High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements

Approximately 80 long interspersed element (LINE-1 or L1) copies are able to retrotranspose actively in the human genome, and these are termed retrotransposition-competent L1s. The 5′ untranslated region (UTR) of the human-specific L1 contains an internal promoter and several transcription factor binding sites. To better understand the effect of the L1 5′ UTR on the evolution of human-specific L1s, we examined this population of elements, focusing on the sequence diversity and accumulated substitutions within their 5′ UTRs. Using network analysis, we estimated the age of each L1 component (the 5′ UTR, ORF1, ORF2, and 3′ UTR). Through the comparison of the L1 components based on their estimated ages, we found that the 5′ UTR of human-specific L1s accumulates mutations at a faster rate than the other components. To further investigate the L1 5′ UTR, we examined the substitution frequency per nucleotide position among them. The results showed that the L1 5′ UTRs shared relatively conserved transcription factor binding sites, despite their high sequence diversity. Thus, we suggest that the high level of sequence diversity in the 5′ UTRs could be one of the factors controlling the number of retrotransposition-competent L1s in the human genome during the evolutionary battle between L1s and their host genomes

Industry portfolio allocation with asymmetric correlations

We develop a new framework of optimal consumption and portfolio choice at industry portfolio level under dynamic and asymmetric correlations between industry and market portfolios. We derive in closed-form the optimal consumption and investment strategies under regime-dependent correlations environment. Overall, we find that ignoring time-varying and asymmetric correlations between portfolios can be costly to investors when applied to a construction of the optimal portfolio. Finally, we empirically test the performance of the model-based investment strategy

Tributyrin and anise mixture supplementation improves growth performance, nutrient digestibility, jejunal villus height, and fecal microbiota in weaned pigs

IntroductionThe objective of this study was to investigate the effects of dietary supplementation of tributyrin and anise mixture (TA) on growth performance, apparent nutrient digestibility, fecal noxious gas emission, fecal score, jejunal villus height, hematology parameters, and fecal microbiota of weaned pigs.MethodsA total of 150 21-day-old crossbred weaned pigs [(Landrace × Yorkshire) × Duroc] were used in a randomized complete block design experiment. All pigs were randomly assigned to 3 groups based on the initial body weight (6.19 ± 0.29 kg). Each group had 10 replicate pens with 5 pigs (three barrows and two gilts) per pen. The experimental period was 42 days and consisted of 3 phases (phase 1, days 1–7; phase 2, days 8–21; phase 3, days 22–42). Dietary treatments were based on a corn-soybean meal-basal diet and supplemented with 0.000, 0.075, or 0.150% TA.Results and discussionWe found that dietary supplementation of graded levels of TA linearly improved body weight, body weight gain, average daily feed intake, and feed efficiency (P < 0.05). TA supplementation also had positive effects on apparent dry matter, crude protein, and energy digestibility (P < 0.05) and jejunal villus height (P < 0.05). The emission of ammonia from feces decreased linearly with the dose of TA increased (P < 0.05). Moreover, TA supplementation was capable to regulate the fecal microbiota diversity, manifesting in a linearly increased Chao1 index and observed species and a linearly decreased Pielou's index (P < 0.05). The abundance of Lactobacillus reuteri, Lactobacillus amylovorus, Clostridium butyricum were increased, while the abundance of Prevotella copri was decreased, by treatment (P < 0.05). Therefore, we speculated that TA supplementation would improve growth performance and reduce fecal ammonia emission through improving nutrient digestibility, which was attributed to the increase of jejunal villus height and the regulation of fecal microbiota

The Time Sequence of Gene Expression Changes after Spinal Cord Injury

Gene expression changes following spinal cord injury (SCI) are time-dependent, and an accurate understanding of these changes can be crucial in determining time-based treatment options in a clinical setting. We performed RNA sequencing of the contused spinal cord of rats at five different time points from the very acute to chronic stages (1 hour, 1 day, 1 week, 1 month, and 3 months) following SCI. We identified differentially expressed genes (DEGs) and Gene Ontology (GO) terms at each time point, and 14,257 genes were commonly expressed at all time points. The biological process of the inflammatory response was increased at 1 hour and 1 day, and the cellular component of the integral component of the synaptic membrane was increased at 1 day. DEGs associated with cell activation and the innate immune response were highly enriched at 1 week and 1 month, respectively. A total of 2841 DEGs were differentially expressed at any of the five time points, and 18 genes (17 upregulated and 1 downregulated) showed common expression differences at all time points. We found that interleukin signaling, neutrophil degranulation, eukaryotic translation, collagen degradation, LGI–ADAM interactions, GABA receptor, and L1CAM-ankyrin interactions were prominent after SCI depending on the time post injury. We also performed gene–drug network analysis and found several potential antagonists and agonists which can be used to treat SCI. We expect to discover effective treatments in the clinical field through further studies revealing the efficacy and safety of potential drugs

Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data

Transposable elements (TEs) are classified into two classes according to their mobilization mechanism. Compared to DNA transposons that move by the “cut and paste” mechanism, retrotransposons mobilize via the “copy and paste” method. They have been an essential research topic because some of the active elements, such as Long interspersed element 1 (LINE-1), Alu, and SVA elements, have contributed to the genetic diversity of primates beyond humans. In addition, they can cause genetic disorders by altering gene expression and generating structural variations (SVs). The development and rapid technological advances in next-generation sequencing (NGS) have led to new perspectives on detecting retrotransposon-mediated SVs, especially insertions. Moreover, various computational methods have been developed based on NGS data to precisely detect the insertions and deletions in the human genome. Therefore, this review discusses details about the recently studied and utilized NGS technologies and the effective computational approaches for discovering retrotransposons through it. The final part covers a diverse range of computational methods for detecting retrotransposon insertions with human NGS data. This review will give researchers insights into understanding the TEs and how to investigate them and find connections with research interests

Effect of Detoxified Nano Sulfur Supplementation on the Growth, Nutrient Digestibility, Meat Quality, Excreta Microbes, Gas Emissions, and Blood Profiles of Broilers

A 35-day experiment was conducted to evaluate the effects of the supplementation of mineral detoxified sulfur dispersion ((DSD); Patent No.: 10-1997773) on the growth performance, meat quality, excreta microbiota, gas emissions, nutrient digestibility, and blood profiles of broilers. In total, 720 one-day-old ROSS 308 broilers, with an initial body weight of 41.9±0.8 g, were divided into two (2) treatment groups with 20 replicate pens/groups composed of 18 birds per pen. Treatments consisted of 1) CON (the control), normal drinking water and 2) TRT (the treatment group), CON+0.001% DSD (1000:1 dilution ratio). Average daily feed intake (ADFI) and feed conversion ratio (FCR) increased in the TRT group (P<0.05) between days 1 to 7 and days 7 to 21 of the experimental period. Similarly, body weight gain (BWG) showed a significant increase (P<0.05) in the DSD-supplemented group throughout in the length of the experiment. With regard to meat quality, redness (a*) was higher, while drip loss was lower, on the 7th day in the DSD group. Furthermore, DSD supplementation increased (P<0.05) Lactobacillus excreta but decreased E. coli concentrations in the TRT group compared to the CON group. Notably, nutrient digestibility, excreta gas emission, and blood profiles did not show any significant differences (P>0.05). DSD supplementation, administered through drinking water, has a positive impact on the growth performance, meat quality, and excreta microbiota of broiler chickens

Phylogeny of Flavobacteria Group Isolated from Freshwater Using Multilocus Sequencing Analysis

Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable technique for the identification or classification of bacteria. The five Flavobacterium species isolated from freshwater and 37 other strains were classified based on six housekeeping genes: gyrB, dnaK, tuf, murG, atpA, and glyA. The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. The results indicated that MLSA, based on the six housekeeping genes, is a trustworthy method for the identification of closely related Flavobacterium species

Transcriptome Profile of Membrane and Extracellular Matrix Components in Ligament-Fibroblastic Progenitors and Cementoblasts Differentiated from Human Periodontal Ligament Cells

Ligament-fibroblastic cells and cementoblasts, two types of progenitor cells that differentiate from periodontal ligament stem cells (hPDLSCs), are responsible for the formation of the adhesive tissues in the tooth root. Since one of the factors that determines the fate of stem cell differentiation is the change in the microenvironment of the stem/progenitor cells, this study attempted to compare and analyze the molecular differences in the membrane and ECM of the two progenitor cells. Single cells derived from hPDLSCs were treated with TGF-β1 and BMP7 to obtain ligament-fibroblastic and cementoblastic cells, respectively. The transcriptome profiles of three independent replicates of each progenitor were evaluated using next-generation sequencing. The representative differentially expressed genes (DEGs) were verified by qRT-PCR, Western blot analysis, and immunohistochemistry. Among a total of 2245 DEGs identified, 142 and 114 DEGs related to ECM and cell membrane molecules were upregulated in ligament-fibroblastic and cementoblast-like cells, respectively. The major types of integrin and cadherin were found to be different between the two progenitor cells. In addition, the representative core proteins for each glycosaminoglycan-specific proteoglycan class were different between the two progenitors. This study provides a detailed understanding of cell–cell and cell–ECM interactions through the specific components of the membrane and ECM for ligament-fibroblastic and cementoblastic differentiation of hPDLSCs

Transcriptome Profile of Membrane and Extracellular Matrix Components in Ligament-Fibroblastic Progenitors and Cementoblasts Differentiated from Human Periodontal Ligament Cells

Ligament-fibroblastic cells and cementoblasts, two types of progenitor cells that differentiate from periodontal ligament stem cells (hPDLSCs), are responsible for the formation of the adhesive tissues in the tooth root. Since one of the factors that determines the fate of stem cell differentiation is the change in the microenvironment of the stem/progenitor cells, this study attempted to compare and analyze the molecular differences in the membrane and ECM of the two progenitor cells. Single cells derived from hPDLSCs were treated with TGF-β1 and BMP7 to obtain ligament-fibroblastic and cementoblastic cells, respectively. The transcriptome profiles of three independent replicates of each progenitor were evaluated using next-generation sequencing. The representative differentially expressed genes (DEGs) were verified by qRT-PCR, Western blot analysis, and immunohistochemistry. Among a total of 2245 DEGs identified, 142 and 114 DEGs related to ECM and cell membrane molecules were upregulated in ligament-fibroblastic and cementoblast-like cells, respectively. The major types of integrin and cadherin were found to be different between the two progenitor cells. In addition, the representative core proteins for each glycosaminoglycan-specific proteoglycan class were different between the two progenitors. This study provides a detailed understanding of cell–cell and cell–ECM interactions through the specific components of the membrane and ECM for ligament-fibroblastic and cementoblastic differentiation of hPDLSCs