Genomic analyses of nitrogen utilization efficiency, its indicator trait blood urea nitrogen and the relationship to classical growth performance and feed efficiency traits in a Landrace × Piétrain crossbred population

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Abstract

Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations. Blood urea nitrogen (BUN) levels in the pig are suitable to predict the NUE and, therefore, might be an indicator trait for NUE because BUN is a relatively easy-to-measure trait. This study investigated the suitability of NUE as a selection trait in future breeding programs. The relationships to classical growth performance and feed efficiency traits were analysed as well as the relationship to BUN to infer the role of BUN as an indicator trait to improve NUE via breeding. The analyzes were based on a Landrace F1 cross population consisting of 502 individuals who descended from 20 Piétrain sires. All animals were genotyped for 48,525 SNPs. They were phenotyped in two different fattening phases, i.e., FP1 and FP2, during the experiment. Uni- and bivariate analyses were run to estimate variance components and to determine the genetic correlation between different traits or between the same trait measured at different time points. Moderate heritabilities were estimated for all traits, whereby the heritability for NUE was h 2 = 0.293 in FP1 and h 2 = 0.163 in FP2 and BUN had the by far highest heritability (h 2 = 0.415 in FP1 and h 2 = 0.460 in FP2). The significant genetic correlation between NUE and BUN showed the potential of BUN to be considered an indicator trait for NUE. This was particularly pronounced when NUE was measured in FP1 (genetic correlations rg=−0.631$$ {r}_g=-0.631 $$ and rg=−0.688$$ {r}_g=-0.688 $$ between NUE and BUN measured in FP1 and FP2, respectively). The genetic correlations of NUE and BUN with important production traits suggest selecting pigs with high growth rates and low BUN levels to breed more efficient pigs in future breeding programs.

Do oral and gut microbiota communicate through redox pathways? A novel asset of the nitrate‐nitrite‐NO pathway

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Do oral and gut microbiota communicate through redox pathways? A novel asset of the nitrate-nitrite-NO pathway

The oral and gut microbiotas are distinct microbial communities with unique compositions and functions but they can communicate and influence each other. Antibiotics disrupt the oral and gut ecosystems, leading to dysbiosis and increased gut epithelial permeability. Nitrate may promote inter-kingdom crosstalk during dysbiosis by either generating redox signalling species or serving as a substrate for bacteria in both ecosystems.


Nitrate may act as a regulator of •NO bioavailability via sequential reduction along the nitrate-nitrite-NO pathway with widespread health benefits, including a eubiotic effect on the oral and gut microbiota. Here, we discuss the molecular mechanisms of microbiota-host communication through redox pathways, via the production of •NO and oxidants by the family of NADPH oxidases, namely hydrogen peroxide (via Duox2), superoxide radical (via Nox1 and Nox2) and peroxynitrite, which leads to downstream activation of stress responses (Nrf2 and NFkB pathways) in the host mucosa. The activation of Nox2 by microbial metabolites is also discussed. Finally, we propose a new perspective in which both oral and gut microbiota communicate through redox pathways, with nitrate as the pivot linking both ecosystems.

ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification

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ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification

Maleimide-based chemical labeling targets inosine in RNA and DNA to identify A-to-I editing sites. Fluorescein conjugation enables visualization via PAGE, and biotin conjugation facilitates streptavidin-mediated enrichment, enhancing the detection and analysis of nucleic acid modifications.


Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.

Effects of food resources on the longevity, survival, and fecundity of Paracentrobia subflava adults, an egg parasitoid of the corn leafhopper pest Dalbulus maidis

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Effects of food resources on the longevity, survival, and fecundity of Paracentrobia subflava adults, an egg parasitoid of the corn leafhopper pest Dalbulus maidis

Process of evaluating longevity and survival to different artificial diets and honeydew of the corn pest Dalbulus maidis in the egg parasitoid Paracentrobia subflava (A). In addition, assess P. subflava's fecundity with food (honey) and without food (B).


Abstract

The diet consumed by adult parasitoids can affect longevity, survival, and fecundity. Honeydew from sap-sucking insects is an abundant food resource in the field; however, artificial diets such as commercial bee honey are often used in lab rearing. The parasitoid Paracentrobia subflava (Girault) (Hymenoptera: Trichogrammatidae) is a natural enemy of Dalbulus maidis (DeLong) (Hemiptera: Cicadellidae). The longevity and survival of P. subflava when fed natural and artificial diets under controlled conditions have not been studied. Further, the fecundity of P. subflava when fed a diet of honey has not been investigated. Therefore, our first objective was to analyse the longevity and survival of P. subflava when fed (1) honeydew of the corn leafhopper D. maidis, (2) honey + water, (3) honey + water + pollen, (4) water, and (5) nothing (control). Our second objective was to evaluate P. subflava fecundity upon exposure to D. maidis eggs, comparing parasitoids fed with honey + water versus controls (no food or water). In the second objective, honey was chosen since it was determined during the first objective to be the optimal food. The longevity of adult parasitoids (laboratory-reared and field-collected) was high when fed on honey and low when fed other diets. The highest longevity was achieved with honey + water: 17 days, while the survival of adult parasitoids was only 3 days for honeydew. Interestingly, fecundity, in terms of the percentage of parasitism and the percentage of emergence, did not differ between parasitoid females that had access to honey + water as a food resource and those that had no food or water.

Genetic diversity, population structure and origin of the native goats in Central Laos

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Abstract

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (F ST: 0.011–0.043) and negligible inbreeding coefficients (F IS: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85 Mb, with short ROH segments (1–5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

Switching from combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate to tenofovir alafenamide fumarate monotherapy in patients with chronic hepatitis B based on nucleotide sequences of hepatitis B virus pregenome RNA

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Switching from combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate to tenofovir alafenamide fumarate monotherapy in patients with chronic hepatitis B based on nucleotide sequences of hepatitis B virus pregenome RNA

We devised a method to analyze drug resistance profile of hepatitis B virus pregenome RNA even when serum hepatitis B virus DNA is undetectable during antiviral therapy. By using this approach, we verified that patients receiving combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate for chronic hepatitis B virus infection due to experiencing viral breakthrough or partial response during initial lamivudine or entecavir hydrate administration were able to safely transition to tenofovir alafenamide fumarate monotherapy.


Abstract

Aim

Patients with chronic hepatitis B virus (HBV) infection experiencing viral breakthrough (BTH) or partial response (PR) during lamivudine (LAM) or entecavir hydrate (ETV) administration often took ETV plus tenofovir alafenamide fumarate (TAF) due to the emergence of a drug-resistance mutation. However, in patients lacking drug-resistance mutation against TAF, sufficient antiviral effects may be achievable with TAF monotherapy. We assessed the drug-resistance profile through nucleotide sequences of HBV pregenome RNA, and subsequently changed to TAF monotherapy from ETV plus TAF.

Methods

This prospective study included 25 patients with serum HBV-DNA below 20 IU/mL under ETV plus TAF administration. Pregenome RNA nucleotide sequences of HBV in the sera were analyzed using direct sequencing and deep sequencing. ETV was discontinued in patients without rtA194T and rtS106C + rtH126Y + rtD134E + rtL269I quadruple mutations in direct sequencing.

Results

LAM-PR, LAM-BTH, ETV-PR, and ETV-BTH were observed in 1, 16, 7, and 1 patient(s), respectively. Pregenome RNA nucleotide sequences were analyzable in 20 patients. Among the 12 patients classified as LAM-BTH, six patients showed rtL180M + rtM204V/I in direct sequencing, and one patient showed minor clones containing rtL180M + rtM204V + A194T in deep sequencing at a frequency of 0.3%. In the six patients classified as ETV-PR, one patient harbored rtM204I. No clones showing rtS106C + rtH126Y + rtD134E + rtL269I quadruple mutation were detected in deep sequencing. Subsequently, ETV was discontinued, and serum HBV-DNA remained undetectable up to 48 weeks in all patients.

Conclusion

Patients receiving ETV plus TAF due to partial response or BTH during initial LAM or ETV administration were able to safely transition to TAF monotherapy based on nucleotide sequences of HBV pregenome RNA in the sera.

Role of PAR1 −506 deletion/insertion polymorphism in primary sclerosing cholangitis

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Role of PAR1 −506 deletion/insertion polymorphism in primary sclerosing cholangitis

We showed that the frequency of PAR1 rs11267092 polymorphism was significantly higher in patients with primary sclerosing cholangitis (PSC) compared to healthy individuals. PSC patients carrying the PAR1 rs11267092 polymorphism showed significantly higher serum levels of alanine aminotransferase and a trend toward shorter transplant-free survival time compared to noncarriers.


Abstract

Aim

Primary sclerosing cholangitis (PSC) is a rare cholestatic liver disease characterized by inflammation of the intra- and extrahepatic bile ducts. Pathogenesis of PSC is still enigmatic but is likely to be multifactorial. Recently, we identified an interleukin-6 (IL-6)-dependent signal transducer and activator of transcription 3 (STAT3) activation in CD4+ TH1 and TH17 cells in PSC. The IL-6/STAT3 pathway was shown to be regulated by protease-activated receptor 1 (PAR1) contributing to inflammation. The role of the PAR1 −506 deletion/insertion (Del/Ins) polymorphism in PSC has not yet been investigated.

Methods

Two hundred eighty four PSC patients (200 patients with inflammatory bowel diseases [IBD] and 84 without IBD) and 309 healthy controls were genotyped for PAR1 rs11267092 (−506 Del/Ins −13 bp). Results were correlated with clinical characteristics and transplant-free survival.

Results

The frequency of PAR1 –506 Ins allele carriers (Del/Ins and Ins/Ins) was significantly higher in PSC patients (57.0%) compared to healthy controls (39.8%). Furthermore, carriers of PAR1 −506 Ins allele were more likely to have PSC than noncarriers (odds ratio 2.01; 95% confidence interval, 1.45–2.79). Patients with PSC carrying the PAR1 −506 Ins allele showed significantly higher alanine aminotransferase serum levels (p = 0.0357) and a trend toward shorter transplant-free survival time compared to noncarriers (8.9 ± 6.6 years vs. 10.5 ± 7.1 years; p = 0.076).

Conclusions

Our study shows that PAR1 −506 Ins is significantly more frequent in people with PSC. As PAR1 −506 Ins allele carriers tended to have a shorter transplant-free survival, PAR1 might play a role in the development and course of PSC.