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  1. Novel Polyvinyl Pyrrolidone-Loaded Olopatadine HCl-Laden Doughnut Contact Lens to Treat Allergic Conjunctivitis
    Xue Y, Zhang W, Lei Y, Dang M
    J Pharm Sci, 2020 05;109(5):1714-1724.
    PMID: 32007507 DOI: 10.1016/j.xphs.2020.01.022
    Olopatadine HCl is an antiallergic drug used for the management of allergic conjunctivitis. Currently, it is delivered via eye drop solution, which is highly inefficient due to low bioavailability. Silicone contact lenses can be used to sustain the release of ophthalmic drugs. However, the presence of drug alters the optical transmittance and physical properties of the contact lens. The objective was to design a novel polyvinyl pyrrolidone (PVP)-coated olopatadine-ethyl cellulose microparticles-laden doughnut contact lens to sustained ocular delivery with limited alteration to the optical and swelling properties of the contact lens. The doughnut was implanted within the periphery of the lens using modified casting technique. Olopatadine HCl was loaded by soaking (SM-OL), direct loading (DL-OL), and doughnut casting method (DNT-OL). PVP (comfort agent) was loaded on the surface of contact lens for all the batches via novel curing technique. The in vitro olopatadine HCl release data of SM-OL (up to 48-72 h) and DL-OL batches (up to 72 h) showed high burst release, whereas DNT-OL batch showed sustained release up to 120 h without significant (p > 0.05) alteration in the optical and swelling properties of contact lens. All the batches showed sustained release of PVP up to 120 h. The in vivo studies in the rabbit tear fluid showed improvement in the olopatadine HCl and PVP retention time in comparison to eye drop solution. The PVP-loaded DNT-OL-500 lens showed tear stabilization (comfort wear) in Schirmer strip test (rabbits) with no protein adherence in comparison to DNT-OL-500 lens without PVP. The study demonstrated the successful delivery of olopatadine HCl and PVP-K30 from the doughnut contact lens for the extended period with limited alteration to the optical and swelling properties of contact lens.
  2. Fulltext Targeted teaching method combined with stepped assessment in public tennis lessons
    Huang P, Saibon JB, Xue Y
    Heliyon, 2023 Jun;9(6):e16680.
    PMID: 37292341 DOI: 10.1016/j.heliyon.2023.e16680
    In order to put students in the spotlight and make it simpler for them to understand and master the teaching topics, public tennis classes in colleges and universities used a combination of targeted teaching techniques and a staged evaluation method. A random sampling was used to select 200 students from public physical education classes at Zhuhai University of Science and Technology as the study population. They were divided into a control group and an experimental group of 100 students each (50 male and 50 female). The study found significant differences between the experimental and control groups in terms of forehand stroke, backhand stroke, technical movements, physical fitness, interest in learning, and motivation to learn. The use of the goal-based teaching technique in combination with the phased evaluation method has been shown to improve students' fundamental tennis skills, as well as their interest and motivation in learning. These results suggest that this teaching method could be effective in the instruction of public sports classes at universities.
  3. How well do we understand the basis of classic selective sweeps in humans?
    Szpak M, Xue Y, Ayub Q, Tyler-Smith C
    FEBS Lett, 2019 07;593(13):1431-1448.
    PMID: 31116407 DOI: 10.1002/1873-3468.13447
    Classic selective sweeps occur when positive selection increases a variant's frequency from low to high in a population, and underlie some long-studied human characteristics such as variation in skin, hair or eye colour. In such well-studied 'gold standard' examples, a known variant has been associated with a plausible phenotype and underlying selective force. Signatures of classic sweeps have more recently been detected in population-genetic data independently of any prior information about the corresponding phenotype or selective force, and usually without suggesting any insights into these. Motivated by the need to understand such candidates, we first review the gold standards and show that our understanding of them is often incomplete or unconvincing; only two of the examples we consider are compellingly explained. We assess approaches for large-scale association of classic sweep candidate variants to phenotypes and selective forces, test these on the gold standards, and discuss the standards of evidence needed to adequately understand a selective sweep.
  4. Fulltext Targeted DNA complementation on a 1,1'-carbonyldiimidazole-functionalized surface for identifying Mycobacterium tuberculosis
    Xu S, Xue Y, Guo F, Xu M, Gopinath SCB, Mao X
    3 Biotech, 2020 May;10(5):227.
    PMID: 32373419 DOI: 10.1007/s13205-020-02216-2
    Herein, a rapid and sensitive current-volt measurement was developed for identifying the IS6110 DNA sequence to diagnose Mycobacterium tuberculosis (TB). An aminated capture probe was immobilized on a 1,1'-carbonyldiimidazole-functionalized interdigitated electrode (IDE) silica substrate, and the target sequence was detected by complementation. It was found that all tested concentrations displayed a higher response in current changes than the control, and the limit of detection was 10 fM. The sensitivity ranged from 1 to 10 fM. The control sequences with single-, triple-mismatch and noncomplementary sequences showed great discrimination. This rapid and easy DNA detection method helps to identify M. tuberculosis for early-stage diagnosis of TB.
  5. Fulltext Inhibition of Heterogeneous Nucleation in Water by Hydrogel Coating
    Li S, Zhu P, Xue Y, Wang L, Wong TW, Yang X, et al.
    Research (Wash D C), 2023;6:0190.
    PMID: 37426472 DOI: 10.34133/research.0190
    Heterogeneous nucleation plays a critical role in the phase transition of water, which can cause damage in various systems. Here, we report that heterogeneous nucleation can be inhibited by utilizing hydrogel coatings to isolate solid surfaces and water. Hydrogels, which contain over 90% water when fully swelled, exhibit a high degree of similarity to water. Due to this similarity, there is a great energy barrier for heterogeneous nucleation along the water-hydrogel interface. Additionally, hydrogel coatings, which possess polymer networks, exhibit higher fracture energy and more robust adhesion to solid surfaces compared to water. This high fracture and adhesion energy acts as a deterrent for fracture nucleation within the hydrogel or along the hydrogel-solid interface. With a hydrogel layer approximately 100 μm thick, the boiling temperature of water under atmospheric pressure can be raised from 100 to 108 °C. Notably, hydrogel coatings also result in remarkable reductions in cavitation pressure on multiple solid surfaces. We have demonstrated the efficacy of hydrogel coatings in preventing damages resulting from acceleration-induced cavitation. Hydrogel coatings have the potential to alter the energy landscape of heterogeneous nucleation on the water-solid interface, making them an exciting avenue for innovation in heat transfer and fluidic systems.
  6. Fulltext Butylparaben weakens female fertility via causing oocyte meiotic arrest and fertilization failure in mice
    Zhang Y, Sun L, Zhang D, Gao Y, Ma H, Xue Y, et al.
    Ecotoxicol Environ Saf, 2023 Nov 01;266:115561.
    PMID: 37837697 DOI: 10.1016/j.ecoenv.2023.115561
    Butylparaben is an ubiquitous environmental endocrine disruptor, that is commonly used in cosmetics and personal care product due to its anti-microbial properties. Butylparaben has been shown to cause developmental toxicity, endocrine and metabolic disorders and immune diseases. However, little is known about the impact on female fertility, especially oocyte quality. In the present study, we reported that butylparaben influenced female fertility by showing the disturbed oocyte meiotic capacity and fertilization potential. Specifically, butylparaben results in the oocyte maturation arrest by impairing spindle/chromosome structure and microtubule stability. Besides, butylparaben results in fertilization failure by impairing the dynamics of Juno and ovastacin and the sperm binding ability. Last, single-cell transcriptome analysis showed that butylparaben-induced oocyte deterioration was caused by mitochondrial dysfunction, which led to the accumulation of ROS and occurrence of apoptosis. Collectively, our study indicates that mitochondrial dysfunction and redox perturbation is the major cause of the weakened female fertility expoesd to butylparaben.
  7. Fulltext FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations
    Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C
    Genome Biol, 2018 Jan 17;19(1):5.
    PMID: 29343290 DOI: 10.1186/s13059-017-1380-2
    We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
  8. Fulltext Copy number variation arising from gene conversion on the human Y chromosome
    Shi W, Massaia A, Louzada S, Banerjee R, Hallast P, Chen Y, et al.
    Hum Genet, 2018 Jan;137(1):73-83.
    PMID: 29209947 DOI: 10.1007/s00439-017-1857-9
    We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0-3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fibre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project. Mapping the changes in copy number to the phylogeny of these Y chromosomes previously established by the Project identified at least 20 mutational events, and investigation of flanking paralogous sequence variants showed that the mutations involved flanking sequences in 18 of these, and could extend over > 30 kb of DNA. While either gene conversion or double crossover between misaligned sister chromatids could formally explain the 0-2 copy events, gene conversion is the more likely mechanism, and these events include the longest non-allelic gene conversion reported thus far. Chromosomes with three copies of this CNV have arisen just once in our data set via another mechanism: duplication of 420 kb that places the third copy 230 kb proximal to the existing proximal copy. Our results establish gene conversion as a previously under-appreciated mechanism of generating copy number changes in humans and reveal the exceptionally large size of the conversion events that can occur.
  9. Fulltext Positive selection in Europeans and East-Asians at the ABCA12 gene
    Sirica R, Buonaiuto M, Petrella V, Sticco L, Tramontano D, Antonini D, et al.
    Sci Rep, 2019 03 19;9(1):4843.
    PMID: 30890716 DOI: 10.1038/s41598-019-40360-9
    Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation. We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation. We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons and the transcription starting site of ABCA12. We found no obvious effect of rs10180970 alleles on ABCA12 gene expression. We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and present in non-Africans 45,000 years ago.
  10. Fulltext A Positively Selected MAGEE2 LoF Allele Is Associated with Sexual Dimorphism in Human Brain Size and Shows Similar Phenotypes in Magee2 Null Mice
    Szpak M, Collins SC, Li Y, Liu X, Ayub Q, Fischer MC, et al.
    Mol Biol Evol, 2021 Dec 09;38(12):5655-5663.
    PMID: 34464968 DOI: 10.1093/molbev/msab243
    A nonsense allele at rs1343879 in human MAGEE2 on chromosome X has previously been reported as a strong candidate for positive selection in East Asia. This premature stop codon causing ∼80% protein truncation is characterized by a striking geographical pattern of high population differentiation: common in Asia and the Americas (up to 84% in the 1000 Genomes Project East Asians) but rare elsewhere. Here, we generated a Magee2 mouse knockout mimicking the human loss-of-function mutation to study its functional consequences. The Magee2 null mice did not exhibit gross abnormalities apart from enlarged brain structures (13% increased total brain area, P = 0.0022) in hemizygous males. The area of the granular retrosplenial cortex responsible for memory, navigation, and spatial information processing was the most severely affected, exhibiting an enlargement of 34% (P = 3.4×10-6). The brain size in homozygous females showed the opposite trend of reduced brain size, although this did not reach statistical significance. With these insights, we performed human association analyses between brain size measurements and rs1343879 genotypes in 141 Chinese volunteers with brain MRI scans, replicating the sexual dimorphism seen in the knockout mouse model. The derived stop gain allele was significantly associated with a larger volume of gray matter in males (P = 0.00094), and smaller volumes of gray (P = 0.00021) and white (P = 0.0015) matter in females. It is unclear whether or not the observed neuroanatomical phenotypes affect behavior or cognition, but it might have been the driving force underlying the positive selection in humans.
  11. Sustainable Approach for the Synthesis of a Semicrystalline Polymer with a Reversible Shape-Memory Effect
    Wong JW, Yang X, Zhao Q, Xue Y, Lok TJ, Wang L, et al.
    ACS Macro Lett, 2023 Apr 13.
    PMID: 37052196 DOI: 10.1021/acsmacrolett.3c00017
    Shape-memory polymers (SMPs) have demonstrated potential for use in automotive, biomedical, and aerospace industries. However, ensuring the sustainability of these materials remains a challenge. Herein, a sustainable approach to synthesize a semicrystalline polymer using biomass-derivable precursors via catalyst-free polyesterification is presented. The synthesized biodegradable polymer, poly(1,8-octanediol-co-1,12-dodecanedioate-co-citrate) (PODDC), exhibits excellent shape-memory properties, as evidenced by good shape fixity and shape recovery ratios of 98%, along with a large reversible actuation strain of 28%. Without the use of a catalyst, the mild polymerization enables the reconfiguration of the partially cured two-dimensional (2D) film to a three-dimensional (3D) geometric form in the middle process. This study appears to be a step forward in developing sustainable SMPs and a simple way for constructing a 3D structure of a permanent shape.
  12. Fulltext Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations
    Arciero E, Kraaijenbrink T, Asan, Haber M, Mezzavilla M, Ayub Q, et al.
    Mol Biol Evol, 2018 Aug 01;35(8):1916-1933.
    PMID: 29796643 DOI: 10.1093/molbev/msy094
    We genotyped 738 individuals belonging to 49 populations from Nepal, Bhutan, North India, or Tibet at over 500,000 SNPs, and analyzed the genotypes in the context of available worldwide population data in order to investigate the demographic history of the region and the genetic adaptations to the harsh environment. The Himalayan populations resembled other South and East Asians, but in addition displayed their own specific ancestral component and showed strong population structure and genetic drift. We also found evidence for multiple admixture events involving Himalayan populations and South/East Asians between 200 and 2,000 years ago. In comparisons with available ancient genomes, the Himalayans, like other East and South Asian populations, showed similar genetic affinity to Eurasian hunter-gatherers (a 24,000-year-old Upper Palaeolithic Siberian), and the related Bronze Age Yamnaya. The high-altitude Himalayan populations all shared a specific ancestral component, suggesting that genetic adaptation to life at high altitude originated only once in this region and subsequently spread. Combining four approaches to identifying specific positively selected loci, we confirmed that the strongest signals of high-altitude adaptation were located near the Endothelial PAS domain-containing protein 1 and Egl-9 Family Hypoxia Inducible Factor 1 loci, and discovered eight additional robust signals of high-altitude adaptation, five of which have strong biological functional links to such adaptation. In conclusion, the demographic history of Himalayan populations is complex, with strong local differentiation, reflecting both genetic and cultural factors; these populations also display evidence of multiple genetic adaptations to high-altitude environments.
  13. Fulltext Association between type 2 diabetes, alcohol intake frequency, age at menarche, and gallbladder cancer: a two-sample Mendelian randomization study
    Cheng M, Zhou X, Xue Y, Zhou E, Hu J, Xu J, et al.
    J Gastrointest Oncol, 2024 Jun 30;15(3):1214-1223.
    PMID: 38989400 DOI: 10.21037/jgo-24-358
    BACKGROUND: Gallbladder cancer (GBC) is a rare malignancy of the digestive tract, characterized by a remarkably poor prognosis. Currently, there is a controversy on the relationship between type 2 diabetes (T2D) and GBC. Additionally, no definitive conclusions were established regarding the causal relationships between alcohol intake frequency (AIF), age at menarche (AAM) and GBC. The objective of this study was to elucidate the causal association between T2D, AIF, AAM, and GBC.

    METHODS: Single-nucleotide polymorphisms (SNPs) associated with exposures and outcomes were sourced from the Integrative Epidemiology Unit (IEU) Open Genome-Wide Association Study (GWAS) database. Specifically, the data of GBC comprised 907 East Asians (pathological results of all cases were registered into Biobank Japan) and 425,707 SNPs; T2D comprised 655,666 Europeans with 5,030,727 SNPs; AIF comprised 462,346 Europeans and 9,851,867 SNPs; AAM comprised 243,944 Europeans and 9,851,867 SNPs. The measurement of exposure traits is collected uniformly from the UK Biobank (UKB) database and presented in the form of standard deviation (SD) or the logarithmic form of the odds ratio (logOR). We employed a two-sample Mendelian randomization (MR) analysis to discern the causalities between T2D, AIF, AAM, and GBC. Sensitivity analyses were conducted to identify and address potential heterogeneity, horizontal pleiotropy, and outliers.

    RESULTS: Our findings indicated that T2D reduced GBC risk [odds ratio (OR) =0.044; 95% confidence interval (CI): 0.004-0.55; P=0.015, inverse variance-weighted (IVW)]. However, no causal relationship was observed between AIF (OR =0.158; 95% CI: 5.33E-05 to 466.84; P=0.65, IVW), AAM (OR =0.19; 95% CI: 0.0003-140.34; P=0.62, IVW), and GBC. Sensitivity analysis revealed no evidence of horizontal pleiotropy, heterogeneity, or outliers, suggesting the robustness and reliability of our conclusions.

    CONCLUSIONS: T2D emerged as a potentially protective factor against GBC, whereas neither AIF nor AAM demonstrated a causal relationship with GBC risk. Regulation of glucose metabolism may be one of the methods for preventing GBC.

  14. Intrinsic Permanent Shape Reconfigurable Semicrystalline Biopolyester Thermoset
    Chen X, Wong JW, Low JT, Lok TJ, Xue Y, Zeng Z, et al.
    ACS Macro Lett, 2024 Aug 20;13(8):1037-1042.
    PMID: 39078044 DOI: 10.1021/acsmacrolett.4c00266
    Catalyst-free, volatile organic solvent (VOC)-free synthesis of biobased cross-linked polymers is an important sustainable feature in polyesterification. To date, these polyesters have been extensively studied for their fundamental sustainability across various uses. The ultimate potential sustainability for these materials, however, is constrained to static structural parts due to their intractable rigid three-dimensional (3D) network. Here, we reveal intrinsic dynamic exchangeable bonds within this type of cross-linked semicrystalline network, poly(1,8-octanediol-co-1,12-docanedioate-co-citrate) (PODDC), enabling permanent shape reconfigurability. Annealing at slightly above melting-transition temperature (Tm) allows for shape reconfigurability up to nine times, comparable in performance to the existing bond-exchange systems. No reagents are involved from synthesis to shape reconfiguration, suggesting an exciting feature exhibited by this sustainable cross-linked material without the need for further chemical modification. We further extend this benefit of reconfigurability to enable flexible shape design in a smart shape-memory polymer (SMP), showing it as one of its potential applications. After its applications, it can undergo hydrolytic degradation. We envision that such multifaceted sustainability for the material will attract interest in environmentally friendly applications such as fabricating external part of soft robots and shape-morphing devices with reduced environmental impact.
  15. Fulltext Bioinspired soft robots for deep-sea exploration
    Li G, Wong TW, Shih B, Guo C, Wang L, Liu J, et al.
    Nat Commun, 2023 Nov 04;14(1):7097.
    PMID: 37925504 DOI: 10.1038/s41467-023-42882-3
    The deep ocean, Earth's untouched expanse, presents immense challenges for exploration due to its extreme pressure, temperature, and darkness. Unlike traditional marine robots that require specialized metallic vessels for protection, deep-sea species thrive without such cumbersome pressure-resistant designs. Their pressure-adaptive forms, unique propulsion methods, and advanced senses have inspired innovation in designing lightweight, compact soft machines. This perspective addresses challenges, recent strides, and design strategies for bioinspired deep-sea soft robots. Drawing from abyssal life, it explores the actuation, sensing, power, and pressure resilience of multifunctional deep-sea soft robots, offering game-changing solutions for profound exploration and operation in harsh conditions.
  16. Fulltext Insights into human genetic variation and population history from 929 diverse genomes
    Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, et al.
    Science, 2020 Mar 20;367(6484).
    PMID: 32193295 DOI: 10.1126/science.aay5012
    Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.
  17. Fulltext Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome
    Shi W, Louzada S, Grigorova M, Massaia A, Arciero E, Kibena L, et al.
    Hum Mol Genet, 2019 Aug 15;28(16):2785-2798.
    PMID: 31108506 DOI: 10.1093/hmg/ddz101
    Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10-3 (95% CI 1.94 × 10-3 to 2.48 × 10-3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.
  18. Fulltext Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders
    Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, et al.
    Curr Biol, 2019 01 07;29(1):149-157.e3.
    PMID: 30581024 DOI: 10.1016/j.cub.2018.11.029
    The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.
  19. Fulltext Ghost admixture in eastern gorillas
    Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, et al.
    Nat Ecol Evol, 2023 Sep;7(9):1503-1514.
    PMID: 37500909 DOI: 10.1038/s41559-023-02145-2
    Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
  20. Fulltext Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique
    Cao Y, Chen L, Chen H, Cun Y, Dai X, Du H, et al.
    Natl Sci Rev, 2023 Apr;10(4):nwac287.
    PMID: 37089192 DOI: 10.1093/nsr/nwac287
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