Biology subjects

Khatun, N.

Publications and source records attributed to Khatun, N..

5 recordsLinked to original sources

bioRxiv2026

XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data

Rapid developments in sequencing technologies have reduced the costs of transcriptomic experiments and resulted in a plethora of publicly available RNA-seq datasets. This is a valuable resource that can be harnessed to obtain novel biological insights through data upcycling. In this wake, we introduce XpBrew, an end-to-end Python workflow that was applied to generate PanXpresso, a comprehensive collection of gene expression datasets covering the taxonomic breadth of plants, animals, fungi, bacteria and archaea. XpBrew (https://github.com/PuckerLab/XpBrew) and PanXpresso (https://doi.org/10.60507/FK2/OBIGQH) are freely available.

bioinformatics↗

bioRxiv2026

Lack of evidence for anthocyanins contributing to pigmentation of Chenopodium quinoa

While most plant lineages are pigmented by anthocyanins, several families in the Caryophyllales represent a major exception by showing a replacement of anthocyanin pigmentation by betalain pigmentation. The mutual exclusion of anthocyanins and betalains at the family level has been well established for over 50 years and has been mechanistically explained. Chenopodiaceae are a betalain-pigmented lineage lacking a key anthocyanin biosynthesis gene and lacking the key activating transcription factor of the anthocyanin biosynthesis. A publication by Zhang et al., 2024 claims that anthocyanins would be responsible for the red pigmentation in leaves of Chenopodium quinoa. Here, we assessed this study and reanalyzed the RNA-seq datasets generated in this study to demonstrate that there is no evidence for anthocyanin biosynthesis, but activity of the betalain and carotenoid biosynthesis could explain the observed pigmentation of quinoa leaves.

plant biology↗

bioRxiv2026

Prefrontal brain-to-brain synchrony during human group hunting: Evidence from fNIRS hyperscanning

Orca, wolves, chimpanzees and humans share a similarly impressive capacity for group hunting, where individuals coordinate behaviour together to capture prey. Studying hunting behaviours has important implications for understanding how behaviour in group contexts may be indicative of cognitive decline. Despite growing interest in brain circuits for prey capture, the brain regions involved in tracking prey during a hunt and the behaviours in group hunt linked to success remain unclear. Here we combined functional near infrared spectroscopy (fNIRS) and a virtual minecraft world to examine behaviour, brain dynamics and brain synchrony involved in group hunting behaviour. We focused on the prefrontal cortex (PFC) due to its known role in planning and social coordination and recorded from pairs of individuals as they either cooperated to hunt another person (prey) or simply followed another person. Hunters were more successful if they managed to keep a smaller distance to the prey and moved at speeds that were more synchronised with their co-predator. At high-range frequencies for fNIRS (0.1-0.2Hz), we found greater brain-to-brain synchrony in lateral and medial (frontopolar) PFC regions during hunting compared with chance levels. Together, these findings provide insights into what behaviours and brain dynamics associated with successful group hunting.

neuroscience↗

bioRxiv2025

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae

Poaceae is a species-rich family of plants in the monocots harboring many important crop species. As grasses, these plants lack striking flowers that are typically pigmented by anthocyanins. Here, we investigated the anthocyanin biosynthesis genes in Poaceae and characterized several striking patterns. (1) An independently evolved MYB lineage (ncaMYB) is responsible for the regulation of the anthocyanin biosynthesis in Poaceae. (2) The independently evolved BZ2 lineage replaced the otherwise widespread TT19/An9 lineage as anthocyanin-related glutathione S-transferase in Poaceae. (3) The anthocyanin biosynthesis genes ANS, arGST (BZ2), and the anthocyanin biosynthesis activating MYB (ncaMYB) appear to be absent from the genus Brachypodium. These observations could be explained by a loss of the anthocyanin biosynthesis at the basis of the Poaceae, followed by an evolutionarily independent regain and again a loss of the anthocyanin biosynthesis in Brachypodium.

plant biology↗

bioRxiv2020

Activation of SnRK2 by the Raf-like kinase ARK represents a common mechanism of ABA response in embryophytes

The Raf-like protein kinase ARK previously identified in the moss Physcomitrella patens acts as an upstream regulator of subgroup III SnRK2, the key regulator of abscisic acid (ABA) and abiotic stress responses. However, the mechanisms underlying activation of ARK by ABA and abiotic stress for the regulation of SnRK2 including the role of ABA receptor-associated group A PP2C (PP2C-A) are not understood. We identified Ser1029 as the phosphorylation site in the activation loop of ARK, which provided a possible mechanism for regulation of its activity. Analysis of transgenic ark lines expressing ARK-GFP with Ser1029-to-Ala mutation indicated that this replacement causes reductions in ABA-induced gene expression, stress tolerance and SnRK2 activity. Immunoblot analysis using an anti-phosphopeptide antibody indicated that ABA treatments rapidly stimulate Ser1029 phosphorylation in wild type. The phosphorylation profile of Ser1029 in ABA-hypersensitive ppabi1 lacking PP2C-A was similar to that in wild type, whereas little Ser1029 phosphorylation was observed in ABA-insensitive ark missense lines. Furthermore, newly isolated ppabi1 ark lines showed ABA-insensitive phenotypes similar to those of ark lines. These results indicate that ARK is a primary activator of SnRK2, preceding negative regulation by PP2C-A in bryophytes, which provides a prototypal mechanism for ABA and abiotic stress-responses in embryophytes. One sentence summaryPhysiological characterization of various moss mutants revealed a common mechanism for phytohormone responses under water deficit in all land plants.

plant biology↗