Biology subjects

Lamichhane, B.

Publications and source records attributed to Lamichhane, B..

7 recordsLinked to original sources

bioRxiv2025

Branch-Enabling N-Methyltransferase in Golgi Reconciles Divergent Models of Galanthamine Biosynthesis

Galanthamine, a therapeutic Amaryllidaceae alkaloid produced exclusively by species within the Amaryllidoideae subfamily, is a key treatment for early-stage symptoms of Alzheimers disease. Elucidating its biosynthetic pathway is essential for strategies aimed at enhancing production through metabolic engineering. Galantamine derives from the metabolic precursor 4'-O-methylnorbelladine, which undergoes cytochrome P450-mediated para-ortho C-C phenol coupling to yield nornarwedine. Two competing terminal routes have been proposed: (i) reduction of nornarwedine to norgalanthamine, followed by N-methylation, or (ii) N-methylation of nornarwedine to narwedine prior to reduction. Here, we identify three N-methyltransferase (NMT) candidates from Leucojum aestivum: LaNMT, related to coclaurine NMTs, and two {gamma}-tocopherol methyltransferases (TMT) homologs, LaTMT1 and LaTMT2. Subcellular localization studies revealed distinct compartmentalization, with LaNMT targeted to the ER-cytosol, LaTMT1 to plastids, and LaTMT2 to the Golgi apparatus. In vitro enzyme assays demonstrated that LaTMT2 methylates both nornarwedine and norgalanthamine, with a kinetic preference for nornarwedine. Agroinfiltration for transient expression in Nicotiana benthamiana further confirmed LaTMT2 as a catalytically efficient and substrate-promiscuous enzyme that supports both terminal routes. These findings identify LaTMT2 as a key branch-enabling N-methyltransferase that reconcile long-standing models of galanthamine biosynthesis and provides a strategic target for metabolic engineering strategies to enhance galanthamine production. Significant statementThis study identifies LaTMT2, a Golgi-localized {gamma}-tocopherol methyltransferase homolog, as a branch-enabling N-methyltransferase that resolves competing models of galanthamine biosynthesis. By revealing an unanticipated Golgi-associated step in Amaryllidaceae alkaloid metabolism, it redefines the subcellular organization of specialized metabolic pathways and provides a strategic enzymatic target for metabolic engineering of high-value therapeutic alkaloids.

plant biology↗

bioRxiv2023

Including organism and environmental heterogeneity in kinematic continuum models of collective behaviour with applications to locust foraging and group structure

Collective behaviour occurs at all levels of the natural world, from cells joining together to form complex structures, to locusts interacting to form large and destructive plagues. These complex behaviours arise from simple individual and environmental interactions, and thus lend themselves well to mathematical modelling. One simplifying assumption, that of relative homogeneity of organisms, is often applied to keep the mathematics tractable. However, heterogeneity arising due to the internal state of individuals has an impact on these interactions and thus plays a role in group structure and dynamics. In this paper, we introduce a continuum model that accounts for this heterogeneity in the form of a state space that models an organisms internal state and converts this to movement characteristics. Using a variety analytic techniques, we investigate the effect of internal state on aggregation density and aggregation formation behaviour, finding that density and formation is most affected by the ratio of attractive to dispersive interactions. We then apply the model to a concrete example of locust foraging to investigate the effect of food, hunger, and gregarisation on locust group formation and structure. Through numerical simulations we find that the most gregarious and satiated locusts tend to be located towards the centre of locust groups. Conversely, hunger drives locusts towards the edges of the group. Finally, we find that locust group dispersal may be driven in part by hunger. Author SummaryCollective behaviour occurs at all levels of the natural world, from cells joining together to form complex structures, to locusts interacting to form large and destructive plagues. We can modelling these complex behaviours using mathematical models however we often need to rely on simplifying assumptions to keep the mathematics easy enough to analyse. One simplifying assumption that is often employed is assuming that all the modelled organisms are the same (or in one of only a few possible states). However, this is often not the case in nature where the differences between individuals arising due to internal characteristics, such as hunger or age, often affects their behaviour and thus can change group dynamics. In this paper we introduce a mathematical model that is able to capture these differences and apply the newly developed model to locust foraging. We find that hunger tends to drive individuals to the edges of aggregations as well as lowers the maximum possible density. These two results combine to give a possible mechanism for the dispersal of locust groups.

animal behavior and cognition↗

bioRxiv2023

APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia

Several genetic risk factors for Alzheimers Disease (AD) implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells. However, the relationship between lipid metabolism in glia and AD pathology remains poorly understood. Through single-nucleus RNA-sequencing of AD brain tissue, we have identified a microglial state defined by the expression of the lipid droplet (LD) associated enzyme ACSL1 with ACSL1-positive microglia most abundant in AD patients with the APOE4/4 genotype. In human iPSC-derived microglia (iMG) fibrillar A{beta} (fA{beta}) induces ACSL1 expression, triglyceride synthesis, and LD accumulation in an APOE-dependent manner. Additionally, conditioned media from LD-containing microglia leads to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for AD with microglial LD accumulation and neurotoxic microglial-derived factors, potentially providing novel therapeutic strategies for AD.

neuroscience↗

bioRxiv2021

Isolation and Genomics of multidrug-resistant Brevundimonas diminuta collected from patients with pertussis-like symptoms

Brevundinomas diminuta is known as an opportunistic pathogen and is rarely associated with invasive infections in humans causing infection in the different parts of the body. In this study, we identified three B. diminuta isolates from three patients with an initial diagnosis of pertussis. Isolates were confirmed using biochemical tests and 16s rRNA sequencing. All isolates were resistant to three different classes of antimicrobial drugs including ceftazidime and ciprofloxacin. We performed Illumina whole-genome sequencing for two isolates. The results showed an average genome size of 3.25 Mbp with the G+C content 67% with multiple predicted virulence factors and genes leading to antibiotic resistance. We found an open pan-genome with 1502 core genes by analysing 13 available global B. diminuta isolated from different environments such as water, soil, or gentamicin fermentation residue. In the phylogenetic analysis, our isolates were grouped with B. diminuta isolate collected from an oral cavity of a patient in the USA.

genomics↗

bioRxiv2020

Modelling locust foraging: How and why food affects hopper band formation

Locust swarms are a major threat to agriculture, affecting every continent except Antarctica and impacting the lives of 1 in 10 people. Locusts are short horned grasshoppers that exhibit two behaviour types depending on their local population density. These are; solitarious, where they will actively avoid other locusts, and gregarious where they will seek them out. It is in this gregarious state that locusts can form massive and destructive flying swarms or plagues. However, these swarms are usually preceded by the formation of hopper bands by the juvenile wingless locust nymphs. It is thus important to understand the hopper band formation process to control locust outbreaks. On longer time-scales, environmental conditions such as rain events synchronize locust lifecycles and can lead to repeated outbreaks. On shorter time-scales, changes in resource distributions at both small and large spatial scales have an effect on locust gregarisation. It is these short time-scale locust-resource relationships and their effect on hopper band formation that are of interest. In this paper we investigate not only the effect of food on both the formation and characteristics of locust hopper bands but also a possible evolutionary explanation for gregarisation in this context. We do this by deriving a multi-population aggregation equation that includes non-local inter-individual interactions and local inter-individual and food interactions. By performing a series of numerical experiments we find that there exists an optimal food width for locust hopper band formation, and by looking at foraging efficiency within the model framework we uncover a possible evolutionary reason for gregarisation. Author summaryLocusts are short horned grass hoppers that live in two diametrically opposed behavioural states. In the first, solitarious, they will actively avoid other locusts, whereas the second, gregarious, they will actively seek them out. It is in this gregarious state that locusts form the recognisable and destructive flying adult swarms. However, prior to swarm formation juvenile flightless locusts will form marching hopper bands and make their way from food source to food source. Predicting where these hopper bands might form is key to controlling locust outbreaks. Research has shown that changes in food distributions can affect the transition from solitarious to gregarious. In this paper we construct a mathematical model of locust-locust and locust-food interactions to investigate how and why isolated food distributions affect hopper band formation. Our findings suggest that there is an optimal food width for hopper band formation and that being gregarious increases a locusts ability to forage when food width decreases.

biochemistry↗

bioRxiv2020

Thyroid Hormones-Thyrotropin Interrelationships in Thyroid Dysfunction States

Objective of this research is to explore the complex correlations among FT3, FT4 and TSH in thyroid dysfunction states. A total of 3425 outpatients were included to analyze their thyroid function tests measured at the university teaching hospital. The subjects under study were categorized as euthyroid (70.45%), subclinical hypothyroid (18.95%), overt hypothyroid (3.30%), subclinical hyperthyroid (5.11%) and overt hyperthyroid (2.19%) patients. The linear and non-linear relations among FT3, FT4 and TSH were modeled statistically to understand their role in thyroid functions. The prevalence of hypothyroidism is higher than hyperthyroidism in which females are more vulnerable than males. The correlation between FT3 and FT4 increases from euthyroidism (r = 0.1, P <0.001) to overt thyroid dysfunctions (r = 0.91, P <0.001). The non-linear complex correlations between FT4 and TSH are significantly explained by well fitted sigmoid curves of four-parameter logistic (4PL) model (R2 = 0.97 and P <0.001) in both hypothyroidism and hyperthyroidism interfaced with euthyroidism. The 4PL curves are response trajectories of pituitary TSH which exhibit the turning points of thyroid dysfunction states by the deviation in serum FT4. The negative slopes and correlations observed in the linear fits in TSH vs FT3 or FT4 are the indicators of negative feedback mechanism in the thyroid cycle.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biochemistry↗

bioRxiv2018

The Subjective Value of Cognitive Effort is Encoded by a Domain-General Valuation Network

Cognitive control is necessary for goal-directed behavior, yet people treat control as costly, discounting goal value by cognitive demands in a similar manner as they would for delayed or risky outcomes. It is unclear, however, whether a putatively domain-general valuation network implicated in other cost domains also encodes the subjective value (SV) of cognitive effort. Here, we demonstrate that a valuation network, centered on the ventromedial prefrontal cortex and ventral striatum, also encodes SV during cognitive effort-based decision-making. We doubly dissociate this network from a primarily frontoparietal network recruited as a function of decision difficulty. We also find evidence that SV signals predict choice and are influenced by state and trait motivation, including sensitivity to reward and anticipated task performance. These findings unify cognitive effort with other cost domains, and inform physiological mechanisms of SV representations underlying the willingness to expend cognitive effort.

neuroscience↗