Miracle-dz/UniFAR-FTUs huggingface dataset:
The rise and fall of the photoinhibition-related energy dissipation qI

Photosynthesis converts sunlight into chemical energy, sustaining the vast majority of the biosphere. Photosystem II (PSII), the oxygen-forming enzyme that initiates photosynthesis, is however particularly prone to light-induced damage in a process known as photoinhibition, which limits the productivity of both aquatic and land photosynthesis. Photoinhibition is associated with an energy dissipation process of unknown origin, termed qI. Here, we present a detailed biophysical and biochemical in vivo study of qI in model green alga Chlamydomonas reinhardtii. Time-resolved fluorescence measurements demonstrate the origin of qI, and indicate the PSII reaction centre as the site of the quencher. Oxygen-dependence of quenching site formation, but not photoinhibition itself, is shown, suggesting that two types of PSII damage – donor and acceptor-side impairment – can be separated. We then demonstrate that the quenching loss takes place in the absence of PSII repair, and is mediated by the degradation of photoinhibited PSII cores by the FtsH protease. Finally, we integrate data ranging from picoseconds to hours in the context of structure-function excitation energy-transferring membrane patches, revealing the extent of PSII heterogeneity from the onset of photoinhibition until the breakdown of damaged PSII. Graphical Abstract Highlights Upon photoinhibition, oxygen sensitization results in an irreversible formation of quenching (qI) and inactivation of Photosystem II qI takes place in the PSII reaction centre Photoinhibition-induced D1 cleavage is much slower than qI formation FtsH metalloprotease is required to degrade quenching PSII reaction centres A multiscale energy transfer model describes heterogeneity of PSII during photoinhibition
The Sugar Porter gene family of Piriformospora indica: Nomenclature, Transcript Profiling and Characterization

Piriformospora indica is one of the prominent mutualistic root endophyte known to overcome phosphate and nitrogen limitation in a wide variety of plant species, reciprocally takes up carbohydrates for its survival and growth. A total of nineteen potential hexose transporters have been identified from P. indica genome, that may contributes to its potential of carbohydrate assimilation from host plant. Phylogenetic analysis assembles it in 10 groups within 3 clusters. To ease the study, systematic nomenclature were provided to 19 putative hexose transporters as “PiST1-PiST19” in accordance to their appearance on the supercontigs genome sequence of P. indica. The protein length ranges from 487 to 608 amino acids. Out of 19 putative hexose transporters, 9 have been predicted to contain 12 transmembrane domains (PiST1, PiST2, PiST5, PiST6, PiST9, PiST10, PiST11, PiST12 and PiST17), along with MFS family and Sugar porter subfamily motif. Therefore, transcripts were detected for these 9 genes. During colonization, three P. indica genes PiST1, PiST5 and PiST9 have shown induction as compared to axenic culture. Similarly during phosphate starvation, revealed PiST12 to be strongly enhanced. Carbon starvation study in liquid axenic culture resulted in induction of 4 genes, PiST6, PiST9, PiST12 and PiST17. We found co-relation in the expression pattern of PiPT and PiST12 during phosphate starvation. In silico analysis revealed the presence of functional conserved fucose permease (FucP) domain, involved in fructose transport. Phylogenetic analysis revealed that PiST12 groups closely with basidiomycetes hexose transporters. Further, functional complementation of Δhxt null mutant revealed, PiST12 is able to complement growth on fructose and galactose but negligible on glucose.
Structure and dynamics of the SARS-CoV-2 envelope protein monomer

Coronaviruses, especially SARS-CoV-2, present an ongoing threat for human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic α-helical transmembrane domain (TMD) and amphiphilic α-helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43 and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the E protein both generates and senses the membrane curvature, preferably localizing with the C-terminus at the convex regions of the membrane. This may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate budding of the viral particles. The presented results may be helpful for better understanding of the function of coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.
METHOD VALIDATION FOR THE DETERMINATION OF FUROSEMIDE IN PLASMA BY LIQUID- LIQUID EXTRACTION AND HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY WITH FLUORESCENCE DETECTION

A practical reversed-phase high-performance liquid chromatography (HPLC) method was developed for 4-chloro-N-furfuryl-5-sulphamoylanthranilic acid (furosemide) determination in plasma. The plasma samples spiked with the drug in presence of propranolol hydrochloride as internal standard, were purified using a liquid - liquid extraction technique. The drugs were separated through a Kromasil 100-5C18 column with a mobile phase composed of acetonitrile and 0.02 M potassium dihydrogen phosphate (34 : 66 v/v) adjusted to pH 3.0 and quantified by fluorescence detection (excitation at 268 nm, emission at 410 nm). The calibration curve was linear ranging between 0.005 and 1.500 mg/mL. The detection limit was 0.001mg/mL and the quantification limit 0.003 mg/mL in plasma. The furosemide recovery from 1mL of plasma was between 99.8 and 101.6 %, with a variation coefficient not higher than 4,85 %. The method is sensitive enough for use in bioavailability and bioequivalence studies after oral administration of 40 mg (a tablet) of furosemide
Phylogeography, codon usages, and DNA barcoding of lesser short nosed fruit bat (Cynopterus brachyotis Muller, 1838) populations in Indonesia

Fruit bat (Pteropodidae) is one of the mammals that is common in environments and widely distributed from subtropical to tropical Asia. Whereas the information on phylogeography of fruit bat Cynopterus brachyotis is still limited. From this situation, this paper aims to assess the phylogeography, codon usage, and DNA barcoding of C. brachyotis populations in Indonesia. Phylogeography was developed based on 657 bp of the mtDNA COI gene for all bat individuals and Bayesian inference to construct the phylogeny tree. The C. brachyotis populations in Indonesia are different to the populations from the Asia’s continent. The results show that C. brachyotis populations in Indonesia were divided into 3 distinct clades. A putative geographical barrier, recent, and rapid range expansion in the Sunda lineage associated with changes in sea levels, possibly coupled with related ecological differences, may have driven population divergence, allopatric, and sympatric speciation. Codon usage and high frequency were also contributing to the dispersal of C. brachyotis forming a distinct population.
Spontaneously Hypertensive Rat substrains show differences in premorbid addiction vulnerability traits and cocaine self-administration: Implications for a novel rat reduced complexity cross

Forward genetic mapping of F2 crosses between closely related substrains of inbred rodents - referred to as a reduced complexity cross (RCC) - is a relatively new strategy for accelerating the pace of gene discovery for complex traits, such as drug addiction. RCCs to date were generated in mice, but rats are thought to be optimal for addiction genetic studies. Based on past literature, one inbred Spontaneously Hypertensive Rat substrain, SHR/NCrl, is predicted to exhibit a distinct behavioral profile as it relates to cocaine vulnerability traits relative to another substrain, SHR/NHsd. Direct substrain comparisons are a necessary first step before implementing an RCC. We evaluated a number of premorbid addiction vulnerability traits and cocaine self-administration behaviors using a longitudinal within-subjects design. Trait impulsivity and compulsivity were greater in SHR/NCrl than SHR/NHsd, as were reactivity to sucrose reward, sensitivity to acute psychostimulant effects of cocaine, and cocaine abuse liability studied under fixed-ratio and chained schedules of cocaine self-administration. Trait compulsivity correlated with the acute psychostimulant effects of cocaine, which in turn correlated with cocaine taking under the chained schedule. Trait compulsivity also was the best predictor of cocaine seeking responses. Heritability estimates indicated that 22%-40% of the variances for the above phenotypes can be explained by additive genetic factors, providing sufficient genetic variance to conduct genetic mapping in F2 crosses of SHR/NCrl and SHR/NHsd. These results provide compelling support for using an RCC approach in SHR substrains to uncover candidate genes and variants that are of relevance to cocaine use disorders. Highlights Closely related SHR substrains have distinct cocaine vulnerability traits Inhibitory control was poorer in SHR/NCrl than SHR/NHsd SHR/NCrl were more sucrose reactive and sensitive to acute cocaine than SHR/NHsd Cocaine abuse liability was greater in SHR/NCrl than SHR/NHsd SHR substrains can be used in an RCC to uncover cocaine vulnerability genes & variants
Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1

Combination of immunofluorescence, Western blot, and ChIP-seq revealed the interplay between HDAC2, HDAC3, and SIRT1 in H3K9 deacetylation during mitosis of mammalian cells. Histone acetylation levels are reduced during mitosis. To study the mitotic regulation of H3K9ac, we used an array of inhibitors targeting specific histone deacetylases. We evaluated the involvement of the targeted enzymes in regulating H3K9ac during all mitotic stages by immunofluorescence and immunoblots. We identified HDAC2, HDAC3, and SIRT1 as modulators of H3K9ac mitotic levels. HDAC2 inhibition increased H3K9ac levels in prophase, whereas HDAC3 or SIRT1 inhibition increased H3K9ac levels in metaphase. Next, we performed ChIP-seq on mitotic-arrested cells following targeted inhibition of these histone deacetylases. We found that both HDAC2 and HDAC3 have a similar impact on H3K9ac, and inhibiting either of these two HDACs substantially increases the levels of this histone acetylation in promoters, enhancers, and insulators. Altogether, our results support a model in which H3K9 deacetylation is a stepwise process—at prophase, HDAC2 modulates most transcription-associated H3K9ac-marked loci, and at metaphase, HDAC3 maintains the reduced acetylation, whereas SIRT1 potentially regulates H3K9ac by impacting HAT activity.
Propranolol reduces sarcoma growth and enhances the response to anti-CTLA4 therapy by modulating the tumor microenvironment

The nonselective beta blocker, propranolol, which for decades has been prescribed for treatment of cardiovascular conditions, has recently been used successfully to treat metastatic angiosarcoma. These results have led to an orphan drug designation by the European Medicines Agency for the treatment of soft tissue sarcomas. The anti-tumor effects of propranolol are suggested to involve the reduction of cancer cell proliferation as well as angiogenesis. Here, we have investigated the anti-angiogenic properties of propranolol in the context of stimulating an anti-tumor immune response. We show that oral administration of propranolol delays tumor progression of MCA205 fibrosarcoma tumors and increases the survival rate of tumor bearing mice. Propranolol works by reducing tumor angiogenesis and facilitating an anti-tumoral microenvironment with increased T cell infiltration and reduced infiltration of myeloid-derived suppressor cells (MDSCs). Using T cell deficient mice, we demonstrate that the full anti-tumor effect of propranolol requires the presence of T cells. Flow cytometry-based analysis and RNA sequencing of FACS-sorted cells show that propranolol-treatment leads to an upregulation of PD-L1 on tumor-associated macrophages (TAMs) and changes in their chemokine expression profile. Lastly, we observe that the co-administration of propranolol significantly enhances the efficacy of anti-CTLA4 therapy. Our results identify propranolol as an immune modulating agent, which can improve immune checkpoint inhibitor therapies in soft tissue sarcoma patients and potentially in other cancers.
Effect of Voluntary Adolescent Alcohol Consumption on Encoding of Decision-Related Variables in Prefrontal Cortex

The medial and orbitofrontal regions of prefrontal cortex (PFC) have been implicated in guiding optimal behavior and updating the economic value of rewards that result from choice behaviors. Both regions mature through adolescence into early adulthood and are thus vulnerable to exposure to neurotoxins, such as alcohol, during this critical developmental window. We sought to examine how voluntary alcohol consumption during adolescence would alter long-term PFC function and subsequent decision-making behavior in adulthood. Male and female rats were given adolescent intermittent ethanol (AIE) exposure to provide voluntary access to alcohol during the period of PFC maturation. In adulthood, we assessed the long-term effects on decision-making behavior using a risk task in adulthood, while concurrently recording neural activity in orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC). While control animals’ preferences for risky rewards increased with the likelihood of their delivery, AIE animals showed an overall reduction in their preferences for the risky option with higher levels of alcohol consumption, suggesting reduced discriminability of uncertain rewards and a shift away from the potential for reward omission. During task performance, neurons in mPFC and OFC responded to events (lever press, reward delivery). In mPFC, neurons with phasic increases at the time of lever press showed a reversal from larger elevations for risky presses in control animals to larger elevations for certain presses as prior alcohol consumption increased. Neurons in mPFC generally showed less discrimination of reward outcome with increased alcohol consumption as well. In OFC, responses to lever press were largely unaffected by AIE exposure. However, encoding of reward size in OFC showed differential effects in males and females. With higher alcohol consumption in males, OFC neurons showed largest excursions from baseline activity in response to largest reward, and smallest excursions for reward omission. This discrimination was reduced as prior alcohol consumption increased. In females, neurons with increased reward-activity, showed an overall higher level of activity due to stronger responses to certain rewards that were selected more frequently. Collectively the results show diminished capacity of PFC to encode decision-related elements to guide adaptive behavior and further clarify the lasting impact of adolescent alcohol use on neural function and behavior, even in the absence of continued use.
Nitric oxide synthases from photosynthetic organisms improve growth and confer nitrosative stress tolerance in E. coli. Insights on the pterin cofactor

Nitric oxide synthase (NOS) synthesizes NO from the substrate L-arginine (Arg). NOS with distinct biochemical properties were characterized from two photosynthetic microorganisms, the unicellular algae Ostreococcus tauri (OtNOS) and the cyanobacteria Synechococcus PCC 7335 (SyNOS). In this work we studied OtNOS and SyNOS recombinantly expressed in E. coli and analyzed bacterial growth and tolerance to nitrosative stress. Results show that the expression of OtNOS and SyNOS promotes bacterial growth and allows metabolizing Arg as N source. In accordance to a high NO producing activity, OtNOS expression induces the hmp flavohemoglobin in E. coli, suggesting that this strain is sensing nitrosative stress. The addition of 1 mM of the NO donor sodium nitroprusside (SNP) is toxic and generates a strong nitrosative stress. The expression of OtNOS or SyNOS reduced SNP toxicity restoring bacterial growth. Finally, using bioinformatic tools and ligand docking analyses, we propose tetrahydromonapterin (MH4), an endogenous pterin found in E. coli, as potential cofactor required for NOS catalytic activity. Our findings could be useful for the development of biotechnological applications using NOS expression to improve growth in bacteria. Key points - The NO synthase (NOS) from photosynthetic microorganisms were expressed in E. coli - Expression of NOS increases bacterial growth and tolerance to nitrosative stress. - Ligand docking analyses indicate tetrahydromonapterin (MH4) as potential NOS cofactor in E. coli.
ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta

Gene expression is governed by several layers of regulation which in addition to genome organization, local chromatin structure, gene accessibility and the presence of transcription factors also includes gene positioning. Although basic mechanisms are expected to be conserved in Eukaryotes, surprisingly little information on the role of gene positioning is available in plant cells, mainly due to the lack of a highly resolutive approach. In this manuscript, we adapted the use of the ANCHOR system to perform real-time single-locus detection in planta. ANCHOR is a DNA-labelling tool derived from the partitioning system. We demonstrate its suitability to monitor a single-locus in planta and used this approach to track chromatin mobility during cell differentiation in Arabidopsis root epidermal cells. Finally, we discuss the potential of this approach to investigate the role of gene positioning during transcription and DNA repair in plants.
A pulse radiolysis study of the oxidation of Br− by Cl2˙− in aqueous solution: formation and properties of ClBr˙−

The oxidation of Br− by Cl2˙− is investigated by pulse radiolysis in aqueous solutions of NaCl and NaBr. Depending on the ratio of the concentration of Br− to Cl−, the main product being observed is either Cl2˙−, ClBr˙− or Br2˙−. The mixed radical anion ClBr˙− exhibits a broad absorption band at 350 nm with e350 = 9300 dm3 mol−1 cm−1. The rate constants of the equilibrium Cl2˙− + Br− ⇌ ClBr˙− + Cl− are determined to be kf = 4 × 109 and kb = 1.1 × 102 dm3 mol−1 s−1.
Female fruitflies use gustatory cues to exhibit reproductive plasticity in response to the social environment

Animals can exhibit remarkable reproductive plasticity in response to their social surroundings, with profound fitness consequences. The study of such plasticity in females, particularly in same-sex interactions, has been severely neglected. Here we measured the impact of variation in the pre-mating social environment on reproductive success in females and tested the underlying mechanisms involved. We used the Drosophila melanogaster model system to test the effect of varying female group size prior to mating and deployed physical and genetic methods to manipulate the perception of different social cues and sensory pathways. We found that socially isolated females were significantly more likely to retain unfertilised eggs before mating, but to show the opposite pattern and lay significantly more fertilised eggs in the 24h after mating, in comparison to grouped females. More than 48h of exposure to other females was necessary for this socially-induced plasticity to be expressed. Neither olfactory nor visual cues were involved in mediating these responses. Instead, we found that females detected other females through direct contact with the deposits they leave behind, even in the absence of eggs. The results demonstrate that females show striking reproductive plasticity in response to their social surroundings and that the nature of their plastic reproductive responses, and the cues they use, differ markedly from those of males. The results emphasise the stark contrasts in how each sex realises reproductive success.
The extracellular milieu of Toxoplasma’s lytic cycle drives lab-adaptation and promotes changes in lipid metabolism primarily driven by transcriptional reprogramming

To map host-independent in vitro virulence traits of Toxoplasma gondii, evolve and resequencing (E&R) during the lab-adaption was applied. Phenotypic assessments of the lytic cycle revealed that only traits needed in the extracellular milieu evolved. Surprisingly, only non-synonymous mutations in a P4 flippase fixed in two populations. However, dramatic changes in the transcriptional signature of extracellular parasites revealed a “pro-tachyzoite” profile as well as upregulation of fatty acid biosynthesis (FASII) pathway genes. More general, a set of 300 genes which expression profile changes during evolution mapped to specific traits. Validation of a select number of genes in this set by knock-outs indeed confirmed their role in lab-adaptation. Finally, assembly of an ApiAP2 and Myb transcription factor network revealed the transcriptional program underlying the adapting extracellular state. Overall, E&R is a new genomic tool successfully applied to map the development of polygenic traits underlying in vitro virulence of T. gondii.
Impaired Cx43 gap junction endocytosis causes cardiovascular defects in zebrafish

Gap junction proteins, termed connexins (Cx), mediate direct cell-to-cell communication by forming channels that physically couple cells, thereby linking their cytoplasm, permitting exchange of molecules, ions, and electrical impulses. The most ubiquitously expressed gap junction protein, connexin43 (Cx43) has been implicated in cardiovascular diseases including arrhythmias, cardiomyopathies, hypertension and diabetes. The Cx43 C-terminal (CT) domain serves as the regulatory hub of the protein affecting all aspects of gap junction function. Here, deletion within the Cx43 CT (amino acids 256-289), a region known to encode key residues regulating gap junction turnover is employed to examine the effects of dysregulated Cx43 gap junction endocytosis using cultured cells (Cx43Δ256-289) and zebrafish model (cx43lh10). We report that this CT deletion causes defective gap junction endocytosis as well as increased gap junction intercellular communication (GJIC). Increased Cx43 protein content in cx43lh10 zebrafish, specifically in the cardiac tissue, larger gap junction plaques and longer Cx43 protein half-lives coincide with severely impaired cardiovascular development. These findings suggest that normal, unimpaired Cx43 gap junction endocytosis and turnover is an essential aspect of gap junction function as demonstrated here for cardiovascular development that when impaired can give rise to arrhythmias, heart malformations and aberrant vasculature structure and function.