Screening of candidate genes related to differences in growth and development between Chinese indigenous and Western pig breeds.

Neijiang (NJ) and Yacha (YC) are two indigenous pig breeds in the Sichuan basin of China, displaying higher resistance to diseases, lower lean ratio, and slower growth rate than the commercial Western pig breed Yorkshire (YS). The molecular mechanisms underlying the differences in growth and development between these pig breeds are still unknown. In the present study, five pigs from NJ, YC, and YS breeds were subjected to the whole genome resequencing, and then the differential single-nucleotide polymorphisms (SNPs) were screened using a 10-kb window sliding in 1-kb step using the Fst method. Finally, 48,924, 48,543, and 46,228 nonsynonymous single-nucleotide polymorphism loci (nsSNPs) were identified between NJ and YS, NJ and YC, and YC and YS, which highly or moderately affected 2,490, 800, and 444 genes, respectively. Moreover, three nsSNPs were detected in the genes of acetyl-CoA acetyltransferase 1 (ACAT1) insulin-like growth factor 2 receptor (IGF2R), insulin-like growth factor 2 and mRNA-binding protein 3 (IGF2BP3), which potentially affected the transformation of acetyl-CoA to acetoacetyl-CoA and the normal functions of the insulin signaling pathways. Moreover, serous determinations revealed significantly lower acetyl-CoA content in YC than in YS, supporting that ACAT1 might be a reason explaining the differences in growth and development between YC and YS breeds. Contents of phosphatidylcholine (PC) and phosphatidic acid (PA) significantly differed between the pig breeds, suggesting that glycerophospholipid metabolism might be another reason for the differences between Chinese and Western pig breeds. Overall, these results might contribute basic information to understand the genetic differences determining the phenotypical traits in pigs.

Lidar attenuation coefficient in the global oceans: insights from ICESat-2 mission.

The attenuation coefficient of natural waters plays a significant role in our understanding of hydrology from both the oceanographic and biological point of view. The advent of near-continuous observations by sophisticated space-based lidars now offers an unprecedented opportunity to characterize attenuation coefficients over open oceans on global and regional scales. At present, however, literature reports of lidar-derived attenuation coefficient estimates (klidar, m-1) in oceanic waters are very limited. In this study, we present a global survey of klidar derived from ATLAS/ICESat-2 nighttime measurements. Our results augment the existing passive sensor ocean color data set with a new diurnal component and extend the record to now include previously unavailable polar nighttime observations. The values of ATLAS measured klidar at 532 nm are between 0.045 and 0.39 m-1 with the higher values (>0.15 m-1) correlated with coastal waters and sea ice covered oceans. The average klidar in clearest oligotrophic ocean gyres is ∼0.058 ± 0.012 m-1 at 532 nm. The results reported here demonstrate the feasibility of using ATLAS/ICESat-2 lidar measurements for global klidar studies, which will in turn provide critical insights that enable climate models to correctly describe the amount of light present under sea ice, and for heat deposition studies in the upper ocean.

Nearshore bathymetry and seafloor property studies from Space lidars: CALIPSO and ICESat-2.

In shallow nearshore waters, seafloor heights and properties can be accurately measured by the current generation of space-based elastic backscatter lidars: CALIOP, flying aboard the CALIPSO satellite and ATLAS aboard ICESat-2. CALIOP's 532 nm volume depolarization ratios, together with the ratios of the attenuated backscatter coefficients measured at 532 nm and 1064 nm, can efficiently distinguish optically shallow waters from nearby land surfaces and deep oceans. ATLAS's high vertical resolution photon measurements can accurately determine seafloor depths in shallow water bodies, characterize seafloor reflectance, and provide assessments of ocean biomass concentrations in the intervening water column. By adding bathymetry, seafloor optical properties (e.g., reflectance, depolarization ratio and attenuated backscatter), and nighttime observations, space lidar measurements obtained in nearshore waters can provide a wealth of unique information to complement existing satellite-based ocean color remote sensing capabilities. The results reported here demonstrate the feasibility of using satellite lidars for nearshore seafloor ecosystem analyses, which in turn provide critical insights for studies of coastal navigation and seabed topography changes due to disasters, as well as the temporal and spatial morphological evolution of coastal systems.

Temporal microRNA expression profile of pig peripheral blood during postnatal development.

Gene expression profiles of blood can reflect the physiopathologic status of the immune system. The dynamic microRNA (miRNA) expression profiles of peripheral blood from pigs at different developmental stages, and how differential expression of miRNAs might relate to immune system development, are unknown. In this study, peripheral blood samples taken at five developmental stages were used to construct 15 miRNA libraries (three biological replicates/stage): 0 days (newborn), 30 days (weaning), 60 days (weaned), and 180 and 360 days (puberty). We identified 295 known mature miRNAs. Hierarchical clustering of the miRNA expression profile showed significant differences between individuals at the neonatal and postnatal stages. Functional enrichment analysis revealed that miRNAs differentially expressed between pairwise comparisons of the developmental stages were over-represented in immune-related pathways such as toll-like receptor signaling. The time-course of expression of the over-representated miRNAs exhibited a pattern of steady decline over time, for both the complete miRNA compendium and immune-related miRNAs. We identified six marker miRNAs that were highly negatively correlated with chronologic age and enriched for genes involved in immune-related pathways. This study of a peripheral blood miRNA transcriptome offers insight into immune system development in swine and provides a resource for pig genome annotation.

Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development.

OBJECTIVE: We investigated the temporal expression profiles of long noncoding RNA (lncRNA) and mRNA in the peripheral blood of pigs during development and identified the lncRNAs that are related to the blood-based immune system. METHODS: Peripheral blood samples were obtained from the pigs at 0, 7, 28, and 180 days and 2 years of age. RNA sequencing was performed to survey the lncRNA and mRNA transcriptomes in the samples. Short time-series expression miner (STEM) was used to show temporal expression patterns in the mRNAs and lncRNAs. Gene ontology and Kyoto encyclopedia of genes and genomes analyses were performed to assess the genes' biological relevance. To predict the functions of the identified lncRNAs, we extracted mRNAs that were nearby loci and highly correlated with the lncRNAs. RESULTS: In total of 5,946 lncRNA and 12,354 mRNA transcripts were identified among the samples. STEM showed that most lncRNAs and mRNAs had similar temporal expression patterns during development, indicating the expressional correlation and functional relatedness between them. The five stages were divided into two classes: the suckling period and the late developmental stage. Most genes were expressed at low level during the suckling period, but at higher level during the late stages. Expression of several T-cell-related genes increased continuously during the suckling period, indicating that these genes are crucial for establishing the adaptive immune system in piglets at this stage. Notably, lncRNA TCONS-00086451may promote blood-based immune system development by upregulating nuclear factor of activated T-cells cytoplasmic 2 expression. CONCLUSION: This study provides a catalog of porcine peripheral blood-related lncRNAs and mRNAs and reveals the characteristics and temporal expression profiles of these lncRNAs and mRNAs during peripheral blood development from the newborn to adult stages in pigs.

Remote Sensing of Daytime Water Leaving Reflectances of Oceans and Large Inland Lakes from EPIC onboard the DSCOVR Spacecraft at Lagrange-1 Point.

The NASA's Earth Polychromatic Imaging Camera (EPIC) on board the Deep Space Climate Observatory (DSCOVR) satellite has been making multiple observations of the entire sunlit Earth in a given day from the Sun-Earth Largangian L1 point since the summer of 2015. EPIC contains 10 narrow channels in the 317⁻780 nm solar spectral range. The data acquired with EPIC have already been used in a variety of scientific investigations, including the study of the global ozone levels, aerosol index and aerosol optical depth, UV reflectivity of clouds over land and ocean, cloud height over land and ocean, and vegetation indices. In this article, we report that EPIC data, particularly for the data measured with narrow channels centered near 443, 551, and 680 nm, can also have important applications in remote sensing of ocean color in different geographical regions. We have modified a version of a multi-channel atmospheric correction algorithm for Moderate Resolution Imaging SpectroRadiometer (MODIS) ocean color applications and adapted the algorithm for processing EPIC data. We present three case studies on water leaving reflectance retrievals from EPIC data acquired over a large turbid river, inland lakes, and oceans. We conclude that a future ocean color instrument on board a satellite at the L1 point, which provides continuous view of the full sunlit disk of the Earth, will complement and extend ocean color observations with the low Earth observing polar orbital and geostationary satellite instruments in both the spatial and time domains.

Passive remote sensing of altitude and optical depth of dust plumes using the oxygen A and B bands: first results from EPIC/DSCOVR at Lagrange-1 point.

We presented an algorithm for inferring aerosol layer height (ALH) and optical depth (AOD) over ocean surface from radiances in oxygen A and B bands measured by the Earth Polychromatic Imaging Camera (EPIC) on the Deep Space Climate Observatory orbiting at Lagrangian-1 point. The algorithm was applied to EPIC imagery of a two-day dust outbreak over the North Atlantic Ocean. Retrieved ALHs and AODs were evaluated against counterparts observed by Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), Moderate Resolution Imaging Spectroradiometer (MODIS), and Aerosol Robotic Network. The comparisons showed 71.5% of EPIC-retrieved ALHs were within ±0.5 km of those determined from CALIOP and 74.4% of EPIC AOD retrievals fell within a ±(0.1+10%) envelope of MODIS retrievals. This study demonstrates the potential of EPIC measurements for retrieving global aerosol height multiple times daily, which are essential for evaluating aerosol profile simulated in climate models and for better estimating aerosol radiative effects.

Snow Grain Size Retrieval over the Polar Ice Sheets with the Ice, Cloud, and land Elevation Satellite (ICESat) Observations.

Snow grain size is an important parameter for cryosphere studies. As a proof of concept, this paper presents an approach to retrieve this parameter over Greenland, East and West Antarctica ice sheets from surface reflectances observed with the Geoscience Laser Altimeter System (GLAS) onboard the Ice, Cloud, and land Elevation Satellite (ICESat) at 1064 nm. Spaceborne lidar observations overcome many of the disadvantages in passive remote sensing, including difficulties in cloud screening and low sun angle limitations; hence tend to provide more accurate and stable retrievals. Results from the GLAS L2A campaign, which began on 25 September and lasted until 19 November, 2003, show that the mode of the grain size distribution over Greenland is the largest (~300 µm) among the three, West Antarctica is the second (~220 µm) and East Antarctica is the smallest (~190 µm). Snow grain sizes are larger over the coastal regions compared to inland the ice sheets. These results are consistent with previous studies. Applying the broadband snow surface albedo parameterization scheme developed by Garder and Sharp (2010) to the retrieved snow grain size, ice sheet surface albedo is also derived. In the future, more accurate retrievals can be achieved with multiple wavelengths lidar observations.

Effects of intrauterine growth retardation and postnatal high-fat diet on hepatic inflammatory response in pigs.

The objective of this study was to investigate the glucose and insulin response of pigs with intrauterine growth retardation (IUGR) to a high-fat (HF) feeding regimen and to observe the underlying toll-like receptor-4 (TLR4) signalling pathway. Weaned piglets with IUGR or normal birthweight (NBW) (n = 20 each) received during the whole fattening period control diets (0% lard) or HF diets (HF, 10% lard). At about 110 kg body weight, pigs were euthanised to collect hepatic samples. Compared with NBW pigs, IUGR pigs had lower daily gain and feed intake. Growth rate of pigs was increased by HF feeding. Pigs fed HF diets had lower peak concentrations of glucose and insulin, which decreased more slowly than in pigs that received the control diets. The mRNA expression abundances of peroxisome proliferator-activated receptor coactivator-1α (PGC-1α), TLR4, myeloid differentiation factor 88 (MyD88), tumour necrosis factor-α (TNF-α), interleukin 6 (IL-6) and IL-1 receptor antagonist (IL-1Rn) were significantly affected by HF feeding, and IL-6 and IL-1Rn mRNA expressions were up-regulated in IUGR pigs compared with NBW pigs. Western blot analysis indicated that HF feeding elevated the protein expressions of TLR4 signalling pathway, as TLR4, MyD88, IκB kinase ß and nuclear factor-κB, and insulin signalling-related proteins, as phosphorylated insulin receptor substrate-1 and phosphorylated protein kinase B. In summary, hepatic TLR4 signalling pathway and inflammatory response induced by HF feeding played an important role in the aggravated development of insulin resistance in pigs.

Comparative evaluation of the fecal microbiota of adult hybrid pigs and Tibetan pigs, and dynamic changes in the fecal microbiota of hybrid pigs.

The breed of pig can affect the diversity and composition of fecal microbiota, but there is a lack of research on the fecal microbiota of hybrid pigs. In this study, feces samples from Chuanxiang black pigs (a hybrid of Tibetan and Duroc pigs) aged 3 days (n = 24), 70 days (n = 31), 10 months (n = 13) and 2 years (n = 30) and Tibetan pigs aged 10 months (n = 14) and 2 years (n = 15) were collected and sequenced by 16S rRNA gene sequencing technology. We also measured the weight of all the tested pigs and found that the 10-month-old and two-year-old Chuanxiang black pigs weighed about three times the weight of Tibetan pigs of the same age. After comparing the genus-level microbiota composition of Tibetan pigs and Chuanxiang black pigs at 10 months and two years of age, we found that Treponema and Streptococcus were the two most abundant bacteria in Chuanxiang black pigs, while Treponema and Chirstensenellaceae_R.7_group were the two most abundant bacteria in Tibetan pigs. Prediction of microbial community function in adult Chuanxiang black pigs and Tibetan pigs showed changes in nutrient absorption, disease resistance, and coarse feeding tolerance. In addition, we also studied the changes in fecal microbiota in Chuanxiang black pigs at 3 days, 70 days, 10 months, and 2 years of age. We found that the ecologically dominant bacteria in fecal microbiota of Chuanxiang black pigs changed across developmental stages. For example, the highest relative abundance of 70-day-old Chuanxiang black pigs at the genus level was Prevotella. We identified specific microbiota with high abundance at different ages for Chuanxiang black pigs, and revealed that the potential functions of these specific microbiota were related to the dominant phenotype such as fast growth rate and strong disease resistance. Our findings help to expand the understanding of the fecal microbiota of hybrid pigs and provide a reference for future breeding and management of hybrid pigs.

Impact of Clouds and Blowing Snow on Surface and Atmospheric Boundary Layer Properties Over Dome C, Antarctica.

Clouds and blowing snow (BLSN) occur frequently over Antarctica, where it is critical to understand their feedbacks to surface and atmospheric boundary layer processes. Dome C, an elevated East Antarctic station, dominated by lengthy periods of surface longwave (LW) radiative cooling, is selected to reveal cloud and BLSN impacts within a largely stable environment. The sky condition is classified as clear, cloudy, or BLSN, using 3 years of Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations satellite data. Co-located and contemporaneous in situ observations are used to investigate the relationship of sky condition with surface and atmospheric boundary layer thermal structure, focusing on seasonal variability. Results show that increased downwelling LW radiation from clouds abate surface radiative cooling losses, contributing to warming during all seasons. An increase of 3°C in the mean surface air temperature is observed during spring, whereas, a more dramatic rise (around 10°C), due to accompanying large-scale subsidence, is observed during fall and winter in association with clouds. For all seasons, the wind speed and wind speed shear are strongest during BLSN events, and the surface-based inversion is weakened by cooling which peaks in a shallow above-surface turbulent layer. The stronger background stability during fall and winter seasons, restricts turbulence and BLSN depths generally to the lowest tens of meters. The Earth's cryosphere is among the most rapidly evolving yet least well-observed regions, and knowledge of clouds and BLSN interactions with the typical stable atmospheric boundary layer can help further understand energy and moisture exchanges.

Enabling Value Added Scientific Applications of ICESat-2 Data With Effective Removal of Afterpulses.

The Advanced Topographic Laser Altimeter System (ATLAS) aboard the Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) has been making very high resolution measurements of the Earth's surface elevation since October 2018. ATLAS uses photomultiplier tubes (PMTs) as detectors in photon counting mode, so that a single photon reflected back to the receiver triggers a detection within the ICESat-2 data acquisition system. However, one characteristic of ICESat-2 detected photons is the possible presence of afterpulses, defined as small amplitude pulses occurring after the primary signal pulse due to photon arrival. The disadvantage of these afterpulses is that they often confound the accurate measurements of low level signals following a large amplitude of signal and can degrade energy resolution and cause errors in pulse counting applications. This paper discusses and summarizes the after-pulsing effects exhibited by the ATLAS PMTs based on on-orbit measurements over different seasons and geographic regions. The potential impacts of these after-pulsing effects on altimetry and ocean subsurface retrievals are discussed.

Analyzing changes in the complexity of climate in the last four decades using MERRA-2 radiation data.

The energy balance of the Earth is controlled by the shortwave and longwave radiation emitted to space. Changes in the thermodynamic state of the system over time affect climate and are noticeable when viewing the system as a whole. In this paper, we study the changes in the complexity of climate in the last four decades using data from the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2). First, we study the complexity of the shortwave and longwave radiation fields independently using Approximate Entropy and Sample Entropy, observing that the rate of complexity change is faster for shortwave radiation. Then, we study the causality of those changes using Transfer Entropy to capture the non-linear dynamics of climate, showing that the changes are mainly driven by the variations in shortwave radiation. The observed behavior of climatic complexity could be explained by the changes in cloud amount, and we research that possibility by investigating its evolution from a complexity perspective using data from the International Satellite Cloud Climatology Project (ISCCP).

Cloud Products from the Earth Polychromatic Imaging Camera (EPIC): Algorithms and Initial Evaluation.

This paper presents the physical basis of the EPIC cloud product algorithms and an initial evaluation of their performance. Since June 2015, EPIC has been providing observations of the sunlit side of the Earth with its 10 spectral channels ranging from the UV to the near-IR. A suite of algorithms has been developed to generate the standard EPIC Level 2 Cloud Products that include cloud mask, cloud effective pressure/height, and cloud optical thickness. The EPIC cloud mask adopts the threshold method and utilizes multichannel observations and ratios as tests. Cloud effective pressure/height is derived with observations from the O2 A-band (780 nm and 764 nm), and B-band (680 nm and 688 nm) pairs. The EPIC cloud optical thickness retrieval adopts a single channel approach where the 780 nm and 680 nm channels are used for retrievals over ocean and over land, respectively. Comparison with co-located cloud retrievals from geosynchronous earth orbit (GEO) and low earth orbit (LEO) satellites shows that the EPIC cloud product algorithms are performing well and are consistent with theoretical expectations. These products are publicly available at the Atmospheric Science Data Center at the NASA Langley Research Center for climate studies and for generating other geophysical products that require cloud properties as input.

Laser pulse bidirectional reflectance from CALIPSO mission.

This paper presents an innovative retrieval method that translate the CALIOP land surface laser pulse returns into the surface bidirectional reflectance. To better analyze the surface returns, the CALIOP receiver impulse response and the downlinked samples' distribution at 30 m resolution are discussed. The saturated laser pulse returns from snow and ice surfaces are recovered based on surface tail information. The retrieved snow surface bidirectional reflectance is compared with reflectance from both CALIOP cloud cover regions and MODIS BRDF/Albedo model parameters. Besides the surface bidirectional reflectance, the column top-of-atmosphere bidirectional reflectance is calculated from the CALIOP lidar background data. It is compared with bidirectional reflectance from WFC radiance measurements. The retrieved CALIOP surface bidirectional reflectance and column top-of-atmosphere bidirectional reflectance results provide unique information to complement existing MODIS standard data products and would have valuable applications for modellers.

Earth Observations from DSCOVR/EPIC Instrument.

The NOAA Deep Space Climate Observatory (DSCOVR) spacecraft was launched on February 11, 2015, and in June 2015 achieved its orbit at the first Lagrange point or L1, 1.5 million km from Earth towards the Sun. There are two NASA Earth observing instruments onboard: the Earth Polychromatic Imaging Camera (EPIC) and the National Institute of Standards and Technology Advanced Radiometer (NISTAR). The purpose of this paper is to describe various capabilities of the DSCOVR/EPIC instrument. EPIC views the entire sunlit Earth from sunrise to sunset at the backscattering direction (scattering angles between 168.5° and 175.5°) with 10 narrowband filters: 317, 325, 340, 388, 443, 552, 680, 688, 764 and 779 nm. We discuss a number of pre-processingsteps necessary for EPIC calibration including the geolocation algorithm and the radiometric calibration for each wavelength channel in terms of EPIC counts/second for conversion to reflectance units. The principal EPIC products are total ozone O3amount, scene reflectivity, erythemal irradiance, UV aerosol properties, sulfur dioxide SO2 for volcanic eruptions, surface spectral reflectance, vegetation properties, and cloud products including cloud height. Finally, we describe the observation of horizontally oriented ice crystals in clouds and the unexpected use of the O2 B-band absorption for vegetation properties.

Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition.

Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.

Uncertainties in cloud phase and optical thickness retrievals from the Earth Polychromatic Imaging Camera (EPIC).

This paper presents an investigation of the expected uncertainties of a single channel cloud optical thickness (COT) retrieval technique, as well as a simple cloud temperature threshold based thermodynamic phase approach, in support of the Deep Space Climate Observatory (DSCOVR) mission. DSCOVR cloud products will be derived from Earth Polychromatic Imaging Camera (EPIC) observations in the ultraviolet and visible spectra. Since EPIC is not equipped with a spectral channel in the shortwave or mid-wave infrared that is sensitive to cloud effective radius (CER), COT will be inferred from a single visible channel with the assumption of appropriate CER values for liquid and ice phase clouds. One month of Aqua MODIS daytime granules from April 2005 is selected for investigating cloud phase sensitivity, and a subset of these granules that has similar EPIC sun-view geometry is selected for investigating COT uncertainties. EPIC COT retrievals are simulated with the same algorithm as the operational MODIS cloud products (MOD06), except using fixed phase-dependent CER values. Uncertainty estimates are derived by comparing the single channel COT retrievals with the baseline bi-spectral MODIS retrievals. Results show that a single channel COT retrieval is feasible for EPIC. For ice clouds, single channel retrieval errors are minimal (< 2%) due to the particle size insensitivity of the assumed ice crystal (i.e., severely roughened aggregate of hexagonal columns) scattering properties at visible wavelengths, while for liquid clouds the error is mostly limited to within 10%, although for thin clouds (COT < 2) the error can be higher. Potential uncertainties in EPIC cloud masking and cloud temperature retrievals are not considered in this study.