Background and Aims: Narrowed or shifted window of implantation (WOI) is acknowledged to be one of the endometrial origins of embryo implantation failure, especially in patients with repeated ...implantation failure (RIF). RNA-Seq-based endometrial receptivity test (rsERT) was developed to assess the endometrial receptivity (ER) and guide the personalized embryo transfer (pET). Clinical studies were conducted to evaluate the clinical utility of rsERT in RIF patients. Method: 566 RIF patients with rsERT and pET in multi-centers from 2019-2022 were included in this retrospective study, which was defined as rsERT-pET group. RIF patients without rsERT and pET in the same period was used as control for comparison. rsERT-pET group was further divided into normal WOI (nWOI) and shifted WOI (sWOI) groups. Clinical pregnancy rate and ongoing pregnancy rate were therefore compared among these groups by nonparametric statistical approaches. Results: The intrauterine pregnancy and ongoing pregnancy rates of rsERT-pET group were receptively 55.0% and 46.2%, which were significantly higher than those of the control group (55.0% vs 35.1%, OR = 2.26, p-value = 2.33×10Formula: see text; 46.2% vs 19.8%, OR = 3.45, p-value = 4.08×10Formula: see text ). We further evaluated the intrauterine pregnancy rates of sWOI and nWOI and found remarkably better pregnancy outcomes in patients from nWOI group compared to those in sWOI group patients (62.4% vs 50.4%, OR = 1.64, p-value = 0.005). Conclusion: The pET guided by the result of rsERT significantly improved the clinical outcomes in patients with RIF based on the intrauterine pregnancy rate and the ongoing pregnancy rate, indicating the clinical potential of rsERT method.
Background and Aims: Chromosomal abnormalities are frequently observed in early human embryos, particularly in patients experiencing repeated pregnancy loss (RPL) or repeated implantation failure ...(RIF). Although preimplantation genetic testing for aneuploidy (PGT-A) is a common technique for screening embryo ploidy, it comes with the risks associated with embryo biopsy. To address this issue, we developed the NICS assay, which evaluates embryos using spent culture medium (SCM) and thus reduces the risks associated with embryo biopsy. However, further evaluation is required to determine the clinical applicability of NICS for patients with RPL or RIF. Method: This retrospective cohort study analyzed 303 patients with RPL or RIF between July 2018 and May 2021. These patients underwent aneuploidy screening using the NICS assay and were thus categorized into the NICS group. The non-NICS group consisted of patients who received conventional morphology embryo transfer during the same period. Routine intracytoplasmic sperm injection (ICSI) was performed, and the embryos were placed in droplets. Approximately 30 Formula: see text L of blastocyst medium from each embryo was transferred into cell lysis buffer, followed by DNA library preparation using the ChromInst kit from Yikon Genomics. Results: In patients with RPL, the NICS group demonstrated significantly lower rates of miscarriage per frozen embryo transfer (FET) than the non-NICS group, 17.9% vs 42.6%. Furthermore, the NICS group exhibited significantly higher rates of ongoing pregnancies (40.7% vs 25.0%) and live births (38.9% vs 20.6%) compared to the non-NICS group. In the case of patients with RIF, the NICS group showed higher clinical pregnancy rates per FET compared to the non-NICS group. Specifically, the clinical pregnancy rates, 46.9% vs 28.7%. Conclusion: The present study demonstrates that the use of NICS for selecting euploid embryos can effectively reduce the incidence of miscarriage in patients experiencing RPL, as well as improve the clinical pregnancy rate in those experiencing RIF.
We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification ...(MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.
Soybean (Glycine max) serves as a major source of protein and edible oils worldwide. The genetic and genomic bases of the adaptation of soybean to tropical regions remain largely unclear. Here, we ...identify the novel locus Time of Flowering 16 (Tof16), which confers delay flowering and improve yield at low latitudes and determines that it harbors the soybean homolog of LATE ELONGATED HYPOCOTYL (LHY). Tof16 and the previously identified J locus genetically additively but independently control yield under short-day conditions. More than 80% accessions in low latitude harbor the mutations of tof16 and j, which suggests that loss of functions of Tof16 and J are the major genetic basis of soybean adaptation into tropics. We suggest that maturity and yield traits can be quantitatively improved by modulating the genetic complexity of various alleles of the LHY homologs, J and E1. Our findings uncover the adaptation trajectory of soybean from its temperate origin to the tropics.
Kindred cells can have different genomes because of dynamic changes in DNA. Single-cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome ...amplification bias, resulting in low genome coverage. Here, we report on a new amplification method—multiple annealing and looping-based amplification cycles (MALBAC)—that offers high uniformity across the genome. Sequencing MALBAC-amplified DNA achieves 93% genome coverage ≥1x for a single human cell at 25x mean sequencing depth. We detected digitized copy-number variations (CNVs) of a single cancer cell. By sequencing three kindred cells, we were able to identify individual single-nucleotide variations (SNVs), with no false positives detected. We directly measured the genome-wide mutation rate of a cancer cell line and found that purine-pyrimidine exchanges occurred unusually frequently among the newly acquired SNVs.
Spiking neural networks (SNNs) are brain-inspired machine learning algorithms with merits such as biological plausibility and unsupervised learning capability. Previous works have shown that ...converting Artificial Neural Networks (ANNs) into SNNs is a practical and efficient approach for implementing an SNN. However, the basic principle and theoretical groundwork are lacking for training a non-accuracy-loss SNN. This paper establishes a precise mathematical mapping between the biological parameters of the Linear Leaky-Integrate-and-Fire model (LIF)/SNNs and the parameters of ReLU-AN/Deep Neural Networks (DNNs). Such mapping relationship is analytically proven under certain conditions and demonstrated by simulation and real data experiments. It can serve as the theoretical basis for the potential combination of the respective merits of the two categories of neural networks.
The quest for ultrahigh detection sensitivity with spectroscopic contrasts other than fluorescence has led to various novel approaches to optical microscopy of biological systems. Coherent nonlinear ...optical imaging, especially the recently developed nonlinear dissipation microscopy (including stimulated Raman scattering and two-photon absorption) and pump-probe microscopy (including excited-state absorption, stimulated emission, and ground-state depletion), provides new image contrasts for nonfluorescent species. Thanks to the high-frequency modulation transfer scheme, these imaging techniques exhibit superb detection sensitivity. By directly interrogating vibrational and/or electronic energy levels of molecules, they offer high molecular specificity. Here we review the underlying principles and excitation and detection schemes, as well as exemplary biomedical applications of this emerging class of molecular imaging techniques.
Adaptive changes in plant phenology are often considered to be a feature of the so-called 'domestication syndrome' that distinguishes modern crops from their wild progenitors, but little detailed ...evidence supports this idea. In soybean, a major legume crop, flowering time variation is well characterized within domesticated germplasm and is critical for modern production, but its importance during domestication is unclear. Here, we identify sequential contributions of two homeologous pseudo-response-regulator genes, Tof12 and Tof11, to ancient flowering time adaptation, and demonstrate that they act via LHY homologs to promote expression of the legume-specific E1 gene and delay flowering under long photoperiods. We show that Tof12-dependent acceleration of maturity accompanied a reduction in dormancy and seed dispersal during soybean domestication, possibly predisposing the incipient crop to latitudinal expansion. Better understanding of this early phase of crop evolution will help to identify functional variation lost during domestication and exploit its potential for future crop improvement.
Whole-genome amplification (WGA) for next-generation sequencing has seen wide applications in biology and medicine when characterization of the genome of a single cell is required. High uniformity ...and fidelity of WGA is needed to accurately determine genomic variations, such as copy number variations (CNVs) and single-nucleotide variations (SNVs). Prevailing WGA methods have been limited by fluctuation of the amplification yield along the genome, as well as false-positive and -negative errors for SNV identification. Here, we report emulsion WGA (eWGA) to overcome these problems. We divide single-cell genomic DNA into a large number (10⁵) of picoliter aqueous droplets in oil. Containing only a few DNA fragments, each droplet is led to reach saturation of DNA amplification before demulsification such that the differences in amplification gain among the fragments are minimized. We demonstrate the proof-of-principle of eWGA with multiple displacement amplification (MDA), a popular WGA method. This easy-to-operate approach enables simultaneous detection of CNVs and SNVs in an individual human cell, exhibiting significantly improved amplification evenness and accuracy.
Photoperiod sensitivity is a key factor in plant adaptation and crop production. In the short-day plant soybean, adaptation to low latitude environments is provided by mutations at the
locus, which ...confer extended flowering phase and thereby improve yield. The identity of
as an ortholog of
, a component of the circadian evening complex (EC), implies that orthologs of other EC components may have similar roles. Here we show that the two soybean homeologs of LUX ARRYTHMO interact with J to form a soybean EC. Characterization of mutants reveals that these genes are highly redundant in function but together are critical for flowering under short day, where the
double mutant shows extremely late flowering and a massively extended flowering phase. This phenotype exceeds that of any soybean flowering mutant reported to date, and is strongly reminiscent of the "Maryland Mammoth" tobacco mutant that featured in the seminal 1920 study of plant photoperiodism by Garner and Allard W. W. Garner, H. A. Allard, J. Agric. Res. 18, 553-606 (1920). We further demonstrate that the J-LUX complex suppresses transcription of the key flowering repressor
and its two homologs via LUX binding sites in their promoters. These results indicate that the EC-E1 interaction has a central role in soybean photoperiod sensitivity, a phenomenon also first described by Garner and Allard. EC and E1 family genes may therefore constitute key targets for customized breeding of soybean varieties with precise flowering time adaptation, either by introgression of natural variation or generation of new mutants by gene editing.
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