Evolving ancient DNA techniques and the future of human history.

Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human health.

The deep population history of northern East Asia from the Late Pleistocene to the Holocene.

Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.

Human population history at the crossroads of East and Southeast Asia since 11,000 years ago.

Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia.

MiR-9 promotes G-MDSC recruitment and tumor proliferation by targeting SOCS3 in breast cancer.

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous group of cells that differentiate from myeloid cells, proliferate in cancer and inflammatory reactions, and mainly exert immunosuppressive functions. Nonetheless, the precise mechanisms that dictate both the accumulation and function of MDSCs remain only partially elucidated. In the course of our investigation, we observed a positive correlation between the content of MDSCs especially G-MDSCs and miR-9 level in the tumor tissues derived from miR-9 knockout MMTV-PyMT mice and 4T1 tumor-bearing mice with miR-9 overexpression. Combined with RNA-seq analysis, we identified SOCS2 and SOCS3 as direct targets of miR-9. Additionally, our research unveiled the pivotal role of the CCL5/CCR5 axis in orchestrating the chemotactic recruitment of G-MDSCs within the tumor microenvironment, a process that is enhanced by miR-9. These findings provide fresh insights into the molecular mechanisms governing the accumulation of MDSCs within the framework of breast cancer development.

Zinc-doped C4N3/BiOBr S-scheme heterostructured hollow spheres for efficient photocatalytic degradation of tetracycline.

Photocatalytic degradation of organic pollutants in water is of great significance to the sustainable development of the environment, but encounters limited efficiency when a single compound is used. Thus, there have been enormous efforts to find novel photocatalytic heterostructured composites with high performance. In this work, a novel S-scheme heterostructure is constructed with BiOBr and Zn2+ doped C4N3 (Zn-C4N3) by a solvothermal method for efficient photodegradation of tetracycline (TC), a residual antibiotic difficult to be removed from the aquatic environment. Thanks to Zn2+-doping induced improvement in chemical affinity between Zn-C4N3 and BiOBr, well-formed Zn-C4N3/BiOBr heterostructured hollow spheres are formed. This structure can efficiently suppress fast recombination of photogenerated electron-hole pairs to enhance the photocatalytic activity of BiOBr dramatically. At a room temperature of 25 °C and neutral pH 7, the catalyst can degrade a significant portion of TC pollutants within 30 min under visible light. Also, the Zn-C4N3/BiOBr heterostructure displays good stability after recycling experiments. Free radical capture experiments and ESR tests show that ˙O2- is the main active substance for photocatalytic degradation of TC. This study provides new insights for constructing heterostructures with an intimate interface between the two phases for photocatalytic applications.

Iso-E-Codelock: A Rebuilding-free Electrochemical Chip with a Customizable Decoding Probe for Real-Time and Portable Pathogen Diagnostics.

In order to realize portable pathogen diagnostics with easier quantitation, digitization and integration, we develop a ready-to-use electrochemical sensing strategy (Iso-E-Codelock) for real-time detection of isothermal nucleic acid amplification. Bridged by a branched DNA as codelock, the isothermal amplicon is transduced into increased current of an electrochemical probe, holding multiple advantages of high sensitivity, high selectivity, signal-on response, "zero" background and one-pot operation. Through a self-designed portable instrument (BioAlex PHE-T), the detection can be implemented on a multichannel microchip and output real-time amplification curves just like an expensive commercial PCR machine. The microchip is a rebuilding-free and disposable component. The branch codelock probe can be customized for different targets and designs. Such high performance and flexibility have been demonstrated utilizing four virus (SARS-CoV-2, African swine fever, FluA and FluB) genes as targets, and two branch (3-way and 4-way) DNAs as codelock probes.

Resolution adjustable Lissajous scanning with piezoelectric MEMS mirrors.

We previously designed a dual-axis piezoelectric MEMS mirror with a low crosstalk gimbal structure, which is utilized as the key device for further research for laser beam scanning. This paper mainly focuses on studying the Lissajous scanning resolution of this MEMS mirror with frequency ratio and phase modulation. For accurately evaluating the scanning resolution, the center angular resolution of Lissajous scanning is redefined by theoretical calculation and verified with experimental measurement. Meanwhile, the scanning nonlinearity of MEMS mirror is studied carefully. Finally, the MEMS mirror works at the state of pseudo-resonance, and the center angular resolution better than 0.16° (H) × 0.03° (V) is achieved at a scanning Field of view (FoV) of 35.0° (H) × 16.5° (V). Moreover, a feasible route of resolution adjustable Lissajous scanning is provided by optimization of frequency ratio and phase modulation, which is helpful for high definition and high frame rate (HDHF) laser scanning imaging with the dual-axis mirror.

Design of low polarization off-axis three-mirror reflective optical systems.

Off-axis optical systems have several important advantages over on-axis ones. However, high polarization aberrations, which play important roles in many applications, become critical disadvantages of off-axis systems. Thanks to the seven free design parameters, three-mirror reflective systems have a good potential to achieve low polarization. A general method to design low polarization off-axis three-mirror reflective optical systems is proposed in this paper. Based on genetic algorithms, several off-axis three-mirror systems with both low polarization aberrations and good wave aberrations are designed. The method proposed in this paper is versatile and can be used to design other types of optical systems that demand low polarization aberrations.

Microfabricated sensor device for CW and pulsed laser power measurements.

On-line measurement is a trend of development toward laser-based applications. We present a fiber-integrated force sensor device for laser power measurement with both CW mode and pulse mode based on laser radiometric heat and radiation force sensing simultaneously. The sensor device is fabricated using a standard microfabrication process. Laser intensity is determined through the displacement of a movable mirror measured by an integrated Fabry-Perot interferometer. Compared with the performance of the device in the ambient condition, a non-linearity error of 0.02% and measurement uncertainty of 2.06% is observed in the quasi-vacuum condition for CW laser illumination. This device can measure a CW laser power with a 46.4 µW/Hz1/2 noise floor and a minimum detection limit of 0.125 mW. For a pulsed laser, a non-linearity error of 0.37% and measurement uncertainty of 2.08% is achieved with a noise floor of 1.3 µJ/Hz1/2 and a minimum detection limit of 3 µJ.

Diode-pumped mode-locked Yb:Sc2SiO5 laser generating 38 fs pulses.

We report on sub-40 fs pulse generation from a Yb:Sc2SiO5 laser pumped by a spatially single-mode fiber-coupled laser diode at 976 nm. A maximum output power of 545 mW was obtained at 1062.6 nm in the continuous-wave regime, corresponding to a slope efficiency of 64% and a laser threshold of 143 mW. A continuous wavelength tuning across 80 nm (1030 -1110 nm) was also achieved. Implementing a SESAM for starting and stabilizing the mode-locked operation, the Yb:Sc2SiO5 laser delivered soliton pulses as short as 38 fs at 1069.5 nm with an average output power of 76 mW at a pulse repetition rate of ∼79.8 MHz. The maximum output power was scaled to 216 mW for slightly longer pulses of 42 fs, which corresponded to a peak power of 56.6 kW and an optical efficiency of 22.7%. To the best of our knowledge, these results represent the shortest pulses ever achieved with any Yb3+-doped rare-earth oxyorthosilicate crystal.

Cytokinin-inducible response regulator SlRR6 controls plant height through gibberellin and auxin pathways in tomato.

Plant height is a key agronomic trait regulated by several phytohormones such as gibberellins (GAs) and auxin. However, little is known about how cytokinin (CK) participates in this process. Here, we report that SlRR6, a type-A response regulator in the CK signaling pathway, positively regulates plant height in tomato. SlRR6 was induced by exogenous kinetin and GA3, but inhibited by indole-3-acetic acid (IAA). Knock out of SlRR6 reduced tomato plant height through shortening internode length, while overexpression of SlRR6 caused taller plants due to increased internode number. Cytological observation of longitudinal stems showed that both knock out and overexpression of SlRR6 generated larger cells, but significantly reduced cell numbers in each internode. Further studies demonstrated that overexpression of SlRR6 enhanced GA accumulation and lowered IAA content, along with expression changes in GA- and IAA-related genes. Exogenous paclobutrazol and IAA treatments restored the increased plant height phenotype in SlRR6-overexpressing lines. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays showed that SlRR6 interacts with a small auxin up RNA protein, SlSAUR58. Moreover, SlSAUR58-overexpressing plants were dwarf with decreased internode length. Overall, our findings establish SlRR6 as a vital component in the CK signaling, GA, and IAA regulatory network that controls plant height.

Quantum Spin Hall States and Topological Phase Transition in Germanene.

We present the first experimental evidence of a topological phase transition in a monoelemental quantum spin Hall insulator. Particularly, we show that low-buckled epitaxial germanene is a quantum spin Hall insulator with a large bulk gap and robust metallic edges. Applying a critical perpendicular electric field closes the topological gap and makes germanene a Dirac semimetal. Increasing the electric field further results in the opening of a trivial gap and disappearance of the metallic edge states. This electric field-induced switching of the topological state and the sizable gap make germanene suitable for room-temperature topological field-effect transistors, which could revolutionize low-energy electronics.

Neutrophils as potential therapeutic targets for breast cancer.

Breast cancer (BC) remains the foremost cause of cancer mortality globally, with neutrophils playing a critical role in its pathogenesis. As an essential tumor microenvironment (TME) component, neutrophils are emerging as pivotal factors in BC progression. Growing evidence has proved that neutrophils play a Janus- role in BC by polarizing into the anti-tumor (N1) or pro-tumor (N2) phenotype. Clinical trials are evaluating neutrophil-targeted therapies, including Reparixin (NCT02370238) and Tigatuzumab (NCT01307891); however, their clinical efficacy remains suboptimal. This review summarizes the evidence regarding the close relationship between neutrophils and BC, emphasizing the critical roles of neutrophils in regulating metabolic and immune pathways. Additionally, we summarize the existing therapeutic approaches that target neutrophils, highlighting the challenges, and affirming the rationale for continuing to explore neutrophils as a viable therapeutic target in BC management.

Identification and evaluation of potential probiotics against skin-ulceration disease in the Chinese tongue sole (Cynoglossus semilaevis).

In this study, three highly pathogenic bacterial strains (Vibrio harveyi TB6, Vibrio alginolyticus TN1, and Vibrio parahaemolyticus TN3) were isolated from skin ulcers and intestines of diseased Chinese tongue sole (Cynoglossus semilaevis). The bacteria were investigated using hemolytic activity tests, in vitro co-culture with intestinal epithelial cells, and artificial infection of C. semilaevis. A further 126 strains were isolated from the intestines of healthy C. semilaevis. The three pathogens were used as indicator bacteria, and the antagonistic strains were identified from the 126 strains. The activities of exocrine digestive enzymes in the strains were also tested. Four strains with antibacterial and digestive enzyme activities were obtained and the best strains, Bacillus subtilis Y2 and Bacillus amyloliquefaciens Y9, were selected according to their ability to protect epithelial cells from infection. In addition, the effects of strains Y2 and Y9 at the individual level were investigated, finding that the activities of the immune-related enzymes superoxide dismutase, catalase, acid phosphatase, and peroxidase were significantly increased in the sera of the treatment group compared with the control group (p < 0.05). The specific growth rate (SGR, %) was also increased, especially in the Y2 group, and was significantly higher compared with the controls (p < 0.05). The result of the artificial infection test showed that the cumulative mortality within 72 h in the Y2 group was the lowest (50.5%), and in the Y9 group (68.5%) it was significantly lower than that in the control group (100%) (p < 0.05). Analysis of the intestinal microbial communities indicated that Y2 and Y9 could alter the composition of the intestinal flora, increasing both species richness and evenness, and inhibiting the growth of Vibrio in the intestine. These results suggested food supplemented with Y2 and Y9 could improve both immune function and disease resistance, as well as have a positive effect on the growth performance and the intestinal morphology of C. semilaevis.

Role of Tim-3 in COVID-19: a potential biomarker and therapeutic target.

T cell immunoglobulin and mucin domain containing protein 3 (Tim-3), an immune checkpoint, is important for maintaining immune tolerance. There is increasing evidence that Tim-3 is aberrantly expressed in patients with COVID-19, indicating that it may play an important role in COVID-19. In this review, we discuss the altered expression and potential role of Tim-3 in COVID-19. The expression of Tim-3 and its soluble form (sTim-3) has been found to be upregulated in COVID-19 patients. The levels of Tim-3 on T cells and circulating sTim-3 have been shown to be associated with the severity of COVID-19, suggesting that this protein could be a potential biomarker of COVID-19. Moreover, this review also highlights the potential of Tim-3 as a therapeutic target of COVID-19.

Prediction of gestational diabetes mellitus at the first trimester: machine-learning algorithms.

PURPOSE: Short- and long-term complications of gestational diabetes mellitus (GDM) involving pregnancies and offspring warrant the development of an effective individualized risk prediction model to reduce and prevent GDM together with its associated co-morbidities. The aim is to use machine learning (ML) algorithms to study data gathered throughout the first trimester in order to predict GDM. METHODS: Two independent cohorts with forty-five features gathered through first trimester were included. We constructed prediction models based on three different algorithms and traditional logistic regression, and deployed additional two ensemble algorithms to identify the importance of individual features. RESULTS: 4799 and 2795 pregnancies were included in the Xinhua Hospital Chongming branch (XHCM) and the Shanghai Pudong New Area People's Hospital (SPNPH) cohorts, respectively. Extreme gradient boosting (XGBoost) predicted GDM with moderate performance (the area under the receiver operating curve (AUC) = 0.75) at pregnancy initiation and good-to-excellent performance (AUC = 0.99) at the end of the first trimester in the XHCM cohort. The trained XGBoost showed moderate performance in the SPNPH cohort (AUC = 0.83). The top predictive features for GDM diagnosis were pre-pregnancy BMI and maternal abdominal circumference at pregnancy initiation, and FPG and HbA1c at the end of the first trimester. CONCLUSION: Our work demonstrated that ML models based on the data gathered throughout the first trimester achieved moderate performance in the external validation cohort.

A Surprising Diversity of Xyloglucan Endotransglucosylase/Hydrolase in Wheat: New in Sight to the Roles in Drought Tolerance.

Drought has become a major limiting factor for wheat productivity, and its negative impact on crop growth is anticipated to increase with climate deterioration in arid areas. Xyloglucan endoglycosylases/hydrolases (XTHs) are involved in constructing and remodeling cell wall structures and play an essential role in regulating cell wall extensibility and stress responses. However, there are no systematic studies on the wheat XTH gene family. In this study, 71 wheat XTH genes (TaXTHs) were characterized and classified into three subgroups through phylogenetic analysis. Genomic replication promoted the expansion of TaXTHs. We found a catalytically active motif and a potential N-linked glycosylation domain in all TaXTHs. Further expression analysis revealed that many TaXTHs in the roots and shoots were significantly associated with drought stress. The wheat TaXTH12.5a gene was transferred into Arabidopsis to verify a possible role of TaXTHs in stress response. The transgenic plants possessed higher seed germination rates and longer roots and exhibited improved tolerance to drought. In conclusion, bioinformatics and gene expression pattern analysis indicated that the TaXTH genes played a role in regulating drought response in wheat. The expression of TaXTH12.5a enhanced drought tolerance in Arabidopsis and supported the XTH genes' role in regulating drought stress response in plants.

Transcriptome Dynamics during Spike Differentiation of Wheat Reveal Amazing Changes in Cell Wall Metabolic Regulators.

Coordinated cell proliferation and differentiation result in the complex structure of the inflorescence in wheat. It exhibits unique differentiation patterns and structural changes at different stages, which have attracted the attention of botanists studying the dynamic regulation of its genes. Our research aims to understand the molecular mechanisms underlying the regulation of spike development genes at different growth stages. We conducted RNA-Seq and qRT-PCR evaluations on spikes at three stages. Our findings revealed that genes associated with the cell wall and carbohydrate metabolism showed high expression levels between any two stages throughout the entire process, suggesting their regulatory role in early spike development. Furthermore, through transgenic experiments, we elucidated the role of the cell wall regulator gene in spike development regulation. These research results contribute to identifying essential genes associated with the morphology and development of wheat spike tissue.

New Fluorophore and Its Applications in Visualizing Polystyrene Nanoplastics in Bean Sprouts and HeLa Cells.

In the domain of environmental science, pollutants of nanoscale plastic dimensions are acknowledged as subjects of intricate significance. Such entities, though minuscule, present formidable challenges to ecological systems and human health. The diminutive dimensions of these contaminants render their detection arduous, thus demanding the inception of avant-garde methodologies. The present manuscript postulates the employment of the tetraphenylethylene functional group with a fused xanthene (TPEF), a distinguished fluorophore, as an exemplary system for the discernment of nanoplastic particulates. The synthesis and characterization of TPEF have been exhaustively elucidated, revealing its paramount fluorescence attributes and inherent affinity for interaction with nanoplastics. When subjected to comparison with TPEF, nanoplastics are observed to manifest a more pronounced fluorescent luminescence than when associated with the conventional Nile Red (NR). Particularly, the TPEF has shown exceptional affinity for polystyrene (PS) nanoplastics. Further, the resilience of nanoplastics within the hypocotyl epidermis of soybeans, as well as their persistence in mung bean sprouts subsequent to rigorous rinsing protocols, has been meticulously examined. Additionally, this investigation furnishes empirical data signifying the existence of nano-dimensional plastic contaminants within HeLa cellular structures. The urgency of addressing the environmental ramifications engendered by these diminutive yet potent plastic constituents is emphatically highlighted in this manuscript. TPEF paves the way for prospective explorations, with the aspiration of devising efficacious mitigation strategies. Such strategies might encompass delineating the trajectories undertaken by nanoplastics within trophic networks or their ingress into human cellular architectures.

In Situ Self-Assembled J-Aggregate Nanofibers of Glycosylated Aza-BODIPY for Synergetic Cell Membrane Disruption and Type†I Photodynamic Therapy.

The in situ self-assembly of exogenous molecules is a powerful strategy for manipulating cellular behavior. However, the direct self-assembly of photochemically inert constituents into supramolecular nano-photosensitizers (PSs) within cancer cells for precise photodynamic therapy (PDT) remains a challenge. Herein, we developed a glycosylated Aza-BODIPY compound (LMBP) capable of self-assembling into J-aggregate nanofibers in situ for cell membrane destruction and type I PDT. LMBP selectively entered human hepatocellular carcinoma HepG2 cells and subsequently self-assembled into intracellular J-aggregate nanovesicles and nanofibers through supramolecular interactions. Detailed studies revealed that these J-aggregate nanostructures generated superoxide radicals (O2 - ⋅) exclusively through photoinduced electron transfer, thus enabling effective PDT. Furthermore, the intracellular nanofibers exhibited an aggregation-induced retention effect, which resulted in selective toxicity to HepG2 cells by disrupting their cellular membranes and synergizing with PDT for powerful tumor suppression efficacy in vivo.