Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Reveals Human–Rodent Differences in H-Current Kinetics Influencing Resonance in Cortical Layer 5 Neurons

While our understanding of human neurons is often inferred from rodent data, inter-species differences between neurons can be captured by building cellular models specifically from human data. This includes understanding differences at the level of ion channels and their implications for human brain function. Thus, we here present a full spiking, biophysically-detailed multi-compartment model of a human layer 5 (L5) cortical pyramidal cell. Model development was primarily based on morphological and electrophysiological data from the same human L5 neuron, avoiding confounds of experimental variability. Focus was placed on describing the behavior of the hyperpolarization-activated cation (h-) channel, given increasing interest in this channel due to its role in pacemaking and differentiating cell types. We ensured that the model exhibited post-inhibitory rebound (PIR) spiking considering its relationship with the h-current, along with other general spiking characteristics. The model was validated against data not used in its development, which highlighted distinctly slower kinetics of the human h-current relative to the rodent setting. We linked the lack of subthreshold resonance observed in human L5 neurons to these human-specific h-current kinetics. This work shows that it is possible and necessary to build human-specific biophysical neuron models in order to understand human brain dynamics.
Single cell reconstruction of human basal cell diversity in normal and IPF lung

Rationale Declining lung function in patients with interstitial lung disease is accompanied by epithelial remodeling and progressive scarring of the gas-exchange region. There is a need to better understand the contribution of basal cell hyperplasia and associated mucosecretory dysfunction to the development of idiopathic pulmonary fibrosis (IPF). Objectives We sought to decipher the transcriptome of freshly isolated epithelial cells from normal and IPF lung to discern disease-dependent changes within basal stem cells. Methods Single cell RNA sequencing was used to map epithelial cell types of the normal and IPF human airway. Organoid and ALI cultures were used to investigate functional properties of basal cell subtypes. Measurements and Main Results We found that basal cells included multipotent and secretory primed subsets in control adult lung tissue. Secretory primed basal cells include an overlapping molecular signature with basal cells obtained from distal lung tissue of IPF lungs. We confirmed that NOTCH2 maintains undifferentiated basal cells and restrict basal-to-ciliated differentiation, and present evidence that NOTCH3 functions to restrain secretory differentiation. Conclusions Basal cells are dynamically regulated in disease and are specifically biased towards expansion of the secretory primed basal cell subset in idiopathic pulmonary fibrosis. Modulation of basal cell plasticity may represent a relevant target for therapeutic intervention in IPF.
Performance characterization of PCR-free whole genome sequencing for clinical diagnosis

Purpose To evaluate the performance of PCR-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection. Methods All the 5 NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing DNA input and library preparation protocol (PCR-based versus PCR-free protocols for library preparation). The DP (depth of coverage) and GQ (genotype quality) of each sample were compared. We developed a systematic WGS pipeline for the analysis of down-sampling samples of the 5 NA12878 samples. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes and CNVs. Results In general, NA12878-2 (PCR-free WGS) showed better DP and GQ distribution than NA12878-1 (PCR-based WGS). With a mean depth of ~40X, the sensitivity of homozyous and heterozygous SNPs of NA12878-2 showed higher sensitivity (>99.77% and > 99.82%) than NA12878-1, and positive predictive value (PPV) exceeded 99.98% and 99.07%. The sensitivity and PPV of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and CNVs are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. Conclusion Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.
Biophysical characterization of the human K0513 protein

Glioblastoma multiforme (GBM) is an aggressive grade IV primary malignant tumour which accounts for 78 % of all brain tumours. K0513 is a GBM biomarker that is upregulated in the invasive phenotype. K0513 is expressed ubiquitously and is reportedly enriched in the cerebral cortex of the brain. K0513 is further implicated in signalling pathways involving neuroplasticity, cytoskeletal regulation and apoptosis. The protein encoded by K0513 is a prospective biomarker for pancreatic cancer prognosis. However, the gene product of K0153 is not well characterised. This study focused on structure-function characterisation of human K0513 protein. To this end, we employed bioinformatics analysis and biophysical approaches to characterize the protein. In silico structural characterisation of the human K0513 protein suggests the presence of a SET binding factor 2 (SBF2) domain and a transmembrane region. The SBF2 domain is found in the Myotubularin-related protein 13 (MTMR13), which may function as a nucleotide exchange factor for the RAS-associated GTPase, Rab28. K0513 was predicted to interact with RAS-associated GTPase, Rab3a. Secondary structure prediction revealed K0513 to be predominantly α-helical in nature. The predicted three-dimensional model of K0513 showed a globular fold, suggesting that the protein is water-soluble. K0513 was heterologously expressed in E. coli XL1-Blue cells and subsequent purification yielded 80 % soluble protein. Biophysical characterisation using tryptophan-based fluorescence spectroscopy and limited proteolysis showed the conformation of K0513 is mostly unperturbed in the presence of nucleotides. Interestingly, K0513 was detected in lung carcinoma, fibrosarcoma and cervical adenocarcinoma cells, supporting its possible role in cancer signalling pathways.
Application of the in vivo oxidative stress reporter Hmox1 as mechanistic biomarker of arsenic toxicity

Inorganic arsenic (iAs) is a naturally occurring metalloid present in drinking water and polluted air exposing millions of people globally. Epidemiological studies have linked iAs exposure to the development of numerous diseases including cognitive impairment, cardiovascular failure and cancer. Despite intense research, an effective therapy for chronic arsenicosis has yet to be developed. Laboratory studies have been of great benefit in establishing the pathways involved in iAs toxicity and providing insights into its mechanism of action. However, the in vivo analysis of arsenic toxicity mechanisms has been difficult by the lack of reliable in vivo biomarkers of the effects of iAs. To resolve this issue we have applied the use of our recently developed stress reporter models to study iAs toxicity. The reporter mice Hmox1 (oxidative stress/inflammation; HOTT) and p21 (DNA damage) were exposed to iAs at acute and chronic, environmentally relevant, doses. We observed induction of the oxidative stress reporters in several cell types and tissues, which was largely dependent on the activation of transcription factor NRF2. We propose that our HOTT reporter model can be used as a surrogate biomarker of iAs-induced oxidative stress, and it constitutes a first-inclass platform to develop treatments in arsenicosis. Indeed, in a proof of concept experiment, the HOTT reporter mice were able to predict the therapeutic utility of the antioxidant N-acetyl cysteine in the prevention of iAs associated toxicity.
Small Non-Coding RNAome of Ageing Chondrocytes

Background Ageing is one of the leading risk factors predisposing cartilage to musculoskeletal diseases, including osteoarthritis. Cumulative evidence suggests that small non-coding RNAs play a role in cartilage-related pathological changes. However, little research has been conducted on the effect of ageing on the expression of small non-coding RNAs in cartilage. By using small RNA sequencing, we investigated changes in the expression of small non-coding RNAs between young and old equine chondrocytes. Methods Chondrocytes were extracted from five young (4±1 years) and five old (17.4±1.9 years) macroscopically normal equine metacarpophalangeal joints. Following RNA extraction cDNA libraries were prepared and subjected to small RNA sequencing using the Illumina MiSeq platform. Differential expression analysis was performed in R using package DESeq2. For tRNA fragment analysis, tRNA reads were aligned to horse tRNA sequences using Bowtie2 version 2.2. 5. Selected microRNA and small nucleolar RNA findings were validated using qRT-PCR in an extended cohort of equine chondrocytes. tRNA fragments were further investigated in low and high grade OA human cartilage tissue. Results In total, 83 sncRNAs were differentially expressed between young and old equine chondrocytes, including microRNAs, snoRNAs, snRNAs and tRNAs. Of these, 34 were expressed higher and 49 were expressed lower in old chondrocytes compared to young. qRT-PCR analysis confirmed findings in an extended cohort of equine chondrocytes. Ingenuity Pathway Analysis of differentially expressed microRNAs and their predicted target genes linked them to cartilage and OA-related pathways and diseases. tRNA fragment analysis revealed that tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1 were reduced in both high grade OA human cartilage and old equine chondrocytes. Conclusion For the first time, we have measured the effect of ageing on the expression of small non-coding RNAs in equine chondrocytes. Changes were detected in a number of different sncRNA species, including microRNAs, small nucleolar RNAs and tRNA fragments. This study supports a role for small non-coding RNAs in ageing cartilage and their potential involvement in age-related cartilage diseases.
Comparative computational analysis of stigmasterol biosynthetic genes and proteins in plants

Plant stigmasterol synthesis involves the partaking of many genes. In the present study, we performed computational comparison of the genes smt2, smo2, ste1, dwf5, dwf1 and c-22 sterol desaturase involved in the phytosterol biosynthetic pathway in different plants. Eleven plants belonging to different botanical families were selected and the gene sequence was retrieved from the KEGG pathway database. Nucleotide sequence homology was observed by Clustal W analysis and phylogeny was studied using MEGA 5 software. Clustal W and MEGA 5 analysis was done for amino acid sequence also. The maximum conserved regions were used in Prosite scan analysis. To determine the domains in protein sequence of the aforesaid genes in eleven plants, Pfam domain database search was performed. Phyre 2 software was used to develop 3D protein models. All the monocots used in the study belong to Poaceae family and hence in our phylogenetic analysis of phytosterol biosynthetic genes showed 90% sequence homology among the plants with same point of origin. The dicot plants chosen for the study belong to different families and hence the genes showed a homology percentile of less than 80.Pfam studies revealed SMT2 protein with a Methyl transf 11 and Sterol MTC domains. SMO2 and STE-1 proteins showed a common FA hydroxylase domain. DWF-5 was found to have domain structure of ERG4/ERG24 family, whereas, DWF-1 showed presence of FAD binding 4 domain. P450 structural domain was represented by sterol c-22 desaturase proteins. The 3D structure prediction revealed structural similarity among all eleven plants for protein involved in the plant stigmasterol biosynthesis.
Effect of Different Fertilization Rates on Cyanogen and Foliage and Tuber Yields of Cassava

This experiment was conducted to determine the effect of different fertilization rates on the cyanogen and yields of cassava foliage and tuber. Nine fertilization rates, three nitrogen and potassium levels (N: 0, 50, 100 kg/ha and K: 0, 100, 250 kg/ha, respectively) with constant phosphorus level (P: 50 kg/ha) (F-0:N0-P50-K0, F-1:N0-P50-K100, F-2:N0-P50-K250, F-3:N50-P50-K0, F-4:N50-P50-K100, F-5:N50-P50-K250, F-6:N100-P50-K0, F-7:N100-P50-K100, F-8:N100P50-K250), were applied in the randomized completely block design. After one year experiment, cassava foliage and tuber were harvested, and determined the yields and cyanogen (HCNp) content. The lowest (P < 0.05) HCNp contents and the highest (P < 0.05) foliage, tuber and protein yields were observed in cassava applied with F-4 (N50-P50-K100) and F-5 (N50-P50-K250) in compare with other fertilization rates. Regarding growth characteristics, the plant height (P < 0.05) was also highest in cassava fertilized by F-4 (N50-P50-K100) and F-5 (N50-P50-K250), whereas the leaf numbers per plant and branches number per plant were highest in cassava applied with F-5 (N50P50-K250) and F-7 (N100-P50-K100), respectively. It could be recommended that the nitrogen (N: 50 kg/ha) and potassium (K: 100-250 kg/ha) should be used to reduce cyanogen contents for safe utilization and increased cassava foliage and tuber yields.
Membrane Insertion of MoS2 Nanosheets: Fresh vs. Aged

Fresh two-dimensional (2D) molybdenum disulfide (MoS2) can absorb the hydrocarbon contamination from the ambient air and cause surface aging. Thus, understanding how the surface aging process of MoS2 affects the interaction with biomolecules is crucial for its applications in the biomedical field. Here, we employed atomistic molecular dynamics simulations to investigate the interactions of fresh and aged MoS2 nanosheets with POPE lipid membranes. Our results show that even though both the fresh and aged MoS2 nanosheets are capable of spontaneous insertion into the POPE bilayer membrane, the fresh MoS2 nanosheet displays significantly more robust interaction than the aged one. The potential mean force (PMF) calculations further confirm that the fresh MoS2 nanosheet is more energetically favorable than the aged one in penetrating into the POPE lipid membranes, with the former having ~17 kJ/mol stronger binding affinity than the later. This work provides a deeper understanding of the surface-aging-dependent interaction of MoS2 nanosheet with biomolecules, which might help the design of better MoS2-based nanodevices with appropriate surface properties.
Nonlinear spatial integration underlies the diversity of retinal ganglion cell responses to natural stimuli

How neurons encode natural stimuli is a fundamental question for sensory neuroscience. In the early visual system, standard encoding models assume that neurons linearly filter incoming stimuli through their receptive fields, but artificial stimuli, such as reversing gratings, often reveal nonlinear spatial processing. We investigated whether such nonlinear processing is relevant for the encoding of natural images in ganglion cells of the mouse retina. We found that standard linear receptive field models fail to capture the spiking activity for a large proportion of cells. These cells displayed pronounced sensitivity to fine spatial contrast, and local signal rectification was identified as the dominant nonlinearity. In addition, we also observed a class of nonlinear ganglion cells with opposite tuning for spatial contrast and a particular sensitivity for spatially homogeneous stimuli. Our work highlights receptive field nonlinearities as a crucial component for understanding early sensory encoding in the context of natural stimuli.
High-speed single-molecule imaging reveals signal transduction by induced transbilayer raft phases

Using single-molecule imaging with enhanced time resolutions down to 5 ms, we found that CD59-cluster rafts and GM1-cluster rafts stably induced in the outer leaflet of the plasma membrane (PM), which triggered the activation of Lyn, H-Ras, and ERK, continually recruited Lyn and H-Ras right beneath them in the inner leaflet, with dwell lifetimes of <0.1 s. The detection was possible due to the enhanced time resolutions employed here. The recruitment depended on the PM cholesterol and saturated alkyl chains of Lyn and H-Ras, whereas it was blocked by the non-raftophilic transmembrane protein moiety and unsaturated alkyl chains linked to the inner-leaflet molecules. Since GM1-cluster rafts recruited Lyn and H-Ras as efficiently as CD59-cluster rafts, and the protein moieties of Lyn and H-Ras were not required for the recruitment, we conclude that the transbilayer raft phases induced by the outer-leaflet stabilized rafts recruit lipid-anchored signaling molecules by lateral raft-lipid interactions, and thus serve as a key signal transduction platform. Summary High-speed single-molecule imaging indicated that CD59-cluster rafts and GM1-cluster rafts stably induced in the plasma membrane outer leaflet generated nano-scale transbilayer raft phases, which continually and transiently recruited Lyn and H-Ras in the inner leaflet by cooperative raft-lipid interactions.
miR156‐independent repression of the ageing pathway by longevity‐promoting AHL proteins in Arabidopsis

Plants age by transition through distinct developmental phases, with the juvenile- to adult vegetative and the adult vegetative to reproductive phase change as two consecutive important post-embryonic phase transitions. During the transition from the juvenile- to adult vegetative phase, also known as the vegetative phase change (VPC), many plants undergo specific morphological and physiological changes. In the model plant Arabidopsis thaliana (Arabidopsis), for example, the VPC is marked by clear heteroblastic changes in leaf shape and size and the appearance of trichomes on the abaxial side of leaves. The VPC and the vegetative to reproductive transition are promoted by the SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE (SPL) family of transcription factors and repressed by miR156 and miR157 that target the SPL transcripts. Here we present data that the plant longevity promoting AT-HOOK MOTIF NUCLEAR LOCALIZED protein 15 (AHL15) and family members also repress the SPL-driven ageing pathway. Arabidopsis ahl loss-of-function mutants showed an accelerated VPC and flowering time, whereas AHL15 overexpression dramatically delayed the VPC and flowering time in both Arabidopsis and Nicotiana tabacum. Expression analysis and tissue-specific AHL15 overexpression revealed that AHL15 affects the VPC and flowering time directly through its expression in the shoot apical meristem and young leaves. In addition, we found evidence that AHL15 represses SPL gene expression in a miR156/157-independent manner. The juvenile traits of spl loss-of-function mutants appeared to be dependent on the enhanced expression of the AHL15 gene, providing evidence for a reciprocal negative feedback between AHL15 and SPL genes. Antagonistically to AHLs, SPLs promote axillary meristem (AM) maturation and thus prevent vegetative growth from these meristems by repressing AHL15 expression. Taken together, our results place AHL15 and family members at a central position in the SPL-driven ageing pathway as suppressors of the VPC, flowering time and AM maturation.
Developmental pathways regulate cytokine-driven effector and feedback responses in the intestinal epithelium

The intestinal tract is a common site for infection, and it relies on an appropriate immune response to defend against pathogens. The intestinal epithelium has an important role in effector responses, which is coordinated by immune-type specific cytokines. It is incompletely understood how cytokines drive epithelial responses. Here, using organoid-cytokine co-cultures, we provide a comprehensive analysis of how key cytokines affect the intestinal epithelium, and relate this to in vivo infection models. We use imaging, based on a convolutional neural network, and transcriptomic analysis to reveal that cytokines use developmental pathways to define intestinal epithelial effector responses. For example, we find IL-22 and IL-13 dichotomously induce goblet cells, in which only IL-13 driven goblet cells are associated with NOTCH signaling. We further show that IL-13 induces BMP signalling to act as a negative feedback loop in IL-13 induced tuft cell hyperplasia, an important aspect of type 2 immunity. Together, we show that targeting developmental pathways may be a useful tool to tailor epithelial effector responses that are necessary for immunity to infection.
An in-silico based clinical insight on the effect of noticeable CD4 conserved residues of SARS-CoV-2 on the CD4-MHC-II interactions

The study is aimed to unveil the conserved residues of CD4 in the context of its purposeful interaction with MHC-II at the receptor-binding domain (RBD) of SARS-CoV-2 compared with the envelope (Env) glycoprotein (gp) 120 of HIV-1. The paired CD4 conserved residues, including the matched CD4 interacting MHC-II epitopes of the structural viral protein domains, were chosen for the protein modelling using the SWISS-MODEL online server. Energy minimization and structural validation of the modelled viral protein domains, including the CD4 and MHC-II protein were achieved by CHIMERA and PROCHECK-Ramachandran Plot respectively. Protein-protein docking was performed by the HADDOCK online tool. The binding affinity score was measured using the PRODIGY online server. As per our docking report, the Env gp120 of HIV-1 with three identical and three conserved residues of CD4 exhibited the highest binding affinity (−13.9 kcal/mol) with MHC-II than the second-highest RBD-S1-SARS-CoV-2 (−12.5 kcal/mol) with three identical and a single conserved residue of CD4. With a noticeable single salt bridge formation identified at the interacting residues Lys305 (of Env gp120-HIV-1) and Glu139 (of MHC-II); the Env gp120 interaction with MHC-II occupied the crucial His144 and Glu194 (salt-bridge) interacting residues of CD4 with the measured buried surface area 2554.8±40.8 Å2. Similarly, the RBD-S1-SARS-CoV-2-MHC-II complex showed two salt bridge formations at the residue sites: 1) Arg567 (of SARS-CoV-2)-Glu194 (of MHC-II) 2) 2) Asp568(of SARS-CoV-2)-Arg165 (of MHC-II) with the increased buried surface area of 1910.9±97.1 Å2 over the SARS-CoV score 1708.2±50.8 Å2; that camouflaged all crucial CD4 interacting residues of MHC-II. In conclusion, the noticeable conserved residues of CD4 at the RBD-S1 sites of SARS-CoV-2 could interrupt the aspired CD4-MHC-II interactions of adaptive immune activation.