Nutrient status changes bacterial interactions in a synthetic community.

Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.IMPORTANCEUnderstanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.

Classification of Benign-Malignant Thyroid Nodules Based on Hyperspectral Technology.

In recent years, the incidence of thyroid cancer has rapidly increased. To address the issue of the inefficient diagnosis of thyroid cancer during surgery, we propose a rapid method for the diagnosis of benign and malignant thyroid nodules based on hyperspectral technology. Firstly, using our self-developed thyroid nodule hyperspectral acquisition system, data for a large number of diverse thyroid nodule samples were obtained, providing a foundation for subsequent diagnosis. Secondly, to better meet clinical practical needs, we address the current situation of medical hyperspectral image classification research being mainly focused on pixel-based region segmentation, by proposing a method for nodule classification as benign or malignant based on thyroid nodule hyperspectral data blocks. Using 3D CNN and VGG16 networks as a basis, we designed a neural network algorithm (V3Dnet) for classification based on three-dimensional hyperspectral data blocks. In the case of a dataset with a block size of 50 × 50 × 196, the classification accuracy for benign and malignant samples reaches 84.63%. We also investigated the impact of data block size on the classification performance and constructed a classification model that includes thyroid nodule sample acquisition, hyperspectral data preprocessing, and an algorithm for thyroid nodule classification as benign and malignant based on hyperspectral data blocks. The proposed model for thyroid nodule classification is expected to be applied in thyroid surgery, thereby improving surgical accuracy and providing strong support for scientific research in related fields.

Rapid Determination of Positive-Negative Bacterial Infection Based on Micro-Hyperspectral Technology.

To meet the demand for rapid bacterial detection in clinical practice, this study proposed a joint determination model based on spectral database matching combined with a deep learning model for the determination of positive-negative bacterial infection in directly smeared urine samples. Based on a dataset of 8124 urine samples, a standard hyperspectral database of common bacteria and impurities was established. This database, combined with an automated single-target extraction, was used to perform spectral matching for single bacterial targets in directly smeared data. To address the multi-scale features and the need for the rapid analysis of directly smeared data, a multi-scale buffered convolutional neural network, MBNet, was introduced, which included three convolutional combination units and four buffer units to extract the spectral features of directly smeared data from different dimensions. The focus was on studying the differences in spectral features between positive and negative bacterial infection, as well as the temporal correlation between positive-negative determination and short-term cultivation. The experimental results demonstrate that the joint determination model achieved an accuracy of 97.29%, a Positive Predictive Value (PPV) of 97.17%, and a Negative Predictive Value (NPV) of 97.60% in the directly smeared urine dataset. This result outperformed the single MBNet model, indicating the effectiveness of the multi-scale buffered architecture for global and large-scale features of directly smeared data, as well as the high sensitivity of spectral database matching for single bacterial targets. The rapid determination solution of the whole process, which combines directly smeared sample preparation, joint determination model, and software analysis integration, can provide a preliminary report of bacterial infection within 10 min, and it is expected to become a powerful supplement to the existing technologies of rapid bacterial detection.

Design of Optical System for Ultra-Large Range Line-Sweep Spectral Confocal Displacement Sensor.

The spectrum confocal displacement sensor is an innovative type of photoelectric sensor. The non-contact advantages of this method include the capacity to obtain highly accurate measurements without inflicting any harm as well as the ability to determine the object's surface contour recovery by reconstructing the measurement data. Consequently, it has been widely used in the field of three-dimensional topographic measuring. The spectral confocal displacement sensor consists of a light source, a dispersive objective, and an imaging spectrometer. The scanning mode can be categorized into point scanning and line scanning. Point scanning is inherently present when the scanning efficiency is low, resulting in a slower measurement speed. Further improvements are necessary in the research on the line-scanning type. It is crucial to expand the measurement range of existing studies to overcome the limitations encountered during the detection process. The objective of this study is to overcome the constraints of the existing line-swept spectral confocal displacement sensor's limited measuring range and lack of theoretical foundation for the entire system. This is accomplished by suggesting an appropriate approach for creating the optical design of the dispersive objective lens in the line-swept spectral confocal displacement sensor. Additionally, prism-grating beam splitting is employed to simulate and analyze the imaging spectrometer's back end. The combination of a prism and a grating eliminates the spectral line bending that occurs in the imaging spectrometer. The results indicate that a complete optical pathway for the line-scanning spectral confocal displacement sensor has been built, achieving an axial resolution of 0.8 µm, a scanning line length of 24 mm, and a dispersion range of 3.9 mm. This sensor significantly expands the range of measurements and fills a previously unaddressed gap in the field of analyzing the current stage of line-scanning spectral confocal displacement sensors. This is a groundbreaking achievement for both the sensor itself and the field it operates in. The line-scanning spectral confocal displacement sensor's design addresses a previously unmet need in systematic analysis by successfully obtaining a wide measuring range. This provides systematic theoretical backing for the advancement of the sensor, which has potential applications in the industrial detection of various ranges and complicated objects.

Safety of early cumulus cell removal combined with early rescue ICSI in the prevention of fertilization failure.

RESEARCH QUESTION: What are the clinical outcomes and safety implications of early cumulus cell removal after short-term insemination combined with early rescue intracytoplasmic sperm injection (ICSI) in preventing fertilization failure? DESIGN: In this retrospective study, a total of 14,360 cycles were divided into four groups based on insemination method and fertilization ability: conventional IVF group (n = 5519); early cumulus cell removal group (n = 4107); conventional ICSI group (n = 4215); and early rescue ICSI group (where failed or low fertilization was predicted, n = 519). Fertilization outcomes, pregnancy outcomes, neonatal outcomes and birth defects were analysed by comparing the early cumulus cell removal group with the conventional IVF group, and the early rescue ICSI group with the conventional ICSI group. RESULTS: There were no significant differences in the outcomes of fertilization, pregnancy, neonates or birth defects between the conventional IVF group and the early cumulus cell removal group (P > 0.05). When compared with the conventional ICSI group, the early rescue ICSI group had similar rates of two pronuclei (2PN) at fertilization, clinical pregnancy, miscarriage, ectopic pregnancy, live birth, sex, mean gestational age, very low birthweight, macrosomia and birth defects (P > 0.05) but a higher polyploidy rate, lower high-quality embryo rate (both P < 0.001), lower twin pregnancy rate (P < 0.01), lower rate of low birthweight, and a higher rate of normal birthweight (both P = 0.024). CONCLUSIONS: Early cumulus cell removal combined with early rescue ICSI led to good pregnancy and neonatal outcomes without an increase in birth defects. This approach could therefore be an effective and safe method for patients with fertilization failure in conventional IVF.

Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs.

Transfer RNA is heavily modified and plays a central role in protein synthesis and cellular functions. Here we demonstrate that ALKBH3 is a 1-methyladenosine (m1A) and 3-methylcytidine (m3C) demethylase of tRNA. ALKBH3 can promote cancer cell proliferation, migration and invasion. In vivo study confirms the regulation effects of ALKBH3 on growth of tumor xenograft. The m1A demethylated tRNA is more sensitive to angiogenin (ANG) cleavage, followed by generating tRNA-derived small RNAs (tDRs) around the anticodon regions. tDRs are conserved among species, which strengthen the ribosome assembly and prevent apoptosis triggered by cytochrome c (Cyt c). Our discovery opens a potential and novel paradigm of tRNA demethylase, which regulates biological functions via generation of tDRs.

METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity.

METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell (mESC). While comparable global hypo-methylation in RNA m6A was observed in Mettl3 or Mettl14 knockout mESCs, respectively. Mettl14 knockout led to a globally decreased nascent RNA synthesis, whereas Mettl3 depletion resulted in transcription upregulation, suggesting that METTL14 might possess an m6A-independent role in gene regulation. We found that METTL14 colocalizes with the repressive H3K27me3 modification. Mechanistically, METTL14, but not METTL3, binds H3K27me3 and recruits KDM6B to induce H3K27me3 demethylation independent of METTL3. Depletion of METTL14 thus led to a global increase in H3K27me3 level along with a global gene suppression. The effects of METTL14 on regulation of H3K27me3 is essential for the transition from self-renewal to differentiation of mESCs. This work reveals a regulatory mechanism on heterochromatin by METTL14 in a manner distinct from METTL3 and independently of m6A, and critically impacts transcriptional regulation, stemness maintenance, and differentiation of mESCs.

Staging of Skin Cancer Based on Hyperspectral Microscopic Imaging and Machine Learning.

Skin cancer, a common type of cancer, is generally divided into basal cell carcinoma (BCC), squamous cell carcinoma (SCC) and malignant melanoma (MM). The incidence of skin cancer has continued to increase worldwide in recent years. Early detection can greatly reduce its morbidity and mortality. Hyperspectral microscopic imaging (HMI) technology can be used as a powerful tool for skin cancer diagnosis by reflecting the changes in the physical structure and microenvironment of the sample through the differences in the HMI data cube. Based on spectral data, this work studied the staging identification of SCC and the influence of the selected region of interest (ROI) on the staging results. In the SCC staging identification process, the optimal result corresponded to the standard normal variate transformation (SNV) for spectra preprocessing, the partial least squares (PLS) for dimensionality reduction, the hold-out method for dataset partition and the random forest (RF) model for staging identification, with the highest staging accuracy of 0.952 ± 0.014, and a kappa value of 0.928 ± 0.022. By comparing the staging results based on spectral characteristics from the nuclear compartments and peripheral regions, the spectral data of the nuclear compartments were found to contribute more to the accurate staging of SCC.

m6 A reader protein YTHDF2 regulates spermatogenesis by timely clearance of phase-specific transcripts.

OBJECTIVES: Accumulating evidences show that the regulatory network of m6 A modification is essential for mammalian spermatogenesis. However, as an m6 A reader, the roles of YTHDF2 remain enigmatic due to the lack of a proper model. Here, we employed the germ cell conditional knockout mouse model and explored the function of YTHDF2 in spermatogenesis. MATERIALS AND METHODS: Ythdf2 germ cell conditional knockout mice were obtained by crossing Ythdf2-floxed mice with Vasa-Cre and Stra8-Cre mice. Haematoxylin and eosin (HE) staining, immunofluorescent staining and Western blotting were used for phenotyping. CASA, IVF and ICSI were applied for sperm function analysis. RNA-seq, YTHDF2-RIP-seq and quantitative real-time PCR were used to explore transcriptome changes and molecular mechanism analysis. RESULTS: Our results showed that YTHDF2 was highly expressed in spermatogenic cells. The germ cell conditional knockout males were sterile, and their sperm displayed malformation, impaired motility, and lost fertilization ability. During differentiated spermatogonia transiting to pachytene spermatocyte, most m6 A-modified YTHDF2 targets that were degraded in control germ cells persisted in pachytene spermatocytes of Ythdf2-vKO mice. These delayed mRNAs were mainly enriched in pathways related to the regulation of transcription, and disturbed the transcriptome of round spermatid and elongated spermatid subsequently. CONCLUSION: Our data demonstrate that YTHDF2 facilitates the timely turnover of phase-specific transcripts to ensure the proper progression of spermatogenesis, which highlights a critical role of YTHDF2 in spermatogenesis.

N6-methyladenosine regulates maternal RNA maintenance in oocytes and timely RNA decay during mouse maternal-to-zygotic transition.

N6-methyladenosine (m6A) and its regulatory components play critical roles in various developmental processes in mammals. However, the landscape and function of m6A in early embryos remain unclear owing to limited materials. Here we developed a method of ultralow-input m6A RNA immunoprecipitation followed by sequencing to reveal the transcriptome-wide m6A landscape in mouse oocytes and early embryos and found unique enrichment and dynamics of m6A RNA modifications on maternal and zygotic RNAs, including the transcripts of transposable elements MTA and MERVL. Notably, we found that the maternal protein KIAA1429, a component of the m6A methyltransferase complex, was essential for m6A deposition on maternal mRNAs that undergo decay after zygotic genome activation and MTA transcripts to maintain their stability in oocytes. Interestingly, m6A methyltransferases, especially METTL3, deposited m6A on mRNAs transcribed during zygotic genome activation and ensured their decay after the two-cell stage, including Zscan4 and MERVL. Together, our findings uncover the essential functions of m6A in specific contexts during the maternal-to-zygotic transition, namely ensuring the stability of mRNAs in oocytes and the decay of two-cell-specific transcripts after fertilization.

Oocyte competence is maintained by m6A methyltransferase KIAA1429-mediated RNA metabolism during mouse follicular development.

KIAA1429 (also known as vir-like m6A methyltransferase-associated protein (VIRMA)), a newly identified component of the RNA m6A methyltransferase complex, plays critical roles in guiding region-selective m6A deposition. However, in mammals, whether KIAA1429 mediates RNA m6A regulatory pathway functions in vivo remains unknown. Here, we show that the Kiaa1429-specific deficiency in oocytes resulted in female infertility with defective follicular development and fully grown germinal vesicle (GV) oocytes failing to undergo germinal vesicle breakdown (GVBD) and consequently losing the ability to resume meiosis. The oocyte growth is accompanied by the accumulation of abundant RNAs and posttranscriptional regulation. We found that the loss of Kiaa1429 could also lead to abnormal RNA metabolism in GV oocytes. RNA-seq profiling revealed that Kiaa1429 deletion altered the expression pattern of the oocyte-derived factors essential for follicular development. In addition, our data show that the conditional depletion of Kiaa1429 decreased the m6A levels in oocytes and mainly affected the alternative splicing of genes associated with oogenesis. In summary, the m6A methyltransferase KIAA1429-mediated RNA metabolism plays critical roles in folliculogenesis and the maintenance of oocyte competence.

Nuclear Exosome Targeting Complex Core Factor Zcchc8 Regulates the Degradation of LINE1 RNA in Early Embryos and Embryonic Stem Cells.

The nuclear exosome targeting (NEXT) complex is responsible for specific nuclear RNA degradation in mammalian cells. However, its function in development remains unknown. Here, we find that the depletion of a central factor of the NEXT complex, Zcchc8, in mouse results in developmental defects, a shortened lifespan, and infertility. We find that Zcchc8-deficient embryonic stem cells (ESCs) exhibit proliferation abnormalities and reduced developmental potencies. Importantly, the transcripts of retrotransposon element LINE1 are found to be targeted by Zcchc8 and degraded by a Zcchc8-mediated mechanism. We further find that sustained expression of higher levels of LINE1 RNA is detected in maternal Zcchc8-depleted oocytes and embryos. Zcchc8-depleted oocytes show higher chromatin accessibility and developmental defects in both meiotic maturation and embryogenesis after fertilization. Collectively, our study defines Zcchc8-mediated RNA degradation as an important post-transcription regulation of LINE1 transcripts in early embryos and ESCs, which play vital roles in the pluripotency and early development.

Author Correction: Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.

In the initial published version of this article, there was an inadvertent omission from the Acknowledgements that this work was supported by Stowers Institute for Medical Research (SIMR-1004) and NIH National Cancer Institute grant to University of Kansas Cancer Center (P30 CA168524). This omission does not affect the description of the results or the conclusions of this work.

Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.

Transplantation of hematopoietic stem cells (HSCs) from human umbilical cord blood (hUCB) holds great promise for treating a broad spectrum of hematological disorders including cancer. However, the limited number of HSCs in a single hUCB unit restricts its widespread use. Although extensive efforts have led to multiple methods for ex vivo expansion of human HSCs by targeting single molecules or pathways, it remains unknown whether it is possible to simultaneously manipulate the large number of targets essential for stem cell self-renewal. Recent studies indicate that N6-methyladenosine (m6A) modulates the expression of a group of mRNAs critical for stem cell-fate determination by influencing their stability. Among several m6A readers, YTHDF2 is recognized as promoting targeted mRNA decay. However, the physiological functions of YTHDF2 in adult stem cells are unknown. Here we show that following the conditional knockout (KO) of mouse Ythdf2 the numbers of functional HSC were increased without skewing lineage differentiation or leading to hematopoietic malignancies. Furthermore, knockdown (KD) of human YTHDF2 led to more than a 10-fold increase in the ex vivo expansion of hUCB HSCs, a fivefold increase in colony-forming units (CFUs), and more than an eightfold increase in functional hUCB HSCs in the secondary serial of a limiting dilution transplantation assay. Mapping of m6A in RNAs from mouse hematopoietic stem and progenitor cells (HSPCs) as well as from hUCB HSCs revealed its enrichment in mRNAs encoding transcription factors critical for stem cell self-renewal. These m6A-marked mRNAs were recognized by Ythdf2 and underwent decay. In Ythdf2 KO HSPCs and YTHDF2 KD hUCB HSCs, these mRNAs were stabilized, facilitating HSC expansion. Knocking down one of YTHDF2's key targets, Tal1 mRNA, partially rescued the phenotype. Our study provides the first demonstration of the function of YTHDF2 in adult stem cell maintenance and identifies its important role in regulating HSC ex vivo expansion by regulating the stability of multiple mRNAs critical for HSC self-renewal, thus identifying potential for future clinical applications.

Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis.

N6-methyladenosine (m6A) is the most common internal modification in eukaryotic mRNA. It is dynamically installed and removed, and acts as a new layer of mRNA metabolism, regulating biological processes including stem cell pluripotency, cell differentiation, and energy homeostasis. m6A is recognized by selective binding proteins; YTHDF1 and YTHDF3 work in concert to affect the translation of m6A-containing mRNAs, YTHDF2 expedites mRNA decay, and YTHDC1 affects the nuclear processing of its targets. The biological function of YTHDC2, the final member of the YTH protein family, remains unknown. We report that YTHDC2 selectively binds m6A at its consensus motif. YTHDC2 enhances the translation efficiency of its targets and also decreases their mRNA abundance. Ythdc2 knockout mice are infertile; males have significantly smaller testes and females have significantly smaller ovaries compared to those of littermates. The germ cells of Ythdc2 knockout mice do not develop past the zygotene stage and accordingly, Ythdc2 is upregulated in the testes as meiosis begins. Thus, YTHDC2 is an m6A-binding protein that plays critical roles during spermatogenesis.