The Relationship Between Cognitive Dysfunction and Symptom Dimensions Across Schizophrenia, Bipolar Disorder, and Major Depressive Disorder

Background: Cognitive dysfunction is considered a core feature among schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD). Despite abundant literature comparing cognitive dysfunction among these disorders, the relationship between cognitive dysfunction and symptom dimensions remains unclear. The study aims are a) to identify the factor structure of the BPRS-18 and b) to examine the relationship between symptom domains and cognitive function across SZ, BD, and MDD.Methods: A total of 716 participants [262 with SZ, 104 with BD, 101 with MDD, and 249 healthy controls (HC)] were included in the study. One hundred eighty participants (59 with SZ, 23 with BD, 24 with MDD, and 74 HC) completed the MATRICS Consensus Cognitive Battery (MCCB), and 507 participants (85 with SZ, 89 with BD, 90 with MDD, and 243 HC) completed the Wisconsin Card Sorting Test (WCST). All patients completed the Brief Psychiatric Rating Scale (BPRS).Results: We identified five BPRS exploratory factor analysis (EFA) factors (“affective symptoms,” “psychosis,” “negative/disorganized symptoms,” “activation,” and “noncooperation”) and found cognitive dysfunction in all of the participant groups with psychiatric disorders. Negative/disorganized symptoms were the most strongly associated with cognitive dysfunctions across SZ, BD, and MDD.Conclusions: Our findings suggest that cognitive dysfunction severity relates to the negative/disorganized symptom domain across SZ, BD, and MDD, and negative/disorganized symptoms may be an important target for effective cognitive remediation in SZ, BD, and MDD

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the pinot noir cultivar (PN40024) using the PacBio HiFi long reads. The T2T reference genome (PN_T2T) was 69 Mb longer with 9026 more genes identified than the 12X.v2 version (Canaguier et al., 2017). We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though the PN40024 sample had been selfed for nine generations, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome, therefore, provides important resources for grapevine genetics and breeding.This work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program (Overseas) to Yongfeng Zhou, the National Key Research and Development Program of China(grant2019YFA0906200), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), the Shenzhen Science and Technology Program (grant KQTD2016113010482651), the BMBF funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI). We thank Bianca Frommer, Marie Lahaye, David Navarro-Payá, Marcela K. Tello-Ruiz and Kapeel Chougule for their help in analyzing the RNA-Seq data and in running the gene annotation pipeline. This study is also based upon work from COST Action CA17111 INTEGRAPE and form COST Innovators Grant IG17111 GRAPEDIA, supported by COST (European Cooperation in Science and Technology).ViticultureT2Tgap-fregene clustercentromeretelomerePublishe

Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, <i>Rhinolophus</i>) Revealed by Three Organs

In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level

Temporal dynamics of the bat wing transcriptome: Insight into gene-expression changes that enable protection against pathogen

ABSTRACT Skin acts as a mechanical barrier between the body and its surrounding environment and plays an important role in resistance to pathogens. However, we still know little regarding skin responses to physiological changes, particularly with regard to responses against potential pathogens. We herein executed RNA-seq on the wing of the Rhinolophus ferrumequinum to assess gene-expression variations at four physiological stages: pre-hibernation, hibernation (early-hibernation and late-hibernation), and post-hibernation, as well as the gene-expression patterns of infected and uninfected bats with the Pseudogymnoascus destructans (Pd). Our results showed that a greater number of differentially expressed genes between the more disparate physiological stages. Functional enrichment analysis showed that the down-regulated response pathways in hibernating bats included phosphorus metabolism and immune response, indicating metabolic suppression and decreased whole immune function. We also found up-regulated genes in post-hibernating bats that included C-type lectin receptor signalling, Toll-like receptor signalling pathway, and cell adhesion, suggesting that the immune response and skin integrity of the wing were improved after bats emerged from their hibernation and that this facilitated clearing Pd from the integument. Additionally, we found that the genes involved in cytokine or chemokine activity were up-regulated in late-hibernation compared to early-hibernation and that FOSB regulation of immune cell activation was differentially expressed in bats infected with Pd during late-hibernation, implying that the host’s innate immune function was enhanced during late-hibernation so as to resist pathogenic infection. Our findings highlight the concept that maintenance of intrinsic immunity provides protection against pathogenic infections in highly resistant bats

Resting frequency of 11 individuals excluding the three outlier samples.

Resting frequency of 11 individuals excluding the three outlier samples.</p

Principal component values of all 14 individuals according to the expression levels of all genes (FPKM) obtained in the reference-free method.

Principal component values of all 14 individuals according to the expression levels of all genes (FPKM) obtained in the reference-free method.</p

GSEA ranked gene list for HN vs. JL.

Differences in gene expression within tissues can lead to differences in tissue function. Understanding the transcriptome of a species helps elucidate the molecular mechanisms underlying phenotypic divergence. According to the presence or absence of a reference genome of for a studied species, transcriptome analyses can be divided into reference‑based and reference‑free methods, respectively. Presently, comparisons of complete transcriptome analysis results between those two methods are still rare. In this study, we compared the cochlear transcriptome analysis results of greater horseshoe bats (Rhinolophus ferrumequinum) from three lineages in China with different acoustic phenotypes using reference‑based and reference‑free methods to explore their differences in subsequent analysis. The results gained by reference-based results had lower false-positive rates and were more accurate because differentially expressed genes among the three populations obtained by this method had greater reliability and a higher annotation rate. Some phenotype-related enrichment terms, including those related to inorganic molecules and proton transmembrane channels, were also obtained only by the reference-based method. However, the reference‑based method might have the limitation of incomplete information acquisition. Thus, we believe that a combination of reference‑free and reference‑based methods is ideal for transcriptome analyses. The results of our study provided a reference for the selection of transcriptome analysis methods in the future.</div

Principal component values of all 14 individuals according to the expression levels of all genes (FPKM) obtained in the reference-based method.

Principal component values of all 14 individuals according to the expression levels of all genes (FPKM) obtained in the reference-based method.</p