The Hoof Color of Australian White Sheep Is Associated with Genetic Variation of the MITF Gene.

Studying the characteristics of mammalian hoof colors is important for genetic improvements in animals. A deeper black hoof color is the standard for breeding purebred Australian White (AUW) sheep and this phenotype could be used as a phenotypic marker of purebred animals. We conducted a genome-wide association study (GWAS) analysis using restriction site associated DNA sequencing (RAD-seq) data from 577 Australian White sheep (black hoof color = 283, grey hoof color = 106, amber hoof color = 186) and performed association analysis utilizing the mixed linear model in EMMAX. The results of GWAS demonstrated that a specific single-nucleotide polymorphism (SNP; g. 33097911G>A) in intron 14 of the microphthalmia-associated transcription factor (MITF) gene was significantly associated with the hoof color in AUW sheep (p = 9.40 × 10-36). The MITF gene plays a key role in the development, differentiation, and functional regulation of melanocytes. Furthermore, the association between this locus and hoof color was validated in a cohort of 212 individuals (black hoof color = 122, grey hoof color = 38, amber hoof color = 52). The results indicated that the hoof color of AUW sheep with GG, AG, and AA genotypes tended to be black, grey, and amber, respectively. This study provided novel insights into hoof color genetics in AUW sheep, enhancing our comprehension of the genetic mechanisms underlying the diverse range of hoof colors. Our results agree with previous studies and provide molecular markers for marker-assisted selection for hoof color in sheep.

Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits.

The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.

Study on the Association between LRRC8B Gene InDel and Sheep Body Conformation Traits.

Marker-assisted selection is an important method for livestock breeding. In recent years, this technology has been gradually applied to livestock breeding to improve the body conformation traits. In this study, the LRRC8B (Leucine Rich Repeat Containing 8 VRAC Subunit B) gene was selected to evaluate the association between its genetic variations and the body conformation traits in two native sheep breeds in China. Four body conformation traits, including withers height, body length, chest circumference, and body weight, were collected from 269 Chaka sheep. We also collected the body length, chest width, withers height, chest depth, chest circumference, cannon bone circumference, and height at hip cross of 149 Small-Tailed Han sheep. Two different genotypes, ID and DD, were detected in all sheep. Our data showed that the polymorphism of the LRRC8B gene was significantly associated with chest depth (p < 0.05) in Small-Tailed Han sheep, and it is greater in sheep with DD than those with ID. In conclusion, our data suggested that the LRRC8B gene could serve as a candidate gene for marker-assisted selection in Small-Tailed Han sheep.

Short variation of the sheep PDGFD gene is correlated with litter size.

Platelet-derived growth factor (PDGF) family, exert plays a key role in embryonic development, cell proliferation, cell migration, angiogenesis and reproduction. Related studies about GWAS analyses have found that PDGFD significantly affected deposition of tail fat in sheep, but there are no studies on reproduction in animals. In this study, three breed of sheep were used to find insertion/deletion (indel) fragment polymorphism of PDGFD which including Australian white (AUW) sheep (Meat type, n = 932), Guiqian semi-fine wool (GSFW) sheep (wool type, n = 60) and East Friensian milk (EFM) sheep (dairy type, n = 60). Only a 18-bp variation was polymorphic in the study AUW sheep population and the genotypes of different sheep breed are also specific. Moreover, the association analysis indicated that this variant was associated with litter size of AUW sheep in the first parity (p < 0.05). The litter size of II genotype was significantly lower than other genotypes in the first parity (p < 0.05). We also revealed that the PDGFD gene was relatively conservative in eight species, PDGFD mRNA expression in 832 sheep samples implying this gene was related to reproduction traits. Hence, these finding demonstrated the one-cause multipotency of PDGFD gene. Collectively, these results suggest that this indel can be used as an effective marker for sheep breeding.

Newly reported 90-bp deletion within the ovine BMPRIB gene: Does it widely distribute, link to the famous FecB (p.Q249R) mutation, and affect litter size?

The study of the BMPRIB gene polymorphisms has become of great importance in sheep, because it provides critical genetic tools to improve reproductive efficiency in ewes. The purposes of this study were: to assess the genetic diversity of the 90-bp deletion polymorphism within the BMPRIB gene in 52 various sheep breeds; to examine its linkage to the p.Q249R variant in the same gene, as well as to analyze its association with litter size. Herein, a total of 2313 various sheep individuals were used to detect the presence of the 90-bp deletion, among them the six breeds (Australian White (AUW), Small-Tail Han (STH), Guiqian semi-fine wool (GQSFW) sheep, etc.) were genotyped using PCR-based genotyping technology (n = 1636), and 47 breeds worldwide (including STH sheep) were genotyped via whole genome sequencing (WGS) method (n = 677). Genotyping outcomes revealed that the polymorphism was segregated in 45 of 52 breeds with varying frequencies (0.05-0.93). It is pertinent to note that the 90-bp deletion is not linked to the famous p.Q249R SNP in population of interest, except in high prolific Hu sheep. The association analysis indicated that the Del-90-bp variant showed no significant association (P > 0.05) with litter size in AUW (n = 625), GQSFW (n = 75) and STH (n = 38) ewes. Nevertheless, further investigation is needed on the importance of the Del-90-bp variant as a DNA marker that could possibly serve as an additional selection criterion in breeding ewes with high productivity.

Novel InDel variations of the Cry2 gene are associated with litter size in Australian White sheep.

Cryptochrome 2 (Cry2) gene regulates circadian rhythm and affects reproduction and pregnancy. Therefore, this study aimed to explore polymorphisms of the Cry2 gene and their associations with litter size at different parity in Australian White (AuW) ewes. Five putative insertion or deletion mutations within the Cry2 gene were selected to study their association with litter size. Two novel deletion mutations were identified in intronic region of Cry2 gene and were genotyped by agarose gel electrophoresis and DNA sequencing. The polymorphism information content (PIC) indicated that both mutations were low polymorphism in tested groups. Statistical analysis revealed that the P1-Del-6-bp was significantly correlated with litter size at third parity (P = 0.010), in which individuals with insertion/deletion (ID) genotype had larger litter size than insertion/insertion (II) genotype (P < 0.05). Whereas, the P2-Del-6-bp was significantly correlated with litter size at first parity (P = 0.036), in which individuals with insertion/insertion (II) genotype had larger litter size than insertion/deletion (ID) genotype (P < 0.05). Collectively, these findings may provide new insights to expedite molecular breeding in sheep through marker-assisted selection strategies (MAS).

Fourier transform infrared spectroscopy and chemometrics for the discrimination of paper relic types.

The paper relic identification is a pending issue to be resolved in the field of cultural heritage. As we all known, heritage paper has significant importance in archaeological research. Nowadays, there are a variety of research methodologies focuses on the analysis of inks for dating documents. While the paper analysis attained little attention. This work is to explore the non-destructive application of ATR-FTIR technique in discrimination of paper relics. 15 types of paper spectra were collected by ATR-FTIR, which wavenumber range were range from 4000 to 650 cm-1. And the moving average smoothing and normalization was used for pretreatment analysis. Five different classification algorithms, principal component analysis-linear discriminant analysis (PCA-LDA), partial least squares discriminant analysis (PLS-DA), soft independent modeling of class analogy (SIMCA), least squares-support vector machine (LS-SVM), partial least squares-linear discriminant analysis (PLS-LDA) were selected to classify the types of paper. PLS-LDA and LS-SVM are effective techniques with 100% classification accuracy. PCA-LDA, PLS-DA and SIMCA give accuracy of 98.67%, 97.33% and 95.56%, respectively. The present experiment suggested that ATR-FTIR combining with chemometrics will be highly useful in paper identification of cultural heritage.

Let's Play Cards: Multi-Component Cognitive Training With Social Engagement Enhances Executive Control in Older Adults.

Cognitive training and social engagement are two of the routes that potentially improve cognitive functions in older adults. The former targets specific functions so that an intervention can trigger the plasticity and efficiency of the underpinning neural systems, and the latter also provides an environment supportive of social and emotional needs. We investigated whether an integration of the two routes could enhance cognitive functions related to executive control, because no prior research has adopted a theory-driven approach to design a group-based cognitive training program for executive control. Forty-six healthy and active older adults living in community settings were randomly assigned to a group-based training program or a group-based active control program. Twenty-three volunteers in a community center were recruited for the waitlist control group. A battery of card games was designed for the cognitive training program based on three theoretical models of executive functions. A set of commercial board games were run in the active control program. Using untrained tests as the outcome measures, we found significant improvement on executive control in the cognitive training group compared with the active and waitlist control groups while the two control groups did not differ in performance. The cognitive training group did not outperform the two groups on a test of reasoning or on a test of delayed episodic memory. The results support the idea that cognitive training with social interaction can improve performance on untrained tests that share overlapping cognitive processes. Despite the inability to adapt to each person's performance, integrating the two routes is beneficial for improving cognitive functions in older adults.

Towards improvement in prediction of iodine value in edible oil system based on chemometric analysis of portable vibrational spectroscopic data.

Iodine value (IV) is a significant parameter to illustrate the quality of edible oil. In this study, three portable spectroscopy devices were employed to determine IV in mixed edible oil system, a new Micro-Electro-Mechanical-System (MEMS) Fourier Transform Infrared Spectrometer (MEMS-FTIR), a MicroNIRTM1700 and an i-Raman Plus-785S. Quantitative model was built by Partial least squares (PLS) regression model and four variable selection methods were applied before PLS model, which are Monte Carlo uninformative variables elimination (MCUVE), competitive reweighted sampling (CARS), bootstrapping soft shrinkage approach (BOSS) and variable combination population analysis (VCPA). The coefficient of determination (R2), and the root mean square error prediction (RMSEP) were used as indicators for the predictability of the PLS models. In MicroNIRTM1700 dataset, MCUVE gave the lowest RMSEP (2.3440), in MEMS-FTIR dataset, CARS showed the best performance with RMSEP (2.2185), in i-Raman Plus-785S dataset, BOSS gave the lowest RMSEP (2.5058). They all had great improvements than full spectrum PLS model. Four variable selection methods take a smaller number of variables and perform significant superiority in prediction accuracy. It was demonstrated that three new portable instruments would be suitable for the on-site determination of edible oil quality in infrared and Raman field.

Mutation p.Leu128Pro in the 1A domain of K16 causes pachyonychia congenita with focal palmoplantar keratoderma in a Chinese family.

UNLABELLED: Pachyonychia congenita (PC), a rare autosomal dominant disorder characterized by hypertrophic nail dystrophy, is classified into two main clinical subtypes: PC-1 and PC-2. PC-1 is associated with mutations in the KRT6A or KRT16 genes, whereas PC-2 is linked to KRT6B or KRT17 mutations. Blood samples were collected from three generations of a new Chinese PC-1 family, including three PC patients and five unaffected family members. A novel missense mutation p.Leu128Pro (c.383T>C) was identified in a highly conserved helix motif in domain 1A of K16. The disease haplotype carried the mutation and cosegregated with the affection status. PolyPhen2 and SIFTS analysis rated the substitution as probably damaging; Swiss-Model analysis indicated that the structure of the mutant protein contained an unnormal α-helix. Overexpression of mutant protein in cultured cells led to abnormal cell morphology. CONCLUSION: The wider spectrum of KRT16 mutations suggests that changes in codons 125, 127, and 132 are most commonly responsible for PC-1 and that proline substitution mutations at codons 127 or 128 may produce more severe disease. This study extends the KRT16 mutation spectrum and adds new information on the clinical and genetic diversity of PC.

Long-term stability of the SGA-WZ strapdown airborne gravimeter.

Accelerometers are one of the most important sensors in a strapdown airborne gravimeter. The accelerometer's drift determines the long-term accuracy of the strapdown inertial navigation system (SINS), which is the primary and most critical component of the strapdown airborne gravimeter. A long-term stability test lasting 104 days was conducted to determine the characteristics of the strapdown airborne gravimeter's long-term drift. This stability test was based on the first set of strapdown airborne gravimeters built in China, the SGA-WZ. The test results reveal a quadratic drift in the strapdown airborne gravimeter data. A drift model was developed using the static data in the two end sections, and then this model was used to correct the test data. After compensating for the drift, the drift effect improved from 70 mGal to 3.46 mGal with a standard deviation of 0.63 mGal. The quadratic curve better reflects the drift's real characteristics. In comparison with other methodologies, modelling the drift as a quadratic curve was shown to be more appropriate. Furthermore, this method allows the drift to be adjusted throughout the course of the entire campaign.

SGA-WZ: a new strapdown airborne gravimeter.

Inertial navigation systems and gravimeters are now routinely used to map the regional gravitational quantities from an aircraft with mGal accuracy and a spatial resolution of a few kilometers. However, airborne gravimeter of this kind is limited by the inaccuracy of the inertial sensor performance, the integrated navigation technique and the kinematic acceleration determination. As the GPS technique developed, the vehicle acceleration determination is no longer the limiting factor in airborne gravity due to the cancellation of the common mode acceleration in differential mode. A new airborne gravimeter taking full advantage of the inertial navigation system is described with improved mechanical design, high precision time synchronization, better thermal control and optimized sensor modeling. Apart from the general usage, the Global Positioning System (GPS) after differentiation is integrated to the inertial navigation system which provides not only more precise altitude information along with the navigation aiding, but also an effective way to calculate the vehicle acceleration. Design description and test results on the performance of the gyroscopes and accelerations will be emphasized. Analysis and discussion of the airborne field test results are also given.

Why does a red snake in the grass capture your attention?

It has been suggested that affective stimuli automatically capture attention; this preferential processing is thought to be related to the evolutionary significance of affective stimuli. However, recent evidence suggests that perceptual salience alone might explain why some affective stimuli are more likely to influence attentional processes in certain contexts. In this study, we manipulated affective and perceptual salience to better understand how affective information is processed and how it impacts attentional processes in different contexts. We used stimuli that are both affectively and perceptually salient, while varying the task requirement to encourage the processing of perceptually salient (Experiment 1) or affectively salient (Experiment 2) information. This design made it possible to observe independent and interdependent relationships between perceptual and affective salience. The results showed that when the task encouraged the processing of perceptually salient information, affective salience did not influence task performance. In contrast, when the task encouraged the processing of affectively salient information, affectively salient information impaired task performance. The findings suggest that the affective nature of the stimuli does not always influence attentional processes.

Affective learning enhances activity and functional connectivity in early visual cortex.

This study examined the impact of task-irrelevant affective information on early visual processing regions V1-V4. Fearful and neutral faces presented with rings of different colors were used as stimuli. During the conditioning phase, fearful faces presented with a certain ring color (e.g., black) were paired with mild electrical stimulation. Neutral faces shown with rings of that color, as well as fearful or neutral faces shown with another ring color (e.g., white), were never paired with shock. Our findings revealed that fearful faces evoked enhanced blood oxygen level dependent (BOLD) responses in V1 and V4 compared to neutral faces. Faces embedded in a color ring that was paired with shock (e.g., black) evoked greater BOLD responses in V1-V4 compared to a ring color that was never paired with shock (e.g., white). Finally, BOLD responses in early visual cortex were tightly interrelated (i.e., correlated) during an affectively potent context (i.e., ring color) but not during a neutral one, suggesting that increased functional integration was present with affective learning. Taken together, the results suggest that task-irrelevant affective information not only influences evoked responses in early, retinotopically organized visual cortex, but also determines the pattern of responses across early visual cortex.

The set switching function of nonclinical dissociators under negative emotion.

Rapid switching may underlie the disruption of some integrated thought processes that characterize dissociation in both nonclinical and clinical populations. We investigated the set switching function under negative emotion with three groups of nonclinical participants that had different degrees of dissociation proneness. In the experiment, participants judged whether the digit in a predefined target color was odd or even on the preswitch trials. In a perseverance condition, participants were required to switch to a new target color while the previous target color became the distractor color. In a learned irrelevance condition, the previously ignored color became the new target color. The results showed that the three groups did not differ in focusing attention in the preswitch trials, for set switching in the baseline condition (in which emotion was not engaged), or for switching in the learned irrelevance condition under negative emotion. However, high dissociators under negative emotion showed faster switching in the perseverance condition. This enhanced ability to divert attention to a new mental set under negative emotion may be a coping strategy related to cognitive symptoms in dissociative disorders.

Attentional capture by emotional stimuli is modulated by semantic processing.

The attentional blink paradigm was used to examine whether emotional stimuli always capture attention. The processing requirement for emotional stimuli in a rapid sequential visual presentation stream was manipulated to investigate the circumstances under which emotional distractors capture attention, as reflected in an enhanced attentional blink effect. Emotional distractors did not cause more interference than neutral distractors on target identification when perceptual or phonological processing of stimuli was required, showing that emotional processing is not as automatic as previously hypothesized. Only when semantic processing of stimuli was required did emotional distractors capture more attention than neutral distractors and increase attentional blink magnitude. Combining the results from 5 experiments, the authors conclude that semantic processing can modulate the attentional capture effect of emotional stimuli.