Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health.

The Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals.

Epstein-Barr virus infection upregulates extracellular OLFM4 to activate YAP signaling during gastric cancer progression.

Extracellular vesicles (EVs) are known to mediate cell communications and shape tumor microenvironment. Compared to the well-studied small EVs, the function of large microvesicles (MVs) during tumorigenesis is poorly understood. Here we show the proteome of MVs in Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC), and identify olfactomedin 4 (OLFM4) is induced by EBV infection and secreted via MVs to promote tumor progression through Hippo signaling.

Modeling metabolic-associated steatohepatitis with human pluripotent stem cell-derived liver organoids.

Background: Metabolic-associated steatohepatitis (MASH) is one of the most prevalent liver diseases worldwide, with a global prevalence estimated between 3% and 5%, posing a significant health burden. Human liver organoids (HLOs) have previously been generated to model steatohepatitis, offering a potential cellular disease model for studying MASH. However, the current HLO model lacks detailed molecular characterizations and requires further improvement.

Engineered IscB-ωRNA system with improved base editing efficiency for disease correction via single AAV delivery in mice.

IscBs, as hypercompact ancestry proteins of Cas9 nuclease, are suitable for in vivo gene editing via single adeno-associated virus (AAV) delivery. Due to the low activity of natural IscBs in eukaryotic cells, recent studies have been focusing on improving OgeuIscB's gene editing efficiency via protein engineering. However, in vivo gene editing efficacy of IscBs for disease correction remained to be demonstrated.

Multiple-Wave Admixture and Adaptive Evolution of the Pamirian Wakhi People.

While whole-genome sequencing has been applied extensively to investigate the genetic diversity of global populations, ethnic minority groups in Pakistan are generally underrepresented. In particular, little is known about the genetic origin and highland adaptation of the Pamirian Wakhi people. According to Chinese historical records, the geographical location and language usage of Wakhi may be closely related to Xinjiang Tajiks.

Desipramine reverses remote memory deficits by activating calmodulin-CaMKII pathway in a UTX knockout mouse model of Kabuki syndrome.

Background: Kabuki syndrome (KS) is a rare developmental disorder characterised by multiple congenital anomalies and intellectual disability. (ubiquitously transcribed tetratricopeptide repeat, X chromosome), which encodes a histone demethylase, is one of the two major pathogenic risk genes for KS. Although intellectual disability is a key phenotype of KS, the role of in cognitive function remains unclear.

dmTGS: Precise Targeted Enrichment Long-Read Sequencing Panel for Tandem Repeat Detection.

Background: Tandem repeats (TRs) are abundant in the human genome and associated with repeat expansion disorders. Our study aimed to develop a tandem repeat panel utilizing targeted long-read sequencing to evaluate known TRs associated with these disorders and assess its clinical utility.

Methods: We developed a targeted long-read sequencing panel for 70 TR loci, termed dynamic mutation third-generation sequencing (dmTGS), using the PacBio Sequel II platform.

Age-related differences of the time-varying features in the brain functional connectivity and cognitive aging.

Brain functional modular organization changes with age. Considering the brain as a dynamic system, recent studies have suggested that time-varying connectivity provides more information on brain functions. However, the spontaneous reconfiguration of modular brain structures over time during aging remains poorly understood.

Evolutionary neural architecture search for automated MDD diagnosis using multimodal MRI imaging.

Major depressive disorder (MDD) is a prevalent mental disorder with serious impacts on life and health. Neuroimaging offers valuable diagnostic insights. However, traditional computer-aided diagnosis methods are limited by reliance on researchers' experience.

BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.

Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references.

Identification of Gene Signatures Associated with COVID-19 across Children, Adolescents, and Adults in the Nasopharynx and Peripheral Blood by Using a Machine Learning Approach.

Background: Significant variations in immune profiles across different age groups manifest distinct clinical symptoms and prognoses in Coronavirus Disease 2019 (COVID-19) patients. Predominantly, severe COVID-19 cases that require hospitalization occur in the elderly, with the risk of severe illness escalating with age among young adults, children, and adolescents.

Objective: This study aimed to delineate the unique immune characteristics of COVID-19 across various age groups and evaluate the feasibility of detecting COVID-19-induced immune alterations through peripheral blood analysis.

Frequency-specific dual-attention based adversarial network for blood oxygen level-dependent time series prediction.

Functional magnetic resonance imaging (fMRI) is currently one of the most popular technologies for measuring brain activity in both research and clinical contexts. However, clinical constraints often result in short fMRI scan durations, limiting the diagnostic performance for brain disorders. To address this limitation, we developed an end-to-end frequency-specific dual-attention-based adversarial network (FDAA-Net) to extend the time series of existing blood oxygen level-dependent (BOLD) data, enhancing their diagnostic utility.

Identification of Key Genes in Fetal Gut Development at Single-Cell Level by Exploiting Machine Learning Techniques.

The study of fetal gut development is critical due to its substantial influence on immediate neonatal and long-term adult health. Current research largely focuses on microbiome colonization, gut immunity, and barrier function, alongside the impact of external factors on these phenomena. Limited research has been dedicated to the categorization of developing fetal gut cells.

AXL and SHC1 confer crizotinib resistance in patient-derived xenograft model of ALK-driven lung cancer.

Anaplastic lymphoma kinase (ALK) inhibitor crizotinib has dramatic effect in non-small cell lung cancer patients with ALK rearrangement. However, most patients eventually develop resistance. To discover therapeutic targets to overcome crizotinib resistance (CR), we generated patient-derived xenograft CR mice and subjected them to phosphorylation profiling, together with CR mice treated with ASP3026 or alectinib.

Erratum to: Aberrant dynamic functional connectivity of thalamocortical circuitry in major depressive disorder.

The online version of the original article can be found at https://doi.org/10.1631/jzus.

Targeting SNRNP200-induced splicing dysregulation offers an immunotherapy opportunity for glycolytic triple-negative breast cancer.

Metabolic dysregulation is prominent in triple-negative breast cancer (TNBC), yet therapeutic strategies targeting cancer metabolism are limited. Here, utilizing multiomics data from our TNBC cohort (n = 465), we demonstrated widespread splicing deregulation and increased spliceosome abundance in the glycolytic TNBC subtype. We identified SNRNP200 as a crucial mediator of glucose-driven metabolic reprogramming.