Genetic Architecture Underlying Nascent Speciation-The Evolution of Eurasian Pigs under Domestication.

Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in the advanced stages of speciation, the genetics of reproductive isolation in nascent stage of speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying the early stages of speciation in great details. Pig breeds have not evolved the large X-effect of hybrid incompatibility commonly observed between "good species." Instead, deleterious epistatic interactions among multiple autosomal loci are common. These weak Dobzhansky-Muller incompatibilities confer partial hybrid inviability with sex biases in crosses between European and East Asian domestic pigs. The genomic incompatibility is enriched in pathways for angiogenesis, androgen receptor signaling and immunity, with an observation of many highly differentiated cis-regulatory variants. Our study suggests that partial hybrid inviability caused by pervasive but weak interactions among autosomal loci may be a hallmark of nascent speciation in mammals.

Development of a flow cytometry-based plating-free system for strain engineering in industrial fungi.

Recent technical advances regarding filamentous fungi have accelerated the engineering of fungal-based production and benefited basic science. However, challenges still remain and limit the speed of fungal applications. For example, high-throughput technologies tailored to filamentous fungi are not yet commonly available for genetic modification. The currently used fungal genetic manipulations are time-consuming and laborious. Here, we developed a flow cytometry-based plating-free system to directly screen and isolate the transformed protoplasts in industrial fungi Myceliophthora thermophila and Aspergillus niger. This system combines genetic engineering via the 2A peptide and the CRISPR-Cas9 system, strain screening by flow cytometry, and direct sorting of colonies for deep-well-plate incubation and phenotypic analysis while avoiding culturing transformed protoplasts in plates, colony picking, conidiation, and cultivation. As a proof of concept, we successfully applied this system to generate the glucoamylase-hyperproducing strains MtYM6 and AnLM3 in M. thermophila and A. niger, respectively. Notably, the protein secretion level and enzyme activities in MtYM6 were 17.3- and 25.1-fold higher than in the host strain. Overall, these findings suggest that the flow cytometry-based plating-free system can be a convenient and efficient tool for strain engineering in fungal biotechnology. We expect this system to facilitate improvements of filamentous fungal strains for industrial applications. KEY POINTS: • Development of a flow cytometry-based plating-free (FCPF) system is presented. • Application of FCPF system in M. thermophila and A. niger for glucoamylase platform. • Hyper-produced strains MtYM6 and AnLM3 for glucoamylase production are generated.

Genome-wide study refines the quantitative trait locus for number of ribs in a Large White × Minzhu intercross pig population and reveals a new candidate gene.

In China, sparerib is one of the most valuable parts of the pork carcass. As a result, candidate gene mining for number of ribs has become an interesting study focus. To examine the genetic basis for this major trait, we genotyped 596 individuals from an F2 Large White × Minzhu intercross pig population using the PorcineSNP60 Genotyping BeadChip. The genome-wide association study identified a locus for number of ribs in a 2.38-Mb region on Sus scrofa chromosome 7 (SSC7 of Sus scrofa genome assembly, Sscrofa10.2). We identified the top significant SNP ASGA0035536, which explained 16.51 % of the phenotypic variance. A previously reported candidate causal mutation (g.19034 A>C) in vertebrae development-associated gene VRTN explained 8.79 % of the phenotypic variation on number of ribs and had a much lower effect than ASGA0035536. Haplotype sharing analysis in F1 boars localized the rib number QTL to a 951-kb interval on SSC7. This interval encompassed 17 annotated genes in Sscrofa10.2, including the previously reported VRTN candidate gene. Of the 17 candidate genes, LTBP2, which encodes a latent transforming growth factor beta binding protein, was previously reported to indirectly regulate the activity of growth differentiation factor Gdf11, which has been shown to increase the number of ribs in knock-out mice. Thus, we propose LTBP2 as a good new candidate gene for number of ribs in the pig population. This finding advances our understanding of the genetic architecture of rib number in pigs.

Mensenchymal stem cells can delay radiation-induced crypt death: impact on intestinal CD44(+) fragments.

Intestinal stem cells are primitive cells found within the intestinal epithelium that play a central role in maintaining epithelial homeostasis through self-renewal and commitment into functional epithelial cells. Several markers are available to identify intestinal stem cells, such as Lgr5, CD24 and EphB2, which can be used to sort intestinal stem cells from mammalian gut. Here, we identify and isolate intestinal stem cells from C57BL/6 mice by using a cell surface antigen, CD44. In vitro, some CD44(+) crypt cells are capable of forming "villus-crypt"-like structures (organoids). A subset strongly positive for CD44 expresses high levels of intestinal stem-cell-related genes, including Lgr5, Bmi1, Hopx, Lrig1, Ascl2, Smoc2 and Rnf43. Cells from this subset are more capable of developing into organoids in vitro, compared with the subset weakly positive for CD44. However, the organoids are sensitive to ionizing irradiation. We investigate the specific roles of mesenchymal stem cells in protecting organoids against radiation-induced crypt death. When co-cultured with mesenchymal stem cells, the crypt domains of irradiated organoids possess more proliferative cells and fewer apoptotic cells than those not co-cultured with mesenchymal stem cells. Cd44v6 continues to be expressed in the crypt domains of irradiated organoids co-cultured with mesenchymal stem cells. Our results indicate specific roles of mesenchymal stem cells in delaying radiation-induced crypt death in vitro.

Photonic-assisted microwave phase shifter using a DMZM and an optical bandpass filter.

We propose and demonstrate a photonic-assisted wideband 360° microwave phase shifter based on a conventional dual-drive Mach-Zehnder modulator (DMZM) and an optical bandpass filter (OBPF). The two arms of the DMZM are driven by the fundamental microwave signal to be phase shifted and its frequency doubled component, respectively. The OBPF followed after the DMZM is used to remove the optical carrier and the sidebands at either side of the optical carrier. As a result, only two sidebands corresponding to the fundamental microwave signal and its frequency doubled component, respectively, are left. Moreover, the phase shift between the two sidebands can be continuously tunable by adjusting the bias voltage of the DMZM. This phase shift is mapped to the fundamental microwave signal which is recovered by beating the two sidebands in a photodetector (PD). The proposed approach is theoretically analyzed and experimentally verified.

Photonic generation of arbitrarily phase-modulated microwave signals based on a single DDMZM.

We propose and demonstrate a compact and cost-effective photonic approach to generate arbitrarily phase-modulated microwave signals using a conventional dual-drive Mach-Zehnder modulator (DDMZM). One arm (arm1) of the DDMZM is driven by a sinusoidal microwave signal whose power is optimized to suppress the optical carrier, while the other arm (arm2) of the DDMZM is driven by a coding signal. In this way, the phase-modulated optical carrier from the arm2 and the sidebands from the arm1 are combined together at the output of the DDMZM. Binary phase-coded microwave pulses which are free from the baseband frequency components can be generated when the coding signal is a three-level signal. In this case, the precise π phase shift of the microwave signal is independent of the amplitude of the coding signal. Moreover, arbitrarily phase-modulated microwave signals can be generated when an optical bandpass filter is attached after the DDMZM to achieve optical single-sideband modulation. The proposed approach is theoretically analyzed and experimentally verified. The binary phase-coded microwave pulses, quaternary phase-coded microwave signal, and linearly frequency-chirped microwave signal are experimentally generated. The simulated and the experimental results agree very well with each other.

Photonic generation of background-free millimeter-wave ultra-wideband pulses based on a single dual-drive Mach-Zehnder modulator.

We propose a novel photonic approach for generating a background-free millimeter-wave (MMW) ultra-wideband (UWB) signal based on a conventional dual-drive Mach-Zehnder modulator (DMZM). One arm of the DMZM is driven by a local oscillator (LO) signal. The LO power is optimized to realize optical carrier suppressed modulation. The other arm is fed by a rectangular signal. The MMW UWB pulses are generated by truncating the continuous wave LO signal into a pulsed one in a photodetector (PD). The generated MMW UWB signal is background-free by eliminating the baseband frequency components because the optical power launched to the PD keeps constant all the time. The proposed method is theoretically analyzed and experimentally verified. The generated MMW UWB signal centered at a frequency of 26 GHz meets the Federal Communications Commission spectral mask very well.

A genome-wide association study of limb bone length using a Large White × Minzhu intercross population.

BACKGROUND: In pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. In this study, an intercross population was constructed between the indigenous Chinese Minzhu pig breed and the western commercial Large White pig breed to examine the genetic basis for variation in limb bone length. The aim of this study was to detect potential genetic variants associated with porcine limb bone length. METHODS: A total of 571 F2 individuals from a Large White and Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for femur length (FL), humerus length (HL), hipbone length (HIPL), scapula length (SL), tibia length (TL), and ulna length (UL). A genome-wide association study was performed by applying the previously reported approach of genome-wide rapid association using mixed model and regression. Statistical significance of the associations was based on Bonferroni-corrected P-values. RESULTS: A total of 39 significant SNPs were mapped to a 11.93 Mb long region on pig chromosome 7 (SSC7). Linkage analysis of these significant SNPs revealed three haplotype blocks of 495 kb, 376 kb and 492 kb, respectively, in the 11.93 Mb region. Annotation based on the pig reference genome identified 15 genes that were located near or contained the significant SNPs in these linkage disequilibrium intervals. Conditioned analysis revealed that four SNPs, one on SSC2 and three on SSC4, showed significant associations with SL and HL, respectively. CONCLUSIONS: Analysis of the 15 annotated genes that were identified in these three haplotype blocks indicated that HMGA1 and PPARD, which are expressed in limbs and influence chondrocyte cell growth and differentiation, could be considered as relevant biological candidates for limb bone length in pig, with potential applications in breeding programs. Our results may also be useful for the study of the mechanisms that underlie human limb length and body height.

Spectral Asymmetry Induces a Re-Entrant Quantum Hall Effect in a Topological Insulator.

The band inversion of topological materials in three spatial dimensions is intimately connected to the parity anomaly of 2D massless Dirac fermions, known from quantum field theory. At finite magnetic fields, the parity anomaly reveals itself as a non-zero spectral asymmetry, i.e., an imbalance between the number of conduction and valence band Landau levels, due to the unpaired zero Landau level. This work reports the realization of this 2D Dirac physics at a single surface of the 3D topological insulator (Hg,Mn)Te. An unconventional re-entrant sequence of quantized Hall plateaus in the measured Hall resistance can be directly related to the occurrence of spectral asymmetry in a single topological surface state. The effect should be observable in any topological insulator where the transport is dominated by a single Dirac surface state.

LC3B-II deacetylation by histone deacetylase 6 is involved in serum-starvation-induced autophagic degradation.

Autophagy is a conserved mechanism for controlling the degradation of misfolded proteins and damaged organelles in eukaryotes and can be induced by nutrient withdrawal, including serum starvation. Although differential acetylation of autophagy-related proteins has been reported to be involved in autophagic flux, the regulation of acetylated microtubule-associated protein 1 light chain 3 (LC3) is incompletely understood. In this study, we found that the acetylation levels of phosphotidylethanolamine (PE)-conjugated LC3B (LC3B-II), which is a critical component of double-membrane autophagosome, were profoundly decreased in HeLa cells upon autophagy induction by serum starvation. Pretreatment with lysosomal inhibitor chloroquine did not attenuate such deacetylation. Under normal culture medium, we observed increased levels of acetylated LC3B-II in cells treated with tubacin, a specific inhibitor of histone deacetylase 6 (HDAC6). However, tubacin only partially suppressed serum-starvation-induced LC3B-II deacetylation, suggesting that HDAC6 is not the only deacetylase acting on LC3B-II during serum-starvation-induced autophagy. Interestingly, tubacin-induced increase in LC3B-II acetylation was associated with p62/SQSTM1 accumulation upon serum starvation. HDAC6 knockdown did not influence autophagosome formation but resulted in impaired degradation of p62/SQSTM1 during serum starvation. Collectively, our data indicated that LC3B-II deacetylation, which was partly mediated by HDAC6, is involved in autophagic degradation during serum starvation.

Photonic generation of widely tunable and background-free binary phase-coded radio-frequency pulses.

We present a novel photonic approach to generating widely tunable and background-free binary phase-coded radio-frequency (RF) pulses by cascading a polarization modulator (PolM) and a phase modulator (PM). The PolM is used to produce an optical carrier and two sidebands with orthogonal polarization states. The phase shift θ between the optical carrier and the sidebands is controlled by the electrical driving signal applied to the PM. For θ>π/2 or <π/2, the phase of the detected RF signal is 0 or π, respectively. For θ=π/2, there is no RF signal recovered in the photodiode (PD). In this way, binary phase-coded RF pulses can be generated, while the optical power launched to the PD keeps constant. The proposed technique is therefore background free by eliminating the baseband frequency components. Moreover, the carrier frequency of the RF pulses is widely tunable and the π phase shift of the RF signal is independent of the amplitude of the electrical driving signal. The proposed scheme is theoretically analyzed and experimentally verified.

High-speed microwave photonic switch for millimeter-wave ultra-wideband signal generation.

We propose a scheme for generating millimeter-wave (MMW) ultra-wideband (UWB) signal that is free from low-frequency components and a residual local oscillator. The system consists of two cascaded polarization modulators and is equivalent to a high-speed microwave photonic switch, which truncates a sinusoidal MMW into short pulses. The polarity switchability of the generated MMW-UWB pulse is also demonstrated.

Widely tunable single-bandpass microwave photonic filter based on polarization processing of a nonsliced broadband optical source.

We propose a new scheme of microwave photonic filter (MPF) based on the polarization processing of a broadband optical source (BOS), which features single-bandpass response and a wide span of operation bandwidth. The BOS is orthogonally polarized by a polarization division multiplexing emulator (PDME) with a tunable time delay between the two polarization states and incident at ± 45° to one principle axis of a polarization modulator (PolM). The PDME cascades a PolM, and a polarizer realizes a microwave modulation making the phase of the carrier able to be tuned while ± 1st sidebands remain unchanged, which after propagating in a dispersive medium results in a tunable single-bandpass response in the RF domain. We experimentally verify the MPF. By adjusting the time delay and the optical spectrum bandwidth, the passband center frequency is continuously tuned from DC to 20 GHz and the 3 dB passband bandwidth changes while the optical spectrum bandwidth ranges from 1 to 4 nm.

Generation of ultra-wideband triplet pulses based on four-wave mixing and phase-to-intensity modulation conversion.

We propose and demonstrate a novel scheme to generate ultra-wideband (UWB) triplet pulses based on four-wave mixing and phase-to-intensity modulation conversion. First a phase-modulated Gaussian doublet pulse is generated by four-wave mixing in a highly nonlinear fiber. Then an UWB triplet pulse is generated by generating the first-order derivative of the phase-modulated Gaussian doublet pulse using an optical filter serving as a frequency discriminator. By locating the optical signal at the linear slope of the optical filter, the phase modulated Gaussian doublet pulse is converted to an intensity-modulated UWB triplet pulse which well satisfies the Federal Communications Commission spectral mask requirements, even in the extremely power-restricted global positioning system band.

Brillouin-assisted microwave frequency measurement with adjustable measurement range and resolution.

We present a reconfigurable microwave frequency measurement technique with adjustable measurement range and resolution. The key novelty of the technique is the employment of stimulated Brillouin scattering, which results in a tunable amplitude comparison function, leading to an adjustable measurement range and resolution. The proposed technique is switchable between a wideband tunable narrow measurement range (~2 GHz) with high resolution (±0.05 GHz) and a fixed wide measurement range (12 GHz) with moderate resolution (±0.25 GHz).

Chaotic ultra-wideband radio generator based on an optoelectronic oscillator with a built-in microwave photonic filter.

We induce a microwave photonic bandpass filter into an optoelectronic oscillator to generate a chaotic ultra-wideband signal in both the optical and electrical domain. The theoretical analysis and numerical simulation indicate that this system is capable of generating band-limited high-dimensional chaos. Experimental results coincide well with the theoretical prediction and show that the power spectrum of the generated chaotic signal basically meets the Federal Communications Commission indoor mask. The generated chaotic carrier is further intensity modulated by a 10 MHz square wave, and the waveform of the output ultra-wideband signal is measured for demonstrating the chaotic on-off keying modulation.

True-time delay line with separate carrier tuning using dual-parallel MZM and stimulated Brillouin scattering-induced slow light.

We experimentally demonstrate a novel tunable true-time delay line with separate carrier tuning using dual-parallel Mach-Zehnder modulator and stimulated Brillouin scattering-induced slow light. The phase of the optical carrier can be continuously and precisely controlled by simply adjusting the dc bias of the dual-parallel Mach-Zehnder modulator. In addition, both the slow light and single-sideband modulation can be simultaneously achieved in the stimulated Brillouin scattering process with three types of configuration. Finally, the true-time delay technique is clearly verified by a two-tap incoherent microwave photonic filter as the free spectral range of the filter is changed.

[Association of polymorphism for porcine BF gene with reproductive traits and placental efficiency in Large White].

Taking BF gene as one of the candidate genes influencing on reproductive traits in present study, this study used PCR-RFLP analyzised the polymorphism of intron 1 of BF gene in Large White sows. A single nucleotide polymorphism (SNP) named as BF-intron 1-C79T was detected. And the three genotypes of CC, CT, TT got fitted Hardy-Weinberg equilibrium with chi2-fitness test. An association analysis was tested between the genetic polymorphism at intron 1 and total number born (TNB), number born alive (NBA), born weight (BW) and placental efficiency (PE) respectively. It showed that, at first parity, the TNB, NBA, BW and PE with CC genotype were higher than those with CT genotype but not significant (P>0.05). Meanwhile, in multiparous sow population, the TNB, NBA and PE with CC genotype were significantly more than those with TT genotype (P<0.05), with increase of 3.45, 3.92, and 23.80%, respectively. Thus BF-intron 1-C79T is suggested to be a potential genetic marker for the breeding on the reproductive traits and placental efficiency.

[Genetic polymorphism of FSH b subunit gene and correlation with reproductive traits in Beijing Black Pig].

FSH beta subunit gene was regarded as a candidate gene for reproductive traits of Beijing Black Pig in this study. The polymorphism of two loci FSHbeta-1 and FSHbeta-2 was detected by electrophoretic method and PCR-RFLP with restriction endonuclease Hae III. Sequencing results showed that a 273 bp sequence, which was a retrotransponsons including a RNA Polymerase III inter promoter, was inserted between the 134th and 135th nucleotide of the PCR product in FSHbeta-1, and the mutation (C-->T) was revealed at the 173th nucleotide of the PCR product in FSHbeta-2. Both alleles (A and B) of both loci were found in the population that showed low polymorphism. Chi-square test indicated that the two polymorphism sites fitted Hardy-Weinberg equilibrium (P>0.05). The effects of polymorphism of FSH b subunit gene on total born number (TNB), number born alive (NBA), and birth weight (WB) were analyzed. For FSHbeta-1 locus, pigs of the first parity with genotype AA had 0.96 and 1.85 TNB more than those with genotypes AB and BB. The pigs of the first parity with genotypes AA and AB had 0.95 and 1.69 NBA more than those with genotype BB, respectively. For FSHbeta-2 locus, pigs of the first parity with genotype AA had1.57 and 2.15 TNB more than those with genotypes AB and BB. The pigs of the first parity with genotypes AA and AB had 1.00 and 0.94 NBA more than those with genotype BB, respectively. The pigs of multiparous with genotype AA had 0.25 kg of WB more than those with genotype BB. The results of combined genotype effects indicated that A allele of FSHbeta-1 locus in all the population and FSHbeta-2 locus in pigs of the first parity had the positive effective on TNB, NBA, and WB.