Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic analyses of feed efficiency traits in pigs

Feed costs amount to approximately 70% of the total costs in pork production, and feed efficiency is, therefore, an important trait for improving pork production efficiency. Production efficiency is generally improved by selection for high lean growth rate, reduced backfat, and low feed intake. These traits have given an effective slaughter pig but may cause problems in piglet production due to sows with limited body reserves. The aim of the present study was to develop a measure for feed efficiency that expressed the feed requirements per 1 kg deposited lean meat and fat, which is not improved by depositing less fat. Norwegian Landrace (n = 8,161) and Duroc (n = 7,202) boars from Topigs Norsvin’s testing station were computed tomography scanned to determine their deposition of lean meat and fat. The trait was analyzed in a univariate animal model, where total feed intake in the test period was the dependent variable and fat and lean meat were included as random regression cofactors. These cofactors were measures for fat and lean meat efficiencies of individual boars. Estimation of fraction of total genetic variance due to lean meat or fat efficiency was calculated by the ratio between the genetic variance of the random regression cofactor and the total genetic variance in total feed intake during the test period. Genetic variance components suggested there was significant genetic variance among Norwegian Landrace and Duroc boars in efficiency for deposition of lean meat (0.23 ± 0.04 and 0.38 ± 0.06) and fat (0.26 ± 0.03 and 0.17 ± 0.03) during the test period. The fraction of the total genetic variance in feed intake explained by lean meat deposition was 12% for Norwegian Landrace and 15% for Duroc. Genetic fractions explained by fat deposition were 20% for Norwegian Landrace and 10% for Duroc. The results suggested a significant part of the total genetic variance in feed intake in the test period was explained by fat and lean meat efficiency. These new efficiency measures may give the breeders opportunities to select for animals with a genetic potential to deposit lean meat efficiently and at low feed costs in slaughter pigs rather than selecting for reduced the feed intake and backfat.
A novel multi-perspective imaging platform (M-PIP) for phenotyping soybean root crowns in the field increases throughput and separation ability of genotype root properties

Background Root crown phenotyping has linked root properties to shoot mass, nutrient uptake, and yield in the field, which increases the understanding of soil resource acquisition and presents opportunities for breeding. The original methods using manual measurements have been largely supplanted by image-based approaches. However, most image-based systems have been limited to one or two perspectives and rely on segmentation from grayscale images. An efficient high-throughput root crown phenotyping system is introduced that takes images from five perspectives simultaneously, constituting the Multi-Perspective Imaging Platform (M-PIP). A segmentation procedure using the Expectation-Maximization Gaussian Mixture Model (EM-GMM) algorithm was developed to distinguish plant root pixels from background pixels in color images and using hardware acceleration (CPU and GPU). Phenes were extracted using MatLab scripts. Placement of excavated root crowns for image acquisition was standardized and is ergonomic. The M-PIP was tested on 24 soybean [Glycine max (L.) Merr. ] cultivars released between 1930 and 2005. Results Relative to previous reports of imaging throughput, this system provides greater throughput with sustained rates of 1.66 root crowns min-1. The EM-GMM segmentation algorithm with hardware acceleration was able to segment images in 10 s, faster than previous methods, and the output images were consistently better connected with less loss of fine detail. Image-based phenes had similar heritabilities as manual measures with the greatest effect sizes observed for Maximum Radius and Fine Radius Frequency. Correlations were also noted, especially among the manual Complexity score and phenes such as number of roots and Total Root Length. Averaging phenes across perspectives generally increased heritability, and no single perspective consistently performed better than others. Angle-based phenes, Fineness Index, Maximum Width, Holes, Solidity and Width-to-Depth Ratio were the most sensitive to perspective with decreased correlations among perspectives. Conclusion The substantial heritabilities measured for many phenes suggest that they are potentially useful for breeding. Multiple perspectives together often produced the greatest heritabilities, and no single perspective consistently performed better than others. Thus, as illustrated here for soybean, multiple perspectives may be beneficial for root crown phenotyping systems. This system can contribute to breeding efforts that incorporate under-utilized root phenotypes to increase food security and sustainability.
A new species of Carpolestes (Mammalia, Plesiadapoidea) from the late Paleocene of southern Wyoming: assessing changes in size and shape during the evolution of a key anatomical feature

Abstract A new and phylogenetically basal species of Carpolestes, the youngest and most derived genus of the plesiadapoid family Carpolestidae in North America, is described from a late Tiffanian (Ti-5) site in Sweetwater County, Wyoming, USA. Carpolestids differ from closely related plesiadapoid clades in having an enlarged, multicuspidate, blade-like P4 that is partly convergent on that of multituberculates and other mammals showing plagiaulacoid dental adaptations. With some notable exceptions, the evolutionary history of North American carpolestids is characterized by the progressive development of larger and more elaborate P4 blades through time. In particular, species of the monophyletic genus Carpolestes differ from species assigned to the earlier and apparently paraphyletic genus Carpodaptes in terms of both the size and shape of their P4. A geometric morphometric analysis reveals that, with respect to P4 shape, the closest approximation to the highly derived morphology of Carpolestes is made by Carpodaptes hobackensis, which is one of the smallest known species of Carpodaptes. In contrast, the largest known species of Carpodaptes, Carpodaptes jepseni, has a P4 that falls within the metric range of variation for species of Carpolestes, yet Carpodaptes jepseni shows a uniquely derived P4 shape that seems to exclude it from any special phylogenetic relationship with Carpolestes. A phylogenetic analysis based on dental characters reconstructs Carpodaptes hobackensis as the sister group of the Carpolestes clade. Shape seems to have been a more important factor than size during the final transformation of the blade-like P4 of North American carpolestids. http://zoobank.org/urn:lsid:zoobank.org:pub:212F9ECC-DA9A-44F8-BE7E-43F3EBAD636A
Transcriptional study of the ABC transporter-encoding genes in response to fungicide treatment and during plant infection in the phytopathogenic fungus Botrytis cinerea

The grey mould fungus Botrytis cinerea causes worldwide losses of commercially important fruits, vegetables and ornamentals. Various fungicides, with different modes of action, are effective against this pathogen, but isolates with multiple fungicide-resistance phenotypes (Multi Drug Resistance, MDR) have been observed with increasing frequency. In fungi, ATP binding cassette (ABC) transporters participate in drug efflux and we report here on the parallel transcriptional study of the predicted ABC transporter-encoding genes in B. cinerea. During plant infection, transcription of all of these genes was activated and over-expression was observed for a few of these genes if the plants were treated with a fungicide prior to infection. In the absence of plant, most of the genes were transcriptionally activated in response to two different fungicides. Both common and specific transcriptional signatures were observed.
Evaluation of 2-Hydroxy-4-(methylthio) Butanoic Acid Isopropyl Ester and Methionine Supplementation on Efficiency of Microbial Protein Synthesis and Rumen Bacterial Populations

Because microorganisms that grow in the rumen flow to the abomasum and are digested, the primary source of protein for milk production is of microbial origin, so increasing microbial protein supply should either increase milk protein or decrease the need for expensive bypass protein. Moreover, improving the consistency of prediction of microbial protein supply decreases the amount of protein that must be fed to the dairy cow, reducing urinary N excretion and decreasing feed costs. Methionine is co-limiting with lysine in most dairy diets. 2-hydroxy-4-(methylthio) butanoic acid (HMBi) is a methionine precursor for bacteria and might be degraded more slowly and, therefore, might be sustained longer over the feeding cycle for bacterial uptake or absorption than methionine itself. HMBi has been shown to increase nitrogen efficiency, expressed as the proportion of ingested nitrogen secreted in milk, when supplemented to dairy cows, but its mode of action (rumen microbial protein synthesis, delayed absorption, or both) has not been ascertained. To show the effect of HMBi and methionine on bacterial population structure and protein synthesis, we used four continuous culture fermenters inoculated with rumen fluid from two lactating Holstein cows. We fed the cultures a normal dairy ration with a 50/50 ratio of concentrate and alfalfa. Our experimental design was a 4x4 Latin square. Our treatments were control (CON), 0.11% HMBi (HMBi), 0.097% methionine (MET), and 0.055% HMBi plus 0.048% methionine (HMBi
The molecular basis for an ancient colour mutant in sweet pea (Lathyrus odoratus)

Abstract: The classic A1 locus in sweet pea (Lathyrus odoratus) was investigated by Bateson, Punnett, and Saunders in the early 20th century history of Mendelian genetics. The mutation, in the form of the pink and white cultivar ‘Painted Lady’, is known from the 18th century. We show that this locus is associated with a single base pair mutation (332 G/A) in the flavonoid 3′,5′-hydroxylase (F3′5′H) gene. This results in an amino acid change (111 glycine/aspartic acid) in the conserved substrate recognition site 1 of the enzyme. The mutant flower lacks the blue pigment delphinidin and is thus pink and white, rather than purple and blue as in the wild-type. This single amino acid change at a functionally important site appears to convert the enzyme from primary F3′5′H activity to a relatively efficient F3′H, as suggested by heterologous transformation into Arabidopsis PAP1D (a mutant line that produces anthocyanin constitutively).
Analysis of crab size structure and the fishing effort applied to a crab fishery in northwest Mexico

The fishing effort of a Sinaloa crab fishery in the Gulf of California in 2014 was analysed based on fishermen’s interviews, official catches and permits, and information from a sample of fishing logbooks from five fishery cooperatives operating in four coastal lagoons that contained the daily catch from individual fishing trips. Unauthorized gear, a double-ring net (DR), was used most frequently (>70% of the fishers) for crab fishing, although authorized single-ring nets and Chesapeake traps (CT) were also used with low frequency. The estimated fishing effort was 641 boats/day in the four coastal lagoons, which was 34% more than authorized, and 818 boats/day were employed in all of Sinaloa. A total of 57 479 fishing gears were estimated for the study area, which was 49.9% greater than the maximum authorized number, and 80 822 nominal fishing gears were estimated for the entire Sinaloa crab fishery, 14.15% more than the total gear limit (70 800). The size of the mesh used in the gear was smaller than the authorized limit of 76 mm, and >50% of the catches included crabs of unlawful size. It is argued that the effort must be regulated in terms of the number of vessels, per unit time, and not the number of gears. The information from this study demonstrates a failure to monitor compliance with current regulations and thus means that other strategies for the sustainable management of the fishery, such as co-management, should be tested.
PAM Nucleotide Deviation with CRISPR-Cas9 and sgRNA

Author(s): Singh, Gurbinder | Abstract: CRISPR-Cas9 is a system that it is not only revolutionary in expeditious sequencing of deoxyribonucleic acids (DNA) but also serves to induce genomic alterations within the sequence as well. The methodology that allows CRISPR to behave in such a manner is its ability to function in conjunction with ribonucleic acids (RNA). A facet of this RNA is its ability to scale from micro to macro organisms and by doing so, represents an observable deviation in its sequence. These sequential changes in RNA are observable in the form of protospacer adjacent motif (PAM) nucleotides which directly associate with the single guiding RNA (sgRNA) systems that direct DNA to the Cas9 enzyme. These PAM nucleotides are segments on RNA that are changed when DNA is altered and can be monitored. Cas9 is the protein component of CRISPR that is responsible for genome editing. However, the problem is that there hasn’t been conclusive evidence that demonstrates sgRNA will scale in complex genomes such as mice or humans. My objective is to observe how the PAM nucleotides behave in a multicellular Mammalia organism such as Mice to determine if RNA is directing DNA to the Cas9 enzyme and inducing genetic alterations. To observe these PAM nucleotides, the Mice genome will be subject to the introduction of Cas9 systems to be observed with PCR, gel electrophoresis, and Illumina sequencing. These are techniques that will yield data that signify if CRISPR is effective in altering mice genomes. With significant observable deviations in the PAM nucleotide sequences, the conclusion will be that CRISPR-Cas9 is able to induce alterations in complex genomes such as Mice and eventually humans.
Morphological and mitochondrial DNA data reshuffle the taxonomy of the genera Atopochetus Attems, Litostrophus Chamberlin and Tonkinbolus Verhoeff (Diplopoda: Spirobolida: Pachybolidae), with descriptions of nine new species

Abstract. Species-level taxonomy and phylogeny of two genera of South-East (SE) Asian pachybolid millipedes are analysed with a combination of morphological characters and DNA sequences (two mitochondrial gene fragments: COI and 16S rRNA). Strong support is found for the genera Litostrophus Chamberlin, 1921 and Atopochetus Attems, 1953 and for a clade consisting of Litostrophus + Atopochetus. Four species of Litostrophus are recognised and (re)described: L. segregatus Chamberlin, 1921 (type species of the genus), L. scaber (Verhoeff, 1938), comb. nov., L. chamaeleon, sp. nov. and L. saraburensis, sp. nov. The genus Tonkinbolus Verhoeff, 1938 (type species T. scaber Verhoeff, 1938) is synonymised under Litostrophus. Atopochetus (type species A. rubropunctatus Attems, 1953), hitherto considered a dubious synonym of Aulacobolus Pocock, 1903, is re-instated for several species until now placed in Tonkinbolus and seven new species. All in all, 10 species of Atopochetus are (re)described: A. dollfusii (Pocock, 1893) (= Aulacobolus rubropunctatus Attems, 1938, syn. nov.), A. moulmeinensis (Pocock, 1893), A. sumatranus (Carl, 1906) (= Trachelomegalus laciniatus Attems, 1937, syn. nov.), A. anaticeps, sp. nov., A. helix, sp. nov., A. setiferus, sp. nov., A. spinimargo, sp. nov., A. truncatus, sp. nov., A. uncinatus, sp. nov. and A. weseneri, sp. nov. Three species recently included in Tonkinbolus are left incertae sedis because they are based exclusively on female type specimens: Spirobolus capucinus Porat, 1896, S. caudulanus Karsch, 1881 and S. macrurus Pocock, 1893. The results of the DNA analysis (COI and 16S rRNA) are congruent with morphological (gonopodal) characters in terms of delimitation of species of Litostrophus and Atopochetus. This is the first DNA study of SE Asian Pachybolidae and as such it provides a basis for further evolutionary and biogeographic studies of SE Asian millipedes.
Collared Lizard Juveniles Use Caudal Displays while Stalking Prey

Abstract Caudal displays that lure or divert the attention of prey are well documented in legless squamates that use sit-and-wait foraging. By contrast, empirical evidence that caudal displays serve to distract prey is lacking in legged lizards. Preliminary observations suggested that juvenile Collared Lizards (Crotaphytus collaris) may give caudal displays when stalking arthropods. Therefore, we conducted field experiments involving introduction of tethered grasshoppers to test whether free-ranging lizards performed more caudal displays when they were stalking prey. Results revealed that lizards performed tail displays more frequently and longer when they were stalking than when not stalking tethered prey. Our results appear to be the first experimental support for the hypothesis that legged lizards use caudal displays when stalking prey, perhaps to distract the attention of prey away from the mouth. Combined with other published results, we demonstrate that caudal displays play a role in both foraging and predator avoidance in juvenile Collared Lizards.
Sensory and preference evaluation of the addition of organic acids to white wines

The aim of this work was to evaluate the response of a trained tasting panel to the addition of organic acids in white wine. The tasters were characterised through questionnaires in relation to age, gender, smoking habits, expertise and wine preference (Vinotype). Two taste functions were also determined, concerning 6-propyl-2-thiouracil (PROP) status and saliva flow. Organic acid detection and recognition thresholds were determined by triangular tests. Perithresholds concentrations of lactic acid and lactic acid plus succinic acid were spiked in two white wines of different acidity and preference was evaluated by visual analogue scale (VAS). The detection and recognition thresholds, expressed in tartaric acid, were of 1.64 g/L and 3.24 g/L for tartaric acid; 1.98 g/L and 3.48 g/L for lactic acid; and 0.88 g/L e 1.05 g/L for succinic acid. The addition of lactic acid (1.92 g/L) and lactic acid (1.92 g/L) plus succinic aci (0.32 g/L) in two white wines did not induce differences (p<0.05) in wine preference. However, tendencies were observed in the increase of preference with acidification in the less sour wine and decrease in the sourer samples. Considering all wines and acidified samples, the preference was higher (p<0.05) in non-smokers, intermediate expertise, sensitive vinotype, PROP tasters and sweet dislikers. This different appreciation was dependent on wine initial acidity. The sourer wine was preferred by intermediate experts, PROP tasters and sweet dislikers. The less acid wine was preferred by non-smokers, sensitive vinotype and PROP tasters. Overall, the results demonstrated the acidity appreciation was dependent on wine initial acidity together with physiological and individual preferences.
Non-genetic factors affecting milk yield, composition and somatic cell count in Hungarian Holstein cows.

The purpose of this study was to determine effects of non-genetic factors on milk yield, milk composition and somatic cell count (SCC) of dairy cows. A total of 4891 records of Hungarian Holstein cows raised in a private dairy farm in South Hungary, between 2007 and 2008 were investigated. Fat, protein and lactose were assessed as milk composition parameters.To evaluate milking cows by effective factors; three different stage of lactation (SL) (SL 1= 90d<, SL 2= 91-150d and SL 3=151 <d), five parity, four calving season (CS) and three body condition score (BCS) groups (groupl =<3 points; group2=3-3.50 points and group3=>3.50 points) were designed. While fat, protein and lactose decreased, daily milk yield (DMY), 305 daily milk yield (305 DMY) and SCC increased with advanced parity. Fat, protein and SCC increased, but lactose and DMY tended to drop with later SL and BCS. These parameters were highest in cows calved in winter-autumn, summer, winter-spring and winter-autumn, respectively. DMY negatively correlated with investigated parameters except for lactose and 305 DMY. The study revealed that non-genetic factors are associated with milk composition, yield and SCC of milk. Therefore, it is suggested that these factors should primarily be considered to obtain more quality and quantity milk from dairy cows.
Chemical speciation distribution characteristics and ecological risk assessment of heavy metals in soil from Sunan mining area, Anhui Province, China

ABSTRACT In this study, the content characteristics, comprehensive pollution assessment, and morphological distribution characteristics of heavy metals (Mn, Cd, Cr, Pb, Ni, Zn, and Cu) were researched based on the processes of field investigation, sample collection, and experimental analysis. Results showed that the mean concentrations of Mn, Pb, Cr, Cu, Cd, Zn, and Ni in surface soils were 522.77, 22.56, 55.10, 25.41, 0.25, 57.02, and 48.47 mg kg−1, respectively. The surface soil from Sunan mining area was contaminated by Cu, Cd, and Ni in different degrees, and high CV values of Cd, Zn, Pb, and Ni were influenced by local human activities possibly. The evaluation results suggested that the mean Igeo values were in the sequence of Cd (0.657) > Ni (0.052) > Cu (−0.293) > Mn (−0.626) > Zn (−0.761) > Cr (−0.884) > Pb (−0.899). Besides, Cd was the most significant potential risk factor among all elements. Nevertheless, the Cd of bioavailable speciations with higher proportion had stronger migration and toxicity, and was more easier to be absorbed and enriched than other elements by some crops (e.g., vegetables, rice), and being at a relatively higher potential ecological risk in soil.
Aspartate: 2-oxoglutarate aminotransferase from Trichomonas vaginalis Identity ofaspartate aminotransferase andaromatic aminoacidaminotransferase

1.Aspartate: 2-oxoglutarate aminotransferase fromtheanaerobic protozoon Trichomonas vaginalis was purified tohomogeneity andcharacterized. Itisadimeric protein ofoverall Mrapprox. 100000. Onlya single isoenzyme wasfound inT.vaginalis. Theoverall molecular andcatalytic properties havefeatures in commonwithboththevertebrate cytoplasmic andmitochondrial isoenzymes. 2.Thepurified aspartate aminotransferase fromT.vaginalis showed veryhighrates ofactivity witharomatic aminoacids asdonors and2-oxoglutarate asacceptor. Thisbroad-spectrum activity wasrestricted toaromatic aminoacids and aromatic 2-oxoacids, andnosignificant activity wasseenwithother commonaminoacids, other thanwith thesubstrates andproducts oftheaspartate:2-oxoglutarate aminotransferase reaction. 3.Co-purification andco-inhibition, bytheirreversible inhibitor gostatin, ofthearomatic aminoacidaminotransferase and aspartate aminotransferase activities, inconjunction withcompetitive substrate experiments, strongly suggest that asingle enzyme isresponsible forbothactivities. Suchhigh rates ofaromatic aminoacid aminotransferase activity havenotbeenreported before ineukaryotic aspartate aminotransferase.