Miracle-dz/UniFAR-FTUs huggingface dataset:
Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature

Stenotrophomonas maltophilia (Smal) is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 ◻) is higher than environmental niches (22-30 ◻). Interestingly, S. rhizophila a phylogenetic neighbour of Smal within genus Stenotrophomonas is unable to grow at 37 ◻. Thus, it is crucial to understand how Smal is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis of S. maltophilia grown at 28 ◻ and 37 ◻ as temperature representative for environmental niches and human body respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene expression levels at 28 ◻ and 37 ◻, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 Type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 ◻. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed by S. maltophilia during adaptation towards the human body. Impact statement Stenotrophomonas maltophilia (Smal) is a WHO listed multidrug resistant nosocomial pathogen. Interestingly, S. maltophilia species can grow both at 28 ◻ and 37 ◻ unlike its closest taxonomic relative, i.e., S. rhizophila and also majority species belonging this genus. Hence this ability to grow at 37 ◻, i.e., human body temperature might have played key role in the unique success and emergence of this species as opportunistic human pathogen. Using transcriptome sequencing, we have identified set of genes which are differentially regulated at 37 ◻ and investigated their evolutionary history. This study has revealed regulation of genes involved in motility, metabolism, energy, replication, transcription, aerotaxis and a type IV secretion system might have a role in successful adaption to a distinct lifestyle. The findings will be helpful in further systematic studies on understanding and management of an emerging human pathogen such as Smal.
Multiomics Integration Elucidates Metabolic Modulators of Drug Resistance in Lymphoma

Background Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL). B-cell NHLs rely on Bruton’s tyrosine kinase (BTK) mediated B-cell receptor signaling for survival and disease progression. However, they are often resistant to BTK inhibitors or soon acquire resistance after drug exposure resulting in the drug tolerant form. The drug tolerant clones proliferate faster, have increased metabolic activity, and shift to oxidative phosphorylation; however, how this metabolic programming occurs in the drug resistant tumor is poorly understood. Methods In this study, we explored for the first time the metabolic regulators of ibrutinib-resistant activated B-cell (ABC) DLBCL using a ‘multi-omics’ analysis that integrated metabolomics (using high-resolution mass spectrometry) and transcriptomic (gene expression analysis). Overlay of the unbiased statistical analyses, genetic perturbation and pharmaceutical inhibition, were further used to identify the key players that contribute to the metabolic reprograming of the drug resistant clone. Results Gene-metabolite integration revealed interleukin 4 induced 1 (IL4I1) at the crosstalk of two significantly altered metabolic pathways involved in the production of various amino acids. We showed for the first time that drug resistant clones undergo metabolic reprogramming from glycolysis towards oxidative phosphorylation & is activated via the BTK-PI3K-AKT-IL4I1 axis and can be targeted therapeutically. Conclusions Our report shows how these cells become dependent on PI3K/AKT signaling for survival after acquiring ibrutinib resistance and shift to sustained Oxidative phosphorylation, additionally we outline the compensatory, pathway that regulates this metabolic reprogramming in the drug resistant cells. These findings from our unbiased analyses highlight the role of metabolic reprogramming during drug resistance development. Furthermore, our work demonstrates that a multi-omics approach can be a powerful and unbiased strategy to uncover genes and pathways that drive metabolic dysregulation in cancer cells.
Molecular population genetics of Sex-lethal (Sxl) in the D. melanogaster species group - a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster

Sex-lethal (Sxl) is the sex determination switch in Drosophila, and also plays a critical role in germ-line stem cell (GSC) daughter differentiation in Drosophila melanogaster. Three female-sterile alleles at Sxl in Drosophila melanogaster were previously shown to genetically interact to varying degrees with the maternally inherited endosymbiont Wolbachia pipientis. Given this genetic interaction and W. pipientis’ ability to manipulate reproduction in Drosophila, we carried out a careful study of both the population genetics (within four Drosophila species) and molecular evolutionary analysis (across 20 Drosophila species) of Sxl. Consistent with earlier studies, we find that selective constraint has played a prominent role in Sxl’s molecular evolution within Drosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection at Sxl. The episodic nature of Sxl’s protein evolution is discussed in light of its genetic interaction with W. pipientis.
SLTRiP induces long lasting and protective T-cell memory response

Major developments have been made in the past many years to characterize and explore potential vaccine candidates that can induce host immune responses against parasite. These advances were based on the fact that the induction of host immune responses could effectively target parasite at different stages of its life cycle and thus, abrogate Plasmodium infections. The role of T-cells against malaria comes from initial studies on rodents showing these cells could inhibit parasite development during pre-erythrocytic stages. Since then, the importance of the cellular immune responses against malaria has been increasingly emphasized, especially for vaccine development against pre-erythrocytic stages. Previous work in our laboratory has confirmed that SLTRiP confers protection against the pre-erythrocytic stage of Plasmodium growth in rodents. Here we report that the protection is mainly due to cell mediated immune responses and PbSLTRiP specific cellular memory responses could be efficiently recalled in mice challenged with P. berghei parasites even after a year following immunization. Our results thereby, highlight the role of the T cell response involved in protection. Characterization of T-cells by intracellular cytokine staining (ICS) revealed that the induced T cells were polyfunctional and involved in secretion of pro-inflammatory cytokines which mediate anti-parasitic activity. The findings contribute to our understanding of the immunological mechanisms underlying the protective vaccines.
Onset of sexual maturity of sexually propagated and wild Favites abdita colonies in northwestern Philippines

Scleractinian corals are modular colonial organisms and are the main framework builders of coral reefs. Most corals reproduce by broadcast spawning with external fertilization and these processes are essential to replenish reef coral populations. Despite decades of research, many aspects of coral reproductive biology remain poorly studied. For example, two important reproductive life history traits, colony size and age at the onset of sexual maturity, are mostly unknown for many reef-building corals. In this study, wild colonies of different size classes and colonies of a known age (i.e. colonies sexually cultured and reared from larvae to adults) of the massive scleractinian Favites abdita were examined for the presence or absence of mature oocytes to determine size and age at the onset of sexual reproduction. Fecundity at the onset of reproductive maturity across size classes of wild colonies was also determined. Surveyed and sampled colonies were grouped into three size classes based on maximum colony diameter (A = 0.1-4.0 cm, B = 4.1-8.0 cm, and C = >8.1 cm). For both wild and sexually propagated colonies, the smallest colonies containing gametes were 1.8 cm in diameter, suggesting that this is the minimum colony size at onset of sexual maturity. Colonies of size class A had lower mean oocyte counts per polyp (44 ± 6.08; mean ± SE) compared to colonies of classes B and C (469 ± 62.41, 278 ± 57.15, respectively). However, mean oocyte geometric mean diameter of size class A colonies was greater (340.38 ± 7.68 μm) than classes B and C (283.96 ± 6.94 μm, 317.57 ± 9.18 μm, respectively). Results of this study bring in to question the widely applied operational definition of coral juveniles being colonies ≤4.0 cm diameter and suggest that even quite small colonies may play a role in contributing to the natural larval pool on reefs than previously thought.
Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by S. Typhimurium within the cytosol, and the bacterial genes required for cytosolic colonization, remain unknown. Here we have exploited the parallel colonization strategies of S. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes/sRNAs with cytosol-specific or vacuole-specific expression signatures. Using these genes/sRNAs as environmental biosensors, we defined that Salmonella is exposed to iron and manganese deprivation and oxidative stress in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal S. Typhimurium replication in the cytosol, as well as entC, fepB, soxS and sitA-mntH. Virulence genes that are typically associated with extracellular bacteria, namely Salmonella pathogenicity island 1 (SPI1) and SPI4, had a cytosolic-specific expression profile. Our study reveals that the cytosolic and vacuolar S. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. Therefore, this archetypical vacuole-adapted pathogen requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol. Author Summary Intracellular pathogens reside either within a membrane-bound vacuole or are free-living in the cytosol and their virulence programs are tailored towards survival within a particular intracellular compartment. Some bacterial pathogens (such as Salmonella enterica) can successfully colonize both intracellular niches, but how they do so is unclear. Here we have exploited the parallel intracellular lifestyles of S. enterica in epithelial cells to identify the niche-specific bacterial expression profiles and environmental cues encountered by S. enterica. We have also discovered bacterial genes that are required for colonization of the cytosol, but not the vacuole. Our results advance our understanding of pathogen-adaptation to alternative replication niches and highlight an emerging concept in the field of bacteria-host cell interactions.
On the Role of Arkypallidal and Prototypical Neurons for Phase Transitions in the External Pallidum

The external pallidum (globus pallidus pars externa [GPe]) plays a central role for basal ganglia functions and dynamics and, consequently, has been included in most computational studies of the basal ganglia. These studies considered the GPe as a homogeneous neural population. However, experimental studies have shown that the GPe contains at least two distinct cell types (prototypical and arkypallidal cells). In this work, we provide in silico insight into how pallidal heterogeneity modulates dynamic regimes inside the GPe and how they affect the GPe response to oscillatory input. We derive a mean-field model of the GPe system from a microscopic spiking neural network of recurrently coupled prototypical and arkypallidal neurons. Using bifurcation analysis, we examine the influence of dopamine-dependent changes of intrapallidal connectivity on the GPe dynamics. We find that increased self-inhibition of prototypical cells can induce oscillations, whereas increased inhibition of prototypical cells by arkypallidal cells leads to the emergence of a bistable regime. Furthermore, we show that oscillatory input to the GPe, arriving from striatum, leads to characteristic patterns of cross-frequency coupling observed at the GPe. Based on these findings, we propose two different hypotheses of how dopamine depletion at the GPe may lead to phase-amplitude coupling between the parkinsonian beta rhythm and a GPe-intrinsic γ rhythm. Finally, we show that these findings generalize to realistic spiking neural networks of sparsely coupled Type I excitable GPe neurons. SIGNIFICANCE STATEMENT Our work provides (1) insight into the theoretical implications of a dichotomous globus pallidus pars externa (GPe) organization, and (2) an exact mean-field model that allows for future investigations of the relationship between GPe spiking activity and local field potential fluctuations. We identify the major phase transitions that the GPe can undergo when subject to static or periodic input and link these phase transitions to the emergence of synchronized oscillations and cross-frequency coupling in the basal ganglia. Because of the close links between our model and experimental findings on the structure and dynamics of prototypical and arkypallidal cells, our results can be used to guide both experimental and computational studies on the role of the GPe for basal ganglia dynamics in health and disease.
Comprehensive multi-omics study of the molecular perturbations induced by simulated diabetes on coronary artery endothelial cells

Coronary artery endothelial cells (CAEC) exert an important role in the development of cardiovascular disease. Dysfunction of CAEC is associated with cardiovascular disease in subjects with type 2 diabetes mellitus (T2DM). However, comprehensive studies of the effects that a diabetic environment exerts on this cellular type scarce. The present study characterized the molecular perturbations occurring on cultured bovine CAEC subjected to a prolonged diabetic environment (high glucose [HG] and high insulin [HI]). Changes at the metabolite and peptide level were assessed by untargeted metabolomics and chemoinformatics, and the results were integrated with proteomics data using published SWATH-based proteomics on the same in vitro model. Our findings were consistent with reports on other endothelial cell types, but also identified novel signatures of DNA/RNA, aminoacid, peptide, and lipid metabolism in cells under a diabetic environment. Manual data inspection revealed disturbances on tryptophan catabolism and biosynthesis of phenylalanine-based, glutathione-based, and proline-based peptide metabolites. Fluorescence microscopy detected an increase in binucleation in cells under treatment that also occurred when human CAEC were used. This multi-omics study identified particular molecular perturbations in an induced diabetic environment that could help unravel the mechanisms underlying the development of cardiovascular disease in subjects with T2DM.
Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens

Allelic diversity of HLA class II genes may help maintain humoral immunity against infectious diseases. We investigated the relative contribution of specific HLA class II alleles, haplotypes and genotypes on the variation of antibody responses to a variety of common pathogens in a cohort of 800 adults representing the general Arab population. We found that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles play a synergistic role in shaping the antibody repertoire. Interestingly, associations of HLA-DRB1 genotypes with specific antigens were identified. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
Real-Time Three-Dimensional Tracking of Single Vesicles Reveals the Abnormal Motion and Vesicle Pools of Synaptic Vesicles in Neurons of Huntington’s Disease Mice

Although defective synaptic transmission was suggested to play a role in neurodegenerative diseases, the dynamics and vesicle pools of synaptic vesicles during neurodegeneration remain elusive. Here, we performed real-time three-dimensional tracking of single synaptic vesicles in cortical neurons from a mouse model of Huntington’s disease (HD). Vesicles in HD neurons had a larger net displacement and radius of gyration compared with wild-type neurons. Vesicles with a high release probability (Pr) were interspersed with low-Pr vesicles in HD neurons, whereas high-Pr and low-Pr vesicle pools were spatially separated in wild-type neurons. Non-releasing vesicles in HD neurons had an abnormally high prevalence of irregular oscillatory motion. These abnormal dynamics and vesicle pools were rescued by overexpressing Rab11, and the abnormal irregular motion was rescued by jasplakinolide. These results suggest the abnormal dynamics and vesicle pools of synaptic vesicles in the early stages of HD, suggesting a possible pathogenic mechanism of neurodegenerative diseases.
Gpr161 ciliary pools prevent hedgehog pathway hyperactivation phenotypes specifically from lack of Gli transcriptional repression

The primary cilium localized G-protein-coupled receptor Gpr161 represses hedgehog pathway via cAMP signaling in multiple tissues. However, whether Gpr161 functions exclusively from inside cilia is unclear. Here, we generated ciliary localization-defective but cAMP signalingcompetent Gpr161mut1 knock-in mice. We uncovered distinctive roles for subcellular Gpr161 pools, contingent upon dependence of the morpho-phenotypic spectrum on downstream Gli transcriptional regulators. Compared to Gpr161 knockout, gene dosage of the Gpr161mut1 allele caused delayed embryonic lethality, reduced upregulation of hedgehog targets and intermediate Gli3 repressor levels. Unlike Gpr161 knockout with aberrant ventral progenitor expansion in neural tube, extraciliary Gpr161 pools in Gpr161mut1 prevented Gli2 activator-mediated ventralization. However, limb buds and midfacial tissues that require Gli repressor for morphogenesis, showed polydactyly and midface widening in Gpr161mut1 from hyperactivation. Thus, Gpr161 ciliary and extraciliary pools functioned as rheostats preventing gradations of hedgehog pathway hyperactivation. Ciliary Gpr161 pools prevented tissue-specific phenotypes dependent specifically on reduced Gli repressor thresholds.
Maribellus comscasis sp. nov., isolated from the deep-sea cold seep

A facultatively anaerobic, Gram-stain-negative, non-motile, curved rod-shaped bacterium, designated WC007T, was isolated from the deep-sea cold seep, P. R. China. Strain WC007T was found to grow at temperatures from 28 to 37 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-5.0% (w/v) NaCl (optimum, 1.0%). The major fatty acids (>10.0%) were iso-C15:0, C16:0, summed feature 3 and summed feature 8. The major isoprenoid quinone was MK-7. Predominant polar lipids were phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The G+C content of the genomic DNA was 38.38%. The average nucleotide identity (ANIb and ANIm), amino acid identity (AAI), the tetranucleotide signatures (Tetra) and in silico DNA-DNA hybridization (isDDH) similarities between the genome sequences of isolate WC007T and Maribellus luteus XSD2T were 70.11%, 84.94%, 71.0%, 0.92022 and 20.40%, respectively, indicating that strain WC007T was distinguished from M. luteus. Phylogenetic analysis based on 16S rRNA gene sequences placed strain WC007T within the genus Maribellus and showed the highest similarity to strain XSD2T (95.70%). In combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, strain WC007T was considered to represent a novel species of the genus Maribellus, for which the name Maribellus comscasis sp. nov. is proposed. The type strain is WC007T (=KCTC 25169T = MCCC 1K04777T). The available of the genome sequence of strain WC007T would be helpful in understanding the degradation mechanism of difficult-to-degrade polysaccharides.
A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

We have developed a simple Agrobacterium-mediated method for the stable transformation of the hornwort Anthoceros agrestis, the fifth bryophyte species for which a genetic manipulation technique becomes available. High transformation efficiency was achieved by using thallus tissue grown under low-light conditions. We generated a total of 216 transgenic A. agrestis lines expressing the β-Glucuronidase (GUS), cyan, green, and yellow fluorescent proteins under the control of the CaMV 35S promoter and several endogenous promoters. Nuclear and plasma membrane localization with multiple color fluorescent proteins was also confirmed. The transformation technique described here should pave the way for detailed molecular and genetic studies of hornwort biology, providing much needed insight into the molecular mechanisms underlying symbiosis, carbon-concentrating mechanism, RNA editing, and land plant evolution in general.
Cysteine is a limiting factor for glioma proliferation and survival

Nutritional intervention is becoming more prevalent as adjuvant therapy for many cancers in view of the tumor dependence on external sources for some nutrients. We report the dependence of glioma cells on exogenous cysteine/cystine, despite this amino acid being nonessential. 13C-tracing and the analysis of cystathionine synthase and cystathioninase levels revealed the metabolic landscape attributable to cysteine deprivation, and the disconnection between the methionine cycle and the transsulfuration pathway. Therefore, we explored the nutritional deprivation in a mouse model of glioma. Animals subjected to a cysteine/cystine-free diet survived longer, with concomitant reductions in glutathione and cysteine plasma levels. At the end point, however, tumors displayed the ability to synthesize glutathione, although higher levels of oxidative stress were detected. We observed a compensation from the nutritional intervention revealed as the recovery of cysteine-related metabolites in plasma. Our study highlights a time window where cysteine deprivation can be exploited for additional therapeutic strategies.