Litter size components in a full diallel cross of four maternal lines of rabbits

[EN] A crossbreeding experiment between 4 Spanish maternal lines of rabbits was performed to estimate crossbreeding effects on litter size components. The experiment was designed as a complete diallel cross involving 4 lines selected for litter size at weaning (A, V, H, and LP [L]) and their 12 simple crosses. Does from these 16 genetic groups were distributed among 4 Spanish farms, but only V line was present in all farms, allowing connectivity of the data. A total of 2,015 does in the third, fourth, or fifth gestations were subjected to laparoscopy. The recorded traits were ovulation rate (OR), number of implanted embryos (IE), total born (TB), embryo survival (ES), foetal survival (FS), and prenatal survival (PS). The differences in direct genetic effects, maternal genetic effects, and individual heterosis between the lines were estimated according to Dickerson s model. Line A was significantly inferior to lines V and H, whereas line LP was similar to A line, but for FS and PS, line A showed the best values, followed by line LP. Comparing crossbred groups to line V, significant differences were shown favoring crossbred groups for OR and IE. The crossbred groups presented high implantation rate, but the foetal survival was lower than in V line. Important values for commercial production were presented by some crosses for OR (HV, 1.26 ova), IE (AH, 1.50 embryos; HV, 1.41 embryos), and TB (AH, 0.82 rabbits; HV, 0.78 rabbits). Relevant and significant reciprocal effects were found, especially for OR in all cases except the LV and VL crosses. These differences become nonsignificant in most of the other traits. Regarding direct genetic effects, line A presented lower estimates than the other lines with important values for OR, but the opposite was observed for FS. The maternal effects were significant only for some contrasts in OR and revealed that the LP line was inferior to the others (1.08 ova compared to the A line, 1.23 compared to the H line, and 0.38 compared to the V line). In general, high positive values for heterosis were found in crossbred does for OR and IE. The crosses, where lines A and H were involved, showed significant heterosis. The highest values were obtained by crossing lines A and H (1.18 ova for OR, 1.87 embryos for IE) followed by the cross between lines H and V. Crosses between line LP and the other lines had a negative heterosis for FS and PS.This work was supported by the Spanish project AGL2011-30170 from the Spanish National Research Plan.Mohamed Ragab, M.; Sánchez Serrano, JP.; Mínguez Balaguer, C.; Vicente Antón, JS.; Baselga Izquierdo, M. (2014). Litter size components in a full diallel cross of four maternal lines of rabbits. Journal of Animal Science. 92(8):3231-3236. https://doi.org/10.2527/jas.2013-7286S3231323692

Selection for ovulation rate in rabbits: Direct and correlated responses estimated with a cryopreserved control population1

The aim of this work was to evaluate the response in 10 generations of selection for ovulation rate in rabbits using a cryopreserved control population. Selection was based on the phenotypic value of ovulation rate estimated at d 12 of second gestation by laparoscopy. To produce the control population, embryos from 50 donor females and 18 males, belonging to the base generation of the line selected for ovulation rate, were recovered. A total of 467 embryos (72-h embryos) were vitrifi ed and stored in liquid N2 for 10 generations. The size of both populations was approximately 10 males and 50 females. The number of records used to analyze the different traits ranged from 99 to 340. Data were analyzed using Bayesian methodology. A difference between the selected and the control populations of 2.1 ova (highest posterior density interval (HPD95%) [1.3, 2.9]) was observed in ovulation rate (OR), but it was not accompanied by a correlated response in litter size (LS; −0.3; HPD95% [−1.1, 0.5]). The number of implanted embryos (IE) increased with selection in 1.0 embryo (HPD95% [−0.6, 2.0]), but this increase was not relevant. Prenatal survival, embryonic survival, and fetal survival (FS) were calculated as LS/OR, IE/OR, and LS/IE, respectively. Prenatal survival was reduced with selection (−0.12; HPD95% [−0.20, −0.04]), basically because of a decrease in FS (−0.12; HPD95% [−0.19, −0.06]). Embryonic survival could have slightly decreased (−0.05; HPD95% [−0.12, 0.02]). In summary, comparison with a control population showed that ovulation rate in rabbits increased with selection without any correlated response in litter size, basically because of a decrease in fetal survival.This study was supported by the Comision Interministerial de Ciencia y Tecnologia CICYT-AGL2005-07624-C03-01 and by funds from the Generalitat Valenciana research program (Prometeo 2009/125). The authors are grateful to Wagdy Mekkawy for letting us use his programs.Laborda Vidal, P.; Santacreu Jerez, MA.; Blasco Mateu, A.; Mocé Cervera, ML. (2015). Selection for ovulation rate in rabbits: Direct and correlated responses estimated with a cryopreserved control population1. Journal of Animal Science. 90(10):3392-3397. https://doi.org/10.2527/jas.2011-4837S33923397901

TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition

Amyotrophic lateral sclerosis (ALS) is an adult-onset motor neuron disease with a mean survival time of three years. The 97% of the cases have TDP-43 nuclear depletion and cytoplasmic aggregation in motor neurons. TDP-43 prevents non-conserved cryptic exon splicing in certain genes, maintaining transcript stability, including ATG4B, which is crucial for autophagosome maturation and Microtubule-associated proteins 1A/1B light chain 3B (LC3B) homeostasis. In ALS mice (G93A), Atg4b depletion worsens survival rates and autophagy function. For the first time, we observed an elevation of LC3ylation in the CNS of both ALS patients and atg4b−/− mouse spinal cords. Furthermore, LC3ylation modulates the distribution of ATG3 across membrane compartments. Antisense oligonucleotides (ASOs) targeting cryptic exon restore ATG4B mRNA in TARDBP knockdown cells. We further developed multi-target ASOs targeting TDP-43 binding sequences for a broader effect. Importantly, our ASO based in peptide-PMO conjugates show brain distribution post-IV administration, offering a non-invasive ASO-based treatment avenue for neurodegenerative diseases

Match-action: the role of motion and audio in creating global change blindness in film

An everyday example of change blindness is our difficulty to detect cuts in an edited moving-image. Edit Blindness (Smith & Henderson, 2008) is created by adhering to the continuity editing conventions of Hollywood, e.g. coinciding a cut with a sudden onset of motion (Match-Action). In this study we isolated the roles motion and audio play in limiting awareness of match-action cuts by removing motion before and/or after cuts in existing Hollywood film clips and presenting the clips with or without the original soundtrack whilst participants tried to detect cuts. Removing post-cut motion significantly decreased cut detection time and the probability of missing the cut. By comparison, removing pre-cut motion had no effect suggesting, contrary to the editing literature, that the onset of motion before a cut may not be as critical for creating edit blindness as the motion after a cut. Analysis of eye movements indicated that viewers reoriented less to new content across intact match-action cuts than shots with motion removed. Audio played a surprisingly large part in creating edit blindness with edit blindness mostly disappearing without audio. These results extend film editor intuitions and are discussed in the context of the Attentional Theory of Cinematic Continuity (Smith, 2012a)

Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress

The expression of ribosomal protein (RP) genes requires a substantial part of cellular transcription, processing and translation resources. Thus, the RP expression must be tightly regulated in response to conditions that compromise cell survival. In Saccharomyces cerevisiae cells, regulation of the RP gene expression at the transcriptional, mature mRNA stability and translational levels during the response to osmotic stress has been reported. Reprogramming global protein synthesis upon osmotic shock includes the movement of ribosomes from RP transcripts to stress-induced mRNAs. Using tiling arrays, we show that osmotic stress yields a drop in the levels of RP pre-mRNAs in S. cerevisiae cells. An analysis of the tiling array data, together with transcription rates data, shows a poor correlation, indicating that the drop in the RP pre-mRNA levels is not merely a result of the lowered RP transcription rates. A kinetic study using quantitative RT-PCR confirmed the decrease in the levels of several RP-unspliced transcripts during the first 15 minutes of osmotic stress, which seems independent of MAP kinase Hog1. Moreover, we found that the mutations in the components of the nonsense-mediated mRNA decay (NMD), Upf1, Upf2, Upf3 or in exonuclease Xrn1, eliminate the osmotic stress-induced drop in RP pre-mRNAs. Altogether, our results indicate that the degradation of yeast RP unspliced transcripts by NMD increases during osmotic stress, and suggest that this might be another mechanism to control RP synthesis during the stress response

Genetic selection for ovulation rate and litter size in rabbits: estimation of genetic parameters and direct and correlated responses

The aim of this work was to estimate direct and correlated responses in survival rates in an experiment of selection for ovulation rate (OR) and litter size (LS) in a line of rabbits (OR_LS). From generation 0 to 6 (first selection period), females were selected only for second gestation OR estimated by laparoscopy. From generation 7 to 13 (second selection period), a 2-stage selection for OR and LS was performed. In stage 1, females having the greatest OR at second gestation were selected. In stage 2, selection was for the greatest average LS of the first 2 parities of the females selected in stage 1. Total selection pressure in females was about 30%. The line had approximately 17 males and 75 females per generation. Traits recorded were OR estimated as the number of corpora lutea in both ovaries, number of implanted embryos (IE) estimated as the number of implantation sites, LS estimated as total number of rabbits born recorded at each parity, embryo survival (ES) estimated as IE/OR, fetal survival (FS) estimated as LS/IE, and prenatal survival (PS) estimated as LS/OR. Data were analyzed using Bayesian methodology. The estimated heritabilities of LS, OR, IE, ES, FS, and PS were 0.07, 0.21, 0.10, 0.07, 0.12, and 0.16, respectively. Direct and correlated responses from this study were estimated in each period of selection as the difference between the average genetic values of last and first generation. In the first selection period, OR increased 1.36 ova, but no correlated response was observed in LS due to a decrease on FS. Correlated responses for IE, ES, FS, and PS in the first selection period were 1.11, 0.00, -0.04, and -0.01, respectively. After 7 generations of 2-stage selection for OR and LS, OR increased 1.0 ova and response in LS was 0.9 kits. Correlated responses for IE, ES, FS, and PS in the second selection period were 1.14, 0.02, 0.02, and 0.07, respectively. Two-stage selection for OR and LS can be a promising procedure to improve LS in rabbits.This study was supported by the Comision Interministerial de Ciencia y Tecnologia CICYT-AGL2005-07624-C03-01 CICYT-AGL2008-05514-C02-01 and by funds from Generalitat Valenciana research programme (Prometeo 2009/125).Ziadi, C.; Mocé Cervera, ML.; Laborda Vidal, P.; Blasco Mateu, A.; Santacreu Jerez, MA. (2013). Genetic selection for ovulation rate and litter size in rabbits: estimation of genetic parameters and direct and correlated responses. Journal of Animal Science. 91(7):3113-3120. https://doi.org/10.2527/jas.2012-6043S3113312091

The HOG Pathway Dictates the Short-Term Translational Response after Hyperosmotic Shock

In the global osmoshock translational response in yeast, some gene products were translationally mobilized without transcriptional up-regulation. Conversely, other transcriptionally up-regulated mRNAs were translationally inhibited. Analogous changes occurred on the protein level. These translational responses were strongly dependent on Hog1 and Rck2

Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein Binds and Protects a Nuclear Noncoding RNA from Cellular RNA Decay Pathways

The control of RNA stability is a key determinant in cellular gene expression. The stability of any transcript is modulated through the activity of cis- or trans-acting regulatory factors as well as cellular quality control systems that ensure the integrity of a transcript. As a result, invading viral pathogens must be able to subvert cellular RNA decay pathways capable of destroying viral transcripts. Here we report that the Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 protein binds to a unique KSHV polyadenylated nuclear RNA, called PAN RNA, and protects it from degradation by cellular factors. ORF57 increases PAN RNA levels and its effects are greatest on unstable alleles of PAN RNA. Kinetic analysis of transcription pulse assays shows that ORF57 protects PAN RNA from a rapid cellular RNA decay process, but ORF57 has little effect on transcription or PAN RNA localization based on chromatin immunoprecipitation and in situ hybridization experiments, respectively. Using a UV cross-linking technique, we further demonstrate that ORF57 binds PAN RNA directly in living cells and we show that binding correlates with function. In addition, we define an ORF57-responsive element (ORE) that is necessary for ORF57 binding to PAN RNA and sufficient to confer ORF57-response to a heterologous intronless β-globin mRNA, but not its spliced counterparts. We conclude that ORF57 binds to viral transcripts in the nucleus and protects them from a cellular RNA decay pathway. We propose that KSHV ORF57 protein functions to enhance the nuclear stability of intronless viral transcripts by protecting them from a cellular RNA quality control pathway

A complete set of nascent transcription rates for yeast genes

The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell

Linguistic theory, linguistic diversity and Whorfian economics

Languages vary greatly in their words, sounds and sentence structures. Linguistic theory has shown that many aspects of variation are superficial and may not reflect underlying formal similarities between languages, which are relevant to how humans learn and process language. In this chapter, I show both how languages can vary and how the surface variations can be manifestations of underlying similarities. Economists have sometimes adopted a ‘Whorfian’ view that differences in languages can cause differences in how their speakers think and behave. Psychological experiments have shown both support for this hypothesis and evidence against it. Specific arguments that language causes thought, which have been made in recent economics papers, are examined in the light of what linguistics tells us about superficial and underlying variatio