Similar Expression Research Articles

Prediction of LncRNA-Protein Interactions Based on Kernel Combinations and Graph Convolutional Networks.

The complexes of long non-coding RNAs bound to proteins can be involved in regulating life activities at various stages of organisms. However, in the face of the growing number of lncRNAs and proteins, verifying LncRNA-Protein Interactions(LPI) based on traditional biological experiments is time-consuming and laborious. Therefore, with the improvement of computing power, predicting LPI has met new development opportunity. In virtue of the state-of-the-art works, a framework called LncRNA-Protein Interactions based on Kernel Combinations and Graph Convolutional Networks (LPI-KCGCN) has been proposed in this article. We first construct kernel matrices by taking advantage of extracting both the lncRNAs and protein concerning the sequence features, sequence similarity features, expression features, and gene ontology. Then reconstruct the existent kernel matrices as the input of the next step. Combined with known LPI interactions, the generated similarity matrices, which can be used as features of the topology map of the LPI network, are exploited in extracting potential representations in the lncRNA and protein space using a two-layer Graph Convolutional Network. The predicted matrix can be finally obtained by training the network to produce scoring matrices w.r.t. lncRNAs and proteins. Different LPI-KCGCN variants are ensemble to derive the final prediction results and testify on balanced and unbalanced datasets. The 5-fold cross-validation shows that the optimal feature information combination on a dataset with 15.5% positive samples has an AUC value of 0.9714 and an AUPR value of 0.9216. On another highly unbalanced dataset with only 5% positive samples, LPI-KCGCN also has outperformed the state-of-the-art works, which achieved an AUC value of 0.9907 and an AUPR value of 0.9267. The code and dataset can be downloaded from https://github.com/6gbluewind/LPI-KCGCN.

Potential Impact of Hypoxic Astrocytes on the Aggravation of Depressive Symptoms in Parkinson's Disease.

Mounting evidence suggests a significant correlation between depressive disorders and neurodegenerative conditions, encompassing Alzheimer's disease and Parkinson's disease (PD). Depression represents a substantial non-motor manifestation frequently identified in individuals with PD, posing a significant threat to patients' overall well-being and necessitating the implementation of effective management strategies. Despite its high prevalence, impacting over 40% of PD patients, the precise cellular and molecular mechanisms underlying depression and its relationship to dopaminergic system degeneration remain largely ambiguous. In this study, we presented our findings demonstrating distinct characteristics of cortical astrocytes in PD patients compared to reactivated glial cells in the substantia nigra. We identified a subset of differentially expressed genes associated with depressive disorders from PD-associated cortical astrocytes. Furthermore, we uncovered the potential involvement of the hypoxia signaling in driving cortical astrocytic dysfunctions. Through a comprehensive investigation utilizing transcriptome and chromatin accessibility analyses on cultured human astrocytes, we revealed that hypoxic treatment could induce similar expression changes observed in cortex from PD patients. Additionally, we provided evidence that activation of the HIF-1 signaling pathway suppressed the expression of key components of mitochondrial ribosomes and electron transport chain proteins COX2 and CYTB, resulting in abnormal mitochondrial membrane potential. Our results underscore the potential impact of glial metabolic abnormalities on the development of depressive disorders associated with Parkinson's disease.

Abstract P35: High-grade B-cell lymphomas with 11q aberrations show a dark zone expression profile similar to Burkitt lymphoma but with additional extension towards intermediate germinal center B-cells

Abstract P35: High-grade B-cell lymphomas with 11q aberrations show a dark zone expression profile similar to Burkitt lymphoma but with additional extension towards intermediate germinal center B-cells

Clinical relevance and therapeutic predictive ability of hypoxia biomarkers in head and neck cancer tumour models.

Tumour hypoxia promotes poor patient outcomes, with particularly strong evidence for head and neck squamous cell carcinoma (HNSCC). To effectively target hypoxia, therapies require selection biomarkers and preclinical models that can accurately model tumour hypoxia. We established 20 patient-derived xenograft (PDX) and cell line-derived xenograft (CDX) models of HNSCC that we characterised for their fidelity to represent clinical HNSCC in gene expression, hypoxia status and proliferation and that were evaluated for their sensitivity to hypoxia-activated prodrugs (HAPs). PDX models showed greater fidelity in gene expression to clinical HNSCC than cell lines, as did CDX models relative to their paired cell lines. PDX models were significantly more hypoxic than CDX models, as assessed by hypoxia gene signatures and pimonidazole immunohistochemistry, and showed similar hypoxia gene expression to clinical HNSCC tumours. Hypoxia or proliferation status alone could not determine HAP sensitivity across our 20 HNSCC and two non-HNSCC tumour models by either tumour growth inhibition or killing of hypoxia cells in an ex vivo clonogenic assay. In summary, our tumour models provide clinically relevant HNSCC models that are suitable for evaluating hypoxia-targeting therapies; however, additional biomarkers to hypoxia are required to accurately predict drug sensitivity.

Contrasting the semantic space of ‘shame’ and ‘guilt’ in English and Japanese

Abstract This article sheds light on the significant yet nuanced roles of shame and guilt in influencing moral behaviour, a phenomenon that became particularly prominent during the COVID-19 pandemic with the community’s heightened desire to be seen as moral. These emotions are central to human interactions, and the question of how they are conveyed linguistically is a vast and important one. Our study contributes to this area by analysing the discourses around shame and guilt in English and Japanese online forums, focusing on the terms shame, guilt, haji (‘shame’) and zaiakukan (‘guilt’). We utilise a mix of corpus-based methods and natural language processing tools, including word embeddings, to examine the contexts of these emotion terms and identify semantically similar expressions. Our findings indicate both overlaps and distinct differences in the semantic landscapes of shame and guilt within and across the two languages, highlighting nuanced ways in which these emotions are expressed and distinguished. This investigation provides insights into the complex dynamics between emotion words and the internal states they denote, suggesting avenues for further research in this linguistically rich area.

Cell wall invertase 3 plays critical roles in providing sugars during pollination and fertilization in cucumber.

In plants, pollen-pistil interactions during pollination and fertilization mediate pollen hydration and germination, pollen tube growth, and seed set and development. Cell wall invertases (CWINs) help provide the carbohydrates for pollen development; however, their roles in pollination and fertilization have not been well established. In cucumber (Cucumis sativus), CsCWIN3 showed the highest expression in flowers, and we further examined CsCWIN3 for functions during pollination to seed set. Both CsCWIN3 transcript and CsCWIN3 protein exhibited similar expression patterns in the sepals, petals, stamen filaments, anther tapetum, and pollen of male flowers, as well as in the stigma, style, transmitting tract, and ovule funiculus of female flowers. Notably, repression of CsCWIN3 in cucumber did not affect the formation of parthenocarpic fruit but resulted in an arrested growth of stigma integuments in female flowers and a partially delayed dehiscence of anthers with decreased pollen viability in male flowers. Consequently, the pollen tube grew poorly in the gynoecia after pollination. In addition, CsCWIN3-RNA interference plants also showed affected seed development. Considering that sugar transporters could function in cucumber fecundity, we highlight the role of CsCWIN3 and a potential close collaboration between CWIN and sugar transporters in these processes. Overall, we used molecular and physiological analyses to determine the CsCWIN3-mediated metabolism during pollen formation, pollen tube growth, and plant fecundity. CsCWIN3 has essential roles from pollination and fertilization to seed set but not parthenocarpic fruit development in cucumber.

ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing.

Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge. If several genes have a similar expression profile across heterogeneous transcriptomics experiments, they could be functionally related. These associations are usually useful for the annotation of uncharacterized genes. In addition, the search for genes with opposite expression profiles is useful for finding negative regulators and proposing inhibitory compounds in drug repurposing projects. Here we present a new web application, Automatic and Serial Analysis of CO-expression (ASACO), which has the potential to discover positive and negative correlator genes to a given query gene, based on thousands of public transcriptomics experiments. In addition, examples of use are presented, comparing with previous contrasted knowledge. The results obtained propose ASACO as a useful tool to improve knowledge about genes associated with human diseases and noncoding genes. ASACO is available at http://www.bioinfocabd.upo.es/asaco/.

Identification and characterization of circadian clock genes in the head transcriptome of Conopomorpha sinensis Bradley

Conopomorpha sinensis Bradley is the most detrimental pest to litchi and longan in China. Adult eclosion, locomotion, mating and oviposition of C. sinensis usually occur at night, regulated by a circadian rhythm. Nevertheless, our understanding of the linkages between adult circadian rhythms and clock genes remains inadequate. To address this gap, transcriptomic analysis was conducted on female and male heads (including antennae) of C. sinensis using the Illumina HiSeq 6000 platform to identify major circadian clock-related genes. The annotated sequences were analyzed by BLASTx, and candidate clock genes were classified based on conservation, predicted domain architectures, and phylogenetic analysis. The analysis revealed a higher conservation of these genes among the compared moths. Further, the expression profile analysis showed a significant spatiotemporal and circadian rhythmic accumulation of some clock genes during development. The candidate clock genes were predominantly expressed in the head, highlighting their crucial function in circadian rhythm regulation. Moreover, CsinPer, CsinTim1, and CsinCry1 displayed similar dynamic expressions with a peak expression level in the 4th age adults, suggesting their involvement in regulation of courtship and mating behaviors. The CsinPer and CsinTim1 mRNA oscillated strongly with a similar phase, containing a peak expression just before the female mating peak. This work will greatly contribute to understanding the circadian clock system of C. sinensis and provide valuable information for further studies of the molecular mechanisms involved in rhythmicity in fruit-boring pests.

Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq.

Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.

Passaged Articular Chondrocytes From the Superficial Zone and Deep Zone Can Regain Zone-Specific Properties After Redifferentiation

Background: Bioengineered cartilage is a developing therapeutic to repair cartilage defects. The matrix must be rich in collagen type II and aggrecan and mechanically competent, withstanding compressive and shearing loads. Biomechanical properties in native articular cartilage depend on the zonal architecture consisting of 3 zones: superficial, middle, and deep. The superficial zone chondrocytes produce lubricating proteoglycan-4, whereas the deep zone chondrocytes produce collagen type X, which allows for integration into the subchondral bone. Zonal and chondrogenic expression is lost after cell number expansion. Current cell-based therapies have limited capacity to regenerate the zonal structure of native cartilage. Hypothesis: Both passaged superficial and deep zone chondrocytes at high density can form bioengineered cartilage that is rich in collagen type II and aggrecan; however, only passaged superficial zone–derived chondrocytes will express superficial zone–specific proteoglycan-4, and only passaged deep zone–derived chondrocytes will express deep zone–specific collagen type X. Study Design: Controlled laboratory study. Methods: Superficial and deep zone chondrocytes were isolated from bovine joints, and zonal subpopulations were separately expanded in 2-dimensional culture. At passage 2, superficial and deep zone chondrocytes were seeded, separately, in scaffold-free 3-dimensional culture within agarose wells and cultured in redifferentiation media. Results: Monolayer expansion resulted in loss of expression for proteoglycan-4 and collagen type X in passaged superficial and deep zone chondrocytes, respectively. By passage 2, superficial and deep zone chondrocytes had similar expression for dedifferentiated molecules collagen type I and tenascin C. Redifferentiation of both superficial and deep zone chondrocytes led to the expression of collagen type II and aggrecan in both passaged chondrocyte populations. However, only redifferentiated deep zone chondrocytes expressed collagen type X, and only redifferentiated superficial zone chondrocytes expressed and secreted proteoglycan-4. Additionally, redifferentiated deep zone chondrocytes produced a thicker and more robust tissue compared with superficial zone chondrocytes. Conclusion: The recapitulation of the primary phenotype from passaged zonal chondrocytes introduces a novel method of functional bioengineering of cartilage that resembles the zone-specific biological properties of native cartilage. Clinical Relevance: The recapitulation of the primary phenotype in zonal chondrocytes could be a possible method to tailor bioengineered cartilage to have zone-specific expression.

Artificial Trachea from Microtissue Engineering and Three-Dimensional Printing for Tracheal Personalized Repair.

Millions of people suffer from tracheal defect worldwide each year, while autograft and allograft cannot meet existing treatment needs. Tissue-engineered trachea substitutes represent a promising treatment for tracheal defect, while lack of precisely personalized treatment abilities. Therefore, development of an artificial trachea that can be used for personalized transplantation is highly desired. In this study, we report the design and fabrication of an artificial trachea based on sericin microsphere (SM) by microtissue engineering technology and three-dimensional (3D) printing for personalized repair of tracheal defect. The SM possessed natural cell adhesion and promoting cell proliferation ability. Then, the microtissue was fabricated by coincubation of SM with chondrocytes and tracheal epithelial cells. This microtissue displayed good cytocompatibility and could support seed cell adhesion and proliferation. After that, this microtissue was individually assembled to form an artificial trachea by 3D printing. Notably, artificial trachea had an encouraging complete cartilaginous and epithelial structure after transplantation. Furthermore, the artificial trachea molecularly resembled native trachea as evidenced by similar expression of trachea-critical genes. Altogether, the work demonstrates the effectiveness of microtissue engineering and 3D printing for individual construction of artificial trachea, providing a promising approach for personalized treatment of tracheal defect.

Bioinformatics characteristics and expression analysis of IL-8 and IL-10 in largemouth bass (Micropterus salmoides) upon Nocardia seriolae infection

IL-8 and IL-10 are crucial inflammatory cytokines that participate in defending host cells against infections. To demonstrate the function of the two interleukin genes in largemouth bass (Micropterus salmoides), we initially cloned and identified the cDNA sequences of il-8 and il-10 in largemouth bass, referred to as Msil-8 and Msil-10, respectively. The open reading frame (ORF) of Msil-8 was 324 bp in length, encoding 107 amino acids, while the ORF of Msil-10 consisted of 726 bp and encoded 241 amino acids. Furthermore, the functional domains of the SCY domain in MsIL-8 and the IL-10 family signature motif in MsIL-10 were highly conserved across vertebrates. Additionally, both MsIL-8 and MsIL-10 showed close relationships with M. dolomieu. Constitutive expression of Msil-8 and Msil-10 was observed in various tissues, with the highest level found in the head kidney. Subsequently, largemouth bass were infected with Nocardia seriolae via intraperitoneal injection to gain a further understanding of the function of these two genes. Bacterial loads were initially detected in the foregut, followed by the midgut, hindgut, and liver. The mRNA expression of Msil-8 was significantly down-regulated after infection, especially at 2 days post-infection (DPI), with a similar expression to Msil-10. In contrast, the expression of Msil-8 and Msil-10 was significantly upregulated in the foregut at 14 DPI. Taken together, these results reveal that the function of IL-8 and IL-10 was likely hindered by N. seriolae, which promoted bacterial proliferation and intercellular diffusion.

Transcriptomic analysis of lipoteichoic acid‑treated undifferentiated and neutrophil‑like differentiated HL‑60 cells.

Toll-like receptor 2 (TLR2) is an important sensor for innate immune cells, including neutrophils, for the recognition of pathogen infection. Lipoteichoic acid (LTA), a cell wall component of gram-positive bacteria, is a TLR2 ligand. LTA-induced TLR2 signaling pathways are well established in neutrophils. However, experimental studies regarding transcriptional regulation and the molecular mechanisms in primary human neutrophils are limited due to their short lifespan. The promyelocytic leukemia cell line, HL-60, can differentiate into a neutrophil-like phenotype following treatment with dimethyl sulfoxide. The aim of the present study was to investigate whether differentiated HL-60 (dHL-60) cells induced a similar gene expression profile upon LTA treatment as that previously determined for primary human neutrophils. After 4 or 24 h of Staphylococcus aureus LTA treatment, undifferentiated HL-60 (uHL-60) and dHL-60 cells were collected for RNA sequencing. The results demonstrated that hundreds of identical differentially expressed genes (DEGs) were observed in 1 and 10 µg/ml LTA-treated dHL-60 cells following 4 and 24 h of incubation, while almost no DEGs between LTA-treated HL-60 and dHL-60 cells were observed. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses (KEGG), it was noted that the pathways of shared DEGs between the 1 and 10 µg/ml LTA-treated dHL-60 cells at both time points were significantly enriched in immune and inflammatory response-related pathways, such as cellular response to tumor necrosis factor, interleukin-1, interferon γ, neutrophil chemotaxis, the NF-κB signaling pathway and the Toll-like receptor signaling pathway. In addition, when comparing the effect of 1 and 10 µg/ml LTA treatment on dHL60 cells, it was found that all enriched GO and KEGG pathways were associated with the TLR signaling pathways of neutrophils. The results of the present study provided important information for the implementation of mRNA profiling in LTA-treated dHL-60 cells and may indicate the feasibility of using dHL-60 cells as a research model for TLR2 signaling in human neutrophils.

Identification of genetics and hormonal factors involved in Quercus robur root growth regulation in different cultivation system

Understanding the molecular processes and hormonal signals that govern root growth is of paramount importance for effective forest management. While Arabidopsis studies have shed light on the role of the primary root in root system development, the structure of root systems in trees is considerably more intricate, posing challenges to comprehend taproot growth in acorn-sown and nursery-cultivated seedlings. In this study, we investigated Quercus robur seedlings using rhizotrons, containers, and transplanted containers to rhizotrons, aiming to unravel the impact of forest nursery practices on processes governing taproot growth and root system development. Root samples were subjected to RNA-seq analysis to identify gene expression patterns and perform differential gene expression and phytohormone analysis. Among studied cultivation systems, differentially expressed genes (DEGs) exhibited significant diversity, where the number of co-occurring DEGs among cultivation systems was significantly smaller than the number of unique DEGs in different cultivation systems. Moreover, the results imply that container cultivation triggers the activation of several genes associated with linolenic acid and peptide synthesis in root growth. Upon transplantation from containers to rhizotrons, rapid enhancement in gene expression occurs, followed by gradual reduction as root growth progresses, ultimately reaching a similar expression pattern as observed in the taproot of rhizotron-cultivated seedlings. Phytohormone analysis revealed that taproot growth patterns under different cultivation systems are regulated by the interplay between auxin and cytokinin concentrations. Moreover, the diversification of hormone levels within the root zone and cultivation systems allows for taproot growth inhibition and prompt recovery in transplanted seedlings. Our study highlights the crucial role of hormone interactions during the early stages of taproot elongation, influencing root system formation across.

The ideology of crisis in higher education

AbstractHigher education seems to be in a perpetual state of ‘crisis’. The many hundreds of books and papers containing this specific, or other relevantly similar expressions, convey a sense of fear and angst. Yet, what are these various crises about, and which values and beliefs are seen as threatened or ‘under attack’? This paper will provide an analysis of the ‘crisis’ literature and identify four major crisis themes – massification, marketisation, restitution and geopolitics, linked to their ideological basis and influences—including meritocracy, liberalism, restorative justice, and justice globalism. The second part of the paper analyses the massification crisis in Britain between the 1940s and the 1970s as a case example identifying how the principles of a meritocratic society played an influential role in the debate. It will be argued that the notion of ‘universities in crisis’ needs to be understood critically in terms of ideology and historically via the shifting and reshaping of such beliefs over time.

Genome-wide study of glutathione transferases and their regulation in flufenacet susceptible and resistant black-grass (Alopecurus myosuroides Huds.).

Glutathione transferases (GSTs) are enzymes with a wide range of functions, including herbicide detoxification. Up-regulation of GSTs and their detoxification activity enables the grass weed black-grass (Alopecurus myosuroides Huds.) to metabolize the very-long-chain fatty acid synthesis inhibitor flufenacet and other herbicides leading to multiple herbicide resistance. However, the genomic organization and regulation of GSTs genes is still poorly understood. In this genome-wide study the location and expression of 115 GSTs were investigated using a recently published black-grass genome. Particularly, the most abundant GSTs of class tau and phi were typically clustered and often followed similar expression patterns but possessed divergent upstream regulatory regions. Similarities were found in the promoters of the most up-regulated GSTs, which are located next to each other in a cluster. The binding motif of the E2F/DP transcription factor complex in the promoter of an up-regulated GST was identical in susceptible and resistant plants, however, adjacent sequences differed. This led to a stronger binding of proteins to the motif of the susceptible plant, indicating repressor activity. This study constitutes the first analysis dealing with the genomic investigation of GST genes found in black-grass and their transcriptional regulation. It highlights the complexity of the evolution of GSTs in black-grass, their duplication and divergence over time. The large number of GSTs allows weeds to detoxify a broad spectrum of herbicides. Ultimately, more research is needed to fully elucidate the regulatory mechanisms of GST expression. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Long noncoding RNA ZFAS1: A novel anti-apoptotic target in Fuchs endothelial corneal dystrophy

Fuchs endothelial corneal dystrophy (FECD) is the leading cause of endothelial keratoplasty without efficacious drug treatment. Recent studies have emphasized the involvement of epigenetic regulation in FECD development. Long non-coding RNAs (lncRNAs) are recognized as crucial epigenetic regulators in diverse cellular processes and ocular diseases. In this study, we revealed the expression patterns of lncRNAs using high-throughput sequencing technology in FECD mouse model, and identified 979 significantly dysregulated lncRNAs. By comparing the data from FECD human cell model, we obtained a series of homologous lncRNAs with similar expression patterns, and revealed that these homologous lncRNAs were enriched in FECD related biological functions, with apoptosis (mmu04210) showing the highest enrichment score. In addition, we investigated the role of lncRNA zinc finger antisense 1 (ZFAS1) in apoptotic process. This study would broaden our understanding of epigenetic regulation in FECD development, and provide potential anti-apoptotic targets for FECD therapy.

인공지능 기반 심리상담에 활용되는 딥러닝 기법 고찰

Objectives This study aims to review and summarize deep learning techniques that have been developed to date and to discuss how they can be applied in practice to artificial intelligence-based psychology counseling robots.
 Methods To examine the latest deep learning techniques utilized in artificial intelligence psychological counseling, an extensive literature search was conducted for research papers and relevant books from both domestic and in-ternational sources in the fields of emotion analysis, facial expression generation, and text generation.. For do-mestic literature, databases such as RISS and KISS were utilized, and for international literature, research paper search sites including ERIC (ProQuest), JSTOR, and Google Scholar were employed.
 Results When applying artificial intelligence in psychological counseling, the prominent technology of interest in-volves recognizing emotions from the interlocutor's facial expressions and generating similar expressions, or rec-ognizing emotions from sentences spoken by the interlocutor and generating responsive sentences. The study in-troduced the concepts of machine learning and deep learning and explained the workings of deep learning techni-ques, such as CNN (Convolutional Neural Network), RNN (Recurrent Neural Network), LSTM (Long Short Term Memory), Transformer, BERT (Bidirectional Encoder Representations from Transformers), GPT (Generative Pretrained Transformer), and GAN (Generative Adversarial Network). These techniques are founded on the princi-ples derived from human brain functioning. Particularly, emotion recognition programs through image analysis have predominantly relied on CNN, while research in the realm of language has advanced with the utilization of GPT-2, LSTM, and similar methods.
 Conclusions Among the existing deep learning techniques, the recognition of emotions from the interlocutor's fa-cial expressions and the generation of similar expressions, or the recognition of emotions from sentences spoken by the interlocutor and the generation of responsive sentences, are the technologies predominantly under scrutiny for their application in artificial intelligence-based psychological counseling. Nevertheless, rule-based chatbots continue to dominate the landscape. This paper explored the merits and demerits of AI-based counseling em-ploying such deep learning techniques. Looking ahead, there is a need for the advancement of technology that en-ables natural interactions, coupled with the essential verification of its effectiveness.

HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development.

The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair.

Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.