Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta) and crab-eating macaques ( M. fascicularis).

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques ( Macaca mulatta, MMU) and crab-eating macaques ( M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Scalable Multipartite Entanglement Created by Spin Exchange in an Optical Lattice.

Ultracold atoms in optical lattices form a competitive candidate for quantum computation owing to the excellent coherence properties, the highly parallel operations over spins, and the ultralow entropy achieved in qubit arrays. For this, a massive number of parallel entangled atom pairs have been realized in superlattices. However, the more formidable challenge is to scale up and detect multipartite entanglement, the basic resource for quantum computation, due to the lack of manipulations over local atomic spins in retroreflected bichromatic superlattices. In this Letter, we realize the functional building blocks in quantum-gate-based architecture by developing a cross-angle spin-dependent optical superlattice for implementing layers of quantum gates over moderately separated atoms incorporated with a quantum gas microscope for single-atom manipulation and detection. Bell states with a fidelity of 95.6(5)% and a lifetime of 2.20±0.13 s are prepared in parallel, and then connected to multipartite entangled states of one-dimensional ten-atom chains and two-dimensional plaquettes of 2×4 atoms. The multipartite entanglement is further verified with full bipartite nonseparability criteria. This offers a new platform toward scalable quantum computation and simulation.

Interrelated Thermalization and Quantum Criticality in a Lattice Gauge Simulator.

Gauge theory and thermalization are both topics of essential importance for modern quantum science and technology. The recently realized atomic quantum simulator for lattice gauge theories provides a unique opportunity for studying thermalization in gauge theory, in which theoretical studies have shown that quantum thermalization can signal the quantum phase transition. Nevertheless, the experimental study remains a challenge to accurately determine the critical point and controllably explore the thermalization dynamics due to the lack of techniques for locally manipulating and detecting matter and gauge fields. We report an experimental investigation of the quantum criticality in the lattice gauge theory from both equilibrium and nonequilibrium thermalization perspectives, with the help of the single-site addressing and atom-number-resolved detection capabilities. We accurately determine the quantum critical point and observe that the Néel state thermalizes only in the critical regime. This result manifests the interplay between quantum many-body scars, quantum criticality, and symmetry breaking.

Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing.

The common marmoset ( Callithrix jacchus) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase ( WWOX) and Tyrosine-protein phosphatase nonreceptor type 21 ( PTPN21) genes may be associated with epilepsy in marmosets. Notably, KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.

Characterization of large-scale genomic differences in the first complete human genome.

BACKGROUND: The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet. RESULTS: Here, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution. CONCLUSION: Our study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.

Levels, consumption, and variations of eight artificial sweeteners in the wastewater treatment plants of Dalian city, China.

Artificial sweeteners (ASs) are emerging contaminants in the environment, primarily derived from wastewater treatment plant (WWTP) effluents. In this study, the influents and effluents of three WWTPs in the Dalian urban area, China, were analyzed for the distribution of 8 typical ASs to investigate their seasonal fluctuations in the WWTPs. The results showed that acesulfame (ACE), sucralose (SUC), cyclamate (CYC), and saccharin (SAC) were both detected in the influent and effluent water samples of WWTPs, with concentrations ranging from not detected (ND) to 14.02 µg·L-1. In addition, SUC was the most abundant ASs type, accounting for 40 %-49 % and 78 %-96 % of the total ASs in the influent and effluent water, respectively. The WWTPs revealed high removal efficiencies of CYC, SAC, and ACE, while the SUC removal efficiency was poor (26 % ± 36 %). The ACE and SUC concentrations were higher in spring and summer, and all ASs showed lower levels in winter, which may be caused by the high consumption of ice-cream in warmer months. The per capita ASs loads in the WWTPs were determined in this study based on the wastewater analysis results. The calculated per capita daily mas loads for individual ASs ranged from 0.45 g·d-1·1000p-1 (ACE) to 2.04 g·d-1·1000p-1 (SUC). In addition, the relationship between per capita ASs consumption and socioeconomic status showed no significant correlation.

Low-noise and high-power second harmonic generation of 532 nm laser for trapping ultracold atoms.

Optical lattices for coherently manipulating ultracold atoms demand high-power, low-noise, narrow-line-width, and continuous-wave lasers. Here, we report the implementation of a 30 W 532 nm low-noise laser by second harmonic generation from a 1064 nm fiber laser, which is capable to generate optical lattices for a quantum gas microscope of Rb87 atoms. The overall conversion efficiency is 59% at an input power of 51 W with a lithium triborate crystal coupled to a ring cavity. The relative intensity noise of the output laser is suppressed to -120 dBc/Hz in the range of 10 Hz-100 kHz with a high dynamic range of over 50 dB, which is suitable for long-term trapping and coherent manipulation of the quantum gases.

A high-power and low-noise 532-nm continuous-wave laser for quantum gas microscopy.

Low-noise, high-power 532-nm lasers are of great interest in many scientific research studies, such as gravitational wave detection and ultracold atom experiments. In particular, in the experiments of quantum gas microscopy, a large power of laser is necessary during the imaging process, while low noise is important for preventing the atoms from being heated up. In this work, we report on the generation of such a 532-nm continuous-wave laser by coherently combining two laser beams produced by single-pass second-harmonic generation. The power of the combined laser is up to 17 W. With the help of intensity stabilization, we are able to suppress the relative intensity noise to below -120 dBc/Hz. The generated laser satisfies the experimental requirements for integrating optical superlattices with a quantum gas microscope.