Biology subjects

Jin, S.-H.

Publications and source records attributed to Jin, S.-H..

6 recordsLinked to original sources

bioRxiv2023

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

In this comprehensive study, we conducted extensive taxon sampling and performed phylogenomic analyses based on plastome and nuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenated and coalescent-based strategies, to generate an accurate phylogeny of the woody Rosaceae genus Pourthiaea. The nrDNA phylogeny of Pourthiaea strongly supported three major clades, which were consistent with morphology. However, the plastid tree provided an alternative phylogenetic topology, indicating cytonuclear discordance. Frequent hybridizations between and among the species of Pourthiaea could explain the cytonuclear discordance. Considering the evidence from morphology and phylogenomic data, we propose a new infrageneric classification for Pourthiaea, consisting of three sections: P. sect. Pourthiaea, P. sect. Amphidoxae B.B.Liu, and P. sect. Impressivenae B.B.Liu.

plant biology↗

bioRxiv2023

Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups identified to have pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model for testing the effect of reticulation on generic circumscription when hybridization and allopolyploidy define a groups evolutionary history. Here, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. The well-inferred phylogenetic backbone revealed an updated generic delimitation of Stranvaesia and a new genus, Weniomeles, characterized by purple-black fruits, trunk and/or branches with thorns, and fruit core with multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Here, we highlight a broadly-applicable workflow for inferring how analyses of reticulate evolution in phylogenomic data can directly shape taxonomic revisions.

evolutionary biology↗

bioRxiv2021

Temporal changes in resting state networks induced by propofol anesthesia.

The cerebral cortical changes associated with propofol-induced unconsciousness remain unknown. While the anesthetic agent affects the entire cerebral cortices, there might be spatiotemporal differences in cortical changes. In particular, we hypothesized that there might be spatiotemporal differences in cortical changes with propofol-anesthesia. To address this hypothesis, we investigated power spectrum changes in electrocorticography (ECoG) signals obtained during the induction phase from awake state to unconsciousness. We found that, 1) the power increased in the range of frequencies < 46 Hz (delta to low gamma), and decreased in the range (62-150) Hz (high gamma), in global channels during the induction phase. 2) The power in the frontoparietal network (FPN), specifically the superior parietal lobule and prefrontal cortex, started to change early, but took a long time to completely change. However, the power in the default mode network (DMN) started to change late, but took a short time to completely change. 3) The power change ({Delta}Power) in the DMN was more conspicuous than that of the dorsal attention network (DAN) in high gamma frequency. Considering that the FPN is involved in communication with the external world and that DMN is involved in communication with self, loss of consciousness induced by general anesthesia results from first, disrupted communication between self and external world, and is then followed by disrupted communication within self, with decreased activity of the FPN, and later, attenuated activity of the DMN. Significance StatementWe investigated the spatiotemporal changes of power spectrum in human electrocorticography (ECoG) during the induction phase from awake state to unconsciousness. We found that from delta to low gamma frequency, the power increased, while in high gamma frequency, the power decreased over all channels. The power in the frontoparietal network (FPN) preferentially changed, then the power in the DMN changed later. The power in DMN decreased more than those in other RSNs in high gamma frequency. Loss of consciousness induced by general anesthesia results from first, disrupted communication between self and external world, followed by disrupted communication within self, with decreased activity of the FPN, and later, attenuated activity of the DMN.

neuroscience↗

bioRxiv2020

Dissociation of connectivity for syntactic irregularity and perceptual ambiguity in musical chord stimuli

Previously syntactic irregularity has been most studied with chord sequences. However, the same chord may be interpreted as having different harmonic functions, implying perceptual ambiguity. Hence, syntactic irregularity and perceptual ambiguity may be processed simultaneously. We devised 3 different 5-chord sequences in which the ending chord differed with the tonic (T), submediant (SM), and supertonic (ST). In terms of syntactic regularity, T is most regular, ST is most irregular. However, in terms of perceptual ambiguity, the most irregular ST had the salient highest voice. Therefore, the SM was the most ambiguous condition. We investigated how the human brain separates syntactic irregularity and perceptual ambiguity in terms of effective connectivity in bilateral inferior frontal gyri (IFGs) and superior temporal gyri (STGs) with magnetoencephalography in 19 subjects. Correct rate was lower for the most ambiguous chord (SM) (P = 0.020) as expected. Connectivity from the right to the left IFG was enhanced for the most irregular chord (ST) (P = 0.024, false discovery rate (FDR) corrected), whereas connectivity from the right to the left STG was enhanced for the most ambiguous chord (SM) (P < 0.001, FDR corrected). The correct rate was negatively correlated with connectivity in the STG, further reflecting perceptual ambiguity (P = 0.026). We found that syntactic irregularity and perceptual ambiguity in music are dissociated in connectivity between bilateral IFGs and STGs, respectively. Significance StatementWe provide the first neurophysiological evidence of the processing of perceptual ambiguity, other than syntactic irregularity, implied in musical chords. We found that the notion of "perceptually ambiguity" is applicable to musical chord stimuli different in syntactic irregularity, and that perceptual ambiguity is separate from syntactic irregularity. Our data demonstrate that the brain interprets the three conditions of musical chords as both "from regular to irregular" and "from ambiguous to unambiguous" conditions simultaneously. This study is the first to unveil dissociation of connectivity by syntactic irregularity and perceptual ambiguity involved in musical chord stimuli.

neuroscience↗

bioRxiv2020

Increased fronto-temporal connectivity by modified melody in real music

In real music, the original melody may appear intact, with little elaboration only, or significantly modified. Since a melody is most easily perceived in music, hearing significantly modified melody may change a brain connectivity. Mozart KV 265 is comprised of a theme with an original melody of "Twinkle Twinkle Little Star" and its significant variations. We studied whether effective connectivity changes with significantly modified melody, between bilateral inferior frontal gyri (IFGs) and Heschls gyri (HGs) using magnetoencephalography (MEG). Among the 12 connectivities, the connectivity from the left IFG to the right HG was consistently increased with significantly modified melody compared to the original melody in 2 separate sets of the same rhythmic pattern with different melody (p = 0.005 and 0.034, Bonferroni corrected). Our findings show that the modification of an original melody in a real music changes the brain connectivity.

neuroscience↗

bioRxiv2019

M. leprae infects human keratinocytes via the interaction of laminin-5 with α-dystroglycan, integrin-β1, or -β4.

Although Mycobacterium leprae (M. leprae) is usually found in macrophages and nerves of the dermis of patients with multibacillary leprosy, it is also present in all layers of the epidermis, basal, suprabasal, prickle cells, and keratin layers. However, the mechanism by which M.leprae invades the dermis remains unknown, whereas the underlying mechanism by which M.leprae invades peripheral nerves, especially Schwann cells, is well defined. M. leprae binds to the -dystroglycan (DG) of Schwann cells via the interaction of -DG and laminin (LN)-2 in the basal lamina, thus permitting it to become attached to and invade peripheral nerves. In the current study, we investigated the issue of how M.leprae infects keratinocytes. LN-5 is the predominant form of laminin in the epidermis and allows the epidermis to be stably attached to the dermis via its interaction with /{beta}-DG as well as integrins that are produced by keratinocytes. We therefore focused on the role of LN-5 in when M. leprae invades keratinocytes. Our results show that M.leprae preferentially binds to LN-5-coated slides and this binding to LN-5 enhances its binding to human epidermal keratinocytes, neonatal (HEKn). The findings also show that pre-treatment with an antibody against -DG, integrin-{beta}1, or -{beta}4 inhibited the binding of LN-5-coated M.leprae to HEKn cells. These results suggest that M. leprae infects keratinocytes by taking advantage of the interaction of LN-5 in the basal lamina of the epidermis and a surface receptor of keratinocytes, such as -DG, integrin-{beta}1, or -{beta}4.\n\nAuthor summaryIn the current study, we investigated the issue of how M.leprae infects keratinocytes. We focused on the role of LN-5, a predominant form of laminin of the epidermis, in the invasion of M. leprae in keratinocytes. Our results show that M. leprae preferentially binds to LN-5-coated slides and coating M.leprae with LN-5 enhanced its binding to human epidermal keratinocytes, neonatal (HEKn). In addition, a pre-treatment with an antibody against -DG, integrin-{beta}1 or -{beta}4 inhibited the binding of LN-5-coated M. leprae to HEKn cells. These results suggest that M. leprae invades keratinocytes by taking advantage of the interaction of LN-5 in the basal lamina of the epidermis and a surface receptor of keratinocytes, such as -DG, integrin-{beta}1, or -{beta}4

microbiology↗