Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes.

Adenine base editors (ABEs) and cytosine base editors (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation of double strand breaks, however, the genomic features that influence the outcomes of base editing in vivo still remain to be characterized. High-throughput datasets from lentiviral integrated libraries were used to investigate the sequence features affecting base editing outcomes, but the effects of endogenous factors beyond the DNA sequences are still largely unknown. Here the base editing outcomes of ABE and CBE were evaluated in mammalian cells for 5012 endogenous genomic sites and 11,868 genome-integrated target sequences, with 4654 genomic sites sharing the same target sequences. The comparative analyses revealed that the editing outcomes of ABE and CBE at endogenous sites were substantially different from those obtained using genome-integrated sequences. We found that the base editing efficiency at endogenous target sites of both ABE and CBE was influenced by endogenous factors, including epigenetic modifications and transcriptional activity. A deep-learning algorithm referred as BE_Endo, was developed based on the endogenous factors and sequence information from our genomic datasets, and it yielded unprecedented accuracy in predicting the base editing outcomes. These findings along with the developed computational algorithms may facilitate future application of BEs for scientific research and clinical gene therapy.

Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints.

The powerful CRISPR genome editing system is hindered by its off-target effects, and existing computational tools achieved limited performance in genome-wide off-target prediction due to the lack of deep understanding of the CRISPR molecular mechanism. In this study, we propose to incorporate molecular dynamics (MD) simulations in the computational analysis of CRISPR system, and present CRISOT, an integrated tool suite containing four related modules, i.e., CRISOT-FP, CRISOT-Score, CRISOT-Spec, CRISORT-Opti for RNA-DNA molecular interaction fingerprint generation, genome-wide CRISPR off-target prediction, sgRNA specificity evaluation and sgRNA optimization of Cas9 system respectively. Our comprehensive computational and experimental tests reveal that CRISOT outperforms existing tools with extensive in silico validations and proof-of-concept experimental validations. In addition, CRISOT shows potential in accurately predicting off-target effects of the base editors and prime editors, indicating that the derived RNA-DNA molecular interaction fingerprint captures the underlying mechanisms of RNA-DNA interaction among distinct CRISPR systems. Collectively, CRISOT provides an efficient and generalizable framework for genome-wide CRISPR off-target prediction, evaluation and sgRNA optimization for improved targeting specificity in CRISPR genome editing.

Heterointerface Engineered Core-Shell Fe2O3@TiO2 for High-Performance Lithium-Ion Storage.

The rational design of the heterogeneous interfaces enables precise adjustment of the electronic structure and optimization of the kinetics for electron/ion migration in energy storage materials. In this work, the built-in electric field is introduced to the iron-based anode material (Fe2O3@TiO2) through the well-designed heterostructure. This model serves as an ideal platform for comprehending the atomic-level optimization of electron transfer in advanced lithium-ion batteries (LIBs). As a result, the core-shell Fe2O3@TiO2 delivers a remarkable discharge capacity of 1342 mAh g-1 and an extraordinary capacity retention of 82.7% at 0.1 A g-1 after 300 cycles. Fe2O3@TiO2 shows an excellent rate performance from 0.1 A g-1 to 4.0 A g-1. Further, the discharge capacity of Fe2O3@TiO2 reached 736 mAh g-1 at 1.0 A g-1 after 2000 cycles, and the corresponding capacity retention is 83.62%. The heterostructure forms a conventional p-n junction, successfully constructing the built-in electric field and lithium-ion reservoir. The kinetic analysis demonstrates that Fe2O3@TiO2 displays high pseudocapacitance behavior (77.8%) and fast lithium-ion reaction kinetics. The capability of heterointerface engineering to optimize electrochemical reaction kinetics offers novel insights for constructing high-performance iron-based anodes for LIBs.

Post-transcriptional regulation of erythropoiesis.

Erythropoiesis is a complex, precise, and lifelong process that is essential for maintaining normal body functions. Its strict regulation is necessary to prevent a variety of blood diseases. Normal erythropoiesis is precisely regulated by an intricate network that involves transcription levels, signal transduction, and various epigenetic modifications. In recent years, research on post-transcriptional levels in erythropoiesis has expanded significantly. The dynamic regulation of splicing transitions is responsible for changes in protein isoform expression that add new functions beneficial for erythropoiesis. RNA-binding proteins adapt the translation of transcripts to the protein requirements of the cell, yielding mRNA with dynamic translation efficiency. Noncoding RNAs, such as microRNAs and lncRNAs, are indispensable for changing the translational efficiency and/or stability of targeted mRNAs to maintain the normal expression of genes related to erythropoiesis. N6-methyladenosine-dependent regulation of mRNA translation plays an important role in maintaining the expression programs of erythroid-related genes and promoting erythroid lineage determination. This review aims to describe our current understanding of the role of post-transcriptional regulation in erythropoiesis and erythroid-associated diseases, and to shed light on the physiological and pathological implications of the post-transcriptional regulation machinery in erythropoiesis. These may help to further enrich our understanding of the regulatory network of erythropoiesis and provide new strategies for the diagnosis and treatment of erythroid-related diseases.

Two-Stage Microporous Layers with Gradient Pore Size Structure for Improving the Performance of Proton Exchange Membrane Fuel Cells.

In this paper, we report the preparation of a gas diffusion layer (GDL) with different gradient pore size structures. The pore structure of microporous layers (MPL) was controlled by the amount of pore-making agent sodium bicarbonate (NaHCO3). We investigated the effects of the two-stage MPL and the different pore size structures in the two-stage MPL on the performance of proton exchange membrane fuel cells (PEMFC). The conductivity and water contact angle tests showed that the GDL had outstanding conductivity and good hydrophobicity. The results of the pore size distribution test indicated that introducing a pore-making agent altered the pore size distribution of the GDL and increased the capillary pressure difference within the GDL. Specifically, there was an increase in pore size within the 7-20 µm and 20-50 µm ranges, which improved the stability of water and gas transmission within the fuel cell. The maximum power density of the GDL03 was increased by 37.1% at 40% humidity, 38.9% at 60% humidity, and 36.5% at 100% humidity when compared to the commercial GDL29BC in a hydrogen-air environment. The design of gradient MPL ensured that the pore size between carbon paper and MPL changed from an initially abrupt state to a smooth transition state, which significantly improved the water and gas management capabilities of PEMFC.

Single-cell profiling of ineffective erythropoiesis in a mouse model of ß-thalassaemia intermedia.

Beta-thalassaemia is an inherited haemoglobin disorder characterised by ineffective erythropoiesis (IE). The detailed pathogenesis of IE remains unclear. In this study, we used single-cell RNA sequencing (scRNA-seq) to examine IE in Th3/+ ß-thalassaemic mice. The results showed that the erythroid group was remarkably expanded, and genes involved in biological processes such as iron metabolism, haeme synthesis, protein folding, and response to heat were significantly upregulated from erythroid progenitors to reticulocytes in ß-thalassaemic mice. In particular, we identified a unique cell population close to reticulocytes, named ThReticulocytes, characterised by a high level of heat shock protein 70 (Hsp70) expression and dysregulation of iron metabolism and haeme synthesis signalling. Treatment of ß-thalassaemic mice with the haeme oxygenase inhibitor tin-mesoporphyrin effectively improved the iron disorder and IE, and the ThReticulocyte population and Hsp70 expression were significantly suppressed. This study revealed in detail the progression of IE at the single-cell level and possibly provided clues to find therapeutic targets in thalassaemia.

Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice.

Base editors have been reported to induce off-target mutations in cultured cells, mouse embryos and rice, but their long-term effects in vivo remain unknown. Here, we develop a Systematic evaluation Approach For gene Editing tools by Transgenic mIce (SAFETI), and evaluate the off-target effects of BE3, high fidelity version of CBE (YE1-BE3-FNLS) and ABE (ABE7.10F148A) in ~400 transgenic mice over 15 months. Whole-genome sequence analysis reveals BE3 expression generated de novo mutations in the offspring of transgenic mice. RNA-seq analysis reveals both BE3 and YE1-BE3-FNLS induce transcriptome-wide SNVs, and the numbers of RNA SNVs are positively correlated with CBE expression levels across various tissues. By contrast, ABE7.10F148A shows no detectable off-target DNA or RNA SNVs. Notably, we observe abnormal phenotypes including obesity and developmental delay in mice with permanent genomic BE3 overexpression during long-time monitoring, elucidating a potentially overlooked aspect of side effects of BE3 in vivo.

TBC1D21 is an essential factor for sperm mitochondrial sheath assembly and male fertility‡.

During spermiogenesis, the formation of the mitochondrial sheath is critical for male fertility. The molecular processes that govern the development of the mitochondrial sheath remain unknown. Whether TBC1D21 serves as a GTPase-activating protein (GAP) for GTP hydrolysis in the testis is unclear, despite recent findings indicating that it collaborates with numerous proteins to regulate the formation of the mitochondrial sheath. To thoroughly examine the property of TBC1D21 in spermiogenesis, we applied the CRISPR/Cas9 technology to generate the Tbc1d21-/- mice, Tbc1d21D125A R128K mice with mutation in the GAP catalytic residues (IxxDxxR), and Tbc1d21-3xFlag mice. Male Tbc1d21-/- mice were infertile due to the curved spermatozoa flagella. In vitro fertilization is ineffective for Tbc1d21-/- sperm, although healthy offspring were obtained by intracytoplasmic sperm injection. Electron microscopy revealed aberrant ultrastructural changes in the mitochondrial sheath. Thirty-four Rab vectors were constructed followed by co-immunoprecipitation, which identified RAB13 as a novel TBC1D21 binding protein. Interestingly, infertility was not observed in Tbc1d21D125A R128K mice harboring the catalytic residue, suggesting that TBC1D21 is not a typical GAP for Rab-GTP hydrolysis. Moreover, TBC1D21 was expressed in the sperm mitochondrial sheath in Tbc1d21-3xFlag mice. Immunoprecipitation-mass spectrometry demonstrated the interactions of TBC1D21 with ACTB, TPM3, SPATA19, and VDAC3 to regulate the architecture of the sperm midpiece. The collective findings suggest that TBC1D21 is a scaffold protein required for the organization and stabilization of the mitochondrial sheath morphology.

The ZFP541-KCTD19 complex is essential for pachytene progression by activating meiotic genes during mouse spermatogenesis.

Meiosis is essential for fertility in sexually reproducing species and this sophisticated process has been extensively studied. Notwithstanding these efforts, key factors involved in meiosis have not been fully characterized. In this study, we investigate the regulatory roles of zinc finger protein 541 (ZFP541) and its interacting protein potassium channel tetramerization domain containing 19 (KCTD19) in spermatogenesis. ZFP541 is expressed from leptotene to the round spermatid stage, while the expression of KCTD19 is initiated in pachytene. Depletion of Zfp541 or Kctd19 leads to infertility in male mice and delays progression from early to mid/late pachynema. In addition, Zfp541-/- spermatocytes show abnormal programmed DNA double-strand break repair, impaired crossover formation and resolution, and asynapsis of the XY chromosomes. ZFP541 interacts with KCTD19, histone deacetylase 1/2 (HDAC1/2), and deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1). Moreover, ZFP541 binds to and activates the expression of genes involved in meiosis and post-meiosis including Kctd19; in turn, KCTD19 promotes the transcriptional activation activity of ZFP541. Taken together, our studies reveal that the ZFP541/KCTD19 signaling complex, acting as a key transcription regulator, plays an indispensable role in male fertility by regulating pachytene progression.

Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods.

Efficient and precise base editors (BEs) for C-to-G transversion are highly desirable. However, the sequence context affecting editing outcome largely remains unclear. Here we report engineered C-to-G BEs of high efficiency and fidelity, with the sequence context predictable via machine-learning methods. By changing the species origin and relative position of uracil-DNA glycosylase and deaminase, together with codon optimization, we obtain optimized C-to-G BEs (OPTI-CGBEs) for efficient C-to-G transversion. The motif preference of OPTI-CGBEs for editing 100 endogenous sites is determined in HEK293T cells. Using a sgRNA library comprising 41,388 sequences, we develop a deep-learning model that accurately predicts the OPTI-CGBE editing outcome for targeted sites with specific sequence context. These OPTI-CGBEs are further shown to be capable of efficient base editing in mouse embryos for generating Tyr-edited offspring. Thus, these engineered CGBEs are useful for efficient and precise base editing, with outcome predictable based on sequence context of targeted sites.

Male fertility in Mus musculus requires the activity of TRYX5 in sperm migration into the oviduct.

Nowadays, abnormal loss of serine proteases appears very frequently in male patients with unexplained sterility. In fact, many testis-specific serine proteases, the largest family among the four protease families implicated in murine spermatogenesis, are indispensable for reproduction. In the present study, we demonstrate that the previously uncharacterized testis-specific serine protease TRYX5 (1700074P13Rik) is required for male fertility in mice. Tryx5-/- male mice are sterile, yet they have normal spermatogenesis and normal sperm parameters. In vivo fertilization experiments showed that the fertilization rate of Tryx5-/- sperm was almost zero. Sperm counting and analysis of paraffin sections of oviducts revealed that Tryx5-/- sperm were unable to migrate into the oviduct, which is likely the cause of the observed infertility of the Tryx5-/- male mice. Importantly, we also found that there was almost no mature ADAM3 present in Tryx5-/- sperm and almost no ADAM3 precursor in Tryx5-/- elongated spermatids of S13-16 stage, even though testes of Tryx5-/- and wild type mice had the same amount of the total precursor ADAM3. Collectively, our results demonstrate that Tryx5 is essential for male fertility in mice and suggest that TRYX5 functions in the stability or localization of ADAM3 precursor in elongated spermatids S13-16 stage, thereby regulating the ability of sperm to migrate from the uterus into the ampulla of the oviduct, the site of fertilization.

GDF11 contributes to hepatic hepcidin (HAMP) inhibition through SMURF1-mediated BMP-SMAD signalling suppression.

Hepcidin (HAMP) synthesis is suppressed by erythropoiesis to increase iron availability for red blood cell production. This effect is thought to result from factors secreted by erythroid precursors. Growth differentiation factor 11 (GDF11) expression was recently shown to increase in erythroid cells of ß-thalassaemia, and decrease with improvement in anaemia. Whether GDF11 regulates hepatic HAMP production has never been experimentally studied. Here, we explore GDF11 function during erythropoiesis-triggered HAMP suppression. Our results confirm that exogenous erythropoietin significantly increases Gdf11 as well as Erfe (erythroferrone) expression, and Gdf11 is also increased, albeit at a lower degree than Erfe, in phlebotomized wild type and ß-thalassaemic mice. GDF11 is expressed predominantly in erythroid burst forming unit- and erythroid colony-forming unit- cells during erythropoiesis. Exogeneous GDF11 administration results in HAMP suppression in vivo and in vitro. Furthermore, exogenous GDF11 decreases BMP-SMAD signalling, enhances SMAD ubiquitin regulatory factor 1 (SMURF1) expression and induces ERK1/2 (MAPK3/1) signalling. ERK1/2 signalling activation is required for GDF11 or SMURF1-mediated suppression in BMP-SMAD signalling and HAMP expression. This research newly characterizes GDF11 in erythropoiesis-mediated HAMP suppression, in addition to ERFE.

Expression pattern of prohibitin, capping actin protein of muscle Z-line beta subunit and tektin-2 gene in Murrah buffalo sperm and its relationship with sperm motility.

OBJECTIVE: The aim of the current study is to investigate the relationship between prohibitin (PHB), capping actin protein of muscle Z-line beta subunit (CAPZB), and tektin-2 (TEKT2) and sperm motility in Murrah buffalo. METHODS: We collected the high-motility and low-motility semen samples, testis, ovary, muscle, kidney, liver, brain and pituitary from Murrah buffalo, and analysed the expression of PHB, CAPZB, and TEKT2 in mRNA (message RNA) and protein level. RESULTS: Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) result showed that the expression of PHB was higher and CAPZB, TEKT2 were specifically expressed in testis as compared to the other 6 tissues, and that in testis, the expression of TEKT2 was higher than that of CAPZB and PHB. Immunohistochemistry test revealed that all three genes were located on the convoluted seminiferous tubule and enriched in spermatogenic cells. Both qRT-PCR and Western Blot results showed that the expression levels of PHB, CAPZB, and TEKT2 were significantly lower in the low-motility semen group compared to the high-motility semen group (p<0.05). CONCLUSION: The expression levels of PHB, CAPZB, and TEKT2 in Murrah buffalo sperm have a high positive correlation with sperm motility. And the three genes may be potential molecular markers for the decline of buffalo sperm motility.

Guilt leads to enhanced facing-the-viewer bias.

As an important moral emotion, guilt plays a critical role in social interaction. It has been found that people tended to exhibit prosocial behavior under circumstances of guilt. However, all extant studies have predominantly focused on the influence of guilt on macro-level behavior. So far, no study has investigated whether guilt affects people's micro-level perception. The current study closes this gap by examining whether guilt affects one's inclination to perceive approaching motion. We achieved this aim by probing a facing-the-viewer bias (FTV bias). Specifically, when an ambiguous walking biological motion display is presented to participants via the point-light display technique, participants tend to perceive a walking agent approaching them. We hypothesized that guilt modulated FTV bias. To test this hypothesis, we adopted a two-person situation induction task to induce guilt, whereby participants were induced to feel that because of their poor task performance, their partner did not receive a satisfactory payment. We found that when participants were told that the perceived biological motion was motion-captured from their partner, the FTV bias was significantly increased for guilty participants relative to neutral participants. However, when participants were informed that the perceived biological motion was from a third neutral agent, the FTV bias was not modulated by guilt. These results suggest that guilt influences one's inclination to perceive approaching motion, but this effect is constrained to the person towards whom guilt is directed.

Identification and analysis of the expression of microRNA from lactating and nonlactating mammary glands of the Chinese swamp buffalo.

To study the role of microRNA (miR) in the lactation physiology of water buffalo, 2 multiparous dairy buffaloes (including an 8-yr-old buffalo that had been lactating for 3 mo, as well as a 10-yr-old nonlactating, nonpregnant buffalo) were used for miR library construction. The profile of differentially expressed miR in lactating and nonlactating mammary gland tissues of these water buffalo were investigated using Illumina-Solexa high-throughput sequencing technology (Illumina, San Diego, CA). The data identified 259 miR families, 359 mature miR, 363 pre-miR, 230 novel buffalo miR, and 5 buffalo-specific miR that were expressed in mammary tissues. Some highly significantly differentially expressed miR were explored, including bbu-miR-497, bbu-miR-30a-5p, bbu-miR-148a, bbu-miR-29a, bbu-miR-125a, bbu-miR-125b, and bbu-miR-103. The expression patterns of 18 miR were confirmed by quantitative real-time PCR in both tissues, and the expression of bbu miR-103 and novel miR-57 constituted the largest differences between lactating and nonlactating tissues. Further functional analysis indicated that the overexpression or suppression of miR-103 in buffalo mammary epithelial cells downregulated or upregulated the expression of pantothenate kinase 3, and also significantly increased the transcription factor steroid regulatory element binding protein, followed by the acceleration of de novo synthesis of fatty acids by upregulation of acetyl coenzyme A carboxylase α expression. The expression levels of 34 predicted target genes of novel-miR-57 in lactating and nonlactating mammary gland tissues were all analyzed by quantitative real-time PCR. Finally, only the expression of docking protein 4 could be upregulated or downregulated selectively by bbu-novel-miR-57 in buffalo mammary epithelial cells and the Bcap-37 cell line. This study provides an overview of the miR expression profile of water buffalo and the interaction between some key miR and their target genes, which may improve understanding of the important roles of miR in buffalo milk fat synthesis.

Object formation in visual working memory: Evidence from object-based attention.

We report on how visual working memory (VWM) forms intact perceptual representations of visual objects using sub-object elements. Specifically, when objects were divided into fragments and sequentially encoded into VWM, the fragments were involuntarily integrated into objects in VWM, as evidenced by the occurrence of both positive and negative object-based attention effects: In Experiment 1, when subjects' attention was cued to a location occupied by the VWM object, the target presented at the location of that object was perceived as occurring earlier than that presented at the location of a different object. In Experiment 2, responses to a target were significantly slower when a distractor was presented at the same location as the cued object (Experiment 2). These results suggest that object fragments can be integrated into objects within VWM in a manner similar to that of visual perception.

BMP-1 participates in the selection and dominance of buffalo follicles by regulating the proliferation and apoptosis of granulosa cells.

BMP1/TLD-related metalloproteinases play a key role in morphogenesis via the proteolytic maturation of a number of extracellular matrix proteins and the activation of a subset of growth factors of the transforming growth factor beta superfamily. Recent data indicated that BMP1 is expressed in sheep ovarian follicles and showed a protease activity. The aim of the present study was to characterize the function of the buffalo BMP1 gene in folliculogenesis. A 3195-bp buffalo BMP1 mRNA fragment was firstly cloned and sequenced, which contained a whole 2967-bp codon sequence. The multialigned results suggested that BMP1 is highly conserved among different species both at the nucleic acid and the amino acid level. BMP1 is located in the oogonium of the fetal buffalo ovary and in the granulosa cells (GCs) and the oocytes of adult ovary from the primordial to the large antral follicles. Further study showed that BMP1 promoted cell cycle and proliferation and inhibited apoptosis in IVC GCs. Adding BMP1 recombinant protein to the culture medium of the GCs increased the expression of the key cell cycle regulators such as cyclin D1 and cyclin D2 and downregulated the expression of cell apoptosis pathway genes such as Cytochrome C, Fas, FasL, and Chop, both at the mRNA and at the protein levels. It also upregulated the expression of PAPP-A, IGF system, and VEGF, and so forth, which play important roles in the selection and dominance of growth follicles. The opposite results were observed by adding BMP1 antibody to the investigation groups. This study suggests that BMP1 regulates the proliferation and apoptosis of IVC GCs by changing the expression pattern of related genes and may potentially promote the selection and dominance of the buffalo follicles.

The working memory Ponzo illusion: Involuntary integration of visuospatial information stored in visual working memory.

Visual working memory (VWM) has been traditionally viewed as a mental structure subsequent to visual perception that stores the final output of perceptual processing. However, VWM has recently been emphasized as a critical component of online perception, providing storage for the intermediate perceptual representations produced during visual processing. This interactive view holds the core assumption that VWM is not the terminus of perceptual processing; the stored visual information rather continues to undergo perceptual processing if necessary. The current study tests this assumption, demonstrating an example of involuntary integration of the VWM content, by creating the Ponzo illusion in VWM: when the Ponzo illusion figure was divided into its individual components and sequentially encoded into VWM, the temporally separated components were involuntarily integrated, leading to the distorted length perception of the two horizontal lines. This VWM Ponzo illusion was replicated when the figure components were presented in different combinations and presentation order. The magnitude of the illusion was significantly correlated between VWM and perceptual versions of the Ponzo illusion. These results suggest that the information integration underling the VWM Ponzo illusion is constrained by the laws of visual perception and similarly affected by the common individual factors that govern its perception. Thus, our findings provide compelling evidence that VWM functions as a buffer serving perceptual processes at early stages.