Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development.

As one of the best-known commercial goat breeds in the world, Boer goat has undergone long-term artificial selection for nearly 100 years, and its excellent growth rate and meat production performance have attracted considerable worldwide attention. Herein, we used single nucleotide polymorphisms (SNPs) called from the whole-genome sequencing data of 46 Australian Boer goats to detect polymorphisms and identify genomic regions related to muscle development in comparison with those of 81 non-specialized meat goat individuals from Europe, Africa, and Asia. A total of 13 795 202 SNPs were identified, and the whole-genome selective signal screen with a π ratio of nucleotide diversity (πcase /πcontrol ) and pairwise fixation index (FST ) was analyzed. Finally, we identified 1741 candidate selective windows based on the top 5% threshold of both parameters; here, 449 candidate genes were only found in 727 of these regions. A total of 433 genes out of the 449 genes obtained were annotated to 2729 gene ontology terms, of which 51 were directly linked to muscle development (e.g., muscle organ development, muscle cell differentiation) by 30 candidate genes (e.g., JAK2, KCNQ1, PDE5A, PDLIM5, TBX5). In addition, 246 signaling pathways were annotated by 178 genes, and two pathways related to muscle contraction, including vascular smooth muscle contraction (ADCY7, PRKCB, PLA2G4E, ROCK2) and cardiac muscle contraction (CACNA2D3, CASQ2, COX6B1), were identified. The results could improve the current understanding of the genetic effects of artificial selection on the muscle development of goat. More importantly, this study provides valuable candidate genes for future breeding of goats.

[Genomic characterization of food-borne Listeria monocytogenes isolates from Nanshan district of Shenzhen during 2009-2019].

Objective: The study aims to investigate the characteristic baseline information about genetic lineages, drug-resistance genes, virulence genes and evolutionary relationships of food-borne Listeria monocytogenes (Lm) isolates from Nanshan district of Shenzhen. Methods: The whole genomes of 46 Lm isolates during 2009-2019 were extracted and sequenced (Illumina PE-150, 100×). The CLC Genomics Workbench 12.0 was used to assemble and align Lm genomes, analyze their housekeeping genes, drug-resistance genes and virulence genes, and construct a k-mer phylogenetic tree. Results: After assembly, all genomes satisfied analytical conditions (contigs N50>20 kb). The medians of GC content, gene count and gene size were 38.3%, 5 960 and 2 952 608 bp, respectively. Based on the Lm genomic reference database, the local k-mer phylogenetic tree had 14 clusters of which the genetic distance was wide. The 46 Lm isolates were classified as Lineage 1 (21), Lineage 2 (23) and Lineage 3 (2). The most common ST type of Lineage 1 was ST87, followed by ST3, ST59, ST224 and ST429, whereas the major ST types of Lineage 2 included ST8 and ST9, the rest being ST121, ST155, ST199, ST204 and ST321. However, Lineage 3 only had ST299. The part of Lm strains carried five drug-resistance genes, such as fosX (17), tetM (6), dfrG (4), catB3 (1) and mefA (1). Furthermore, all strains possessed nine virulence genes, including flaA, iap, actA, hly, mpl, prfA, plcA, plcB and inlB. Nevertheless, six isolates and three of them respectively carried the mutant inlA and inlJ, and other two isolates lacked inlC. Conclusion: The food-borne Lm isolates from Nanshan district of Shenzhen presented genetic and evolutionary diversity. Noted that the drug-resistant strains, which also owned abundant virulence genes with specific functions, could lead to serious infections, particularly those isolates from raw poultry and Flammulina velutipes. It was implied that the local region was at risk due to Listeriosis by food. This study offered reference for prevention, control and treatment of Lm infection to the Greater Bay Area.

On-Demand Semiconductor Source of Entangled Photons Which Simultaneously Has High Fidelity, Efficiency, and Indistinguishability.

An outstanding goal in quantum optics and scalable photonic quantum technology is to develop a source that each time emits one and only one entangled photon pair with simultaneously high entanglement fidelity, extraction efficiency, and photon indistinguishability. By coherent two-photon excitation of a single InGaAs quantum dot coupled to a circular Bragg grating bull's-eye cavity with a broadband high Purcell factor of up to 11.3, we generate entangled photon pairs with a state fidelity of 0.90(1), pair generation rate of 0.59(1), pair extraction efficiency of 0.62(6), and photon indistinguishability of 0.90(1) simultaneously. Our work will open up many applications in high-efficiency multiphoton experiments and solid-state quantum repeaters.

Photocatalytic membrane combined with biodegradation for toluene oxidation.

Photocatalytic membrane coupled to biodegradation offers potential for degrading volatile organic compounds (VOCs) in photocatalytic membrane biofilm reactor. An intimately coupled photocatalysis and biodegradation reactor was operated in continuous operation for 500 days to treat simulated waste gas containing toluene. Toluene removal efficiency obtained 99%, with the elimination capacity of 550 g m-3·h-1. Membrane photocatalysis coupled to biodegradation was created to improve toluene removal from 11 to 20%. The dominant genera were Lysinibacillus, Hydrogenophaga, Pseudomonas at 30 d, Rudaea, Dongia, Litorilinea at 230 d xyl, Tod, Tcb, Bed, Tmo, Tbu, Tou, Dmp, Cat were functional genes of toluene metabolism, as shown by16S rDNA and metagenomic sequencing. Photocatalysis destroyed part of the toluene into biodegradable intermediates that were immediately mineralized by microorganisms in biofilm, some toluene was directly degraded by toluene degrading bacterial community into carbon dioxide and water. The novel hybrid photocatalytic membrane biofilm reactor is a cost-effective and robust alternative to VOCs treatment.

Toward Scalable Boson Sampling with Photon Loss.

Boson sampling is a well-defined task that is strongly believed to be intractable for classical computers, but can be efficiently solved by a specific quantum simulator. However, an outstanding problem for large-scale experimental boson sampling is the scalability. Here we report an experiment on boson sampling with photon loss, and demonstrate that boson sampling with a few photons lost can increase the sampling rate. Our experiment uses a quantum-dot-micropillar single-photon source demultiplexed into up to seven input ports of a 16×16 mode ultralow-loss photonic circuit, and we detect three-, four- and fivefold coincidence counts. We implement and validate lossy boson sampling with one and two photons lost, and obtain sampling rates of 187, 13.6, and 0.78 kHz for five-, six-, and seven-photon boson sampling with two photons lost, which is 9.4, 13.9, and 18.0 times faster than the standard boson sampling, respectively. Our experiment shows an approach to significantly enhance the sampling rate of multiphoton boson sampling.

Time-Bin-Encoded Boson Sampling with a Single-Photon Device.

Boson sampling is a problem strongly believed to be intractable for classical computers, but can be naturally solved on a specialized photonic quantum simulator. Here, we implement the first time-bin-encoded boson sampling using a highly indistinguishable (∼94%) single-photon source based on a single quantum-dot-micropillar device. The protocol requires only one single-photon source, two detectors, and a loop-based interferometer for an arbitrary number of photons. The single-photon pulse train is time-bin encoded and deterministically injected into an electrically programmable multimode network. The observed three- and four-photon boson sampling rates are 18.8 and 0.2 Hz, respectively, which are more than 100 times faster than previous experiments based on parametric down-conversion.

Near-Transform-Limited Single Photons from an Efficient Solid-State Quantum Emitter.

By pulsed s-shell resonant excitation of a single quantum dot-micropillar system, we generate long streams of 1000 near-transform-limited single photons with high mutual indistinguishability. The Hong-Ou-Mandel interference of two photons is measured as a function of their emission time separation varying from 13 ns to 14.7 µs, where the visibility slightly drops from 95.9(2)% to a plateau of 92.1(5)% through a slow dephasing process occurring at a time scale of 0.7 µs. A temporal and spectral analysis reveals the pulsed resonance fluorescence single photons are close to the transform limit, which are readily useful for multiphoton entanglement and interferometry experiments.

Investigating the recheck rules for urine analysis in children.

The aim of this study was to establish recheck rules of urinalysis in children by investigating the concordance rate of the results obtained using the LabUMat urine dry chemistry analyzer (referred to as dry chemistry) and the UriSed tangible composition analyzer with that of the microscopic examination. First, 1040 urine samples from children (mean age 6.5 years) were analyzed using LabUMat and UriSed analyzers, and subsequently subjected to microscopic examination. The missed detection rate was evaluated and recheck rules were established to avoid missed diagnoses of abnormal renal function. Finally, clinical validations of the recheck rules were performed on 200 additional specimens. Among the samples used to investigate the recheck rules, the samples with positive microscopic examination results accounted for 58.65% of the total, while the samples with negative results accounted for 41.35%. Of the positive samples, a major portion (>50%) were RBC positive. The samples that were WBC positive and CAST positive accounted for 23.08 and 7.69%, respectively. The concordance rate was 87.5% and the missed detection rate was 2.9%. For the validation of the recheck rules in 200 urine samples, the concordance rate was 87.5% and the missed detection rate was 2.4%. When the detection of occult blood, WBC, and protein by dry chemistry, and the detection of RBC, WBC, and CAST by the UriSed analyzer are inconsistent, or the differences between them greater than 2 levels, recheck by microscopic examination is suggested.

Identification a novel HLA-B*27:105 allele in a Chinese bone marrow donor by polymerase chain reaction sequence-based typing.

HLA-B*27:105 has one nucleotide change from HLA-B*27:04:01 at nucleotide position 404 from G to A.

A novel HLA-A*32 allele, A*32:67 was identified by polymerase chain reaction sequence-based typing in a Chinese individual.

HLA-A*32:67 has a single nucleotide difference at position 286 C>A compared with HLA-A*32:01:01.

Dynamically controlled resonance fluorescence spectra from a doubly dressed single InGaAs quantum dot.

We report the first experimental demonstration of the interference-induced spectral line elimination predicted by Zhu and Scully [Phys. Rev. Lett. 76, 388 (1996)] and Ficek and Rudolph [Phys. Rev. A 60, R4245 (1999)]. We drive an exciton transition of a self-assembled quantum dot in order to realize a two-level system exposed to a bichromatic laser field and observe the nearly complete elimination of the resonance fluorescence spectral line at the driving laser frequency. This is caused by quantum interference between coupled transitions among the doubly dressed excitonic states, without population trapping. We also demonstrate a multiphoton ac Stark effect with shifted subharmonic resonances and dynamical modifications of resonance fluorescence spectra by using double dressing.

KIR3DL1 genetic diversity and phenotypic variation in the Chinese Han population.

Allelic polymorphism and expression variation of killer cell immunoglobulin-like receptor (KIR) 3DL1 on natural killer (NK) cells differ among populations. To determine whether the phenotypic variants are due to KIR polymorphism, transcription or copy number, the allelic polymorphism, mRNA levels and antigen expression of KIR3DL1 were assessed in 162 individuals. We characterized 13 KIR3DL1 alleles, five of which were novel. In addition, 21 genotypes were identified. The correlation between the binding patterns of NK cells to anti-KIR3DL1 and KIR3DL1 alleles was also examined. NK cells with different 3DL1 alleles showed distinct binding levels to anti-KIR3DL1. The binding frequencies of NK cells to anti-KIR3DL1 were not accordant with their binding levels, but both associated with the allele copy numbers. The mRNA expression amounts of individuals with two copy alleles were higher than those of individuals with one copy allele. Our data indicate that both the allele copy number and polymorphism of KIR3DL1 influence the antigen expression on the NK-cell surface, but only the copy number was associated with mRNA expression.

Identification of a novel HLA-DPB1 allele, HLA-DPB1*167:01, in a Chinese individual.

HLA-DPB1*167:01 allele differs from HLA-DPB1*10:01 by a single nucleotide substitution at codon 65 (ATC>CTC.

Identification of two novel HLA-B*54 alleles, B*54:01:03 and B*54:01:04 by polymerase chain reaction sequence-based typing.

HLA-B*54:01:03 and HLA-B*54:01:04 show one nucleotide change compared to HLA-B*54:01:01.

Identification of the novel HLA-A*26:79 allele by polymerase chain reaction sequence-based typing in a Chinese individual.

HLA-A*26:79 was different from HLA-A*26:01:01 at nucleotide position 406 from G to A.

Identification of a novel HLA-DQB1*03:03:04 allele by polymerase chain reaction sequence-based typing in a Chinese leukemia patient.

Nucleotide sequence of HLA-DQB1*03:03:04 allele was different from that of HLA-DQB1*03:03:02 by a single nucleotide substitution at position 603 C>T.

Identification of a novel HLA-DQB1*03:38 allele by polymerase chain reaction sequence-based typing in a Chinese bone marrow donor.

HLA-DQB1*03:38 differs from HLA-DQB1*03:03:02:01 at nucleotide position 184 T>C in exon 2.

Exogenous abscisic acid increases antioxidant enzymes and related gene expression in pepper (Capsicum annuum) leaves subjected to chilling stress.

To elucidate how physiological and biochemical mechanisms of chilling stress are regulated by abscisic acid (ABA) pretreatment, pepper variety (cv. 'P70') seedlings were pretreated with 0.57 mM ABA for 72 h and then subjected to chilling stress at 10°/6°C (day/night). Chilling stress caused severe necrotic lesions on the leaves and increased malondialdehyde and H(2)O(2) levels. Activities of monodehydroascorbate reductase (DHAR), dehydroascorbate reductase, glutathione reductase, guaiacol peroxidase, ascorbate peroxidase, ascorbate, and glutathione increased due to chilling stress during the 72 h, while superoxide dismutase and catalase activities decreased during 24 h, suggesting that chilling stress activates the AsA-GSH cycle under catalase deactivation in pepper leaves. ABA pretreatment induced significant increases in the above-mentioned enzyme activities and progressive decreases in ascorbate and glutathione levels. On the other hand, ABA-pretreated seedlings under chilling stress increased superoxide dismutase and guaiacol peroxidase activities and lowered concentrations of other antioxidants compared with untreated chilling-stressed plants. These seedlings showed concomitant decreases in foliage damage symptoms, and levels of malondialdehyde and H(2)O(2). Induction of Mn-SOD and POD was observed in chilling-stressed plants treated with ABA. The expression of DHAR1 and DHAR2 was altered by chilling stress, but it was higher in the presence than in the absence of ABA at 24 h. Overall, the results indicate that exogenous application of ABA increases tolerance of plants to chilling-induced oxidative damage, mainly by enhancing superoxide dismutase and guaiacol peroxidase activities and related gene expression.

Identification of a new HLA-A*02 allele, HLA-A*02:230, using polymerase chain reaction sequence-based typing in a Chinese individual.

Nucleotide sequence of HLA-A*02:230 allele was different from that of HLA-A*02:03:01 by a single nucleotide substitution at codon 139 (GCA > ACA), resulting in one amino acid change (Ala to Thr).

Identification of a new HLA-A*11:78N allele by polymerase chain reaction sequence-based typing.

Nucleotide sequence of HLA-A*11:78N allele was different from that of HLA-A*11:01:01 by two nucleotides deletion at positions 286 and 287, resulting in reading frameshift and has premature stop codon at position 73 in exon 2.