Identification of a histone acetyltransferase as a novel regulator of Drosophila intestinal stem cells

AbstractOne of the major challenges in stem cell research is to decipher the controlling mechanisms/genes of stem cell homeostasis. Through an RNAi mediated genetic screen of living animals, we identified an evolutionarily conserved histone acetyltransferase Atac2 as a novel regulator of Drosophila intestinal stem cells (ISCs). Expression of Atac2-RNAi or a dominant negative allele of Atac2 generated more ISCs, while excessive Atac2 or a histone deacetylase inhibitor promoted ISC differentiation without affecting ISC survival or lineage specification. These findings extend our knowledge of epigenetic mechanisms in stem cell regulation

Estimation of genetic parameters for predicted nitrogen use efficiency and losses in early lactation of Holstein cows

peer reviewedThe objective of this study was to estimate genetic parameters of predicted N use efficiency (PNUE) and N losses (PNL) as proxies of N use and loss for Holstein cows. Furthermore, we have assessed approximate genetic correlations between PNUE, PNL, and dairy production, health, longevity, and conformation traits. These traits are considered important in many countries and are currently evaluated by the International Bull Evaluation Service (Interbull). The values of PNUE and PNL were obtained by using the combined milk mid-infrared (MIR) spectrum, parity, and milk yield–based prediction equations on test-day MIR records with days in milk (DIM) between 5 and 50 d. After editing, the final data set comprised 46,163 records of 21,462 cows from 154 farms in 5 countries. Each trait was divided into primiparous and multiparous (including second to fifth parity) groups. Genetic parameters and breeding values were estimated by using a multitrait (2-trait, 2-parity classes) repeatability model. Herd-year-season of calving, DIM, age of calving, and parity were used as fixed effects. Random effects were defined as parity (within-parity permanent environment), nongenetic cow (across-parity permanent environment), additive genetic animal, and residual effects. The estimated heritability of PNUE and PNL in the first and later parity were 0.13, 0.12, 0.14, and 0.13, and the repeatability values were 0.49, 0.40, 0.55, and 0.43, respectively. The estimated approximate genetic correlations between PNUE and PNL were negative and high (from −0.89 to −0.53), whereas the phenotypic correlations were also negative but relatively low (from −0.45 to −0.11). At a level of reliability of more than 0.30 for all novel traits, a total of 504 bulls born after 1995 had also publishable Interbull multiple-trait across-country estimated breeding values (EBV). The approximate genetic correlations between PNUE and the other 30 traits of interest, estimated as corrected correlations between EBV of bulls, ranged from −0.46 (udder depth) to 0.47 (milk yield). Obtained results showed the complex genetic relationship between efficiency, production, and other traits: for instance, more efficient cows seem to give more milk, which is linked to deeper udders, but seem to have lower health, fertility, and longevity. Additionally, the approximate genetic correlations between PNL, lower values representing less loss of N, and the 30 other traits, were from −0.32 (angularity) to 0.57 (direct calving ease). Even if further research is needed, our results provided preliminary evidence that the PNUE and PNL traits used as proxies could be included in genetic improvement programs in Holstein cows and could help their management

Result Diversification in Search and Recommendation: A Survey

Diversifying return results is an important research topic in retrieval systems in order to satisfy both the various interests of customers and the equal market exposure of providers. There has been growing attention on diversity-aware research during recent years, accompanied by a proliferation of literature on methods to promote diversity in search and recommendation. However, diversity-aware studies in retrieval systems lack a systematic organization and are rather fragmented. In this survey, we are the first to propose a unified taxonomy for classifying the metrics and approaches of diversification in both search and recommendation, which are two of the most extensively researched fields of retrieval systems. We begin the survey with a brief discussion of why diversity is important in retrieval systems, followed by a summary of the various diversity concerns in search and recommendation, highlighting their relationship and differences. For the survey's main body, we present a unified taxonomy of diversification metrics and approaches in retrieval systems, from both the search and recommendation perspectives. In the later part of the survey, we discuss the open research questions of diversity-aware research in search and recommendation in an effort to inspire future innovations and encourage the implementation of diversity in real-world systems.Comment: 20 page

Genetic parameters analysis of milk citrate for Holstein cows in early lactation

peer reviewedDelivering innovative and holistic monitoring and decision-making PLF tools relies on the availability of critical biomarkers. Negative energy balance is a difficult trait complex as there is a difference between perceived imbalance and physiological imbalance. Milk citrate is considered to be an early biomarker of negative energy balance for dairy cows in early lactation, but its genetic analysis is lacking. The objectives of this study were to (1) show the distribution of milk citrate content in early lactation; (2) analyze the genetic parameters of milk citrate. The coefficient of determination (R2) and root mean square error (RMSE) of the predicted milk citrate model by milk mid-infrared (MIR) spectra in external validation were 0.86 and 0.76 mmol/L, and available from DIM 5 to 50 d. Records were divided into three traits according to the first (citrate1), second (citrate2), and from third to fifth party (citrate3+). After editing, the data included 134,517 records, from 52,198 cows, and 4,479 animals in the pedigree with 566,170 SNPs. A multiple-trait repeatability model was used in this study. The citrate is decreasing in early lactation, on average from 10.04 to 8.58 mmol/L from DIM 5 to 50 d. When cows start to be in energy balance (DIM ≈ 40 d), milk citrate was 8.82 mmol/l. The average of citrate1 was 8.93 mmol/l; citrate2 was 8.93 mmol/l; citrate3+ was 9.17 mmol/l. The heritability for citrate1 was 0.40; for citrate2, 0.37 and for citrate3+, 0.35. The ranges of genetic correlations between the three traits were from 0.98 to 0.99, and of phenotypic correlations, from 0.41 to 0.42. This study shows that considering MIR-based milk citrate as an indicator to identify negative energy balance should be possible in early lactation and that this indicator could help select for animals less affected by negative energy balance

A review of Vietnamese Schistoloma Kobelt, 1902 with a list of all known species of the genus (Caenogastropoda: Cyclophoroidea: Pupinidae)

Fig 2. A, Schistoloma maydelineae new species, holotype HNHM 103476; B, Sculpture and suture of upper whorls; C, Sculpture of the last whorl. Photographs by: B. Páll-Gergely. Scale "a" = 10 mm and refers to fig. A, scale "b" = 5 mm and refers to figs. B and C.Published as part of Páll-Gergely, Barna, Nguyen, Phi Khanh & Chen, Yansen, 2019, A review of Vietnamese Schistoloma Kobelt, 1902 with a list of all known species of the genus (Caenogastropoda: Cyclophoroidea: Pupinidae), pp. 322-327 in Raffles Bulletin of Zoology 67 on page 325, DOI: 10.26107/RBZ-2019-0023, http://zenodo.org/record/457705

Genetic analyses of principal components of milk mid-infrared spectra from Holstein cows

peer reviewedMilk mid-infrared (MIR) spectra are widely used to predict milk composition and phenotypes linked to animal health, efficiency, emissions, resilience, and even milk processability. However, the milk phenome represented by the large number of individual MIR wavenumbers (hereafter called MIR spectral traits) could allow strategies to develop innovative and holistic monitoring and decision-making PLF tools by avoiding phenotypic calibrations. The objectives of this study were to start exploring the complete genetic architecture of MIR spectral traits by studying principal components of milk MIR traits from Holstein cows and their genetic correlations with milk fat percent. In total, 27,855 records for 311 MIR spectral traits and fat percent from 3,303 first-parity Holstein cows were used. All principal components (PCs) of 311 wavenumbers were extracted and single-traits and bivariate (PC and fat percentage) repeatability models were used. The first 75 PCs explained already 99.99% of the phenotypic variance across the 311 wavenumbers. However, the genetic variances of these 75 PCs explained only 85.54% of the total genetic variances of the 311 PCs. Their range of heritability was from 0.00 to 0.47. The mean and standard deviation of genetic correlations (absolute value) between 311 PCs and fat percent were 0.25 and 0.28, respectively. After first 75 PCs, some PCs (e.g., PC 86) still had genetic correlations (here 0.37) with fat percent. This preliminary study showed that phenotypic rank reduction using first 75 PCs might be dangerous, also as even some PCs (e.g., PC 145) with very low phenotypic variances (< 0.001%) showed heritability (here 0.05) over 0.01. By estimating heritability and in future studies genetic correlations among MIR spectral traits associated with genomics, understanding the genetic architecture of MIR spectral traits will not only help us optimize their use for breeding, but also manage by avoiding phenotypic calibration steps

Relationship between proxies of energy states and nitrogen use efficiency for Holstein cows in early lactation

peer reviewedThe purposes of this study were to estimate the genetic parameters of the energy status indicator (C18:1 cis-9) of Holstein cows in early lactation and its relationship with nitrogen use efficiency (NUE) (predicted NUE and milk urea concentration). After editing, the data included 143,517 records within 5 to 50 days in milk from 52,198 cows, and 3,546 animals in the pedigree with 28,427 SNPs. Two multiple-trait repeatability models were used in this study. In early lactation, the average C18:1 cis-9 was gradually decreasing and was highest in May. The heritabilities of C18:1 cis-9 for primiparous and multiparous cows were 0.12 and 0.09, respectively. The C18:1 cis-9 had positive genetic correlations with predicted NUE (from 0.28 to 0.67), and weak genetic correlations with milk yield, milk urea concentration (from-0.15 to 0.14). This study suggests that breeding for NUE alone may enhance energy troubles in early lactation

Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein.

peer reviewedThe aims of this study were to conduct a single-step genome-wide association to identify genomic regions associated with milk urea (MU) and to estimate genetic correlations between MU and milk yield (MY), milk composition (calcium content (CC), fat percentage (FP), protein percentage (PP), and casein percentage (CNP)), and cheese-making properties (CMP) (coagulation time (CT), curd firmness after 30 min from rennet addition (a30), and titratable acidity (TA)). The used data have been collected from 2015 to 2020 on 78,073 first-parity (485,218 test-day records), and 48,766 s-parity (284,942 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA) of 6,617 animals (1,712 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 Kb) was calculated, and the top-3 genomic regions explaining the largest rate of the genetic variance were considered promising regions and used to identify potential candidate genes. Mean (standard deviation) MU was 25.38 (8.02) mg/dl and 25.03 (8,06) mg/dl in the first and second lactation, respectively. Mean heritability estimates for daily MU were 0.21 and 0.23 for the first and second lactation, respectively. The genetic correlations estimated between MU and MY, milk composition, and CMP were quite low (ranged from -0.10 (CC) to 0.10 (TA) and -0.05 (CT) to 0.13 (TA) for the first and second lactations, respectively). The top-3 regions associated with MU were located from 80.61 to 80.74 Mb on BTA6, 103.26 to 103.41 Mb on BTA11, and 1.59 to 2.15 Mb on BTA14. Genes including KCNT1, MROH1, SHARPIN, TSSK5, CPSF1, HSF1, TONSL, DGAT1, SCX, and MAF1 were identified as positional candidate genes for MU. The findings of this study can be used for a better understanding of the genomic architecture underlying MU in Holstein cattle

Defining a nitrogen efficiency index in Holstein cows and assessing its potential effect on the breeding program of bulls.

peer reviewedThe purposes of this study were (1) to explore the relationship between 3 milk mid-infrared predicted features including nitrogen intake (NINT), milk true protein N (MTPN), and milk urea-N yield (MUNY); (2) to integrate these 3 features into an N efficiency index (NEI) and analyses approximate genetic correlations between the NEI and 37 traits (indices) of interest; and (3) to assess the potential effect of including the NEI into breeding programs of bulls. The edited data were 1,043,171 test-day records on 342,847 cows in 1,931 herds and 143,595 test-day records on 53,660 cows in 766 herds used for estimating breeding values (EBV) and variance components, respectively. The used records were within 5 to 50 d in milk. The records were grouped into primiparous and multiparous. The genetic parameters for the included mid-infrared features and EBV of the animals included in the pedigree were estimated using a multiple-trait repeatability animal model. Then, the EBV of the NINT, MTPN, MUNY were integrated into the NEI using a selection index assuming weights based on the N partitioning. The approximate genetic correlations between the NEI and 37 traits of interest were estimated using the EBV of the selected bulls. The bulls born from 2011 to 2014 with NEI were selected and the NEI distribution of these bulls having EBV for the 8 selected traits (indices) was checked. The heritability and repeatability estimates for NINT, MTPN, and MUNY ranged from 0.09 to 0.13, and 0.37 to 0.65, respectively. The genetic and phenotypic correlations between NINT, MTPN, and MUNY ranged from -0.31 to 0.87, and -0.02 to 0.42, respectively. The NEI ranged from -13.13 to 12.55 kg/d. In total, 736 bulls with reliability ≥0.50 for all included traits (NEI and 37 traits) and at least 10 daughters distributed in at least 10 herds were selected to investigate genetic aspects of the NEI. The NEI had positive genetic correlations with production yield traits (0.08-0.46), and negative genetic correlations with the investigated functional traits and indices (-0.71 to -0.07), except for the production economic index and functional type economic index. The daughters of bulls with higher NEI had lower NINT and MUNY, and higher MTPN. Furthermore, 26% of the bulls (n = 50) with NEI born between 2011 to 2014 had higher NEI and global economic index than the average in the selected bulls. Finally, the developed NEI has the advantage of large-scale prediction and therefore has the potential for routine application in dairy cattle breeding in the future.13. Climate actio

Single-step genome-wide association for milk urea concentration in Walloon Holstein

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