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The upper deg-centric graph of a simple, connected graph G, denoted by [G.sub.ud], is a graph constructed from G such that V([G.sub.ud]) = V(G) and E([G.sub.ud]) = [v.sub.i][v.sub.j]: [d.sub.G][v.sub.i], [v.sub.j]) [v.sub.j] [deg.sub.G]([v.sub.i]). This paper introduces and discusses the concepts of upper degcentric graphs and iterated upper deg-centrication of a graph. Keywords: Distance, eccentricity, deg-centric graphs, upper deg-centric graphs, upper deg-centrication process. AMS Subject Classification: 83-02, 99A00

[This corrects the article DOI: 10.3389/fnins.2022.1086168.].

[This corrects the article DOI: 10.3389/fimmu.2023.1198211.].

[This corrects the article DOI: 10.3389/fimmu.2023.1129513.].

Alzheimer's disease (AD) is a common, refractory, progressive neurodegenerative disorder in which cognitive and memory deficits are highly correlated with abnormalities in hippocampal brain regions. There is still a lack of hippocampus-related markers for AD diagnosis and prevention. Differently expressed genes were identified in the gene expression profile GSE293789 in the hippocampal brain region. Enrichment analyses GO, KEGG, and GSEA were used to identify biological pathways involved in the DEGs and AD-related group. WGCNA was used to identify the gene modules that are highly associated with AD in the samples. The intersecting genes of the genes in DEGs and modules were extracted and the top ten ranked hub genes were identified. Finally GES48350 was used as a validation cohort to predict the diagnostic efficacy of hub genes. From GSE293789, 225 DEGs were identified, which were mainly associated with calcium response, glutamatergic synapses, and calcium-dependent phospholipid-binding response. WGCNA analysis yielded dark green and bright yellow modular genes as the most relevant to AD. From these two modules, 176 genes were extracted, which were taken to be intersected with DEGs, yielding 51 intersecting genes. Then 10 hub genes were identified in them: HSPA1B, HSPB1, HSPA1A, DNAJB1, HSPB8, ANXA2, ANXA1, SOX9, YAP1, and AHNAK. Validation of these genes was found to have excellent diagnostic performance. Ten AD-related hub genes in the hippocampus were identified, contributing to further understanding of AD development in the hippocampus and development of targets for therapeutic prevention.

BACKGROUND: Photosystem II (PSII) is the light-driven water:plastoquinone oxidoreductase of oxygenic photosynthesis and is found in the thylakoid membrane of chloroplasts and cyanobacteria. Considerable attention is focused on how PSII is assembled in vivo and how it is repaired following irreversible damage by visible light (so-called photoinhibition). Understanding these processes might lead to the development of plants with improved growth characteristics especially under conditions of abiotic stress. SCOPE: Here we summarize recent results on the assembly and repair of PSII in cyanobacteria, which are excellent model organisms to study higher plant photosynthesis. CONCLUSIONS: Assembly of PSII is highly co-ordinated and proceeds through a number of distinct assembly intermediates. Associated with these assembly complexes are proteins that are not found in the final functional PSII complex. Structural information and possible functions are beginning to emerge for several of these 'assembly' factors, notably Ycf48/Hcf136, Psb27 and Psb28. A number of other auxiliary proteins have been identified that appear to have evolved since the divergence of chloroplasts and cyanobacteria. The repair of PSII involves partial disassembly of the damaged complex, the selective replacement of the damaged sub-unit (predominantly the D1 sub-unit) by a newly synthesized copy, and reassembly. It is likely that chlorophyll released during the repair process is temporarily stored by small CAB-like proteins (SCPs). A model is proposed in which damaged D1 is removed in Synechocystis sp. PCC 6803 by a hetero-oligomeric complex composed of two different types of FtsH sub-unit (FtsH2 and FtsH3), with degradation proceeding from the N-terminus of D1 in a highly processive reaction. It is postulated that a similar mechanism of D1 degradation also operates in chloroplasts. Deg proteases are not required for D1 degradation in Synechocystis 6803 but members of this protease family might play a supplementary role in D1 degradation in chloroplasts under extreme conditions.

This study investigated the differences in gene expression profiles of diploid and autotetraploid in cowpea, and provided theoretical basis for screening key genes of differential expression and ploidy breeding. The phenotypes and contents of chlorophyll, soluble sugar and soluble protein of diploid and autotetraploid of cowpea were compared and transcriptome sequencing was performed. The autotetraploid leaves of cowpea were thicker and darker green than diploid leaves, and the contents of chlorophyll, soluble sugar and soluble protein in leaves were higher. A total of 2678 differentially expressed genes (DEGs) were analyzed in the diploid and autotetraploid of cowpea. Among them, there were 421 genes with higher expression of tetraploid than diploid, and 2257 genes with lower expression of tetraploid than diploid. All 2678 DEGs were annotated into the Gene Ontology (GO) functional library. The DEGs were mainly concentrated in metabolism and cell composition. Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway analysis showed that cowpea diploid and autotetraploid have significant differences in flavonoid biosynthesis, degradation of other glycan, phenylpropane biosynthesis, starch sucrose metabolism, keratin, amber and wax biosynthesis, circadian rhythm and plant pathways. RESUMO: O objetivo deste estudo foi investigar as diferenças nos perfis de expressão gênica de diplóides e autotetraplóides em feijão-caupi e fornecer base teórica para a triagem de genes-chave de expressão diferencial e melhoramento de ploidia. Os fenótipos e teores de clorofila, açúcar solúvel e proteína solúvel de diplóides e autotetraplóides de feijão-caupi foram comparados e o sequenciamento do transcriptoma foi realizado. As folhas autotetraploides do feijão-caupi apresentaram-se mais espessas e de cor verde mais escura que as folhas diplóides, e os teores de clorofila, açúcar solúvel e proteína solúvel nas folhas foram maiores. Um total de 2678 genes diferencialmente expressos (DEG) foram analisados no diplóide e autotetraploide do feijão-caupi. Entre eles, havia 421 genes com maior expressão de tetraploide do que diplóides, e 2257 genes com menor expressão de tetraploide do que diplóides. Todos os 2678 DEGs foram anotados na biblioteca funcional GO. Os DEGs foram concentrados principalmente no metabolismo e na composição celular. A análise da via KEGG mostrou que o diplóides e o autotetraplóide do feijão-caupi apresentam diferenças significativas na biossíntese de flavonoides, degradação de outros glicanos, biossíntese de fenilpropano, metabolismo da sacarose do amido, biossíntese de queratina, âmbar e cera, ritmo circadiano e vias vegetais.

Soil salinity is becoming a growing issue nowadays, severely affecting the world’s most productive agricultural landscapes. With intersecting and competitive challenges of shrinking agricultural lands and increasing demand for food, there is an emerging need to build resilience for adaptation to anticipated climate change and land degradation. This necessitates the deep decoding of a gene pool of crop plant wild relatives which can be accomplished through salt-tolerant species, such as halophytes, in order to reveal the underlying regulatory mechanisms. Halophytes are generally defined as plants able to survive and complete their life cycle in highly saline environments of at least 200-500 mM of salt solution. The primary criterion for identifying salt-tolerant grasses (STGs) includes the presence of salt glands on the leaf surface and the Na + exclusion mechanism since the interaction and replacement of Na + and K + greatly determines the survivability of STGs in saline environments. During the last decades or so, various salt-tolerant grasses/halophytes have been explored for the mining of salt-tolerant genes and testing their efficacy to improve the limit of salt tolerance in crop plants. Still, the utility of halophytes is limited due to the non-availability of any model halophytic plant system as well as the lack of complete genomic information. To date, although Arabidopsis ( Arabidopsis thaliana ) and salt cress ( Thellungiella halophila ) are being used as model plants in most salt tolerance studies, these plants are short-lived and can tolerate salinity for a shorter duration only. Thus, identifying the unique genes for salt tolerance pathways in halophytes and their introgression in a related cereal genome for better tolerance to salinity is the need of the hour. Modern technologies including RNA sequencing and genome-wide mapping along with advanced bioinformatics programs have advanced the decoding of the whole genetic information of plants and the development of probable algorithms to correlate stress tolerance limit and yield potential. Hence, this article has been compiled to explore the naturally occurring halophytes as potential model plant species for abiotic stress tolerance and to further breed crop plants to enhance salt tolerance through genomic and molecular tools.

This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn’s disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.

The aim of this work was to study the physiological quality of ‘BRS’ passion fruit seeds grown at different altitudes stored in cold chamber and in natural environment for six months.  Hybrid passion fruit seeds (BRS Gigante Amarelo, BRS Sol do Cerrado and BRS Rubi do Cerrado) grown at three altitudes (104; 711; 1016 meters) in the southern region of the state of Espírito Santo were used. Germination was carried out in germitest paper rolls, placed in BOD-type germination chambers at temperature of 20-30 ºC. The following parameters were analyzed: germination, germination speed index, shoot and root length and dry mass of seedlings. The experimental design used was completely randomized in a factorial scheme with split plot in time 4x(3x3) (four bimonthly analyses x three hybrids x three altitudes), with two independent storage environments and three replicates of 100 seeds. Hybrid Passiflora edulis f. flavicarpa seeds can be stored in natural environment or cold chamber. Hybrid yellow passion fruit seeds grown at altitudes of 104 and 711 meters show higher germination and vigor percentages. Hybrid ‘Gigante Amarelo’ seeds had lower averages for variables under study, regardless of altitude. Hybrid ‘Rubi do Cerrado’ seeds grown at altitude of 1016 meters and hybrid ‘Sol do Cerrado’ seeds grown at altitudes of 104 and 711 meters have higher germination and vigor percentages and can be stored for 180 days in natural environment or cold chamber without viability loss. Flavicarpa can be stored in natural environment or cold chamber. Hybrid yellow passion fruit seeds grown at altitudes of 104 and 711 meters show higher germination and vigor percentages. Hybrid ‘Gigante Amarelo’ seeds had lower averages for variables under study, regardless of altitude. Hybrid ‘Rubi do Cerrado’ seeds grown at altitude of 1016 meters and hybrid ‘Sol do Cerrado’ seeds grown at altitudes of 104 and 711 meters have higher germination and vigor percentages and can be stored for 180 days in natural environment or cold chamber without viability loss. Passiflora edulis f. flavicarpa can be stored in natural environment or cold chamber. Hybrid yellow passion fruit seeds grown at altitudes of 104 and 711 meters show higher germination and vigor percentages. Hybrid ‘Gigante Amarelo’ seeds had lower averages for variables under study, regardless of altitude. Hybrid ‘Rubi do Cerrado’ seeds grown at altitude of 1016 meters and hybrid ‘Sol do Cerrado’ seeds grown at altitudes of 104 and 711 meters have higher germination and vigor percentages and can be stored for 180 days in natural environment or cold chamber without viability loss. Hybrid ‘Gigante Amarelo’ seeds had lower averages for variables under study, regardless of altitude. Hybrid ‘Rubi do Cerrado’ seeds grown at altitude of 1016 meters and hybrid ‘Sol do Cerrado’ seeds grown at altitudes of 104 and 711 meters have higher germination and vigor percentages and can be stored for 180 days in natural environment or cold chamber without viability loss.  Hybrid ‘Gigante Amarelo’ seeds had lower averages for variables under study, regardless of altitude. Hybrid ‘Rubi do Cerrado’ seeds grown at altitude of 1016 meters and hybrid ‘Sol do Cerrado’ seeds grown at altitudes of 104 and 711 meters have higher germination and vigor percentages and can be stored for 180 days in natural environment or cold chamber without viability loss.