Genomic data for 78 chickens from 14 populations

Background: Since the domestication of the red jungle fowls (Gallus gallus; dating back to~10 000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production, and skin color. Population genomic variations through diversifying selection have not been fully investigated. Findings: The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of five wild red jungle fowls and eight Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ~21.30 gigabases (Gb) of high-quality data from each individual to the reference chicken genome, we identified ~6.44 million (M) single nucleotide polymorphisms (SNPs) for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries. Conclusions: The current data is important for population genetics and further studies in chickens and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chickens.Peer reviewedAnimal Scienc

Design of a Micromachined Z-axis Tunneling Magnetoresistive Accelerometer with Electrostatic Force Feedback

This paper presents the design, simulation, fabrication and experiments of a micromachined z-axis tunneling magnetoresistive accelerometer with electrostatic force feedback. The tunneling magnetoresistive accelerometer consists of two upper differential tunneling magnetoresistive sensors, a middle plane main structure with permanent magnetic films and lower electrostatic feedback electrodes. A pair of lever-driven differential proof masses in the middle plane main structure is used for sensitiveness to acceleration and closed-loop feedback control. The tunneling magnetoresistive effect with high sensitivity is adopted to measure magnetic field variation caused by input acceleration. The structural mode and mass ratio between inner and outer proof masses are optimized by the Ansys simulation. Simultaneously, the magnetic field characteristic simulation is implemented to analyze the effect of the location of tunneling magnetoresistive sensors, magnetic field intensity, and the dimension of permanent magnetic film on magnetic field sensitivity, which is beneficial for the achievement of maximum sensitivity. The micromachined z-axis tunneling magnetoresistive accelerometer fabricated by the standard deep dry silicon on glass (DDSOG) process has a device dimension of 6400 μm (length) × 6400 μm (width) × 120 μm (height). The experimental results demonstrate the prototype has a maximal sensitivity of 8.85 mV/g along the z-axis sensitive direction under the gap of 1 mm. Simultaneously, Allan variance analysis illustrate that a noise floor of 86.2 μg/Hz0.5 is implemented in the z-axis tunneling magnetoresistive accelerometer

Analysis of Morphological Variability, Correlation and Principal Component in a Cultivated Population of an Important Medicinal Plant, Atractylodes macrocephala Koidz. (Asteraceae)

Abstract: Although Atractylodes macrocephala is an important economically medicinal plant with a centuries' cultivation history, our understanding of its morphological variation remains rudimentary. Here, in order to generate information on character association, and influence of characters on rhizome yield of cultivated Atractylodes macrocephala, variability, correlation and principal component analysis for 21 morphological characters were studied on 100 morphologically distinct accessions of this medicinal crop. The significant and positive correlation for dry rhizome yield per plant was observed with the largest diameter, number of buds, number of branches and shape of the rhizome, and closely followed by primary branches per plant, plant height, plant crown, and apical lobule length and width of the largest lower leaf. Factor analysis was also used for defining of the determinant factors and the characters constituted in each factor. In Principal component analysis (PCA), the first four main and independent factors could explain 65.75% of the total variation related to main effective characters. Additionally, the results grouped the accessions into two clusters based the scatter plot of principal component analysis defined by the first two axes, which separated accessions with more than two-branched rhizome from other accessions. This characterization on the basis of morphological analysis will help in identification of economically useful accessions for further germplasm conservation programmes and crop improvement

Dietary Methionine Increased the Growth Performances and Immune Function of Partridge Shank Broilers after Challenged with Coccidia

The present study investigated the effects of methionine (Met) on growth, immune function, and antioxidant capacity in partridge shank broilers, which were treated with either an anticoccidial drug or a coccidia vaccine. Chickens were fed five graded levels of Met (0.33%, 0.39%, 0.45%, 0.51%, or 0.57%) for 21 days in combination with the drug or vaccine. The results revealed that an optimal level of Met supplementation (1) increased ADFI (average daily feed intake), ADG (average daily gain), and F/G values (feed-to-gain ratio), indicating improved production; (2) increased OPG levels (oocysts per gram feces), intestinal lesion scores, bursa of Fabricius and thymus indexes, and sIgA content; (3) improved GSH-Px activities, and increased content levels of T-protein, albumin, and urea nitrogen. In addition, birds in the anticoccidial drug group had higher final weights, higher ADFI and ADG values, as well as lower F/G values, compared with birds in the vaccine group, indicating that coccidia vaccine reduces the performance of broilers. In conclusion, we found that an optimal level of dietary Met improved the production of partridge shank broilers, and this result might be related to immune function and antioxidant capacity. Optimal levels of digestible Met in terms of production performance (ADG and F/G) and immune function (sIgA in ileum mucosa) in partridge shank broilers (1–21 days) were found to be 0.418, 0.451, and 0.451 of diet, respectively, when birds were given anticoccidial drug treatment, with corresponding figures of 0.444, 0.455, and 0.452% when the coccidia vaccine was administered

The comparison of blood characteristics in low- and high-altitude chickens

Tibetan chicken (TC) is a unique chicken breed that has inhabited the Tibetan Plateau for thousands of years and has adapted to the harsh environment of an altitude of over greater than 4000 m. The changes in blood characteristics that occur in high-altitude rearing of TCs are unknown. To obtain a deeper insight into the blood characteristics of chickens in low and high altitudes, we focussed on four chicken populations to compare the variations among them. In the present study, we found significant differences in white blood cell (WBC) count, red blood cell (RBC) count and haematocrit (HCT) values between TCs and other chicken populations. When TCs were reared at low altitude, there was a significant (p < .05) decrease in the WBC, RBC and HCT values compared with the TCs reared at high altitude; however, whether the mean corpuscular volume (MCV) value is related to oxygen transport and hypoxia adaptation requires further study. It is likely that haemoglobin (HGB), mean corpuscular haemoglobin (MCH) and MCH concentration (MCHC) values are decrease at high-altitude hypoxic environments. Therefore, the increase in WBC, RBC and HCT values may be the common haematological mechanism for TCs to adapt to high-altitude hypoxia. These research results provide the scientific basis and theory to explain how TCs are able to adapt to high-altitude hypoxia

Direct Generation of Human Neuronal Cells from Adult Astrocytes by Small Molecules

Astrocytes, due to the proximity to neuronal lineage and capability to proliferate, are ideal starting cells to regenerate neurons. Human fetal astrocytes have been successfully converted into neuronal cells by small molecules, which offered a broader range of further applications than transcription factor-mediated neuronal reprogramming. Here we report that human adult astrocytes could also be converted into neuronal cells by a different set of small molecules. These induced cells exhibited typical neuronal morphologies, expressed neuronal markers, and displayed neuronal electrophysiological properties. Genome-wide RNA-sequencing analysis showed that the global gene expression profile of induced neuronal cells resembled that of human embryonic stem cell-differentiated neurons. When transplanted into post-natal mouse brains, these induced neuronal cells could survive and become electrophysiologically mature. Altogether, our study provides a strategy to directly generate transgene-free neuronal cells from human adult astrocytes by small molecules