Biology subjects

Er, S.

Publications and source records attributed to Er, S..

8 recordsLinked to original sources

bioRxiv2026

Comparative analysis of adhesin-like proteins from Methanobacteriales species

Methanogenic archaea are key syntrophic partners in animal and human guts. However, the molecular basis of physical and functional interactions of methanogens with other cells remains poorly understood. Adhesin-like proteins (ALPs) are abundant, unusually large, and repeat-rich surface proteins and are potential prime candidates for mediating cell-cell interactions, however, due to poor characterization, ALPs often remain neglected in annotations of genomes and large-scale datasets. Here, we combined structure-guided analysis with comparative genomics to map ALP domain architectures across Methanobacteriales species, with emphasis on intestinal and rumen lineages. We curated predicted ALP structures and manually delineated domain boundaries to build a reference set encompassing ABD, RBH, membrane-anchoring domains (MAD), and miscellaneous accessory domains. Leveraging on a novel approach for ALP domain annotations, we generate ALP annotations and domain architectures for 17 Methanobacteriales species without reliance on primary-sequence homology. Applying this approach to strains of Methanobrevibacter smithii and Methanobrevibacter intestini, we assembled species-level "adhesiomes" and assessed conservation patterns of ALPs. Network analysis indicated that ALPs are more commonly shared among strains within a species than between species, suggesting species-specific adhesin repertoires. While total ALP counts differed significantly between M. smithii and M. intestini (Wilcoxon rank-sum p = 0.00295), median ALP lengths did not (p = 0.606). Our results provide a comprehensive overview of the ALP domain architectures in Methanobacteriales species and reveals species-specific adhesiomes that likely contribute to niche adaptation and syntrophic partnerships in gut ecosystems.

microbiology↗

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2025

Comparative genomics of DH5α-inhibiting Escherichia coli isolates from human feces reveals common co-occurrence of bacteriocin genes with virulence factors and antibiotic resistance genes.

The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producing Escherichia coli strains from the gut microbiota of healthy individuals in Singapore. Using a large-scale screening approach, we analyzed 3,107 E. coli isolates from 109 fecal samples for inhibitory activity against E. coli DH5 and performed whole-genome sequencing on 37 representative isolates. Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread, with colicins and microcins dominating the profiles. Notably, we identified a hcp-et3-4 gene cluster, encoding an effector linked to Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain. Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenic E. coli (ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract. Our study highlights the co-occurrence of bacteriocins, ARGs, and virulence genes in gut-residing E. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications. ImportanceThis study provides genomic insights into the diverse repertoire of potential bacteriocin production in E. coli strains isolated from a cohort of healthy human subjects in Southeast Asia. Our findings suggest that the co-occurrence of bacteriocin genes with multiple antibiotic resistance and virulence genes is a common feature among non-clinical isolates. This genetic linkage could contribute to the increased abundance of multi-drug-resistant and virulent strains within individual hosts. Moreover, this co-occurrence may facilitate the host colonization with strains carrying antibiotic resistance and virulence determinants, potentially also contributing to the dissemination of resistant and pathogenic strains within the local population and beyond.

microbiology↗

bioRxiv2024

The Interplay of Prior Information and Motion Cues in Resolving Visual Ambiguity in Agent Perception

Agent perception is essential for social interaction, allowing individuals to interpret and respond to the actions of others within dynamic environments. In this study, we examined on how prior knowledge and motion cues are integrated to influence the temporal dynamics of perceiving agents. In order to make realistic but ambiguous stimuli in motion and form characteristics, we used human, robot, and android agents. Using temporal representational similarity analysis (RSA) on EEG recordings, we analyzed the representation of agent identities under varying conditions--Still versus Moving stimuli and Prior versus Naive contexts. Our findings revealed that prior knowledge and motion cues interact to produce distinct temporal patterns of representation. In the naive condition, information about the agent persisted longer during still presentations than during moving ones, suggesting that the processing of agents depends on the availability of motion information and prior information. Moreover, motion information affects the temporal processing of agents when no prior information about agents is available. These results highlight the critical roles of both bottom-up sensory inputs and top-down expectations and their interactions in resolving the ambiguities inherent in agent perception.

neuroscience↗

bioRxiv2024

Predictive processing in biological motion perception: Evidence from human behavior

Biological motion perception plays a crucial role in understanding the actions of other animals, facilitating effective social interactions. While foundation of biological motion perception is rooted in bottom-up processes, as evidenced by point-light display studies, real-world complexities necessitate the involvement of top-down processes, such as attention and expectation. This study investigates the impact of expectations on biological motion perception using a cued individuation task with point-light display stimuli. We conducted three experiments, each providing advance information about distinct aspects of the subsequent biological motion stimuli - specifically information about action, emotion, and gender. Our results revealed a pattern in the action experiment, where participants demonstrated significantly slower response times for incongruent trials than congruent ones, but only under the 75% cue validity condition. This effect was notably absent in the emotion and gender experiments. Our exploration underscores the multi-faceted nature of biological motion perception, highlighting that while the brain adeptly harnesses prior cues to anticipate and interpret stimuli, the nature and reliability of these cues play a pivotal role on their effects. Specifically, action-related information stands out as an important modulator, possibly due to its evolutionary significance and unique neural processing pathway. These findings not only agree with the principles of predictive processing but also pave the way for future research, emphasizing the need to utilize naturalistic, complex stimuli together with neuroimaging methods to create more comprehensive models of biological motion perception.

neuroscience↗

bioRxiv2023

Comparison of tet(X4)-containing contigs from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects.

The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacteriaceae strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analysed. A metagenomic sequencing (MS) dataset of the same samples was mined for contigs that harboured the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and catD (also annotated as estT) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in two out of 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. Contig sequences are relatively short ([~]14-33 kb) but show high similarity to the respective plasmid sequences of the isolates. The frequent co-occurrence of florR and catD with tet(X4) corroborates the hypothesis that the transmission of tet(X4) may have originated from the veterinary sector. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism have a low abundance. Further optimisation is required if MS is to be utilised in antibiotic resistance surveillance.

microbiology↗

bioRxiv2022

PKB/AKT attenuates Lewy Body-like pathology in primary neurons via Cathepsins B and D

Motor symptoms of Parkinsons disease (PD) are caused by the loss of dopamine neurons in the substantia nigra pars compacta. Current PD therapies offer only symptomatic relief, and the research on novel ways to stop or slow down the degeneration of dopamine neurons in PD attracts considerable efforts. A characteristic feature of PD is the abnormal accumulation and spread of misfolded -synuclein (-syn) protein leading to the formation of Lewy neurites and bodies in different neuronal populations, including dopamine neurons. The process of Lewy body formation compromises neuronal functions and contributes to the progression of the disease and neurodegeneration in PD patients. Treatments preventing -syn misfolding, aggregation and/or spread may therefore provide much-needed disease-modifying therapies for PD. We and others have demonstrated that -syn aggregation and Lewy body formation can be modelled in primary neuronal cultures treated with -syn pre-formed fibrils (PFFs). Using this approach, we have identified several factors preventing the accumulation of phosphorylated -syn in dopamine neurons in vitro and in vivo. In particular, we and others have demonstrated a prominent role of PKB/AKT pathway activation in promoting the survival of dopamine neurons. Here, we utilize lentiviral vectors (LVs) to express constitutively active myristoylated serine-threonine protein kinase AKT1 (mAKT1) in primary dopamine neurons. We show that lentivirally-delivered mAKT1 promoted survival of dopamine neurons after thapsigargin-induced endoplasmic reticulum (ER) stress and prevented fibril-induced accumulation of phosphorylated -syn. Furthermore, using pharmacological tools, we demonstrate that this activity of mAKT1 is dependent on the functional Cathepsins B and D. These proof-of-principle results demonstrate the critical importance of lysosomal enzymes for processing misfolded -syn and establish a basis for the use of LVs to develop neuroprotective gene therapy strategies for dopamine neurons in PD.

neuroscience↗

bioRxiv2019

GDNF/RET signaling pathway activation eliminates Lewy Body pathology in midbrain dopamine neurons

Neurodegenerative diseases are associated with proteostasis disturbances and accumulation of fibrillar proteins into insoluble aggregates. Progressive age-related degeneration of dopamine neurons is a primary cause of motor dysfunctions in Parkinsons disease (PD) and substantial evidence supports critical involvement of -synuclein (-syn) in the etiology of PD. -syn is a cytosolic protein present in high concentrations in pre-synaptic neuronal terminals and a primary constituent of intracellular protein aggregates known as Lewy Neurites or Lewy Bodies. Progression of Lewy pathology is a characteristic feature in the PD brains caused by the prion-like self-templating properties of misfolded -syn. Modelling Lewy pathology progression with application of exogenously prepared -syn preformed fibrils, we discovered that glial cell line-derived neurotrophic factor (GDNF) prevented formation of -syn aggregates in dopamine neurons in culture and in vivo after viral vector expression of GDNF. These effects were abolished by CRISPR/Cas9-mediated deletion of receptor tyrosine kinase Ret, the major GDNF signaling pathway. Similar to GDNF, expression of mutated constitutively active RET (RET_MEN2B) was able to protect dopamine neurons. GDNF protection against -syn pathology progression was abolished by Src and attenuated by Akt pathway inhibitors. For the first time, we have shown the neurotrophic factor-mediated protection against the misfolded -syn propagation in dopamine neurons, uncovered underlying receptor and intracellular signaling pathways. These results for the first time demonstrate that activation of GDNF/RET signaling can be an effective therapeutic approach to prevent Lewy pathology spread at early stages of PD.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=145 HEIGHT=200 SRC=\"FIGDIR/small/752899v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (57K):\norg.highwire.dtl.DTLVardef@1f5109dorg.highwire.dtl.DTLVardef@15e4a2org.highwire.dtl.DTLVardef@15571c8org.highwire.dtl.DTLVardef@a10f7d_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗