Integration of Single-Cell RNA-Seq Datasets: A Review of Computational Methods.

With the increased number of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, integrative analysis of multiple scRNA-seq datasets has become commonplace. Batch effects among different datasets are inevitable because of differences in cell isolation and handling protocols, library preparation technology, and sequencing platforms. To remove these batch effects for effective integration of multiple scRNA-seq datasets, a number of methodologies have been developed based on diverse concepts and approaches. These methods have proven useful for examining whether cellular features, such as cell subpopulations and marker genes, identified from a certain dataset, are consistently present, or whether their condition-dependent variations, such as increases in cell subpopulations in particular disease-related conditions, are consistently observed in different datasets generated under similar or distinct conditions. In this review, we summarize the concepts and approaches of the integration methods and their pros and cons as has been reported in previous literature.

Piperlongumine decreases cognitive impairment and improves hippocampal function in aged mice.

Piperlongumine (PL), a biologically active compound from the Piper species, has been shown to exert various pharmacological effects in a number of conditions, including tumours, diabetes, pain, psychiatric disorders and neurodegenerative disease. In this study, we evaluated the therapeutic effects of PL on hippocampal function and cognition decline in aged mice. PL (50 mg/kg/day) was intragastrically administrated to 23­month­old female C57BL/6J mice for 8 weeks. Novel object recognition and nest building behaviour tests were used to assess cognitive and social functions. Additionally, immunohistochemistry and western blot analysis were performed to examine the effects of PL on the hippocampus. We found that the oral administration of PL significantly improved novel object recognition and nest building behaviour in aged mice. Although neither the percentage area occupied by astrocytes and microglia nor the level of 4­hydroxynonenal protein, a specific marker of lipid peroxidation, were altered by PL treatment, the phosphorylation levels of N­methyl­D­aspartate receptor subtype 2B (NR2B), calmodulin­dependent protein kinase II alpha (CaMKIIα) and extracellular signal­regulated kinase 1/2 (ERK1/2) were markedly increased in the hippocampus of aged mice following the administration of PL. We also found that PL treatment resulted in a CA3­specific increase in the phosphorylation level of cyclic AMP response element binding protein, which is recognized as a potent marker of neuronal plasticity, learning and memory. Moreover, the number of doublecortin­positive cells, a specific marker of neurogenesis, was significantly increased following PL treatment in the dentate gyrus of the hippocampus. On the whole, these data demonstrate that PL treatment may be a potential novel approach in the treatment of age­related cognitive impairment and hippocampal changes.

Synthesis and biological evaluation of carbocyclic analogues of pachastrissamine.

A series of carbocyclic analogues of naturally-occurring marine sphingolipid pachastrissamine were prepared and biologically evaluated. The analogues were efficiently synthesized via a tandem enyne/diene-ene metathesis reaction as a key step. We found that the analogue 4b exhibited comparable cytotoxicity and more potent inhibitory activity against sphingosine kinases, compared to pachastrissamine. Molecular modeling studies were conducted to provide more detailed insight into the binding mode of 4b in sphingosine kinase. In our docking model, pachastrissamine and 4b were able to effectively bind to the binding pocket of sphingosine kinase 1 as co-crystalized sphingosine. However, 4b showed a hydrophobic interaction with Phe192, which suggests that it contributes to its increased inhibitory activity against sphingosine kinase 1.