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Biology subjects

Duru, I. C.

Publications and source records attributed to Duru, I. C..

4 recordsLinked to original sources

BpLAZY1A Mediates Transcriptional Polarity and Drives Adaxial Tension Wood Like Tissue Formation in Silver Birch (Betula pendula) Branches

A defining feature of most trees is the architectural distinction between a vertically growing main stem and laterally growing branches. This growth habit increases fitness by increasing photosynthetically active surface area and shading competitors. Here, we studied the weeping birch cultivar Betula pendula Youngii to uncover the mechanisms that maintain lateral branch growth. We identified a loss-of-function mutation in BpLAZY1A, a core component of the gravitropic signalling pathway, as the cause of the weeping phenotype. Forward genetic analysis demonstrated that the weeping phenotype is recessive in silver birch. Transgenic BpLAZY1A RNAi lines phenocopied Youngii, confirming the functional role of BpLAZY1A. Reporter analysis revealed that BpLAZY1A is expressed predominantly in gravity-sensing starch sheath cells, with occasional expression in the main stem phloem. Time lapse imaging revealed two distinct gravitropic responses during branch development - an early response associated with establishment of the branch apex gravitropic set-point angle, and a later response associated with polar reinforcement at the branch base. The main stem retained normal gravitropic responses in BpLAZY1A RNAi lines, indicating a branch-specific role for BpLAZY1A. Integrative analyses combining transcriptomics, chemical profiling, and histochemistry indicated that BpLAZY1A establishes adaxial-abaxial polarity during early branch development. In wild-type branches, pectin-rich tension wood-like tissue formed preferentially in the adaxial xylem, accompanied by adaxial expression of pectin- and tension wood-associated genes, including BpRRT1 and BpCOBRA-LIKE4. Auxin-related genes, including BpIAA29 and BpSAURs, were preferentially upregulated in the abaxial side. This transcriptional asymmetry was reduced in BpLAZY1A RNAi line 1, where tension wood-like tissue formed in both adaxial and abaxial sides of the xylem, indicating a loss of polarity. Together, these findings demonstrate that BpLAZY1A functions specifically in branch gravitropism and links spatially asymmetric gene expression with branch growth orientation and biomechanical reinforcement. Our results identify BpLAZY1A as a key regulator coordinating gravitropic signalling, tissue polarity, and the developmental biomechanics underlying lateral branch growth.

plant biology↗

Comparison of phage and plasmid populations present in the gut microbiota of Parkinson's disease patients

The aging population worldwide is on the rise, leading to a higher number of Parkinsons disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We found over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and healthy controls (n = 68). Significant associations emerged between Body Mass Index (BMI) and plasmid alpha diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and healthy controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. Moreover, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes. We built a classification system based on a selection of the phages differentially abundant in the groups. A machine learning approach based on phage abundances allowed a classification of the subjects into the PD or control group with an area under curve (AUC) of 0.969.

microbiology↗

Metagenome-assembled microbial genomes from Parkinson's disease fecal samples

The human gut microbiome composition has been linked to Parkinsons disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAG) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different versions of Collinsella and Prevotella MAGs, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.

genomics↗

Improved chromosome level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) based on SMRT Sequencing and linkage map.

The Glanville fritillary (Melitaea cinxia) butterfly is a long-term model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome level assembly of the butterflys genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO, indicates that the genome contains 93 - 95% of the BUSCO genes in complete and single copies. We predicted 14,830 gene models using the MAKER pipeline and manually curated 1,232 of these gene models. The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome and genetics studies on this species.

genomics↗