Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain

In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely related populations. The biological material comprised 171 triplets (sire/dam/offspring) from seven populations of autochthonous beef cattle in Spain (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta, and Rubia Gallega), which were genotyped for 777,962 SNPs with the BovineHD BeadChip. After standard quality filtering, we reconstructed the haplotype phases in the parental individuals and calculated the LD by the correlation -r- between each pair of markers that had a genetic distance < 1 Mb. Subsequently, these correlations were used to calculate the persistency of LD phase between each pair of populations along the autosomal genome. Therefore, the distribution of the recombination rate along the genome can be inferred since the effect of the number of generations of divergence should be equivalent throughout the genome. In our study, the recombination rate was highest in the largest chromosomes and at the distal portion of the chromosomes. In addition, the persistency of LD phase was highly heterogeneous throughout the genome, with a ratio of 25.4 times between the estimates of the recombination rates from the genomic regions that had the highest (BTA18-7.1 Mb) and the lowest (BTA12-42.4 Mb) estimates. Finally, an overrepresentation enrichment analysis (ORA) showed differences in the enriched gene ontology (GO) terms between the genes located in the genomic regions with estimates of the recombination rate over (or below) the 95^th (or 5^th) percentile throughout the autosomal genome.

Genetic effects of season on the preweaning growth of beef cattle: A first approach to Retinta calves

Background: Heat stress derived from global warming is causing major economic losses in the livestock industry. Objective: To develop a novel methodological approach for determining the influence of climatic factors on the estimation of genetic parameters for growth traits in Retinta cattle breed by using reaction-norm models. Methods: Live weight records (n=7,753) from 3,162 Retinta calves born from 1,249 dams and 85 sires and raised in the Andalusian region (Spain) were analyzed. The effect of heat stress was measured using the temperature-humidity index, calculated with climatological data obtained from four weather stations. A bivariate-random-regression reaction-norm model was used to estimate the (co)variance components of weight until weaning in two different climatic seasons corresponding to warm and cold months. Results: The heritability pattern of individuals reared under diverse environments during the first 90 days of age was different. However, differences were not significant at the end of the growing period. Weaned calves reared during the cold season showed greater growth from 70 to 160 days in comparison with those reared during the warm season. Conclusions: Highly significant evidence of genotype-climatic condition interaction was found during the calf´s first three months of growth.

Correction to: Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment

Following publication of the original article [1], the author reported that the two curves in the sub-diagram WSR4 in Fig. 2a should be the other way round.

Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment

BACKGROUND

Plant cell walls participate in all plant-environment interactions. Maintaining cell wall integrity (CWI) during these interactions is essential. This realization led to increased interest in CWI and resulted in knowledge regarding early perception and signalling mechanisms active during CWI maintenance. By contrast, knowledge regarding processes mediating changes in cell wall metabolism upon CWI impairment is very limited.

RESULTS

To identify genes involved and to investigate their contributions to the processes we selected 23 genes with altered expression in response to CWI impairment and characterized the impact of T-DNA insertions in these genes on cell wall composition using Fourier-Transform Infrared Spectroscopy (FTIR) in Arabidopsis thaliana seedlings. Insertions in 14 genes led to cell wall phenotypes detectable by FTIR. A detailed analysis of four genes found that their altered expression upon CWI impairment is dependent on THE1 activity, a key component of CWI maintenance. Phenotypic characterizations of insertion lines suggest that the four genes are required for particular aspects of CWI maintenance, cell wall composition or resistance to Plectosphaerella cucumerina infection in adult plants.

CONCLUSION

Taken together, the results implicate the genes in responses to CWI impairment, cell wall metabolism and/or pathogen defence, thus identifying new molecular components and processes relevant for CWI maintenance.

Relationship between patient-reported outcomes and clinical outcomes in metastatic castration-resistant prostate cancer: post hoc analysis of COU-AA-301 and COU-AA-302

Background

Patient-reported outcomes (PROs) are used to assess benefit-risk in drug development. The relationship between PROs and clinical outcomes is not well understood. We aim to elucidate the relationships between changes in PRO measures and clinical outcomes in metastatic castration-resistant prostate cancer (mCRPC).

Patients and methods

We investigated relationships between changes in self-reported fatigue, pain, functional well-being (FWB), physical well-being (PWB) and prostate cancer-specific symptoms with overall survival (OS) and radiographic progression-free survival (rPFS) after 6 and 12 months of treatment in COU-AA-301 (N = 1195) or COU-AA-302 (N = 1088). Eligible COU-AA-301 patients had progressed after docetaxel and had Eastern Cooperative Oncology Group performance status (ECOG PS) ≤ 2. Eligible COU-AA-302 patients had no prior chemotherapy and ECOG PS 0 or 1. Patients were treated with abiraterone acetate (1000 mg/day) plus prednisone (10 mg/day) or prednisone alone daily. Association between self-reported fatigue, pain and functional status, and OS and/or rPFS, using pooled data regardless of treatment, was assessed. Cox proportional hazard regression modeled time to death or radiographic progression.

Results

In COU-AA-301 patients, PRO improvements were associated with longer OS and longer time to radiographic progression versus worsening or stable PROs (P < 0.0001). In multivariate models, all except pain intensity remained associated with OS. Pain intensity, PWB and FWB improvements remained associated with rPFS. In COU-AA-302 patients, worsening PROs were associated with higher likelihood of radiographic progression (P ≤ 0.025) compared with improved or stable PROs. In multivariate models, worsening PWB remained associated with worse rPFS. The 12-month analysis confirmed the 6-month results.

Conclusions

PROs are significantly associated with clinically relevant time-to-event efficacy outcomes in clinical trials and may complement and help predict traditional clinical practice methods for monitoring patients for disease progression.

Mitogen-Activated Protein Kinase Phosphatase 1 (MKP1) Negatively Regulates the Production of Reactive Oxygen Species During Arabidopsis Immune Responses

Genetic ablation of the β subunit of the heterotrimeric G protein complex in agb1-2 confers defective activation of microbe-associated molecular pattern (MAMP)-triggered immunity, resulting in agb1-2 enhanced susceptibility to pathogens like the fungus Plectosphaerella cucumerina BMM. A mutant screen for suppressors of agb1-2 susceptibility (sgb) to P. cucumerina BMM identified sgb10, a new null allele (mkp1-2) of the mitogen-activated protein kinase phosphatase 1 (MKP1). The enhanced susceptibility of agb1-2 to the bacterium Pseudomonas syringae pv. tomato DC3000 and the oomycete Hyaloperonospora arabidopsidis is also abrogated by mkp1-2. MKP1 negatively balances production of reactive oxygen species (ROS) triggered by MAMPs, since ROS levels are enhanced in mkp1. The expression of RBOHD, encoding a NADPH oxidase-producing ROS, is upregulated in mkp1 upon MAMP treatment or pathogen infection. Moreover, MKP1 negatively regulates RBOHD activity, because ROS levels upon MAMP treatment are increased in mkp1 plants constitutively overexpressing RBOHD (35S::RBOHD mkp1). A significant reprograming of mkp1 metabolic profile occurs with more than 170 metabolites, including antimicrobial compounds, showing differential accumulation in comparison with wild-type plants. These results suggest that MKP1 functions downstream of the heterotrimeric G protein during MAMP-triggered immunity, directly regulating the activity of RBOHD and ROS production as well as other immune responses.

[Assessment of muscular toxicity due to chemotherapy by cardio-pulmonary exercise testing]

INTRODUCTION

Cardio-pulmonary exercise testing (CPET) is frequently used to assess aerobic capacity, to evaluate respiratory tolerance and to provide prognostic information. Therefore, CPET is often incorporated in the preoperative assessment of cancer patients. This clinical case report presents the preoperative assessment of a patient before thoracic surgery, in whom an important decrease of aerobic capacity was noted, possibly because of muscular toxicity linked to chemotherapy.

CASE REPORT

This clinical case concerns a fit, 66-year-old man with a large cell carcinoma of the bronchus. He had received 2 cycles of adjuvant chemotherapy. Subsequently, a left pneumonectomy had been proposed and preoperative assessment performed. CPET showed no further increase in oxygen uptake after the first ventilatory threshold, in spite of increases in carbon dioxide output, minute ventilation and heart rate. Moreover, maximal oxygen uptake was low and there was a decrease of oxygen pulse at maximal effort.

CONCLUSION

We suggest that the limitation of effort was due to a limitation of muscular oxygen extraction, which could be explained by possible muscular toxicity due to chemotherapy.

Generation and characterization of a novel knockin minipig model of Hutchinson-Gilford progeria syndrome

Hutchinson-Gilford progeria syndrome (HGPS) is an extremely rare genetic disorder for which no cure exists. The disease is characterized by premature aging and inevitable death in adolescence due to cardiovascular complications. Most HGPS patients carry a heterozygous de novo LMNA c.1824C > T mutation, which provokes the expression of a dominant-negative mutant protein called progerin. Therapies proven effective in HGPS-like mouse models have yielded only modest benefit in HGPS clinical trials. To overcome the gap between HGPS mouse models and patients, we have generated by CRISPR-Cas9 gene editing the first large animal model for HGPS, a knockin heterozygous LMNA c.1824C > T Yucatan minipig. Like HGPS patients, HGPS minipigs endogenously co-express progerin and normal lamin A/C, and exhibit severe growth retardation, lipodystrophy, skin and bone alterations, cardiovascular disease, and die around puberty. Remarkably, the HGPS minipigs recapitulate critical cardiovascular alterations seen in patients, such as left ventricular diastolic dysfunction, altered cardiac electrical activity, and loss of vascular smooth muscle cells. Our analysis also revealed reduced myocardial perfusion due to microvascular damage and myocardial interstitial fibrosis, previously undescribed readouts potentially useful for monitoring disease progression in patients. The HGPS minipigs provide an appropriate preclinical model in which to test human-size interventional devices and optimize candidate therapies before advancing to clinical trials, thus accelerating the development of effective applications for HGPS patients.

Quantitative phosphoproteomic analysis reveals common regulatory mechanisms between effector- and PAMP-triggered immunity in plants

Plant immunity consists of two arms: pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), induced by surface-localized receptors, and effector-triggered immunity (ETI), induced by intracellular receptors. Despite the little structural similarity, both receptor types activate similar responses with different dynamics. To better understand phosphorylation events during ETI, we employed a phosphoproteomic screen using an inducible expression system of the bacterial effector avrRpt2 in Arabidopsis thaliana, and identified 109 differentially phosphorylated residues of membrane-associated proteins on activation of the intracellular RPS2 receptor. Interestingly, several RPS2-regulated phosphosites overlap with sites that are regulated during PTI, suggesting that these phosphosites may be convergent points of both signaling arms. Moreover, some of these sites are residues of important defense components, including the NADPH oxidase RBOHD, ABC-transporter PEN3, calcium-ATPase ACA8, noncanonical Gα protein XLG2 and H⁺ -ATPases. In particular, we found that S343 and S347 of RBOHD are common phosphorylation targets during PTI and ETI. Our mutational analyses showed that these sites are required for the production of reactive oxygen species during both PTI and ETI, and immunity against avirulent bacteria and a virulent necrotrophic fungus. We provide, for the first time, large-scale phosphoproteomic data of ETI, thereby suggesting crucial roles of common phosphosites in plant immunity.

Characteristics of ripened Tronchón cheese from raw goat milk containing legally admissible amounts of antibiotics

The aim of this study was to evaluate the transfer of the most widely used antibiotics in dairy goats from milk to cheese as well as their effect on the cheese-making process and cheese characteristics during ripening. Antibiotic-free milk was spiked individually with 7 veterinary drugs (amoxicillin, benzylpenicillin, cloxacillin, erythromycin, ciprofloxacin, enrofloxacin, and oxytetracycline) at an equivalent concentration of the European Union maximum residue limit. Spiked goat milk was used to make mature Tronchón cheeses, which were analyzed at 0, 30, and 60 d of maturation to determine pH, chemical composition, proteolytic and lipolytic activities, and color and textural properties. A sensory evaluation of 60-d ripened cheeses was carried out. Cheeses from raw antibiotic-free goat milk were made simultaneously to be used as reference. The cheese-making process was unaffected by the presence of most antibiotics evaluated. Only erythromycin and oxytetracycline significantly increased the time required for cheese production (122 ± 29 and 108 ± 25 min, respectively). However, variable amounts of antibiotics, ranging from 7.4 to 68%, were transferred from milk to cheese, with oxytetracycline and quinolones showing the highest retention rates. In general, antibiotic residues present in the cheeses at the beginning of maturation decrease significantly along time. Thus, β-lactams and erythromycin residues were not detectable after 30 d of ripening. However, relatively high concentrations of enrofloxacin (148 ± 12 µg/kg) and ciprofloxacin (253 ± 24 µg/kg) residues were found in the cheeses after 60 d of maturation. The quality characteristics of the Tronchón cheeses were only slightly affected by such substances, with few significant differences in the free fatty acid concentration and color and textural properties of the cheeses. Results herein indicate that the use of goat milk containing antibiotics, such as quinolones, at the European Union maximum residue limit for cheese production could adversely affect the safety of the final products because relatively high concentrations of these substances could be retained in soft and semi-mature cheeses, making it necessary to assess the risk for consumer health. Studies on the partition of the antibiotic substances during cheese-making, using specific technologies, would be convenient to guarantee the safety of cheese and related products.

Abstract P1-15-17: Liposomal-encapsulated doxorubicin (Myocet)as part of primary systemic therapy in HER2-positive operable breast cancer: Efficacy data, cardiotoxicity and long-term follow-up in 81 patients diagnosed from 2005-2016 at a single institution

Objectives

To evaluate the efficacy, cardiotoxicity profile and long-term benefits of liposomal doxorubicin (Myocet) as part of neoadjuvant therapy in HER2-positive operable breast cancer patients.

Methods

The treatment consisted of a sequential regimen of paclitaxel and liposomal doxorubicin (Myocet) plus trastuzumab. Clinical and pathologic response were evaluated and correlated with clinical and biological factors. Cardiotoxicity profile and long-term benefits were analyzed.

Results

Median age was 48 years and 4%, 69%, and 27% were stage I, II, and III, respectively, while 12% had inflammatory breast cancer at diagnosis. Hormone receptor (HR) status was negative in 43% and 70% were grade III.

Patients Characteristics Total number (%)Age, years Median (Range)48 (30-79)Tumor (cT)* Tx1 (1)T14 (5)T253 (66)T313 (16)T410 (12)Nodal Status N024 (30)N1-257 (70)Stage I3 (4)II56 (69)III22 (27)Hormone Receptor Status HR+35 (43)HR-46 (57)HER2 IHC 3+74 (91)IHC 2+7 (9)FISH/SISH21 (26)Grade I1(1)II22 (27)III57 (71)Unknown1 (1)Ki-67 &lt;20%6 (7)20-35%32 (40)&gt;35%43 (53)Surgical Indication at Diagnosis Mastectomy58 (72)Tumorectomy22 (27)Any surgery in breast*1 (1)* One patient had an occult carcinoma.

pCR by SubgroupsPathologic ResponsepCRNo pCR(n=81)n (%)n (%)Tumor Size (MRI)  &lt;/=5 cm26 (49)27 (51)&gt; 5 cm10 (67)5 (33)Nodes  Positive26 (46)31 (54)Negative18 (75)6 (25)Histological Subtype  Ductal43 (56)34 (44)Lobular0 (0)2 (100)Other1 (50)1 (50)Hormone Receptor  Negative23 (66)12 (34)Positive21 (46)25 (54)Ki-67  &lt;204 (67)2 (33)20-3512 (38)20 (62)&gt;3528 (65)15 (35)Grade  I0 (0)1 (100)II12 (55)10 (45)III31 (54)26 (46)

The clinical complete response rate by ultrasound and MRI were 47% and 65%, respectively, and allowed a high rate of conservative surgery (72%).

The pathologic complete response (pCR) rate in breast and axilla was 54%, higher in HR-negative (66%) than in HR-positive (46%),in ki-67&gt;35% (65%) than ki-67 between 20-35% (38%) and similar in grade III (54%) and grade II (55%).

Patients who achieved pCR had longer DFS and a trend to improve OS.

Four percent of patients showed a decrease in the left ventricular ejection fraction below 50% during treatment. All except one of them recovered after discontinuation of trastuzumab.

Conclusion: A sequential regimen of taxanes and liposomal doxorubicin (Myocet) plus trastuzumab was active with high pCR rates and long-term benefit with a very good cardiotoxicity profile.

Citation Format: Antolin S, Calvo L, Prato J, Molina A, Reboredo C, Mosquera J. Liposomal-encapsulated doxorubicin (Myocet)as part of primary systemic therapy in HER2-positive operable breast cancer: Efficacy data, cardiotoxicity and long-term follow-up in 81 patients diagnosed from 2005-2016 at a single institution [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-17.

Screening for epistatic selection signatures: A simulation study

Detecting combinations of alleles that diverged between subpopulations via selection signature statistics can contribute to decipher the phenomenon of epistasis. This research focused on the simulation of genomic data from subpopulations under divergent epistatic selection (ES). We used D’_IS² and F_ST statistics in pairs of loci to scan the whole-genome. The results showed the ability to identify loci under additive-by-additive ES (ES_aa) by reporting large statistical departures between subpopulations with a high level of divergence, while it did not show the same advantage in the other types of ES. Despite this, limitations such as the difficulty to distinguish between the quasi-complete fixation of one locus by ES_aa from other events were observed. However, D’_IS² can detect loci under ES_aa by defining a minimum boundary for the minor allele frequency on a multiple subpopulation analysis where ES only takes place in one subset. Even so, the major limitation was distinguishing between ES and single-locus selection (SS); therefore, we can conclude that divergent locus can be also a result of ES. The test conditions with D-statistics of both Ohta (1982a, 1982b) and Black and Krafsur (1985) did not provide evidence to differentiate ES in our simulation framework of isolated subpopulations.

A new molecular screening tool for the detection of chromosomal abnormalities in donkeys

Chromosomal abnormalities are a major cause of infertility and reproductive problems in equids. Nowadays, their detection is rising due to the use of new diagnostic tools based on molecular markers instead of karyotyping. Reports of this kind of genetic aberrations in domestic donkeys (Equus asinus) are extremely scarce, despite their importance in human activities. In the present study, we analysed the implementation of a short-tandem-repeat (STR)-based molecular method initially developed for horses, as a diagnostic tool to detect chromosomal abnormalities in donkeys. The frequency of five X-linked (LEX003, LEX026, TKY38, TKY270 and UCEDQ502) and one Y-linked (ECAYM2) molecular markers and one Y-linked gene (sex-determining region Y, SRY) was characterized in 121 donkeys from two diverse breeds, the Spanish Andalusian and the African Moroccan breeds. The molecular panel showed 100% sensitivity and 99.67% specificity in detecting 10 different chromosomal abnormalities in the species. In conclusion, this methodology is a valid, rapid and low-cost tool for the detection and characterization of chromosomal abnormalities in domestic donkeys.

Evidence for the effect of serotoninergic and dopaminergic gene variants on stress levels in horses participating in dressage and harness racing

Eye temperature assessed with infrared thermography is an adequate tool for stress level assessment in sport horses’ competitions having a moderate heritability. Serotonin and dopamine signal transduction-linked gene variants have been associated with anxiety-related traits in several species. In this study we examined the association between 10 gene variants in BDNF, COMT, HTR1A, TPH2 and SLC6A4 genes (and the haplotypes at SLC6A4 gene) with stress level (measured with eye temperature and heart rate) in 270 animals, 135 Spanish Trotter Horses (STH) participating in trotting races and 135 ‘Pura Raza Español’ (PRE) horses in dressage. Association analyses were performed using a unified mixed model (counting for population structure and individual relatedness) for the whole population and for each horse breed. The g.43865600G &gt; A intronic gene variant located 11.0 kb downstream from the transcription start site of SLC6A4 gene was associated with an increase in eye temperature before competition with a relative contribution of this gene variant of 38.8% (P = 0.001), 31.8% just after (P = 0.001) and 29.8% 2 h after the competition (P = 0.003). In STH, the g.43865600G &gt; A gene variant showed the same association with eye temperature before (P = 0.001, contribution 27.2%), just after (P = 0.0003, 29.0%) and after the competition (P = 0.002, 17.5%); and the c.*111G &gt; A gene variant located at the 3′UTR region of COMT gene was associated with eye temperature 2 h after the competition (P = 0.001, 22.3%). These results showed that SLC6A4 and COMT gene variants are associated with stress level measured as eye temperature increase during competitions, and may be promising tools for genetic testing against resistance at high stress levels in trotter horses.