<i>C14orf132</i> gene is possibly related to extremely low birth weight

BackgroundDespite extensive research the genetic component of extremely low birth weight (ELBW) in newborns has remained obscure.ResultsThe aim of the case study was to identify candidate gene(s) causing ELBW in newborns and hypotrophy in infants. A family of four was studied: mother, father and two ELBW-phenotype children. Studies were made of the medical conditions of the second child at birth and post-partum - peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy and suspected metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate the genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene - C14orf132 (chromosome 14 open reading frame 132) differentially expressed, with the level of the transcript significantly lower in the blood samples of the children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children.ConclusionWe demonstrated the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the pre- and early postnatal developmental delay through the altered gene expression

Culling reasons and risk factors in Estonian dairy cows

Background: Culling is a major cost for dairy farms but also an essential part in managing herd productivity. This study aimed to identify the culling rates of Estonian dairy cows, identify the farmers' stated reasons and risk factors for culling. This observational study used registry data of all cows from herds with >= 20 cow-years in 2013-2015. Cow lactation-level analyses included data of 86,373 primiparous cows from 409 herds and 177,561 lactations of 109,295 multiparous cows from 410 herds. Weibull proportional hazard regression models were used to identify risk factors for culling due to slaughter or death. Results: The overall culling rate of Estonian dairy cows was 26.24 (95% CI 26.02; 26.46) per 100 cow-years. The most common reasons farmers stated for culling were feet/claw disorders (26.4%), udder disorders (22.6%), metabolic and digestive disorders (18.1%) and fertility problems (12.5%). Animal-level risk factors for culling were Holstein breed, older parity, lower milk yield breeding value, older age at first calving, longer previous calving interval, having assisted calving, stillbirth and birth of twins/triplets. Lower milk yield, somatic cell count over 200,000 cells/ml and fat/protein ratio over 1.5 at first test-milking after calving were associated with greater culling hazard during the lactation. Cows from larger herds, herds with decreasing size and higher milk yields had a higher culling probability. Conclusions: This study emphasises the need for improved management of hoof health and prevention of mastitis and metabolic diseases. It is essential to ensure easy calving and good health of cows around calving in order to lower the culling hazard

Multiblock analysis reveals key areas and risk factors for dairy cow losses

Describe the relative contribution of the production areas (thematic blocks) to cow losses characterized by herd on farm mortality risk (MR), culling rates (CR) and mean age of culled cows (MAofCC). Also, the study aimed to identify within each block, the variables mostly contributing to the cow losses.This work was financed by the Estonian Research Council grant (PSG 268).This work was financed by the Estonian Research Council grant (PSG 268

Attitudes and personality of farm managers and association with cow culling rates and longevity in large-scale commercial dairy farms

The farmer has the central role in determining cow culling policies on their farm and thus affecting cow longevity. The present study aimed to examine farm managers´ satisfaction, attitudes, personality traits and analyse the associations with dairy cow culling and longevity in large commercial dairy farms. Farm managers of 116 dairy herds rearing at least 100 cows in freestall barns were included. A questionnaire for the farm managers registered personal background information of respondent and included statements capturing their satisfaction, opinions and attitudes regarding dairy cow culling and longevity, farming in general, and a Ten Item Personality Inventory scoring. For each herd, the last 12 months cow culling rate (CR, excluding dairy sale) and herd mean age of culled cows (MAofCC) was obtained from the Estonian Livestock Performance Recording Ltd. A K-mean clustering algorithm was applied to subgroup farm managers based on their attitudes, opinions and personality traits. The yearly mean herd CR was 33.0% and MAofCC was 60.6 months. Farm managers´ were mostly dissatisfied with cow longevity and culling rates in their farms. Dissatisfaction with culling rates and longevity, priority for producing high milk yields over longevity and production-oriented attitude was associated with high culling rates and poor longevity. Farm managers' personality had an effect on herd culling rates and their attitudes explained one third of the variability of culling rates and longevity.Explaining the economic consequences of high culling rates and decreased longevity, improving the visibility of these parameters together with benchmarking could bring these issues into focus

In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages

Although chromosomal instability (CIN) is a common phenomenon in cleavage-stage embryogenesis following in vitro fertilization (IVF)1,2,3, its rate in naturally conceived human embryos is unknown. CIN leads to mosaic embryos that contain a combination of genetically normal and abnormal cells, and is significantly higher in in vitro-produced preimplantation embryos as compared to in vivo-conceived preimplantation embryos4. Even though embryos with CIN-derived complex aneuploidies may arrest between the cleavage and blastocyst stages of embryogenesis5,6, a high number of embryos containing abnormal cells can pass this strong selection barrier7,8. However, neither the prevalence nor extent of CIN during prenatal development and at birth, following IVF treatment, is well understood. Here we profiled the genomic landscape of fetal and placental tissues postpartum from both IVF and naturally conceived children, to investigate the prevalence and persistence of large genetic aberrations that probably arose from IVF-related CIN. We demonstrate that CIN is not preserved at later stages of prenatal development, and that de novo numerical aberrations or large structural DNA imbalances occur at similar rates in IVF and naturally conceived live-born neonates. Our findings affirm that human IVF treatment has no detrimental effect on the chromosomal constitution of fetal and placental lineages

Attitudes and personality of farm managers and association with cow culling rates and longevity in large-scale commercial dairy farms

The farmer has the central role in determining cow culling policies on their farm and thus affecting cow longevity. The present study aimed to examine farm managers satisfaction, attitudes, personality traits and analyse the associations with dairy cow culling and longevity in large commercial dairy farms.Farm managers of 116 dairy herds rearing at least 100 cows in freestall barns were included. A questionnaire for the farm managers registered personal background information of respondent and included statements capturing their satisfaction, opinions and attitudes regarding dairy cow culling and longevity, farming in general, and a Ten Item Personality Inventory scoring. For each herd, the last 12 months cow culling rate (CR, excluding dairy sale) and herd mean age of culled cows (MAofCC) was obtained from the Estonian Livestock Performance Recording Ltd. A K-mean clustering algorithm was applied to subgroup farm managers based on their attitudes, opinions and personality traits.The yearly mean herd CR was 33.0% and MAofCC was 60.6 months. Farm managers acute accent were mostly dissatisfied with cow longevity and culling rates in their farms. Dissatisfaction with culling rates and longevity, priority for producing high milk yields over longevity and production-oriented attitude was associated with high culling rates and poor longevity. Farm managers' personality had an effect on herd culling rates and their attitudes explained one third of the variability of culling rates and longevity.Explaining the economic consequences of high culling rates and decreased longevity, improving the visibility of these parameters together with benchmarking could bring these issues into focus

Additional file 1: of C14orf132 gene is possibly related to extremely low birth weight

Timeline summarizing the clinical course of the children described in this case report. (PDF 210 kb

rs10732516 polymorphism at the IGF2/H19 locus associates with genotype-specific effects on placental DNA methylation and birth weight of newborns conceived by assisted reproductive technology

BackgroundAssisted reproductive technology (ART) has been associated with low birth weight of fresh embryo transfer (FRESH) derived and increased birth weight of frozen embryo transfer (FET)-derived newborns. Owing to that, we focused on imprinted insulin-like growth factor 2 (IGF2)/H19 locus known to be important for normal growth. This locus is regulated by H19 imprinting control region (ICR) with seven binding sites for the methylation-sensitive zinc finger regulatory protein (CTCF). A polymorphism rs10732516 G/A in the sixth binding site for CTCF, associates with a genotype-specific trend to the DNA methylation. Due to this association, 62 couples with singleton pregnancies derived from FRESH (44 IVF/18 ICSI), 24 couples from FET (15 IVF/9 ICSI), and 157 couples with spontaneously conceived pregnancies as controls were recruited in Finland and Estonia for genotype-specific examination. DNA methylation levels at the H19 ICR, H19 DMR, and long interspersed nuclear elements in placental tissue were explored by MassARRAY EpiTYPER (n = 122). Allele-specific changes in the methylation level of H19 ICR in placental tissue (n = 26) and white blood cells (WBC, n = 8) were examined by bisulfite sequencing. Newborns' (n = 243) anthropometrics was analyzed by using international growth standards.ResultsA consistent trend of genotype-specific decreased methylation level was observed in paternal allele of rs10732516 paternal A/maternal G genotype, but not in paternal G/maternal A genotype, at H19 ICR in ART placentas. This hypomethylation was not detected in WBCs. Also genotype-specific differences in FRESH-derived newborns' birth weight and head circumference were observed (P = 0.04, P = 0.004, respectively): FRESH-derived newborns with G/G genotype were heavier (P = 0.04) and had larger head circumference (P = 0.002) compared to newborns with A/A genotype. Also, the placental weight and birth weight of controls, FRESH- and FET-derived newborns differed significantly in rs10732516 A/A genotype (P = 0.024, P = 0.006, respectively): the placentas and newborns of FET-derived pregnancies were heavier compared to FRESH-derived pregnancies (P = 0.02, P = 0.004, respectively).ConclusionsThe observed DNA methylation changes together with the phenotypic findings suggest that rs10732516 polymorphism associates with the effects of ART in a parent-of-origin manner. Therefore, this polymorphism should be considered when the effects of environmental factors on embryonic development are studied