Fecal calprotectin is a novel biomarker to predict the clinical outcomes of patients with ruptured intracranial aneurysm.

BACKGROUND: Intracranial aneurysm (IA) is a common cerebrovascular disease and the leading cause of spontaneous subarachnoid hemorrhage. Recent evidence suggests that gut microbiota is involved in the pathophysiological process of IA through the gut-brain axis. However, the role of gut inflammation in the development of IA has yet to be clarified. Our study aimed to investigate whether fecal calprotectin (FC) level, a sensitive marker of gut inflammation, is correlated with the development of IA and the prognosis of patients with ruptured IA (RIA). METHODS: 182 patients were collected from January 2022 to January 2023, including 151 patients with IA and 31 healthy individuals. 151 IA patients included 109 patients with unruptured IA (UIA) and 42 patients with RIA. The FC level was measured by enzyme-linked immunosorbent assay. Other detailed information was obtained from an electronic medical record system. RESULTS: Compared with healthy controls, the FC levels in patients with IA were increased (P < 0.0001). Patients with RIA had significantly higher FC levels than UIA patients (P < 0.0001). Moreover, the FC level in RIA patients with unfavorable outcomes was higher than in RIA patients with favorable outcomes. Logistic regression analysis showed that the elevated FC level was an independent risk factor for a 3-month poor prognosis in patients with RIA (OR=1.005, 95% CI = 1.000 -1.009, P = 0.044). CONCLUSION: Fecal calprotectin level is significantly elevated in IA patients, especially those with RIA. FC is a novel biomarker of 3-month poor outcomes in RIA patients.

From salt water to bioceramics: Mimic nature through pressure-controlled hydration and crystallization.

Modern synthetic technology generally invokes high temperatures to control the hydration level of ceramics, but even the state-of-the-art technology can still only control the overall hydration content. Magically, natural organisms can produce bioceramics with tailorable hydration profiles and crystallization traits solely from amorphous precursors under physiological conditions. To mimic the biomineralization tactic, here, we report pressure-controlled hydration and crystallization in fabricated ceramics, solely from the amorphous precursors of purely inorganic gels (PIGs) synthesized from biocompatible aqueous solutions with most common ions in organisms (Ca2+, Mg2+, CO32-, and PO43-). Transparent ceramic tablets are directly produced by compressing the PIGs under mild pressure, while the pressure regulates the hydration characteristics and the subsequent crystallization behaviors of the synthesized ceramics. Among the various hydration species, the moderately bound and ordered water appears to be a key in regulating the crystallization rate. This nature-inspired study offers deeper insights into the magic behind biomineralization.

Turing structuring with multiple nanotwins to engineer efficient and stable catalysts for hydrogen evolution reaction.

Low-dimensional nanocrystals with controllable defects or strain modifications are newly emerging active electrocatalysts for hydrogen-energy conversion and utilization; however, a crucial challenge remains in insufficient stability due to spontaneous structural degradation and strain relaxation. Here we report a Turing structuring strategy to activate and stabilize superthin metal nanosheets by incorporating high-density nanotwins. Turing configuration, realized by constrained orientation attachment of nanograins, yields intrinsically stable nanotwin network and straining effects, which synergistically reduce the energy barrier of water dissociation and optimize the hydrogen adsorption free energy for hydrogen evolution reaction. Turing PtNiNb nanocatalyst achieves 23.5 and 3.1 times increase in mass activity and stability index, respectively, compared against commercial 20% Pt/C. The Turing PtNiNb-based anion-exchange-membrane water electrolyser with a low Pt mass loading of 0.05 mg cm-2 demonstrates at least 500 h stability at 1000 mA cm-2, disclosing the stable catalysis. Besides, this new paradigm can be extended to Ir/Pd/Ag-based nanocatalysts, illustrating the universality of Turing-type catalysts.

Plasmoelectric Potential in Plasmon-Mediated Electrochemistry.

Plasmon-mediated chemical reactions have attracted intensive research interest as a means of achieving desirable reaction yields and selectivity. The energetic charge carriers and elevated local temperature induced by the nonradiative decay of surface plasmons are thought to be responsible for improving reaction outcomes. This study reports that the plasmoelectric potential is another key contributor in plasmon-mediated electrochemistry. Additionally, we disclose a convenient and reliable method for quantifying the specific contributions of the plasmoelectric potential, hot electrons, and photothermal heating to the electroreduction of oxygen at the plasmonic Ag electrode, revealing that the plasmoelectric potential is the dominating nonthermal factor under short-wavelength illumination and moderate electrode bias. This work elucidates novel mechanistic understandings of plasmon-mediated electrochemistry, facilitating high-performance plasmonic electrocatalyst design optimization.

Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation.

Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation.

Activation of SIRT1 Alleviates Ferroptosis in the Early Brain Injury after Subarachnoid Hemorrhage.

Ferroptosis is a regulated cell death that characterizes the lethal lipid peroxidation and iron overload, which may contribute to early brain injury (EBI) pathogenesis after subarachnoid hemorrhage (SAH). Although Sirtuin 1 (SIRT1), a class III histone deacetylase, has been proved to have endogenous neuroprotective effects on the EBI following SAH, the role of SIRT1 in ferroptosis has not been studied. Hence, we designed the current study to determine the role of ferroptosis in the EBI and explore the correlation between SIRT1 and ferroptosis after SAH. The pathways of ferroptosis were examined after experimental SAH in vivo (prechiasmatic cistern injection mouse model) and in HT-22 cells stimulated by oxyhemoglobin (oxyHb) in vitro. Then, ferrostatin-1 (Fer-1) was used further to determine the role of ferroptosis in EBI. Finally, we explored the correlation between SIRT1 and ferroptosis via regulating the expression of SIRT1 by resveratrol (RSV) and selisistat (SEL). Our results showed that ferroptosis was involved in the pathogenesis of EBI after SAH through multiple pathways, including acyl-CoA synthetase long-chain family member 4 (ACSL4) activation, iron metabolism disturbance, and the downregulation of glutathione peroxidase 4 (GPX4) and ferroptosis suppressor protein 1 (FSP1). Inhibition of ferroptosis by Fer-1 significantly alleviated oxidative stress-mediated brain injury. SIRT1 activation could suppress SAH-induced ferroptosis by upregulating the expression of GPX4 and FSP1. Therefore, ferroptosis could be a potential therapeutic target for SAH, and SIRT1 activation is a promising method to inhibit ferroptosis.

Insertable, Scabbarded, and Nanoetched Silver Needle Sensor for Hazardous Element Depth Profiling by Laser-Induced Breakdown Spectroscopy.

Sensing of hazardous metals is urgent in many areas (e.g., water pollution and meat products) as heavy metals threaten people's health. Laser-induced breakdown spectroscopy (LIBS), as a rapid, in situ, and multielemental analytical technique, has been widely utilized in rapid hazardous heavy metal sensing. However, loose and water-containing samples (e.g., meat, plant, and soil) are hard to analyze by LIBS directly, and heavy metal depth profiling for bulk samples remains suspenseful. Here, inspired by the Needle, the sword of Arya Stark in Game of Thrones, we propose an insertable, scabbarded, and nanoetched silver (NE-Ag) needle sensor for rapid hazardous element sensing and depth profiling. The NE-Ag needle sensor features a micro-nanostructure surface for inserting into the bulk sample and absorbing hazardous analytes. For accurate elemental depth profiling, we design a stainless-steel scabbard to wrap and protect the NE-Ag needle from pollution (unexpected contaminant absorption) during the needle insertion and extraction process. The results for cadmium (Cd) show that the relative standard deviation equals to 6.7% and the limit of detection reaches 0.8 mg/L (ppm). Furthermore, the correlations (Pearson correlation coefficient) for Cd and chromium (Cr) depth profiling results are no less than 0.96. Furthermore, the total testing time could be less than 1 h. All in all, the insertable and scabbarded NE-Ag needle senor has high potential in rapid hazardous heavy metal depth profiling in different industries.

Genome-Wide Association Studies and Haplotype-Sharing Analysis Targeting the Egg Production Traits in Shaoxing Duck.

Age at first egg (AFE) and egg number (EN) are economically important traits related to egg production, as they directly influence the benefits of the poultry industry, but the molecular genetic research that affects those traits in laying ducks is still sparse. Our objective was to identify the genomic regions and candidate genes associated with AFE, egg production at 43 weeks (EP43w), and egg production at 66 weeks (EP66w) in a Shaoxing duck population using genome-wide association studies (GWASs) and haplotype-sharing analysis. Single-nucleotide polymorphism (SNP)-based genetic parameter estimates showed that the heritability was 0.15, 0.20, and 0.22 for AFE, EP43w, and EP66w, respectively. Subsequently, three univariate GWASs for AFE, EP43w, and EP66w were carried out independently. Twenty-four SNPs located on chromosome 25 within a 0.01-Mb region that spans from 4.511 to 4.521 Mb were associated with AFE. There are two CIs that affect EP43w, i.e., twenty-five SNPs were in strong linkage disequilibrium region spanning from 3.186 to 3.247 Mb on chromosome 25, a region spanning from 4.442 to 4.446 Mb on chromosome 25, and two interesting genes, ACAD8 and THYN1, that may affect EP43w in laying ducks. There are also two CIs that affect EP66w, i.e., a 2.412-Mb region that spans from 127.497 to 129.910 Mb on chromosome 2 and a 0.355-Mb region that spans from 4.481 to 4.837 Mb on chromosome 29, and CA2 and GAMT may be the putative candidate genes. Our study also found some haplotypes significantly associated with these three traits based on haplotype-sharing analysis. Overall, this study was the first publication of GWAS on egg production in laying ducks, and our findings will be helpful to provide some candidate genes and haplotypes to improve egg production performance based on breeding in laying duck. Additionally, we learned from a method called bootstrap test to verify the reliability of a GWAS with small experimental samples that users can access at https://github.com/xuwenwu24/Bootstrap-test.

Immunopotentiators improve the antioxidant defense, apoptosis, and immune response in Shaoxing ducklings.

The abuse of antibiotics for agricultural purposes has been under scrutiny. Therefore, there is an urgent need to find antibiotic substitutes in animal production. The effects of chlorogenic acid, ß-D-Glucan, astragalus flavone, CpG-DNA, and chicken IgG on spleen antioxidant capacity, apoptosis, and the immune response in Shaoxing ducklings were investigated in this study. The ducklings treated with ß-D-Glucan, astragalus flavone, CpG-DNA, and chicken IgG showed significant reduction in catalase and superoxide dismutase activities. The five immunopotentiators facilitated caspase 3 expression and reduced Bcl2 expression in the spleen. Compared to the control group, the protein level of COX2 was significantly upregulated in the chlorogenic acid, CpG-DNA, and chicken IgG groups. The protein level of iNOS expression was significantly improved in all immunopotentiator groups, except for the astragalus flavone group. The five immunopotentiators induced IL-1ß, IFN-α, IFN-ß, TNF-α, RIG-I, TLR3, and TLR7 gene expression. In summary, chlorogenic acid, ß-D-Glucan, astragalus flavone, CpG-DNA, and chicken IgG, as immunopotentiators, improved the innate immune response in the ducklings, which not only provides a new avenue for the development of efficient approaches to prevent pathogen infections, but also offers an alternative to antibiotics in animal production.

Alpha-Enolase Protects Hepatocyte Against Heat Stress Through Focal Adhesion Kinase-Mediated Phosphatidylinositol 3-Kinase/Akt Pathway.

Accumulating pieces of evidence showed that α-enolase (ENO1) is a multifunctional protein that plays a crucial role in a variety of pathophysiological processes. In our previous study, differential expression of ENO1 was observed in different heat-tolerance duck breeds. Here, we examined in vitro expression level of ENO1 in hepatocytes against heat stress. The mechanisms of ENO1 on cell glycolysis, growth, and its potential regulatory pathways were also analyzed. The results showed that ENO1 expression in messenger RNA and protein levels were both greatly increased in heat-treated cells compared with non-treated cells. ENO1-overexpressed cells significantly elevated cell viability and glycolysis levels. It was further shown that stably upregulated ENO1 activated focal adhesion kinase-phosphatidylinositol 3-kinase/Akt and its downstream signals. In addition, the interaction between ENO1 and 70-kDa heat shock protein was detected using co-immunoprecipitation. Our research suggests that ENO1 may interact with 70-kDa heat shock protein to protect hepatocyte against heat stress through focal adhesion kinase-mediated phosphatidylinositol 3-kinase/Akt pathway.

Facile Surfactant-, Reductant-, and Ag Salt-free Growth of Ag Nanoparticles with Controllable Size from 35 to 660 nm on Bulk Ag Materials.

Morphologically and dimensionally controlled growth of Ag nanocrystals has long been plagued by surfactants or capping agents that complicate downstream applications, unstable Ag salts that impaired the reproducibility, and multistep seed injection that is troublesome and time-consuming. Here, we report a one-pot electro-chemical method to fast (∼2 min) produce Ag nanoparticles from commercial bulk Ag materials in a nitric acid solution, eliminating any need for surfactants or capping agents. Their size can be easily manipulated in an unprecedentedly wide range from 35 to 660 nm. Furthermore, the Ag nanoparticles are directly grown on the Ag substrate, highly desirable for promising applications such as catalysis and plasmonics. The mechanistic studies reveal that the concentration of Ag+ in the diffusion layer nearby the surface, controlled by the magnitude and duration of voltage, is critical in governing the nanoparticle formation (<1.3 mM) and its dimensional adjustability.

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China.

BACKGROUND: Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. RESULTS: Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. CONCLUSION: Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity.

Plasmonic metal nanostructures: concepts, challenges and opportunities in photo-mediated chemical transformations.

Plasmonic metal nanostructures (PMNs) are characterized by the plasmon oscillation of conduction band electron in response to external radiation, enabling strong light absorption and scattering capacities and near-field amplification. Owing to these enhanced light-matter interactions, PMNs have garnered extensive research interest in the past decades. Notably, a growingly large number of reports show that the energetics and kinetics of chemical transformations on PMNs can be modified upon photoexcitation of their plasmons, giving rise to a new paradigm of manipulating the reaction rate and selectivity of chemical reactions. On the other hand, there is urgent need to achieve clear understanding of the mechanism underlying the photo-mediated chemical transformations on PMNs for unleashing their full potential in converting solar energy to chemicals. In this perspective, we review current fundamental concepts of photo-mediated chemical transformations executed at PMNs. Three pivotal mechanistic questions, i.e., thermal and nonthermal effects, direct and indirect charge transfer processes, and the specific impacts of plasmon-induced potentials, are explored based on recent studies. We highlight the critical aspects in which major advancements should be made to facilitate the rational design and optimization of photo-mediated chemical transformations on PMNs in the future.

High-temperature exposure alters the community structure and functional features of the intestinal microbiota in Shaoxing ducks (Anas platyrhynchos).

The gut microbiome is a complex ecosystem that contributes to host nutrition and health. However, our current knowledge of the relationship between ambient temperature and gut microbiota of poultry is still limited. The objective of the present study was to characterize the intestinal microbiota of ducks exposed to high ambient temperature. Sixty 60-day-old Shaoxing ducks were allocated to control and heat-treated groups. The ducks in the control group were kept at 25°C, and the ducks in the heat treatment group were raised at 30-40°C, which simulated the temperature change of day and night in summer. After 15 D, the intestinal contents of the duodenum, jejunum, and ileum were obtained from 6 ducks of each group. Genomic DNA was extracted and amplified based on the V4-V5 hypervariable region of 16S rRNA. The results showed that Firmicutes was the dominant bacterial phylum with the highest abundance in the contents of the small intestine of ducks, and the relative abundance of the phylum Firmicutes in all 3 intestinal segments was increased by high temperature. At the genus level, Lactobacillus was found to be the most dominant bacterial genus across 3 gut segments, and its abundance was increased in ducks under heat treatment. Compared with the corresponding intestine segment of control ducks, a total of 36 genera in the duodenum, 19 genera in the jejunum, and 6 genera in the ileum of heat-treated ducks were found to be significantly different in the abundance (linear discriminant analysis score >3.0, P < 0.05). Functional prediction of gut microbiota revealed that high temperature caused changes in the abundance of metabolism and transcription-related pathways. It is noteworthy that most of the altered pathways are related to metabolism. In conclusion, high temperature induced remarkable taxonomic changes in the gut microbiome of ducks, which might be related to the negative effects of high temperature in ducks. Our present study provided an important theoretical ground for high-temperature intervention.

Thermal and Nonthermal Effects in Plasmon-Mediated Electrochemistry at Nanostructured Ag Electrodes.

Hot carriers (HCs) and thermal effects, stemming from plasmon decays, are crucial for most plasmonic applications. However, quantifying these two effects remains extremely challenging due to the experimental difficulty in accurately measuring the temperature at reaction sites. Herein, we provide a novel strategy to disentangle HCs from photothermal effects based on the different traits of heat dissipation (long range) and HCs transport (short range), and quantitatively uncover the dominant and potential-dependent role of photothermal effect by investigating the rapid- and slow-response currents in plasmon-mediated electrochemistry at nanostructured Ag electrode. Furthermore, the plasmoelectric surface potential is found to contribute to the rapid-response currents, which is absent in the previous studies.

Changes in morphology and miRNAs expression in small intestines of Shaoxing ducks in response to high temperature.

During summer days the extreme heat may cause damage to the integrity of animal intestinal barrier. Little information is available concerning morphological changes in the duck intestines in response to high temperature. And the molecular mechanisms underlying the pathogenesis of high temperature-induced intestinal injury remain undefined. MicroRNAs (miRNAs) are known to play key roles in post-transcriptional regulation of gene expression that influences various biological processes. The purpose of this study was to explore the changes in morphology and miRNA expression profiles of the three intestinal segments (duodenum, jejunum and ileum) of ducks in response to high temperature. Sixty female Shaoxing ducks (Anas platyrhynchos), 60 days old, were allocated in two groups, including control ducks kept at 25 °C, and ducks subjected to high ambient temperatures of 30-40 °C for 15 successive days, which mimicked the diurnal temperature variations experienced in hot seasons. Three ducks from each group were executed at the end of feeding experiment, and the samples of three intestinal segments were collected for morphological examination and Illumina deep sequencing analyses. Histopathological examination of the intestinal mucous membrane was performed with HE staining method. The results demonstrated that varying degrees of damage to each intestinal segment were found in heat-treated ducks, and there were more severe injuries in duodenum and jejunum than those in ileum. Illumina high-throughput sequencing and bioinformatic methods were employed in this study to identify the miRNA expression profile of three different intestinal tissues in control and heat-treated ducks. A total of 75,981,636, 88,345,563 and 100,179,422 raw reads were obtained from duodenum, jejunum and ileum, respectively, from which 74,797,633 clean reads in duodenal libraries, 86,406,445 clean reads in jejunal libraries, and 98,518,858 lean reads in ileal libraries were derived after quality control, respectively. And a total of 276 known and 182 novel miRNAs were identified in the three intestinal segments of ducks under control and heat-treated conditions. By comparing the same tissues in different conditions, 16, 18 and 15 miRNAs were found to be significantly differentially expressed between control and heat-treated ducks in duodenum, jejunum and ileum, respectively, of which 1 miRNA was expressed in both the duodenum and jejunum, 2 miRNAs were expressed in both the duodenum and ileum, and 3 miRNAs were found to be expressed in both the jejunum and ileum. In addition, two differentially expressed miRNAs in each comparison were randomly selected and validated by quantitative qRT-PCR. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that the differentially expressed miRNAs may be involved in the high temperature-induced intestinal injury in ducks. Our work provides the comprehensive miRNA expression profiles of small intestines in the normal and heat-treated ducks. These findings suggest the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the high temperature-induced changes in the duck small intestine.

Digital gene-expression profiling analysis of the fatty liver of Landes geese fed different supplemental oils.

The goose liver is an ideal model for deciphering lipogenesis molecular mechanisms. This study was designed to investigate the effect of different lipid sources on hepatic lipogenesis in overfed geese. Sixty Landes geese were fed ad libitum with no fat (control) or overfed diets containing 2% goose fat (GF) or rapeseed oil (RO) for 20 days. We measured fatty acid composition of the liver at day 20 of overfeeding. We performed a transcriptomic comparison of fatty liver between GF and RO-fed geese to gain insights into the molecular and cellular events mediating lipogenesis activity. The results showed that there was no substantial effect on fatty liver performance between GF- and RO-fed geese. Significant differences in fatty acid composition were detected between GF- and RO-fed geese. Total ω-6 PUFAs increased and saturated fatty acid decreased (P < 0.05) with RO supplementation when compared with GF, but ω-3 PUFAs did not differ between the two diets. Concentrations of C16:1, C18:1, C18:2, C20:2, and C22:1 were higher (P < 0.05) in the fatty liver of RO-fed geese compared to those in the GF group. Analysis of transcriptome sequencing showed that there were 124 up-regulated and 129 down-regulated differentially expressed genes in the fatty liver of RO and GF-fed geese. Many of these genes code for proteins involved in the lipid metabolic process, including bile secretion, adipocytokine signalling pathway, biosynthesis of unsaturated fatty acids, linoleic acid metabolism, fatty acid elongation and fatty acid biosynthesis, and fat digestion and absorption. Moreover, genes involved in lipid-related pathways such as peroxisome, steroid biosynthesis, steroid hormone biosynthesis, retinol metabolism, and apoptosis were altered, suggesting that the fatty liver of goose fed different oils undertakes both an oxidation function and hormone-related metabolic function. In conclusions, these data suggest that RO supplementation reduces liver lipid oxidation and improves lipogenesis. These findings provide new insights into the molecular mechanisms involved in fatty liver formation and provide valuable resources for analysing mechanisms underlying the effects of oils from different sources on the goose fatty liver.

Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks.

Emerging evidences have linked the gut microbiota to poultry physiology. Gut microbiota composition in Shaoxing ducks were profiled under different rearing conditions: raised on the litter floor and the plastic mesh floor. A total of 46 and 39 luminal content samples from the duodenum, ileum, and cecum of the ducks reared under the two conditions were analyzed by 16S rRNA gene amplicon sequencing analysis. Proteobacteria (48.66%), Proteobacteria (33.38%), and Bacteroidetes (55.35%) were the dominant phyla in the duodenum, ileum, and cecum of the ducks reared on the litter floor respectively, while Firmicutes (30.80%), Firmicutes (66.62%) and Bacteroidetes (47.15%) were the topmost phyla in the duodenum, ileum, and cecum of the ducks reared on the plastic mesh floor. Physiologically, the height of villi and the ratio of villus height to crypt depth in the ileum and duodenum were significantly greater in the ducks reared on plastic mesh floor. Furthermore, our results demonstrate that the gut microbiota was significantly associated with the duck phenotypes, such as chest depth and serum estradiol levels (p < 0.05), which were altered by the different rearing conditions. Collectively, our results showed that the rearing floor types have an important effect on the gastrointestinal microbial composition of ducks.

Divergently expressed gene identification and interaction prediction of long noncoding RNA and mRNA involved in duck reproduction.

Long noncoding RNAs (lncRNAs) and divergently expressed genes exist widely in different tissues of mammals and birds, in which they are involved in various biological processes. However, there is limited information on their role in the regulation of normal biological processes during differentiation, development, and reproduction in birds. In this study, whole transcriptome strand-specific RNA sequencing of the ovary from young ducks (60days), first-laying ducks (160days), and old ducks, i.e., ducks that stopped laying eggs (490days) was performed. The lncRNAs and mRNAs from these ducks were systematically analyzed and identified by duck genome sequencing in the three study groups. The transcriptome from the duck ovary comprised 15,011 protein-coding genes and 2905 lncRNAs; all the lncRNAs were identified as novel long noncoding transcripts. The comparison of transcriptome data from different study groups identified 2240 divergent transcription genes and 135 divergently expressed lncRNAs, which differed among the groups; most of them were significantly downregulated with age. Among the divergent genes, 38 genes were related to the reproductive process and 6 genes were upregulated. Further prediction analysis revealed that 52 lncRNAs were closely correlated with divergent reproductive mRNAs. More importantly, 6 remarkable lncRNAs were correlated significantly with the conversion of the ovary in different phases. Our results aid in the understanding of the divergent transcriptome of duck ovary in different phases and the underlying mechanisms that drive the specificity of protein-coding genes and lncRNAs in duck ovary.

Transcriptome analysis of the livers of ducklings hatched normally and with assistance.

OBJECTIVE: "Hatchability" is an important economic trait in domestic poultry. Studies on poultry hatchability focus mainly on the genetic background, egg quality, and incubation conditions, whereas the molecular mechanisms behind the phenomenon that some ducklings failed to break their eggshells are poorly understood. METHODS: In this study, the transcriptional differences between the livers of normally hatched and assisted ducklings were systematically analyzed. RESULTS: The results showed that the clean reads were de novo assembled into 161,804 and 159,083 unigenes (≥200-bp long) by using Trinity, with an average length of 1,206 bp and 882 bp, respectively. The defined criteria of the absolute value of log2 fold-change ≥1 and false discovery rate≤0.05 were differentially expressed and were significant. As a result, 1,629 unigenes were identified, the assisted ducklings showed 510 significantly upregulated and 1,119 significantly down-regulated unigenes. In general, the metabolic rate in the livers of the assisted ducklings was lower than that in the normal ducklings; however, compared to normal ducklings, glucose-6-phosphatase and ATP synthase subunit alpha 1 associated with energy metabolism were significantly upregulated in the assisted group. The genes involved in immune defense such as major histocompatibility complex (MHC) class I antigen alpha chain and MHC class II beta chain 1 were downregulated in the assisted ducklings. CONCLUSION: These data provide abundant sequence resources for studying the functional genome of the livers in ducks and other poultry. In addition, our study provided insight into the molecular mechanism by which the phenomenon of weak embryos is regulated.