Characterization of Alternaria alternata isolates from different citrus species grown in Tunisian Cap Bon peninsula

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Abstract

The prospection of citrus trees affected by Alternaria alternata in Tunisian Cap Bon peninsula for 2 years, 2018 and 2019, showed a variation in the percentage of isolation frequency depending on the region, age of citrus trees and citrus species and varieties. Thirty isolates of A. alternata from citrus species were characterized and studied for their variability. The isolates were subjected to morphological identification using macroscopic and microscopic features and molecular characterization through PCR amplification of their internal transcribed spacer regions. A high morphological and molecular diversity within A. alternata isolates was detected. The molecular sequencing results precisely confirmed that these fungal isolates belong to A. alternata strains. Pathogenicity test showed that A. alternata T1 and T9 isolates were capable of causing disease symptoms only on young leaves of clementine plant (MA3 variety). These findings are useful in the development of sustainable strategies to manage Alternaria in citrus-growing areas in Tunisia.

Draft genome sequence of Colletotrichum fructicola causing leaf spot on tea plants (Camellia sinensis)

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Draft genome sequence of Colletotrichum fructicola causing leaf spot on tea plants (Camellia sinensis)

Draft whole-genome sequence of Colletotrichum fructicola SX-6 annotated 15,243 predicted protein-coding genes; four gene families whose genes were significantly more abundant were identified by comparative genome analyses.


Abstract

Colletotrichum fructicola, one of the dominant pathogens isolated from the main tea region in China, causes leaf spot in mature leaves of tea plants, affecting their growth and yield. Here, we present the draft whole-genome sequence of the C. fructicola strain SX-6 previously used for morphological and transcriptomic analyses. The assembly consists of 510 contigs with an estimated genome size of 56.8 Mb. A total of 15,243 predicted protein-coding genes in the SX-6 genome were annotated using NR, Swiss-Prot, KEGG, KOG, TCDB, GO, PHI, DFVF, P450, SignalP and CAZy databases. We identified 833 carbohydrate-active enzymes, 1803 secreted proteins, 79 secondary metabolite gene clusters and 576 fungal virulence factors that may be involved in the pathogenicity of this fungus. Comparative genome analyses with 25 Colletotrichum species revealed their evolutionary relationships via a constructed phylogenetic tree and identified four gene families whose genes were significantly more abundant in strain SX-6. The resulting assembly will provide a valuable resource for further research on the gene functions of C. fructicola.

A Human Neuron/Astrocyte Co‐culture to Model Seeded and Spontaneous Intraneuronal Tau Aggregation

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Abstract

Communication and contact between neurons and astrocytes is important for proper brain physiology. How neuron/astrocyte crosstalk is affected by intraneuronal tau aggregation in neurodegenerative tauopathies is largely elusive. Human induced pluripotent stem cell (iPSC)-derived neurons provide the opportunity to model tau pathology in a translationally relevant in vitro context. However, current iPSC models inefficiently develop tau aggregates, and co-culture models of tau pathology have thus far utilized rodent astrocytes. In this article, we describe the co-culture of human iPSC-derived neurons with primary human astrocytes in a 96-well format compatible with high-content microscopy. By lentiviral overexpression of different mutated tau variants, this protocol can be flexibly adapted for the efficient induction of seeded or spontaneous tau aggregation. We used this novel co-culture model to identify cell type–specific disease mechanisms and to provide proof of concept for intervention by antisense therapy. These results show that this human co-culture model provides a highly translational tool for target discovery and drug development for human tauopathies. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Human neuron/astrocyte co-culture for seeded and spontaneous intraneuronal tau aggregation

Support Protocol 1: Human induced pluripotent stem cell culture

Support Protocol 2: Human primary astrocyte culture

Neuroprotective effects of vitamin D in an Alzheimer’s disease rat model: Improvement of mitochondrial dysfunction via calcium/calmodulin‐dependent protein kinase kinase 2 activation of Sirtuin1 phosphorylation

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Neuroprotective effects of vitamin D in an Alzheimer's disease rat model: Improvement of mitochondrial dysfunction via calcium/calmodulin-dependent protein kinase kinase 2 activation of Sirtuin1 phosphorylation

The study investigated the potential role of vitamin D3 (Vit.D) in mitigating cognitive impairment and mitochondrial dysfunction in an Alzheimer's disease (AD) rat model. The results showed that Vit.D improved memory abilities, reduced Aβ aggregation and elevated p-Tau levels, restored normal mitochondrial function, and reduced inflammatory and oxidative stress via CAMKK2-AMPK/SIRT1 pathway upregulation. These findings suggest that Vit.D may have a neuroprotective effect against AD.


Abstract

Mitochondrial dysfunction is an early event in Alzheimer's disease (AD) pathogenesis. To assess the impact of vitamin D3 (Vit.D) on neurogenesis, we investigated its role in mitigating cognitive impairment and mitochondrial dysfunction through calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2)-mediated phosphorylation of Sirtuin1 (SIRT1) in an aluminum-chloride-D-galactose (AlCl3-D-gal)-induced AD rat model. Rats were distributed into four groups: control, AlCl3 + D-gal (10 + 60 mg/kg, ip), Vit.D (500 IU/kg, po), and AlCl3 + D-gal+Vit.D. Novel object recognition (NOR), Morris Water Maze, and passive avoidance (PA) tests were used to measure memory abilities. The hippocampal tissue was used to assess vitamin D3 receptor (VDR) and peroxisome-proliferator-activated-receptor-γ-coactivator-1α ( PGC-1α) expression by quantitative real-time polymerase chain reaction (qRT-PCR), CAMKK2, p-SIRT1, phosphorylated-AMP-activated protein kinase (p-AMPK), dynamin-related-protein-1 (Drp1), and mitofusin-1 (Mnf1) proteins by western blot and Ca2+ levels, endothelial nitic oxide synthase (eNOS), superoxide dismutase (SOD), amyloid beta (Aβ), and phospho tau (p-Tau) via enzyme-linked immunosorbent assay(ELISA) in addition to histological and ultrastructural examination of rat's brain tissue. Vit.D-attenuated hippocampal injury reversed the cognitive decline and Aβ aggregation, and elevated p-Tau levels in the AlCl3 + D-gal-induced AD rat model. In AlCl3 + D-gal-exposed rats, Vit.D induced VDR expression, normalized Ca2+ levels, elevated CAMKK2, p-AMPK, p-SIRT1, and PGC-1α expression. Vit.D reduced Drp1, induced Mnf1, increased mitochondrial membrane potential, preserved mitochondrial structure, restored normal mitochondrial function, and retained normal eNOS level and SOD activity in AlCl3 + D-gal rats. In conclusion, our findings proved that Vit.D may ameliorate cognitive deficits in AlCl3 + D-gal-induced AD by restoring normal mitochondrial function and reducing inflammatory and oxidative stress via CAMKK2-AMPK/SIRT1 pathway upregulation.

Coat protein genealogy and complete genome characterization of field isolates of rice yellow mottle virus from Zambia

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Abstract

Rice yellow mottle virus (RYMV) is widespread in mainland Africa and adjoining islands but to date its occurrence in Zambia is unknown. In March 2022, field surveys were conducted in Luapula, Northern, Western and Eastern provinces of Zambia to determine the occurrence of RYMV and its genetic relationship with global isolates of the virus. Thirty-three paddy rice fields were visited and 108 leaf tissue samples were collected for analysis. The incidence of yellow mottle symptoms ranged from 25% to 43% in 10 (30.3%) of 33 fields and RYMV was detected in 35 (32.4%) of 108 samples by RT-PCR with virus-specific primers. A subset of 27 RYMV-positive samples was constituted from which full-length (720 bp) coat protein (CP) regions were amplified followed by bidirectional Sanger sequencing. Phylogenetic analysis of the CP cistron revealed distinct clustering of the isolates from Zambia in a monophyletic clade as subtype of the RYMV strain S4. Three isolates were randomly selected and used to obtain complete RYMV genomes of 4448–4449 nucleotides (nt). Comparative analysis of both the CP and the complete RYMV genomes from Zambia with their corresponding sequences in GenBank revealed that they shared 92%–93.2% nt identities with strain S4 isolates. These results confirm for the first time occurrence of RYMV strain S4 in Zambia and further reinforce the need for phytosanitary vigilance to safeguard rice production in Zambia.

All nonhomologous chromosomes and rearrangements in Saccharum officinarum × Saccharum spontaneum allopolyploids identified by oligo-based painting

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Modern sugarcane cultivars (Saccharum spp., 2n = 100~120) are complex polyploids primarily derived from interspecific hybridization between S. officinarum and S. spontaneum. Nobilization is the theory of utilizing wild germplasm in sugarcane breeding, and is the foundation for utilizing S. spontaneum for stress resistance. However, the exact chromosomal transmission remains elusive due to a lack of chromosome-specific markers. Here, we applied chromosome-specific oligonucleotide (oligo)-based probes for identifying chromosomes 1-10 of the F1 hybrids between S. officinarum and S. spontaneum. Then, S. spontaneum-specific repetitive DNA probes were used to distinguish S. spontaneum in these hybrids. This oligo- fluorescence in situ hybridization (FISH) system proved to be an efficient tool for revealing individual chromosomal inheritance during nobilization. We discovered the complete doubling of S. officinarum-derived chromosomes in most F1 hybrids. Notably, we also found defective S. officinarum-derived chromosome doubling in the F1 hybrid Yacheng75-4191, which exhibited 1.5n transmission for all nonhomologous chromosomes. Altogether, these results highlight the presence of variable chromosome transmission in nobilization between S. officinarum and S. spontaneum, including 1.5n + n and 2n + n. These findings provide robust chromosome markers for in-depth studies into the molecular mechanism underlying chromosome doubling during the nobilization, as well as tracing chromosomal inheritance for sugarcane breeding.