Biology subjects

Suo, L.

Publications and source records attributed to Suo, L..

5 recordsLinked to original sources

bioRxiv2026

YGEP: An Integrated Web Platform for Genomic Evaluation and Intelligent Breeding in Yak

Background: The yak (Bos grunniens) is an essential livestock species in high-altitude alpine ecosystems, serving key roles in meat, milk, and wool production as well as ecological maintenance. However, traditional yak breeding systems face several limitations, including fragmented herd data management, inefficient phenotypic collection, missing pedigree records, and high technical barriers to applying genomic technologies. These factors constrain the widespread application of modern genetic evaluation methods in yak breeding programs. Description: We developed the Yak Genomic Evaluation Platform (YGEP, https://yakbreeding.swun.edu.cn/en/), an integrated digital system for yak genetic selection and herd management. YGEP integrates three core analytical modules: pedigree reconstruction, genotype imputation and genomic breeding value estimation. Benchmarking on 706 yaks showed that GBLUP achieved a prediction accuracy of r = 0.96 for cannon bone circumference (CCB), and KBeagle reached 84.0% imputation accuracy with the combined reference panel. Conclusion: YGEP bridges the gap between advanced genomic analytics and practical yak breeding. By integrating pedigree reconstruction, genotype imputation, and GEBV estimation into a user-friendly cloud platform, YGEP effectively eliminates technical and data bottlenecks. Overall, it provides an accessible, scalable, and standardized solution to advance digital herd management and precision genetic improvement in alpine livestock.

bioinformatics↗

bioRxiv2026

ITK Deficiency Attenuates Alveolar Hemorrhage by Enhancing Regulatory T Cell-Mediated Tissue Resilience

Pulmonary hemorrhage (PH) is a life-threatening manifestation of systemic autoimmunity caused by immune-mediated disruption of the alveolar capillary barrier. Despite high mortality, the molecular checkpoints that shift destructive inflammation toward protective immune regulation remain poorly defined. Here, using the pristane-induced PH model, we identify interleukin-2-inducible T cell kinase (ITK) as a critical regulator of autoimmune lung injury. ITK deficiency (ITK-/- ) conferred near-complete protection from PH and associated multiorgan injury, accompanied by reduced proinflammatory monocytes and neutrophils and increased Foxp3 regulatory T cells (Tregs). Adoptive transfer of ITK-/-; Tregs protected wild-type recipients from PH and suppressed systemic proinflammatory cytokines, identifying Tregs as key mediators of tissue protection. Mechanistically, lung ITK-/- ; Tregs exhibited increased amphiregulin, a mediator of tissue repair. Transcriptomic profiling further showed that ITK loss reprogrammed Tregs toward a metabolically and functionally enhanced state, with enrichment of oxidative phosphorylation, mTORC1 and STAT5 signaling, and tissue-repair programs. These findings establish ITK as a regulator of the balance between pulmonary injury and reparative immunity and support targeting the ITK axis in severe inflammatory lung disease.

immunology↗

bioRxiv2025

Trans-generational maintenance of mitochondrial DNA integrity in oocytes during early folliculogenesis

Mutations in mitochondrial DNA (mtDNA) can lead to mitochondrial and cellular dysfunction. However, recent studies suggest that there is purifying selection against mutant mtDNAs during transgenerational transmission. We investigated the mtDNA dynamics during ovarian follicle development. Using base-editing, we generated mice harboring a 3177 G>A mutation corresponding to the human Leber hereditary optic neuropathy (LHON)-related mtDNA mutation and confirmed the transgenerational reduction of mutant mtDNA. Using a mouse follicle culture system in which pathogenic mtDNA mutations were introduced in vitro followed by mtDNA sequencing and digital PCR, we found this germline heteroplasmy shift during early folliculogenesis was induced by the decrease of mutant mtDNA together with compensatory replication of wild-type mtDNA. In contrast, synonymous mtDNA mutations did not impact the mtDNA dynamics. These findings show that mice can eliminate certain pathogenic mtDNA mutations in the germline during early folliculogenesis, maintaining mitochondrial integrity across generations.

genetics↗

bioRxiv2020

Assessment of whether published non-Cochrane systematic reviews of nursing follow the review protocols registered in the International Prospective Register of Systematic Reviews (PROSPERO): A comparative study

Purpose We compare published non-Cochrane reviews of nursing with their pre-registered protocols on PROSPERO to quantify the prevalence of differences and the extent to which the differences were explained.Methods We searched for protocols and their corresponding reviews in PROSPERO’s nursing group that were “completed and published” from inception to September 8th, 2019. Two authors independently identified differences and classified the difference as none, partial, or complete, and determined if the existed differences had been explained. Frequency (n), percentage (%), median, and inter-quartile ranges were used to analyze the extent of differences and explanations.Results We identified 22 pre-registered protocols and their reviews. All 22 pairs (100%) exhibited differences. Eighteen pairs (82%) showed differences in at least six methodological sections, while 21 pairs (95%) involved completed difference in at least one section. The median number of differences per review was 8.00 (upper quartile = 6.00, lower quartile = 9.75). The differences involved all 13 compared methodology-related sections. Only 5 (3%) of all differences were explained in the systematic reviews.Conclusions We observed widespread differences between non-Cochrane reviews of nursing and their protocols recorded in PROSPERO, with relatively few explanations for the changes. Measures including establishing a new item in the reporting guideline of systematic reviews to guide reporting and explaining the reasons for differences between protocols and systematic reviews or even requiring authors to do so at the Journal’s author guideline are recommended to improve transparency.View Full Text

scientific communication and education↗

bioRxiv2017

Pyk2 suppresses contextual fear memory in a kinase-independent manner

Post-traumatic stress disorder (PTSD) is a psychological illness characterized by recalling a feeling of distress when re-experiencing the original trauma-related cues. This associative fear response plays an important role in some psychiatric disorders and elucidation of the underlying mechanisms is of great importance. Here, we constructed Pyk2 null mice and found that these mutant mice showed enhancement in contextual-fear memory, but no changes in auditory-cued and spatial-referenced learning and memory. Moreover, using kinase mutant mice, we observed that Pyk2 suppressed contextual fear memory in a kinase-independent pathway. Using high-throughput RNA sequencing, we found that immediate early genes (IEGs), such as Npas4, cFos, Zif268/Egr1, Arc, and Nr4a1, were enhanced in Pyk2 null mice. We further demonstrated that Pyk2 disruption affected pyramidal neuronal complexity and spine dynamics. Thus, we demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2 null mice provides a model for understanding fear-related disorders.

genetics↗