Improving tilapia (Oreochromis mossambicus) resistance to streptococcal disease by improving the gut biome through administration of the microorganisms Bacillus subtilis and Enterococcus faecalis

The destruction of microbial communities within the gut of farmed tilapia (Oreochromis mossambicus) by Streptococcus agalactiae infection can result in considerable impacts to the health of the host. It is necessary to find a more effective treatment to improve the gut biome of farmed tilapia. We applied a tilapia culture method incorporating microorganisms in the diet and tracked gut bacteria over a 15-week period. A model of S. agalactiae infected individuals was constructed by detecting blood parameters and actual observation. Good’s coverage index (> 0.98) and 60 %) were higher than CGs. The application of the combined microorganisms within the diet of cultured O. mossambicus may therefore benefit their health by promoting a gut microbiome of greater diversity and increasing their resistance to disease

Comparing the Effects of Pond and Rice Field Culture Methods on Muscle Quality of Rice Flower Carp

Rice flower carp (Cyprinus carpio rubrofuscus) has high economic value because of its tender meat. However, a comprehensive scientific evaluation of the meat quality and nutritional value of rice flower carp is still needed. At the same time, because of its fast growth and strong disease resistance, rice flower carp is widely popularized in rice field culture but without any research comparing its quality with the pond culture method. Although rice farming has high ecological value, the fish yield is low and its specifications are abnormal, which cannot guarantee the stability and safety of the commercial fish supply and limit the potential rice flower carp industrial benefits. In addition, some studies have shown that fish muscle quality can be affected by environmental conditions. This study aimed to comprehensively evaluate the muscle quality and nutritional value of the rice flower carp and investigate the relationships between the nutritional values and its culture conditions, providing data to increase the rice flower carp yield, economic efficiency, and farmed varieties available. Therefore, 6 000 Quanzhou rice flower carp (2.35±0.08 g) were randomly divided into ponds and rice field groups for the experiment (three replicates per group, with a density of 15 000/hm2). The pond culture group was fed with 3% of the commercially established everyday food per fish weight, while the rice field group was not fed. After 12 weeks, the fish were submitted to a 24 h period without food and anesthetized using MS-222 (USA, Sigma). The length and weight of 100 fish were measured for each treatment. For the rice field group and pond group, respectively, the lengths were (13.56±0.49) cm and (14.10±0.23) cm, and the weights were (73.19±7.02) g and (101.20±4.57) g. The muscle quality of 30 fish from each treatment was measured, including basic nutritional components, texture characteristics, and amino acid and fatty acid compositions. The nutritional level was compared between the pond and rice field groups using the FAO/WHO amino acid score, whole egg protein comparison, protein amino acid score (AAS), chemical score (CS), and essential amino acid index (EAAI). Moreover, no significant differences between the two culture methods were observed in relation to the total ash (P > 0.05). The crude protein and crude fat contents in the rice field group were significantly lower than in the pond group (P 0.05). Essential amino acids (EAA) in both groups met the FAO/WHO standard. Among the 18 amino acids measured, the total amino acids (TAA), delicious amino acids (DAA), essential and nonessential amino acids (NEAA) were significantly lower in rice field conditions than in pond (P 0.05). In contrast, the contents of linoleic, linolenic, and arachidonic acids in the pond group were significantly higher than those in the rice field group (P < 0.05), while 14 other fatty acids showed significantly lower contents in the pond group (P < 0.05). The monounsaturated fatty acid (MUFA) contents in the pond group were significantly higher (P < 0.05), while the EPA+DHA and n-3PUFA/n-6PUFA were significantly lower than those in the rice field group (P < 0.05). Overall, the contents of four main flavor amino acids (glutamic acid, glycine, alanine, and aspartic acid) in the rice field group were significantly lower than those in the pond group (P < 0.05). In conclusion, rice flower carp reared in both pond and rice field is a high-quality protein source. However, different cultural environments significantly influence the rice flower carp muscle nutritional value and quality, wherein a higher nutrient composition and amino acid score were observed in the pond environment. Concerning the fatty acids content, the muscle of rice flower carp reared in rice fields had higher EPA+DHA content and N-3/N-6 polyunsaturated fatty acid ratio, which is more suitable for people with hyperlipidemia and cardiovascular diseases. In addition, in terms of texture, the muscle of rice flower carp is chewier under the rice field rearing condition. Nevertheless, N-3PUFA shortages were observed in both culture conditions. Besides, fish in the pond group had better muscle nutrition than the rice field group. Different culture conditions can change rice flower carp's fatty acid composition and content to a certain extent, but none of the two conditions tested here could completely allay the lower N-3PUFA problem. Therefore, increasing the N-3PUFA content of rice flower carp is the key to improving its nutritional value, and pond culture conditions make this process easier to be manually controlled

Lipoteichoic acid obtained from Lactobacillus paracasei via low-temperature pasteurization alleviates the macrophage inflammatory response by downregulating the NF-κB signaling pathway

This study compared the anti-inflammatory properties of Lactobacillus paracasei 6–1 lipoteichoic acid (LTA) obtained via different heat treatments to clarify the effect of heat intensity on its immunomodulatory activity. LTA exposed to low-temperature pasteurization (65 °C for 30 min) contained more acetylglucosamine and exhibited the strongest anti-inflammatory activity. It significantly down-regulated the pro-inflammatory cytokine levels (tumor necrosis factor-alpha (TNF-α), IL-1, IL-6, and IL-12) and increased that of the IL-10 anti-inflammatory cytokine (p < 0.05). LTA effectively improved cytokine imbalance in mice repaired the intestinal oxidative damage caused by enteritis, and regulated inflammation by downregulating MyD88, TLR4, p-ERK, NF-κB p65, and p-NF-κB p65 expression (p < 0.05) on the protein and transcript levels. In summary, low-temperature pasteurized LTA more effectively regulated the inflammatory response by downregulating the TLR4-MyD88-MAPK and NF-κB signaling pathways

Tissue Structure and Full-Length Transcriptome Analysis of the Scaly Sublayer of Cyprinus carpio var. Quanzhounensis

Cyprinus carpio var. Quanzhounensis, native to Quanzhou County, Guilin City, Guangxi, has a dark brown body color, translucent gill cover, and abdominal skin, and is an important farmed species in the local integrated rice-fishery industry. A comparative study on the skin of Cyprinus carpio var. Quanzhounensis revealed a lack of reflective guanine crystals on the body surface and a significantly higher melanin content than that of C. carpio var. Jian, which was tentatively considered the direct cause of variations in body color of this group. Iridocytes are a pigment cell species that contain regularly arranged guanine crystals, which are the key material basis for the metallic luster of the fish body surface. In species such as medaka (Oryzias latipes) and zebrafish (Danio rerio), the absence of guanine crystals is considered a manifestation of the absence of iridocyte differentiation and therefore is ideal for studying the mechanism of pigment cell differentiation. The pnp4a, Gbx2, sox10, tfec genes and other iridocyte-related genes have been mined using mutant materials, and we have uncovered the differentiation mechanism that regulates the formation of iridescent cells. C. carpio var. color has abundant genetic variation in body color and is a good material for studying the mechanism of body color determination in fish. The roles of ASIP and MC1R in the aggregation and distribution of melanin and formation of black spots in C. carpio var. color were verified. The guanine crystalline deletion trait of C. carpio var. Quanzhounensis may be loaded with regulatory mechanism diversity and mutation loci related to guanine crystal formation or iridescent cell differentiation. In addition, as a rice-fish culture species, the living environment of C. carpio var. Quanzhounensis harvestmen differ significantly from pond and net-pen culture species, requiring high resistance to disease, adversity, and transport. It is unclear whether the absence of guanine crystals in their skin leads to changes in their basal physiological state, and in-depth studies are beneficial for accurate assessment of culture performance. To reveal the structural basis and transcriptomic characteristics of guanine crystalline deficiency traits in the skin of C. carpio var. Quanzhounensis in this study, we selected the subscale tissues with the most significant differences in guanine crystalline distribution as the control material, and transmission electron microscopy was used to observe the tissue structure and full-length transcriptome sequencing to understand the structural and transcriptomic characteristics of guanine crystalline deficiency in the skin of C. carpio var. Quanzhounensis. The results of this study provide information for the analysis of body color traits, identification of economic traits, and utilization of germplasm resources. Transmission electron microscopy of the subscale tissue sections revealed two significant differences in the histological structure of C. carpio var. Quanzhounensis, and C. carpio var. Jian. First, guanine crystals were absent in C. carpio var. Quanzhounensis, whereas guanine crystals were widely present in the tissues of C. carpio var. Jian and cascading cavities were observed in the sections after guanine crystals were dislodged. Second, the number and density of melanin particles in the tissues of C. carpio var. Quanzhounensis harvestmen were significantly higher than those of C. carpio var. Jian, showing smaller, darker, and more numerous particles, which is consistent with the darker color and lack of silvery reflective material on the body surface of C. carpio var. Quanzhounensis harvestmen. The transcriptome characteristics were analyzed using Oxford Nanopore (ONT) sequencing technology, and 2.88~3.26 Gb of high-quality data were obtained for each sample. The number of full-length sequences after filtering ribosomal RNA for all sample data was 2 203 826~2 412 500, and the proportion of full-length sequences for each sample was 87.06%~88.57%. The comparison rate was 90.35%~92.46%. Variable splicing events in the transcripts were counted; 3 075 variable splicing events and 57 624 variable polyadenylation events were detected; and 15 615 new coding region sequences and 771 long-stranded non-coding RNAs were predicted. The number of exon jumps and intron retention in variable splicing events differed significantly (P<0.01) between species, and the number of transcripts with five polyadenylation sites differed significantly (P<0.01) between species, indicating that variable splicing and polyadenylation are involved in regulatory processes related to trait formation. A total of 15 615 open reading frames (ORFs), including 9 890 complete ORFs, were predicted in this study. A total of 841 differentially expressed transcripts were screened in this study; 183 transcripts were upregulated and 658 transcripts were downregulated in C. carpio var. Quanzhounensis compared to C. carpio var. Jian (JH), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed enrichment in extracellular matrix-receptor interactions and adherent spots. KEGG pathway analysis showed that it was enriched for extracellular gaps, transcription factor complexes, integrin complexes, and other terms. The most significantly enriched KEGG pathway and GO terms were closely associated with the extracellular matrix, and it is speculated that these transcriptional changes may lead to changes in the composition, density, and conformation of the skin extracellular matrix

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

Background: Cancers arise through an evolutionary process in which cell populations are subjected to selection; however, to date, the process of bladder cancer, which is one of the most common cancers in the world, remains unknown at a single-cell level. Results: We carried out single-cell exome sequencing of 66 individual tumor cells from a muscle-invasive bladder transitional cell carcinoma (TCC). Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading to two distinct tumor cell subpopulations. By analyzing recurrently mutant genes in an additional cohort of 99 TCC tumors, we identified genes that might play roles in the maintenance of the ancestral clone and in the muscle-invasive capability of subclones of this bladder cancer, respectively. Conclusions: This work provides a new approach of investigating the genetic details of bladder tumoral changes at the single-cell level and a new method for assessing bladder cancer evolution at a cell-population level. © 2012 Li et al.; licensee BioMed Central Ltd

Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm

SummaryTumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level. To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell sequencing method using two lymphoblastoid cell line single cells. We then carried out whole-exome single-cell sequencing of 90 cells from a JAK2-negative myeloproliferative neoplasm patient. The sequencing data from 58 cells passed our quality control criteria, and these data indicated that this neoplasm represented a monoclonal evolution. We further identified essential thrombocythemia (ET)-related candidate mutations such as SESN2 and NTRK1, which may be involved in neoplasm progression. This pilot study allowed the initial characterization of the disease-related genetic architecture at the single-cell nucleotide level. Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients

Common genetic variants influence human subcortical brain structures

The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction

Common genetic variants influence human subcortical brain structures

The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction