Miracle-dz/UniFAR-FTUs huggingface dataset:
A universal mechanism of biomass density homeostasis via ribosomal counterions

In all growing cells, the cell envelope must expand in concert with cytoplasmic biomass to prevent lysis or molecular crowding. The complex cell wall of microbes and plants makes this challenge especially daunting and it unclear how cells achieve this coordination. Here, we uncover a striking linear increase of cytoplasmic pressure with growth rate in E. coli. Remarkably, despite this increase in turgor pressure with growth rate, cellular biomass density was constant across a wide range of growth rates. In contrast, perturbing pressure away from this scaling directly affected biomass density. A mathematical model, in which endopeptidase-mediated cell wall fluidization enables turgor pressure to set the pace of cellular volume expansion, not only explains these confounding observations, but makes several surprising quantitative predictions that we validated experimentally. The picture that emerges is that changes in turgor pressure across growth rates are mediated by counterions of ribosomal RNA. Profoundly, the coupling between rRNA and cytoplasmic pressure simultaneously coordinates cell wall expansion across growth rates and exerts homeostatic feedback control on biomass density. Because ribosome content universally scales with growth rate in fast growing cells, this universal mechanism may control cell wall biosynthesis in microbes and plants and drive the expansion of ribosome-addicted tumors that can exert substantial mechanical forces on their environment.
A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
Finding Expression of MUC1 and MUC4 in the Respiratory System of the Iraqi Common Quail (Coturnix coturnix)

Background This study focused on the major components of mucus, known as mucins, within the mucosal epithelium of the respiratory system in Iraqi Common Quail. Six quail were utilized in accordance with animal ethics guidelines from the College of Veterinary Medicine at the University of Al-Qadisiyah. Histological analysis, utilizing H&E staining, aimed to identify key respiratory system structures. PAS plus Alcian blue stains were employed to identify specific carbohydrates in the trachea, bronchi, and lungs. RT-qPCR was used to assess the gene expression levels of MUC1 and MUC4. Results The trachea and bronchi encompassed four distinct layers: tunica mucosa, tunica submucosa, hyaline cartilage, and tunica adventitia. The mucosa consisted of pseudostratified epithelium that transitioned into simple columnar cells toward the primary and secondary bronchioles. This transition further progressed into simple cuboidal and squamous epithelium at smaller tertiary branches of the secondary bronchioles. Notably, the bronchial tunica submucosa was thinner than the trachea. While hyaline cartilage was prominently present in the trachea, it became fragmented in the bronchi and diminished towards the lungs and secondary bronchioles. Lung tissue was characterized by numerous lobules housing alveoli connected to alveolar ducts and sacs, alongside an intricate network of blood vessels. The respiratory tissues, including the trachea, bronchi, and lungs, exhibited a strong affinity for PAS-combined Alcian blue stains. This confirmed the substantial presence of both acidic and neutral mucins within the epithelial cells and glands. The trachea demonstrated significantly elevated levels of acidic mucins and a concentrated amount? of neutral mucins. Transcriptome analysis indicated the expression of both MUC1 and MUC4 genes. Importantly, MUC4 expression surpassed that of MUC1 in the trachea, bronchi, and lungs. Conclusion This study highlights the similarity of histological structures in the trachea, bronchi, and lungs of quail to typical avian species. Moreover, it underscored the substantial presence of both acidic and neutral mucins, with MUC4 being the predominant mucin, potentially playing a pivotal role in regulating mucosal barrier functions and interacting with pathogens. Nonetheless, further investigation is warranted to elucidate MUC4’s role in respiratory epithelial cells.
Methods for tagging an ectoparasite, the salmon louse Lepeophtheirus salmonis

Monitoring individuals within populations is a cornerstone in evolutionary ecology, yet individual tracking of invertebrates and particularly parasitic organisms remains rare. To address this gap, we describe here a method for attaching radio frequency identification (RFID) tags to individual adult females of a marine ectoparasite, the salmon louse Lepeophtheirus salmonis. Comparing two alternative types of glue, we found that one of them (2-octyl cyanoacrylate, 2oc) gave a significantly higher tag retention rate than the other (ethyl 2-cyanoacrylate, e2c). This glue comparison test also resulted in a higher loss rate of adult ectoparasites from the population where tagging was done using 2oc, but this included males not tagged and thus could also suggest a mere tank effect. Corroborating this, a more extensive analysis using data collected over two years showed no significant difference in mortality after repeated exposure to the 2oc glue, nor did it show any significant effect of the tagging procedure on the reproduction of female salmon lice. The proportion of RFID-tagged individuals followed a negative exponential decline, with tag retention among the living female population generally high. The projected retention was found to be about 88% after 30 days or 80% after 60 days, although one of the four batches of glue used, purchased from a different supplier, appeared to give significantly lower tag retention and with greater initial loss (74% and 60% respectively). Overall, we find that RFID tagging is a simple and effective technology that enables documenting individual life histories for invertebrates of a suitable size, including marine and parasitic species, and that it can be used over long periods of study.
Sexual antagonism and sex determination in three syngnathid species alongside male pregnancy gradient and varying sex roles.

Teleost fish show an enormous diversity of sex determination systems, varying from environmental sex determination to full sex chromosomes. Traditionally sex chromosomes are considered within a framework of sexually antagonistic relationships and are viewed not only as sex determination systems but also as a means to resolve sexual conflict by confining conflicting genes to one sex. However, the relationship between emergence sexually-antagonistic loci, resolution of sexual conflict and sex determination is not fully understood. In this study we take a look at genomic and transcriptomic signatures of sexual antagonism, and relate them to putative sex determination systems in three species from the family Syngnathidae: Nerophis ophidion , Syngnathus typhle and Hippocampus erectus . The family is famous for their extreme form of parental care - male pregnancy. Male pregnancy forms a parental investment gradient among species of the family. We selected species alongside this gradient to investigate the effects male pregnancy has on sexual conflict in syngnathids. We found that both S.typhle and N.ophidion seem to have environmental sex determination and that sexual conflict is primarily resolved via differential gene and allele expression. On the other hand H.erectus possess an XY sex chromosome system. Strikingly, the identified homomorphic Y chromosome is not homologous to the Y chromosome of H.erectus identified in an independent study. We hypothesize that both sex-linked chromosomes evolved due to captive breeding and represent transition states between sex determination systems. Furthermore, we propose that the master sex determination gene is located outside of these sex-linked chromosomes.
Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures

Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs, which enable kinases to adopt various conformational states. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the kinase conformation(s) they bind. However, the limited availability of experimentally determined structural data for kinases in inactive states restricts drug discovery efforts for this major protein family. Modern AI-based structural modeling methods hold potential for exploring the previously experimentally uncharted druggable conformational space for kinases. Here, we first evaluated the currently explored conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) (1) and ESMFold (2), two prominent AI-based structure prediction methods. We then investigated AF2’s ability to predict kinase structures in different conformations at various multiple sequence alignment (MSA) depths, based on this parameter’s ability to explore conformational diversity. Our results showed a bias within the PDB and predicted structural models generated by AF2 and ESMFold toward structures of kinases in the active state over alternative conformations, particularly those conformations controlled by the DFG motif. Finally, we demonstrate that predicting kinase structures using AF2 at lower MSA depths allows the exploration of the space of these alternative conformations, including identifying previously unobserved conformations for 398 kinases. The results of our analysis of structural modeling by AF2 create a new avenue for the pursuit of new therapeutic agents against a notoriously difficult-to-target family of proteins. Significance Statement Greater abundance of kinase structural data in inactive conformations, currently lacking in structural databases, would improve our understanding of how protein kinases function and expand drug discovery and development for this family of therapeutic targets. Modern approaches utilizing artificial intelligence and machine learning have potential for efficiently capturing novel protein conformations. We provide evidence for a bias within AlphaFold2 and ESMFold to predict structures of kinases in their active states, similar to their overrepresentation in the PDB. We show that lowering the AlphaFold2 algorithm’s multiple sequence alignment depth can help explore kinase conformational space more broadly. It can also enable the prediction of hundreds of kinase structures in novel conformations, many of whose models are likely viable for drug discovery.
Vitamin D promotes DNase1L3 to degrade ecDNA and inhibit the malignant progression of hepatocellular carcinoma

Extrachromosomal DNA (ecDNA) is an important carrier of oncogene amplification. However, the degradation mechanism of ecDNA is not well understood. We found that endogenous natural molecular vitamin D (VD) reduces ecDNA and inhibits the progression of hepatocellular carcinoma. VD reduces ecDNA depending on its binding protein GC, which can interact with the endonuclease DNase1L3 and stabilize DNase1L3 protein level. The DNase1L3 protein directly degrades ecDNA, and its N-terminus has a lipophilic region capable of affinity for lipid droplets. Intranuclear lipid droplets are abundantly distributed around ecDNA, so DNase1L3 can affinitize ecDNA through its lipophilic region. VD, as a lipid-soluble molecule, can increase the area of lipid droplets and further improve the degradation of DNase1L3 on ecDNA. Therefore, we designed two mRNA-based therapeutics, DNase1L3 and GC-DNase, both of which had an anti-tumor effect on PDX models. The above results showed that treatments targeting ecDNA in cancer are prospective in clinical practice. One-Sentence Summary Vitamin D reduces ecDNA and inhibits cancer progression. DNase1L3 was found to degrade ecDNA with the help of lipid droplets.
Transcriptomic Response to Nitrogen Availability Highlights Signatures of Adaptive Plasticity During Tetraploid Wheat Domestication

The domestication of crops, with the development of the agroecosystems, is associated with major environmental changes and represent a model to test the role of phenotypic plasticity. Here we investigated 32 genotypes representing key stages of tetraploid wheat domestication. We developed a dedicated pipeline combining RNA-Seq data, estimates of evolvability and QST to characterize the plasticity of gene expression and identify signatures of selection under different nitrogen conditions. The analysis of gene expression diversity showed contrasting results between primary and secondary domestication in relation to nitrogen availability. Indeed, nitrogen triggered the expression of twice the number of genes in durum wheat compared to emmer and wild emmer. QST distributions and QST–FST comparisons revealed distinct selection signatures at each domestication stage. While primary domestication affected the expression of genes involved in biotic interactions, secondary domestication was associated with changes in expression of genes involved in metabolism of amino acids, particularly lysine. Selection signatures were found also in differentially expressed genes, specifically involved in nitrogen metabolism, such as glutamate dehydrogenase. Overall, our findings show that nitrogen availability had a pivotal role during the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.
Neural activity is modulated by spontaneous and volitionally controlled breathing

Recent studies have provided evidence regarding respiration-brain coupling, but how continuously varying dynamics of breathing modulate neural activity is not known. We examined whether the neural state differs between spontaneous and volitionally controlled breathing and across the phases of breathing, inspiration and expiration. Magnetoencephalography with a respiratory belt was used to record cortical oscillatory activity during spontaneous, deep, and square breathing (n=33). Alpha power was suppressed during inspiration and increased during expiration (p<0.01) indicating dynamically fluctuating neural states across the respiratory cycle. Compared to spontaneous and square breathing, alpha power increased during deep breathing (p<0.01). We also observed a steeper aperiodic slope and a broadband shift in the power spectrum during square breathing in comparison with spontaneous breathing suggesting that spectral characteristics of neural activity are modulated by the rate, depth, and pattern of breathing. Altogether, we demonstrate that neural activity is modulated by breathing techniques and phases of breathing.
Forcing and variability of the hydroclimate in Central Asia

Central Asia is the semiarid region whose territory is roughly defined by the boundaries of Kazakhstan, Uzbekistan, Kyrgyzstan, Turkmenistan, Tajikistan, and the northern part of Afghanistan. It is located in the interior of the Eurasian land mass at about equal distance from the Atlantic and Pacific Oceans, just upstream of the planet’s largest topographic barriers, and in the transition zone between temperate and subtropical continental climates. In addition, it is situated close to the regions known to benefit from summer monsoon precipitation, but is isolated from them by the Karakorum and Hindu Kush mountains. Central Asia has received the attention of a global public regarding the rapid desiccation of the Aral Sea. The combination of these facts highlights that a sound understanding of the Central Asian hydroclimate is imperative both for purely academic interest and potential societal benefit. This thesis addresses a number of key issues in order to contribute to a better understanding of this kind. Chapter 2 complements the introductory first chapter. In terms of widely used techniques of multivariate statistics (principal component analysis and maximum covariance analysis), the dominant modes of the wintertime 500 hPa geopotential height variability over western Eurasia are identified and their covariability with the climate in Central Asia is analysed. It is shown that the Scandinavia Pattern is particularly relevant in this context, since its connexion with both temperature and precipitation in Central Asia is comparatively close. Thereafter, an intercomparison of a wide range of observational and numerical precipitation data sets is presented in chapter 3. Data sets based on re-analyses, direct observations, and numerical downscaling are validated and compared with respect to their ability to represent the Central Asian precipitation climate. The mutual agreement between different observational data sets is used as an indication of whether these data can be used for the validation of data from other sources. In particular, it is shown that the observational data usually agree qualitatively on the occurrence of anomalous years or seasons, while there is considerable disagreement regarding the amplitude of interannual variability. The climate high resolution model (CHRM) is shown to improve the spatial characteristics of the precipitation distribution. At the same time, it strongly underestimates summer precipitation and its variability, while interannual variations are well represented in other seasons, in particular during winter and spring.
Evolution of hierarchical switching pattern in antigenic variation of Plasmodium falciparum under variable host immunity

The var genes family encoding the variants of the erythrocyte membrane protein of Plasmodium falciparum is crucial for virulence of the parasite inside host. The transcriptional output of the var genes switches from one variant to other in a mutually exclusive fashion. It is proposed that a biased hierarchical switching pattern optimizes the growth and survival of the parasite inside the host. Apart from the hierarchical switching pattern, it is also well established that the intrinsic switching rates vary widely among the var genes. The centromeric protein like Var2csa is much more stable than the genes located at the telomeric and sub-telomeric regions of the chromosomes. In this study, we explored the evolutionary advantage achieved through selecting variable switching rates. Our theoretical analysis based on a mathematical model coupled with single cell RNA-seq data suggests that the variable switching rate is beneficial when cells expressing different variants are deferentially amenable to be cleared by the immune response. In fact, the variants which are cleared by the immune systems more efficiently are more stably expressed compared to a variant attacked by the immune system much less vigorously. The cells turn off expression of the variant quickly which is not cleared very efficiently. The evolutionary simulation shows that this strategy maximizes the growth of the parasite population under the presence of immune attack by the host. In corroboration with the result, we observed that stable variant has higher binding affinity to IgM from experimental data. Our study provides an evolutionary basis of widely variable switching rates of the var genes in Plasmodium falciparum.
Optimization of RNAi efficiency in PVD neuron of C. elegans

PVD neuron of C. elegans has become an attractive model for the study of dendrite development and regeneration due to the elaborate and stereotype dendrite morphology in this neuron. The molecular basis for dendrite maintenance and regeneration is poorly understood. RNA interference (RNAi) by feeding E. coli expressing dsRNA has been the basis of several genome wide screens performed using C. elegans. However, the feeding method often fails when it comes to nervous system. Using an optimal induction condition for the dsRNA expression in E coli, we fed the worm strains with HT115 bacteria expressing dsRNA against genes like mec-3, hpo-30, and tiam-1, whose loss of function are known to show dendrite morphology defects in PVD neuron. We found that RNAi of these genes in the strains such as nre-1(-) lin-15b(-), lin-15b(-) and sid-1(-); lin-15b(-); Punc-119::sid-1[+] resulted in significant reduction of dendrite branching. However, the phenotypes were significantly modest compared to the respective loss of function mutants. To obtain stronger phenotype for PVD specific genes, we have made a strain, which strongly expresses sid-1 under mec-3 promoter specific for PVD. When Pmec-3::sid-1 is expressed in either nre-1(-);lin-15b(-) or lin-15b(-) background, the higher order branching phenotype after RNAi of mec-3, hpo-30, and tiam-1 was significantly enhanced as compared to nre-1(-);lin-15b(-) and lin-15b(-) background alone. Next we tested the nre-1(-) lin-15b(-), Pmec-3-sid-1[+] strain for the knockdown of genes playing role in dendrite regeneration process. We found that when aff-1 and ced-10 genes were knocked down in the nre-1(-) lin-15b(-), Pmec-3-sid-1[+] background, the dendrite regeneration was significantly reduced and the extent of reduction was comparable to that of the mutants of aff-1 and ced-10. Essentially, our strain expressing sid-1 in PVD neuron optimizes the condition for RNAi for high throughput screening for PVD development, maintenance and regeneration.