Among 16,063 expressed genes, several cancer-related genes were identified after further investigation was made. The experimental results demonstrate the great effectiveness and efficiency of the proposed framework in terms of multiclass biomedical data classification.
Motivation: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) ...requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity. However, the time complexity of designing mu-primers with the best heuristic method available is too vast. We have formulated minimum-set mu-primer design problem as a set covering problem (SCP), and used modified compact genetic algorithm (MCGA) to solve this problem optimally and efficiently. We have also proposed new strategies of primer/probe design algorithm (PDA) on combining both minimum-set (MS) mu-primers and unique (UniQ) probes. Designed primer/probe set by PDA-MS/UniQ can amplify multiple genes simultaneously upon physical presence with minimum-set mu-primer amplification (MMA) before intended differential detection with probes-array hybridization (PAH) on the selected target set of SRP. Results: The proposed PDA-MS/UniQ method pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12 669 target sequences, the performance of our method with 68% reduction on required mu-primers number seems to be superior to the compared heuristic approaches in both computation efficiency and reduction percentage. Our integrated PDA-MS/UniQ method is applied to the differential detection on 9 plant viruses from 4 genera with MMA and PAH of 11 mu-primers instead of 18 unique ones in conventional PCR while amplifying overall 9 target sequences. The results of wet lab experiments with integrated MMA-PAH system have successfully validated the specificity and sensitivity of the primers/probes designed with our integrated PDA-MS/UniQ method. Contact: cykao@csie.ntu.edu.tw Supplementary information:
DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this ...study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues.
Our method achieves high precision and recall for 66 families of DNA-binding domains, with a false positive rate less than 5% for 250 non-DNA-binding proteins. In addition, experimental results show that our method is able to identify the different DNA-binding behaviors of proteins in the same SCOP family based on the use of evolutionary conservation of DNA-contact residues.
This study shows the conservation of DNA-contact residues in DNA-binding domains. We conclude that the members in the same subfamily bind DNA specifically and the members in different subfamilies often recognize different DNA targets. Additionally, we observe the co-evolution of DNA-contact residues and interacting DNA base-pairs.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
It was proposed that Epstein-Barr virus (EBV) is closely associated with nasopharyngeal carcinoma (NPC); however, the molecular mechanisms involved in the effect of EBV on NPC host genes have not yet ...been well defined. For this study, two sets of microarray experiments, NPC (EBV-free) vs normal epithelial cells and EBV⁺ vs EBV- NPC arrays, were analyzed and the datasets were cross-compared to identify any correlation between gene clusters involved in EBV targeting and the NPC host gene expression profiles. Statistical analysis revealed that EBV seems to have a preference for targeting more genes from the differentially expressed group in NPC cells than those from the ubiquitously expressed group. Furthermore, this trend is also reflected in log ratios where the EBV target genes of the differentially expressed group origin showed greater log ratios than genes with an origin from the ubiquitously expressed NPC group. Taken together, the genome-wide comparative scanning of EBV and NPC transcriptomes has successfully demonstrated that EBV infection has an intensifying effect on the signals involved in NPC gene expression both in breadth (the majority of the genes) and in depth (greater log ratios).
PDF
