32 research outputs found
Small proteins: untapped area of potential biological importance
No full textPolypeptides containing ≤ 100 amino acid residues are generally considered to be small proteins. Many studies have shown that some small proteins are involved in important biological processes, including cell signaling, metabolism and growth. Small protein generally has a simple domain and has an advantage to be used as model system to overcome folding speed limits in protein folding simulation and drug design. But small proteins were once thought to be trivial molecules in biological processes compared to large proteins. Because of the constraints of experimental methods and bioinformatics analysis, many genome projects have used a length threshold of 100 amino acid residues to minimize erroneous predictions and small proteins are relatively under-represented in earlier studies. The general protein discovery methods have potential problems to predict and validate small proteins, and very few effective tools and algorithms were developed specially for small proteins identification. In this review, we mainly consider the diverse strategies applied to small proteins prediction and discuss the challenge for differentiate small protein coding genes from artifacts. We also summarize current large-scale discovery of small proteins in species at the genome level. In addition, we present an overview of small proteins with regard to biological significance, structural application and evolution characterization in an effort to gain insight into the significance of small proteins
Lactobacillus protects the integrity of intestinal epithelial barrier damaged by pathogenic bacteria
No full textPathogens invade intestinal mucosal barrier through phagocytosis of antigen presenting cells (dendritic cell, microfold cells), or through the invasion into the intestinal epithelial directly. Some pathogens could damage the cell junction between epithelial cells and use the paracellular pathway as an entrance to invade. Moreover, some Lactobacillus could inhibit the adhesion of the pathogens and protect the integrity of the cell junction and mucosal barrier. This research focused on the potential therapeutic effect of Lactobacillus fructosus (L. fructosus) C2 to attenuate ETEC K88 or S. typhimurium SL1344 induced changes to mucosal barrier. The results demonstrated that treatment of polarized Caco-2 cells with L. fructosus C2 reduced the permeation of dextran, and expression of IL-8, p-ERK and p-JNK when cells were infected with pathogenic bacteria. The findings indicated that L. fructosus C2 exerted a protective effect against the damage to the integrity of Caco-2 cells by ETEC or S. typhimurium infection
Stigmatic bodies: The corporeal Qiu Miaojin
No full textB1 - Research Book ChaptersDeposited with permission of University of Hawaii PressQiu Miaojin (1969–1995) is Taiwan’s best-known lesbian author. In local lesbian (nütongzhi) subcultures, Qiu’s books are frequently cited as classics, particularly her 1994 novel The Crocodile’s Journal (Eyu shouji), the first novel in Taiwan’s modern literary history to be written by an author commonly known to be a lesbian that takes erotic relationships between women as its central theme. Qiu’s fiction is much celebrated, too, in the mainstream literary establishment; The Crocodile’s Journal won the prestigious China Times Honorary Prize for Literature for Qiu posthumously, following her suicide in mid-1995. Qiu’s unique literary style—mingling cerebral, experimental language use, psychological realism, biting social critique through allegory, and a surrealist effect deriving from the use of arrestingly unusual metaphors—is strongly influenced by both European and Japanese literary and cinematic modernisms. Although her fiction has been compared, in its principal subject-matter, to Radclyffe Hall’s 1920s classic of lesbian alienation, The Well of Loneliness, most frequently cited in Qiu’s writings are male modernist and postmodernist ‘masters’ (many of whose work shows a strongly homoerotic aesthetic) including Andre Gide, Jean Genet, Kobo Abe, Yukio Mishima, Haruki Murakami, Andrei Tarkovsky, and Derek Jarman—locally, Qiu’s work has been critiqued for this apparent masculinist bias. Qiu’s early short stories ‘Zero Degree’ (‘Linjiedian,’ 1988) and ‘Platonic Hair’ (‘Bolatu zhi fa,’ 1990), to be discussed in this chapter, appeared in her first collection, The Revelry of Ghosts (Guide kuanghuan) in 1991, following their earlier serialization in local daily newspapers. They are Qiu’s first works to treat thematically homoerotic desire between women
FMRI evidence for the interaction between orthography and phonology in reading Chinese compound words
No full textCompound words make up a major part of modern Chinese vocabulary. Behavioral studies have demonstrated that access to lexical semantics of compound words is driven by the interaction between orthographic and phonological information. However, little is known about the neural underpins of compound word processing. In this fMRI study, we asked participants to perform lexical decision to pseudohomophones, which were constructed by replacing one or both constituents of two-character compound words with orthographically dissimilar homophonic characters. Mixed pseudohomophones, which shared the first constituent with the base words, were more difficult to reject than non-pseudohomophone nonwords. This effect was accompanied by the increased activation of bilateral inferior frontal gyrus (IFG), left inferior parietal lobule (IPL), and left angular gyrus. The pure pseudohomophones, which shared no constituent with their base words, were rejected as quickly as nonword controls and did not elicit any significant neural activation. The effective connectivity of a phonological pathway from left IPL to left IFG was enhanced for the mixed pseudohomophones but not for pure pseudohomophones. These findings demonstrated that phonological activation alone, as in the case of the pure pseudohomophones, is not sufficient to drive access to lexical representations of compound words, and that orthographic information interacts with phonology, playing a gating role in the recognition of Chinese compound words
The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng
No full textPanax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS) and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥ 0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains typing
A Study of Tapping by the Unaffected Finger of Patients Presenting with Central and Peripheral Nerve Damage
No full textAim: Whether the unaffected function of the hand of patients presenting with nerve injury is affected remains inconclusive. We aimed to evaluate whether there are differences in finger tapping following central or peripheral nerve injury compared with the unaffected hand and the ipsilateral hand of a healthy subject.Methods: 30 right brain stroke patients with hemiplegia, 30 left arm peripheral nerve injury cases and 60 healthy people were selected. We tested finger tapping of the right hands, and each subject performed the test twice.Results: Finger tapping following peripheral nerve injury as compared with the unaffected hand and the dominant hand of a healthy person was significantly higher than was found for central nerve injury (P<0.05). Finger tapping of the male peripheral group’s unaffected hand and the control group’s dominant hand was significantly higher than the central group (P<0.001). However, finger tapping of the female control group’s dominant hand was markedly higher than the central group’s unaffected hand (P<0.01, P=0.002), the peripheral group’s unaffected hand (P<0.05, P=0.034). Conclusion: The unaffected function of the hand of patients with central and peripheral nerve injury was different as compared with the ipsilateral hand of healthy individuals. The rehabilitation therapist should intensify the practice of normal upper limb fine activities and coordination of the patient
AtHD2D gene plays a role in plant growth, development and response to abiotic stresses in Arabidopsis thaliana
No full textAbstracts: The histone deacetylases play important roles in the regulation of gene expression and the subsequent control of a number of important biological processes, including those involved in the response to environmental stress. A specific group of histone deacetylase genes, HD2, is present in plants. In Arabidopsis, HD2s include HD2A, HD2B, HD2C and HD2D. Previous research showed that HD2A, HD2B and HD2C are more related in terms of expression and function, but not HD2D. In this report, we studied different aspects of AtHD2D in Arabidopsis with respect to plant response to drought and other abiotic stresses. Bioinformatics analysis indicates that HD2D is distantly related to other HD2 genes. Transient expression in Nicotiana benthamiana and stable expression in Arabidopsis of AtHD2D fused with gfp showed that AtHD2D was expressed in the nucleus. Overexpression of AtHD2D resulted in developmental changes including fewer main roots, more lateral roots, and a higher root:shoot ratio. Seed germination and plant flowering time were delayed in transgenic plants expressing AtHD2D, but these plants exhibited higher degrees of tolerance to abiotic stresses, including drought, salt and cold stresses. Physiological studies indicated that the malondialdehyde (MDA) content was high in wild-type plants but in plants overexpressing HD2D the MDA level increased slowly in response to stress conditions of drought, cold, and salt stress. Furthermore, electrolyte leakage in leaf cells of wild type plants increased but remained stable in transgenic plants. Our results indicate that AtHD2D is unique among HD2 genes and it plays a role in plant growth and development regulation and these changes can modulate plant stress responses
Effects of a Macro-nutrient Preload on Type 2 Diabetic Patients
No full textAims: Macro-nutrient preloads given 30 minutes before regular meals may improve metabolism. The aim was to investigate how type 2 diabetic patients react to a preload consisting of a blend of macro-nutrients with a low glycemic index (Inzone Preload ®). Methods: In a before-after study design, 30 subjects with type 2 diabetes mellitus (T2DM) were enrolled in a 12-week program. All subjects were given Inzone Preload (43 % proteins, 29% carbohydrates, 10 % lipids and 9 % fibers,71 kcal), 30 min before each meal during 12 weeks. Fasting glucose, postprandial 2h glucose were monitored every second week. Body weight (BW) and waist circumference were measured each month. Fasting plasma glucose, glycosylated hemoglobin, serum lipids, fasting insulin, C-reactive protein and homeostasis model assessment were evaluated before and after the intervention. Subjective appetite was monitored using visual analogue scales after the Inzone Preload. Results: The dietary intervention significantly influenced several metabolic parameters compared to base line. Inzone Preload treatment reduced mean postprandial plasma glucose levels (12.2 ± 1.2 mmol/L vs 10.5 ± 2.0 mmol/L), HbA1c (7.4 ± 0.3 % vs 7.1 ± 0.2 %), mean total cholesterol (4.8 ± 0.9 mmol/L vs 4.3 ± 0.8 mmol/L), low-density lipoprotein cholesterol (2.8 ± 0.6 mmol/L vs 2.5 ± 0.4 mmol/L) and CRP (1.5 ± 1.4 mg/L vs 0.7 ± 0.7 mg/L) BW loss of more than 3% was seen in 13 participants (43%). Feelings of satiety were significantly higher after Inzone Preload than after habitual breakfast (p < 0.05). No significant changes in fasting blood glucose, high-density lipoprotein and total triacylglycerol, HOMA-IR, and HOMA-β were observed. Conclusions: A macro-nutrient preload treatment reduces postprandial glucose, inflammatory markers and serum lipids in patients with T2DM. Approximately half of the study group also displayed reduced body weight
Sequence variation and expression analysis of seed dormancy- and germination-associated ABA- and GA-related genes in rice cultivars
No full textAbscisic acid (ABA) and Gibberellic acid (GA) play key roles in regulating seed dormancy and germination. First, when examining germination of different rice cultivars, we found that their germination timing and dormancy status are rather distinct, coupled with different GA/ABA ratio. Second, we studied genomic sequences of ABA and GA dormancy- and germination-associated genes in rice and discovered single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) in both coding and regulatory sequences. We aligned all these variations to the genome assemblies of 9311 and PA64s and demonstrated their relevance to seed dormancy both quantitatively and qualitatively based on gene expression data. Third, we surveyed and compared differentially-expressed genes in dry seeds between 9311 and PA64s to show that these differentially-expressed genes may play roles in seed dormancy and germination
Transcriptome analysis of Dendrobium officinale and its application to the identification of genes associated with polysaccharide synthesis
No full textDendrobium officinale is one of the most important Chinese medicinal herbs. Polysaccharides are one of the main active ingredients of D. officinale. To identify the genes that maybe related to polysaccharides synthesis, two cDNA libraries were prepared from juvenile and adult D. officinale, and were named Dendrobium-1 and Dendrobium-2, respectively. Illumina sequencing for Dendrobium-1 generated 102 million high quality reads that were assembled into 93,881 unigenes with an average sequence length of 790 base pairs. The sequencing for Dendrobium-2 generated 86 million reads that were assembled into 114,098 unigenes with an average sequence length of 695 base pairs. Two transcriptome databases were integrated and assembled into a total of 145,791 unigenes. Among them, 17,281 unigenes were assigned to 126 KEGG pathways while 135 unigenes were involved in fructose and mannose metabolism. Gene Ontology analysis revealed that the majority of genes were associated with metabolic and cellular processes. Furthermore, 430 glycosyltransferase and 89 cellulose synthase genes were identified. Comparative analysis of both transcriptome databases revealed a total of 32,794 differential expression genes (DEGs), including 22,051 up-regulated and 10,743 down-regulated genes in Dendrobium-2 compared to Dendrobium-1. Furthermore, a total of 1142 and 7918 unigenes showed unique expression in Dendrobium-1 and Dendrobium-2, respectively. These DEGs were mainly correlated with metabolic pathways and the biosynthesis of secondary metabolites. In addition, 170 DEGs belonged to glycosyltransferase genes, 37 DEGs were related to cellulose synthase genes and 627 DEGs encoded transcription factors. This study substantially expands the transcriptome information for D. officinale and provides valuable clues for identifying candidate genes involved in polysaccharide biosynthesis and elucidating the mechanism of polysaccharide biosynthesis
