Integrating spatial transcriptomics and single-cell RNA-sequencing reveals the alterations in epithelial cells during nodular formation in benign prostatic hyperplasia.

OBJECTIVE: Proliferative nodular formation represents a characteristic pathological feature of benign prostatic hyperplasia (BPH) and serves as the primary cause for prostate volume enlargement and consequent lower urinary tract symptoms (LUTS). Its specific mechanism is largely unknown, although several cellular processes have been reported to be involved in BPH initiation and development and highlighted the crucial role of epithelial cells in proliferative nodular formation. However, the technological limitations hinder the in vivo investigation of BPH patients. METHODS: The robust cell type decomposition (RCTD) method was employed to integrate spatial transcriptomics and single cell RNA sequencing profiles, enabling the elucidation of epithelial cell alterations during nodular formation. Immunofluorescent and immunohistochemical staining was performed for verification. RESULTS: The alterations of epithelial cells during the formation of nodules in BPH was observed, and a distinct subgroup of basal epithelial (BE) cells, referred to as BE5, was identified to play a crucial role in driving this progression through the hypoxia-induced epithelial-mesenchymal transition (EMT) signaling pathway. BE5 served as both the initiating cell during nodular formation and the transitional cell during the transformation from luminal epithelial (LE) to BE cells. A distinguishing characteristic of the BE5 cell subgroup in patients with BPH was its heightened hypoxia and upregulated expression of FOS. Histological verification results confirmed a significant association between c-Fos expression and key biological processes such as hypoxia and cell proliferation, as well as the close relationship between hypoxia and EMT in BPH tissues. Furthermore, a strong link between c-Fos expression and the progression of BPH was also been validated. Additionally, notable functional differences were observed in glandular and stromal nodules regarding BE5 cells, with BE5 in glandular nodules exhibiting enhanced capacities for EMT and cell proliferation characterized by club-like cell markers. CONCLUSIONS: This study elucidated the comprehensive landscape of epithelial cells during in vivo nodular formation in patients, thereby offering novel insights into the initiation and progression of BPH.

Anisotropic Sensing Performance in a High-Sensitivity Surface Plasmon Resonance Sensor Based on Few-Layer Black Phosphorus.

Few-layer black phosphorus (FLBP) is a highly promising material for high sensitivity label-free surface plasmon resonance (SPR) sensors due to its exceptional electrical, optical, and mechanical properties. FLBP exhibits inherent anisotropy with different refractive indices along its two main crystal orientations, the zigzag and armchair axes. However, this anisotropic property is often overlooked in FLBP-based sensors. In this study, we conducted a comprehensive investigation of the SPR reflectivity and phase in a BK7-Ag-FLBP structure to understand the influence of the stacking sequence and the number of FLBP layers on the sensing performance. Clear resonant angle shifts caused by different stacking sequences of FLBP could be observed both theoretically and experimentally. In the theoretical study, the highest reflective and phase sensitivities were achieved with a 12-layer black phosphorus (BP) structure. The reflectivity sensitivity reached 287.9°/refractive index units (RIU) with the zz stacking 12-layer BP film exhibiting a sensitivity 76°/RIU higher than the ac stacking structure. Similarly, the phase sensitivity reached 1162°/RIU with the zz stacking 12-layer BP structure showing a sensitivity 276.9°/RIU higher than the ac stacking structure. The electric field distribution of the 12-layer BP structure with four different stacking sequences has also been analyzed. In the experiment study, the well-known Attenuated Total Reflection (ATR) θ-2θ SPR setup is utilized to detect the reflectivity and phase of BK7-Ag-FLBP structures. The FLBP samples with the same thickness but different stacking sequences show significant resonant angle shift (0.275°) and maximum phase difference variation (34.6°). The FLBP sample thickness and crystal orientations have been demonstrated using the angular-resolved polarized Raman spectroscopy (ARPRS). These theoretical and experimental results provide strong evidence that the stacking sequences of FLBP have a significant impact on the sensing performance of SPR sensors. By harnessing the anisotropic properties of materials like FLBP, novel structures of anisotropic-2D material-based SPR sensors could open up exciting possibilities for innovative applications.

Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution.

Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.

Frontiers of soybean pan-genome studies.

Artificial domestication provided the original motivation to the blooming of agriculture, following with the dramatic change of the genetic background of crops and livestock. According to theory and technology upgradation that contributing to the omics, we appreciate using the pan-genome instead of single reference genome for crop study. By comparison and integration of multiple genomes under the guidance of pan-genome theory, we can estimate the genomic information range of a species, leading to a global understanding of its genetic diversity. Combining pan-genome with large size chromosomal structural variations, high throughput population resequencing, and multi-omics data, we can profoundly study the genetic basis behind species traits we focus on. Soybean is one of the most important commercial crops over the world. It is also essential to our food security. Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently. In this review, we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly, iterative assembly and graph-based genome. Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome. We highlighted the contribution of structural variation (SV) to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits. By those, we approved the value of graph-based pan-genome for data integration and SV calculation. Future research directions are also discussed for crop genomics and data science.

Identification of crucial metabolites in colored grain wheat (Triticum aestivum L.) regulated by nitrogen application.

Colored wheats have drawn attention due to their nutritional compounds. However, limited information is obtained on the effects of nitrogen fertilizer on crucial metabolites and grain quality of wheats with different color grain. In the study, the pot experiment was conducted with white (W), blue (B), and purple (P) grain wheats treated with three levels of N (LN, 0 g kg-1; MN, 0.05 g kg-1; HN, 0.1 g kg-1). Higher N level could promote wheat growth, improve grain indexes, and nutrient uptake. SPAD values of flag leaves remained in the order HN > MN > LN across all wheat varieties, and maintained increasing during tested stages under purple wheat. Metabolomics analysis showed that the annotated 358 metabolites mainly belonged to 29 classes, including carboxylic acids and their derivatives, fatty acids, flavonoids, and phenols. 35, 39, and 70 differential accumulated metabolites were respectively found between the WLN vs. WHN, the BHN vs. BLN, and the PHN vs. PLN, which were mainly enriched in "biosynthesis of plant secondary metabolites", "cGMP-PKG signaling pathway", "sphingolipid signaling pathway", "biosynthesis of alkaloids derived from histidine and purine", and "biosynthesis of plant hormones". Additionally, erucic acid was dominated in the three wheat cultivars, and was decreased after treated with high N levels. Our study preliminarily revealed the different response mechanisms to different N levels in the white, blue, and purple grain wheats, and lay a theoretical foundation for further breeding of excellent colored grain varieties.

Metabolomics Uncovers the Mechanisms of Nitrogen Response to Anthocyanins Synthesis and Grain Quality of Colored Grain Wheat (Triticum aestivum L.).

Nitrogen (N) is a key factor for plant growth and affects anthocyanin synthesis. This study aimed to clarify the potential mechanisms of N levels (LN, 0 kg·ha-1; MN, 150 kg·ha-1; HN, 225 kg·ha-1) in anthocyanin synthesis and grain quality of colored grain wheat. HN increased the yield component traits and grain morphology traits in colored grain wheat while decreasing the processing and nutrient quality traits. Most quality traits were significantly negatively correlated with the yield composition and morphological traits. Anthocyanin was more accumulated under LN conditions, but other related yield and morphological traits of colored grain wheat declined. The anthocyanin content was the highest in blue wheat, followed by that in purple wheat. Cyanidin-3-O-(6-O-malonyl-ß-d-glucoside) and cyanidin-3-O-rutinoside were the predominant anthocyanins in blue and purple wheat. The identified anthocyanin-related metabolites were associated with flavonoid biosynthesis, anthocyanin biosynthesis, and secondary metabolite biosynthesis. Therefore, the study provided information for optimizing nitrogen fertilizer management in producing high quality colored wheat and verified the close relationship between anthocyanin and low N condition.

AutoNet-Generated Deep Layer-Wise Convex Networks for ECG Classification.

The design of neural networks typically involves trial-and-error, a time-consuming process for obtaining an optimal architecture, even for experienced researchers. Additionally, it is widely accepted that loss functions of deep neural networks are generally non-convex with respect to the parameters to be optimised. We propose the Layer-wise Convex Theorem to ensure that the loss is convex with respect to the parameters of a given layer, achieved by constraining each layer to be an overdetermined system of non-linear equations. Based on this theorem, we developed an end-to-end algorithm (the AutoNet) to automatically generate layer-wise convex networks (LCNs) for any given training set. We then demonstrate the performance of the AutoNet-generated LCNs (AutoNet-LCNs) compared to state-of-the-art models on three electrocardiogram (ECG) classification benchmark datasets, with further validation on two non-ECG benchmark datasets for more general tasks. The AutoNet-LCN was able to find networks customised for each dataset without manual fine-tuning under 2 GPU-hours, and the resulting networks outperformed the state-of-the-art models with fewer than 5% parameters on all the above five benchmark datasets. The efficiency and robustness of the AutoNet-LCN markedly reduce model discovery costs and enable efficient training of deep learning models in resource-constrained settings.

Lossy Mode Resonance Sensors Based on Anisotropic Few-Layer Black Phosphorus.

Lossy mode resonance (LMR) sensors offer a promising avenue to surpass the constraints of conventional surface plasmon resonance (SPR) sensors by delivering enhanced label-free detection capabilities. A notable edge of LMR over SPR is its excitation potential by both transverse electric (TE) and transverse magnetic (TM) polarized light. Yet this merit remains underexplored due to challenges to achieving high sensing performance under both TM and TE polarization within a singular LMR model. This study introduces a theoretical model for an LMR prism refractive index sensor based on a MgF2-few layer black phosphorus-MgF2 configuration, which can achieve angular sensitivity nearing 90° refractive index unit-1 (RIU-1) for both polarizations. Leveraging the distinct anisotropic nature of black phosphorus, the figure of merit (FOM) values along its two principal crystal axes (zigzag and armchair) show great difference, achieving an impressive FOM of 1.178 × 106 RIU-1 along the zigzag direction under TE polarized light and 1.231 × 104 RIU-1 along the armchair direction under TM polarized light. We also provide an analysis of the electric field distribution for each configuration at its respective resonant conditions. The proposed structure paves the way for innovative applications of anisotropic-material-based LMR sensors in various applications.

Vascular network-inspired fluidic system (VasFluidics) with spatially functionalizable membranous walls.

In vascular networks, the transport across different vessel walls regulates chemical compositions in blood over space and time. Replicating such trans-wall transport with spatial heterogeneity can empower synthetic fluidic systems to program fluid compositions spatiotemporally. However, it remains challenging as existing synthetic channel walls are typically impermeable or composed of homogeneous materials without functional heterogeneity. This work presents a vascular network-inspired fluidic system (VasFluidics), which is functionalizable for spatially different trans-wall transport. Facilitated by embedded three-dimensional (3D) printing, elastic, ultrathin, and semipermeable walls self-assemble electrostatically. Physicochemical reactions between fluids and walls are localized to vary the trans-wall molecules among separate regions, for instance, by confining solutions or locally immobilizing enzymes on the outside of channels. Therefore, fluid compositions can be regulated spatiotemporally, for example, to mimic blood changes during glucose absorption and metabolism. Our VasFluidics expands opportunities to replicate biofluid processing in nature, providing an alternative to traditional fluidics.

Somatostatin receptor subtype 2A expression and genetics in 184 paragangliomas: a single center retrospective observational study.

PURPOSE: Adrenal and extra-adrenal paragangliomas (PGLs) are a group of neuroendocrine tumors (NETs) with strong heterogeneity, which often express somatostatin receptor subtype 2 A (SSTR2A). However, the association between SSTR2A expression and genetic status of PGLs remains unclear. The purpose of the study was to identify whether various pathogenic variants (PVs) had an impact on SSTR2A expression in PGLs. METHODS: This retrospective study included 184 patients with pathologically confirmed PGLs. The immunohistochemical expression of SSTR2A were studied in 184 tumors and PVs were tested in 159 tumor samples. Clinical and genetic data were compared in SSTR2A positive and negative PGLs. RESULTS: SSTR2A was positive in 63.6% (117/184) of all tumors. PGLs with negative SSTR2A were more likely to be extra-adrenal (37.0% vs 18.0%; P = 0.005) and exhibited a considerably greater proportion of PVs (75.4% vs. 49.0%; P = 0.001) than those with positive SSTR2A. Compared to those without PVs, a higher proportion of PGLs with PVs in cluster 1B (P = 0.004) and cluster 2 (P = 0.004) genes, especially VHL (P = 0.009), FGFR1 (P = 0.010) and HRAS (P = 0.007), were SSTR2A negative. SSTR2A was positive in all tumors (4/4) with SDHx PVs and in 87.5% (7/8) of metastatic PGLs. CONCLUSIONS: SSTR2A negativity was correlated with extra-adrenal tumor location and PVs in cluster 1B and cluster 2 genes such as VHL, FGFR1 and HRAS. Immunohistochemistry of SSTR2A should be taken into consideration in the personalized management of PGLs.

[Corrigendum] FKBP11 protects intestinal epithelial cells against inflammation­induced apoptosis via the JNK­caspase pathway in Crohn's disease.

Subsequently to the publication of the above article, the authors realized that Fig. 4 in their paper had been assembled containing two erroneously placed gel slices; essentially, the GAPDH bands featured in Fig. 4A had also been included in Fig. 5, and the data for the FKBP11 bands in Fig. 4A had also been included to show the GRP78 bands in Fig. 4. The authors were able to revisit their original data and to correct the data that had been featured incorrectly in Fig. 4. The corrected version of Fig. 4, now showing the true data for the GRP78 protein bands in Fig. 4C and the correct GAPDH protein bands for Fig. 4A, is shown on the next page. Note that these errors did not significantly affect the results or the conclusions reported in this paper. All the authors agree to the publication of this Corrigendum, and are grateful to the Editor of Molecular Medicine Reports for allowing them the opportunity to correct this error. Moreover, the authors apologize to the readership for any inconvenience caused. [Molecular Medicine Reports 18: 4428­4438, 2018; DOI: 10.3892/mmr.2018.9485].

A non-image-forming visual circuit mediates the innate fear of heights in male mice.

The neural basis of fear of heights remains largely unknown. In this study, we investigated the fear response to heights in male mice and observed characteristic aversive behaviors resembling human height vertigo. We identified visual input as a critical factor in mouse reactions to heights, while peripheral vestibular input was found to be nonessential for fear of heights. Unexpectedly, we found that fear of heights in naïve mice does not rely on image-forming visual processing by the primary visual cortex. Instead, a subset of neurons in the ventral lateral geniculate nucleus (vLGN), which connects to the lateral/ventrolateral periaqueductal gray (l/vlPAG), drives the expression of fear associated with heights. Additionally, we observed that a subcortical visual pathway linking the superior colliculus to the lateral posterior thalamic nucleus inhibits the defensive response to height threats. These findings highlight a rapid fear response to height threats through a subcortical visual and defensive pathway from the vLGN to the l/vlPAG.

Genetic background and intraoperative haemodynamic instability in patients with pheochromocytoma and paraganglioma: a multicenter retrospective study.

BACKGROUND: Perioperative management to maintain intraoperative haemodynamic stability is crucial during surgical treatment of pheochromocytomas and paragangliomas (PPGLs). Although approximately 70% of PPGLs carry pathogenic variants (PVs) in susceptibility genes, whether intraoperative haemodynamic instability (IHI) is associated with genetic background remains unclear. This study aimed to analyse IHI in patients with PPGL due to PVs in different genes. MATERIALS AND METHODS: This retrospective study recruited 756 patients with abdominal PPGL from two tertiary care centres. Clinical information including sex, age, catecholamine-associated signs and symptoms (CAS), tumour location and size, biochemistry, and perioperative characteristics were collected. Genetic mutations were investigated using next-generation sequencing. RESULTS: Among the 671 patients included in the analysis, 61.8% (415/671) had IHI. IHI was significantly associated with genetic background in patients with PPGL. Most (80.9%, 89/110) patients with PPGL due to PVs in HRAS suffered IHI. In contrast, only half (31/62) of patients with PPGL due to PVs in VHL had IHI. In the multivariate regression analysis, compared to those with negative genetic testing results, patients with PPGL due to PVs in HRAS (OR 3.82, 95% CI 2.187-6.679, P<0.001), the other cluster 2 genes (OR 1.95, 95% CI 1.287-2. 569, P< 0.05), and cluster 1 genes other than VHL (OR 2.35, 95% CI 1.338-4.111, P<0.05) were independent risk factors for IHI, while PVs in VHL was not independent risk factor (OR 1.09, 95% CI 0.605-1.953, P>=0.05). In addition, age at diagnosis of primary tumour, presenting of CAS, and tumour size were identified as independent factors for IHI. The nomogram illustrated that genetic background as sharing the largest contribution to IHI, followed by tumour size, age, and presenting of CAS. CONCLUSION: IHI is associated with the genetic background in patients with PPGL. The perioperative management of patients with PPGL can be personalized according to their genetic backgrounds, tumour size, age, and presenting of CAS.

Readthrough events in plants reveal plasticity of stop codons.

Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor tRNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of basic transcription factor 3. Furthermore, the SCR events exhibit non-conserved signature, and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.