Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring molecular determinants of polysaccharide Lyase family 6-1 enzyme activity.

The Polysaccharide Lyase Family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.
Rapid, green and inexpensive synthesis of high quality UiO-66 amino-functionalized materials with exceptional capability for removal of hexavalent chromium from industrial waste

We describe a new synthetic method for the isolation of the UiO-66 amino-functionalized material (called metal organic resin-1, MOR-1) and its composite with alginic acid (HA). MOR-1 can be prepared in high yield (∼70%) and purity within an hour via a reflux reaction of ZrCl4 and 2-amino-terephthalic acid in acifidied aqueous solution, whereas addition of sodium alginate to the fine suspension of MOR-1 resulting from the reflux synthesis affords the MOR-1-HA composite. This inexpensive, green and fast preparation method results in UiO-66 amino-functionalized materials (MOR-1 and MOR-1-HA) of the same quality and microporous features as those of compounds isolated with the slower solvothermal synthesis involving toxic and costly organic solvents. Field Emission-Scanning Electron Microscopy (FE-SEM) studies revealed that MOR-1 consists of spongy nanoparticles (150–300 nm in size), whereas MOR-1-HA nanoparticles are relatively compact. Thus, for the first time we could visualize the effect of alginic acid partially coating the surface of the MOR particles. The composite prepared by this method can be successfully utilized as a stationary phase, mixed with sand, in an anion-exchange column. The column shows excellent hexavalent chromium sorption properties and can be easily regenerated and reused several times with almost no loss of its initial Cr(VI) removal capacity. Remarkably, this ion exchange column is capable of eliminating Cr(VI) ions from chrome plating wastewater samples, thus indicating its potential for applications in industrial wastewater treatment.
A Novel Method for the Preparation of Narrow-Disperse Nanoencapsulated Phase Change Materials by Phase Inversion Emulsification and Suspension Polymerization

Narrow-disperse nanoencapsulated phase change materials with methyl methacrylate as shell material and n-octadecane as core material were successfully prepared by phase inversion emulsification and suspension polymerization. We characterized the structure, surface morphology, particle size distribution, and thermal properties of prepared nanocapsules using methods such as the Fourier infrared spectrum, scanning electron microscopy analysis, transmission electron microscopy (TEM), differential scanning calorimetry analysis, and thermogravimetric analysis. The effects of surfactant concentration and monomer/n-octadecane mass ratios on the average diameter and phase change properties of nanoencapsulated n-octadecane were investigated. The average diameter of nanocapsules is ∼300–500 nm. The surface is quite smooth and compact. An obvious core–shell structure can be observed from TEM images, and the thickness of the shell is ∼50 nm. When the n-octadecane/monomer mass ratio is 5:4, the encapsulation efficiency.
Morphological and genetic diversity of traditional varieties of agave in Hidalgo State, Mexico

The agaves are plants of cultural importance which have been used by humans for about 10,000 years and about 40 specific uses. The most culturally and economically important of those uses are for the production of fermented (pulque) and distilled beverages (mescal). Pulque continues to be produced in nearly all of Mexico, and the agaves used for this purpose have shown domestication syndrome. We carry out an ethnobotanical, morphological, and genetic analysis of the traditional varieties of pulque agave used in the production of aguamiel (agave sap) and pulque in the state of Hidalgo. We did semi-structured interviews, free listings, and tours with 11 agave managers. We analyzed morphology and studied genetic diversity and structure using nuclear microsatellites. We found wild-collected, tolerated, transplanted, and cultivated varieties of agave. This comprised 19 traditional varieties of pulque agave, 12 of them in production during the study, which corresponded to the species Agave americana, A. salmiana y A. mapisaga and five intraspecific entities. The varieties were grouped morphologically according to a management gradient; the wild-collected varieties were the smallest, with more lateral teeth and a larger terminal spine. The cultivated varieties clearly exhibited domestication syndrome, with larger plants and smaller dentition. The expected heterozygosity (He) of the varieties ranged from 0.204 to 0.721. Bayesian clustering suggested the existence of three genetic groups, both at the level of traditional varieties of pulque agaves and for management categories, a result that matches multivariate clustering. Pulque producers in the studied localities maintain high agrobiodiversity. The cultivated varieties exhibit domestication syndrome, as has been reported for other species of the genus with the same selection purposes. Our results support the hypothesis of a decrease in genetic diversity in crops compared to wild-growing agaves, which seems to be due to vegetative propagation, among other factors.
Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction

Chromosome segregation errors in oocytes lead to the production of aneuploid eggs, which are the leading cause of pregnancy loss and of several congenital diseases such as Down syndrome. The frequency of chromosome segregation errors in oocytes increases with maternal age, especially at a late stage of reproductive life. How aging at various life stages affects oocytes differently remains poorly understood. In this study, we describe aging‐associated changes in the transcriptome profile of mouse oocytes throughout reproductive life. Our single‐oocyte comprehensive RNA sequencing using RamDA‐seq revealed that oocytes undergo transcriptome changes at a late reproductive stage, whereas their surrounding cumulus cells exhibit transcriptome changes at an earlier stage. Calorie restriction, a paradigm that reportedly prevents aging‐associated egg aneuploidy, promotes a transcriptome shift in oocytes with the up‐regulation of genes involved in chromosome segregation. This shift is accompanied by the improved maintenance of chromosomal cohesin, the loss of which is a hallmark of oocyte aging and causes chromosome segregation errors. These findings have implications for understanding how oocytes undergo aging‐associated functional decline throughout their reproductive life in a context‐dependent manner.
Cortical alpha oscillations in cochlear implant users reflect subjective listening effort during speech-in-noise perception

Listening to speech in noise is effortful for individuals with hearing loss, even if they have received a hearing prosthesis such as a hearing aid or cochlear implant (CI). At present, little is known about the neural functions that support listening effort. One form of neural activity that has been suggested to reflect listening effort is the power of 8–12 Hz (alpha) oscillations measured by electroencephalography (EEG). Alpha power in two cortical regions has been associated with effortful listening—left inferior frontal gyrus (IFG), and parietal cortex—but these relationships have not been examined in the same listeners. Further, there are few studies available investigating neural correlates of effort in the individuals with cochlear implants. Here we tested 16 CI users in a novel effort-focused speech-in-noise listening paradigm, and confirm a relationship between alpha power and self-reported effort ratings in parietal regions, but not left IFG. The parietal relationship was not linear but quadratic, with alpha power comparatively lower when effort ratings were at the top and bottom of the effort scale, and higher when effort ratings were in the middle of the scale. Results are discussed in terms of cognitive systems that are engaged in difficult listening situations, and the implication for clinical translation.
Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor

Significance Dynamin is a protein that is a central player in endocytosis, a process that mediates the entry of diverse particles into cells, from nutrients to viruses. Dynamin’s primary activity is to use guanosine triphosphate as fuel to constrict and cut membrane tubes. Key quantitative aspects of its function remain yet unclear. In this work, we determine the strength of an individual dynamin motor. Then, by building a detailed computational model resolving individual motors, we demonstrate that dynamin produces sufficient force to tightly constrict a membrane tube when most of its motors are simultaneously cooperating. Hence, we quantitatively validate the prevailing constriction-by-ratchet model for nature’s strongest torque-generating motor: the dynamin “nanomuscle. ” Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful enough stroke is produced and how the motor modules would cooperate in the constriction process. Here, we characterized the dynamin motor modules by single-molecule Förster resonance energy transfer (smFRET) and found strong nucleotide-dependent conformational preferences. Integrating smFRET with molecular dynamics simulations allowed us to estimate the forces generated in a power stroke. Subsequently, the quantitative force data and the measured kinetics of the GTPase cycle were incorporated into a model including both a dynamin filament, with explicit motor cross-bridges, and a realistic deformable membrane template. In our simulations, collective constriction of the membrane by dynamin motor modules, based on the ratchet mechanism, is directly reproduced and analyzed. Functional parallels between the dynamin system and actomyosin in the muscle are seen. Through concerted action of the motors, tight membrane constriction to the hemifission radius can be reached. Our experimental and computational study provides an example of how collective motor action in megadalton molecular assemblies can be approached and explicitly resolved.
Sex Differences and Caffeine Impact in Adenosine-Induced Hyperemia

Visual Abstract Caffeine consumption before adenosine stress myocardial perfusion imaging (MPI) is known to affect the hemodynamic response and, thus, reduce the stress myocardial blood flow (MBF) and myocardial flow reserve (MFR) assessments. However, it is not clear if any sex-specific differences in the hemodynamic response after caffeine consumption exist. This study aimed to evaluate if such differences exist and, if so, their impact on MBF and MFR assessments. Methods: This study comprised 40 healthy volunteers (19 women). All volunteers underwent 4 serial rest/stress MPI sessions using 82Rb; 2 sessions were acquired without controlled caffeine consumption, and 2 sessions after oral ingestion of either 100 and 300 mg of caffeine or 200 and 400 mg of caffeine. For the caffeine imaging sessions, caffeine was ingested orally 1 h before the MPI scan. Results: Increase in plasma caffeine concentration (PCC) (mg/L) after consumption of caffeine was larger in women (MPI session without caffeine vs. MPI session with caffeine: women = 0.3 ± 0.2 vs. 5.4 ± 5.1, men = 0.1 ± 0.2 vs. 2.7 ± 2.6, both P < 0.001). Caffeine consumption led to reduced stress MBF and MFR assessments for men whereas no changes were reported for women (women [PCC < 1 mg/L vs. PCC ≥ 1 mg/L]: stress MBF = 3.3 ± 0.6 vs. 3.0 ± 0.8 mL/g/min, P = 0.07; MFR = 3.7 ± 0.6 vs. 3.5 ± 1.0, P = 0.35; men [PCC < 1 mg/L vs. PCC ≥ 1 mg/L]: stress MBF = 2.7 ± 0.7 vs. 2.1 ± 1.0 mL/g/min, P = 0.005; MFR = 3.8 ± 1.0 vs. 3.1 ± 1.4, P = 0.018). Significant differences in the stress MBF were observed for the 2 sexes (both P ≤ 0.001), whereas similar MFR was reported (both P ≥ 0.12). Conclusion: Associations between increases in PCC and reductions in stress MBF and MFR were observed for men, whereas women did not have the same hemodynamic response. Stress MBF was affected at lower PCCs in men than women.
An intradialytic non-immersive virtual reality exercise program: a crossover randomized controlled trial.

BACKGROUND Chronic kidney disease is closely related to a high risk of death and disability, poor physical performance, and frailty. The main objective of this research was to analyse how intradialytic administration of a non-immersive virtual reality (VR) exercise program would affect physical function and adherence to exercise in these patients. METHODS A total of 56 individuals participated in two 12-week periods in a crossover randomised controlled trial. Each patient underwent a functional capacity evaluation before and after each study period. The functional tests administered included the 4-metre gait speed test, Short Physical Performance Battery (SPPB), timed up-and-go (TUG) test, one-legged stance test (OLST) for balance, sit-to-stand 10 (STS-10) and sit-to-stand 60 (STS-60) tests, and 6-minute walking test (6MWT). Adherence to the exercise program was also recorded. To assess the effect of VR exercise on the functional test outcomes over time, the patients were analysed using a 2-way repeated-measures ANOVA with time and treatment as the within-participant factors. RESULTS By the end of the 12 weeks of exercise, compared to the control period, 33 participants showed significant change in physical function as measured through the 4-metre gait speed (0.14 m/s), SPPB (1.2 points), TUG (-1.7 seconds), OLST (7.1 seconds), STS-10 (-5.8 seconds), STS-60 (5.0 repetitions), and 6MWT (85.2 metres) with adherence rates exceeding 70%. There were no changes in the biochemical data or in the medications in the period of the study. CONCLUSION An intradialytic non-immersive VR exercise program improves patient physical function.
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing

The expansion of three‐dimensional protein structures and enhanced computing power have significantly facilitated our understanding of protein sequence/structure/function relationships. A challenge in structural genomics is to predict the function of uncharacterized proteins. Protein function deconvolution based on global sequence or structural homology is impracticable when a protein relates to no other proteins with known function, and in such cases, functional relationships can be established by detecting their local ligand binding site similarity. Here, we introduce a sequence order‐independent comparison algorithm, PocketShape, for structural proteome‐wide exploration of protein functional site by fully considering the geometry of the backbones, orientation of the sidechains, and physiochemical properties of the pocket‐lining residues. PocketShape is efficient in distinguishing similar from dissimilar ligand binding site pairs by retrieving 99.3% of the similar pairs while rejecting 100% of the dissimilar pairs on a dataset containing 1538 binding site pairs. This method successfully classifies 83 enzyme structures with diverse functions into 12 clusters, which is highly in accordance with the actual structural classification of proteins classification. PocketShape also achieves superior performances than other methods in protein profiling based on experimental data. Potential new applications for representative SARS‐CoV‐2 drugs Remdesivir and 11a are predicted. The high accuracy and time‐efficient characteristics of PocketShape will undoubtedly make it a promising complementary tool for proteome‐wide protein function inference and drug repurposing study.
Temporal compartmentalization of viral infection in bacterial cells

Significance Virus lytic infection disrupts host cell homeostasis and takes over the cell space for virus multiplication. Viral-induced reorganization of prokaryotic cells must meet the challenge to restructure the cytoplasm open space of a small-sized cell. We discovered that the bacterial siphovirus SPP1 builds two types of independent compartments in the host cytoplasm to confine viral DNA enzymatic reactions and to store viral particles. This spatial partition responds to the requirements for exponential replication of SPP1 genomes and for the assembly of hundreds of viral particles. Its similarities to remodeling of the cell nucleus by herpesviruses led to the hypothesis that ancestral strategies used by viruses to invade the cell space were conserved to infect hosts of different domains of life. Virus infection causes major rearrangements in the subcellular architecture of eukaryotes, but its impact in prokaryotic cells was much less characterized. Here, we show that infection of the bacterium Bacillus subtilis by bacteriophage SPP1 leads to a hijacking of host replication proteins to assemble hybrid viral–bacterial replisomes for SPP1 genome replication. Their biosynthetic activity doubles the cell total DNA content within 15 min. Replisomes operate at several independent locations within a single viral DNA focus positioned asymmetrically in the cell. This large nucleoprotein complex is a self-contained compartment whose boundaries are delimited neither by a membrane nor by a protein cage. Later during infection, SPP1 procapsids localize at the periphery of the viral DNA compartment for genome packaging. The resulting DNA-filled capsids do not remain associated to the DNA transactions compartment. They bind to phage tails to build infectious particles that are stored in warehouse compartments spatially independent from the viral DNA. Free SPP1 structural proteins are recruited to the dynamic phage-induced compartments following an order that recapitulates the viral particle assembly pathway. These findings show that bacteriophages restructure the crowded host cytoplasm to confine at different cellular locations the sequential processes that are essential for their multiplication.
Reactions of hydroperoxo and superoxide with iodine and bromine and the iodide (I2-) and iodine atom reduction potentials

The equilibrium constant for reaction of HO/sub 2/ with I/sub 2/ to form H/sup +/, O/sub 2/, and I/sub 2//sup -/ was measured to be 30 M at 25 /sup 0/C. Derived free energies are . delta.G/sub f//sup 0/(I/sub 2//sup -/) = -0.9 kcal/mol and . delta.G/sub f//sup 0/(I/sub aq/) = 18.3 kcal/mol. Reduction potentials are E/sup 0/(I/sub 2(aq)//I/sub 2//sup -/) = 0.21 V, E/sup 0/(I/sub 2//sup -//2I/sup -/) = 1.03 V, and E/sup 0/(I/I/sup -/) = 1.33 V. Rate constants for reaction of HO/sub 2/ with I/sub 2/ and Br/sub 2/ are 1.8 x 10/sup 7/ and 1.3 x 10/sup 8/ M/sup -1/ s/sup -1/. Rate constants for O/sub 2//sup -/ reactions with I/sub 2/, I/sub 3//sup -/, Br/sub 2/, Br/sub 3//sup -/, and HOBr are 6.0 x 10/sup 9/, 0.25 x 10/sup 9/, 5 x 10/sup 9/, 1.5 x 10/sup 9/, and 3.5 x 10/sup 9/, and 3.5 x 10/sup 9/ M/sup -1/ s/sup -1/. The activation energies for reaction of O/sub 2//sup -/ with I/sub 2/ and with I/sub 3//sup -/ are 3.3 and 4.9 kcal/mol. 15 references, 4 figures, 1 table.
Age- and sex-associated differences in hematology and biochemistry parameters of Dunkin Hartley guinea pigs (Cavia porcellus)

The Dunkin Hartley is the most common guinea pig strain used in biomedical research, particularly for studies of asthma, allergy, infectious disease, reproduction, and osteoarthritis. Minimally invasive blood tests, such as complete blood counts and serum biochemistry profiles, are often collected for diagnostics and laboratory analyses. However, reference intervals for these assays have not yet been well-documented in this strain. The purpose of this study was to establish reference intervals for hematologic and biochemical parameters of Dunkin Hartley guinea pigs and determine age- and sex-related differences. Hematologic and biochemical parameters were retrospectively obtained from 145 male and 68 female guinea pigs between 2 and 15 months of age. All blood parameters were analyzed by a veterinary clinical pathology laboratory. Reference intervals were established according to the American Society for Veterinary Clinical Pathology guidelines. Age- and sex-related differences were determined using unpaired t-tests or nonparametric Mann-Whitney tests. Hematocrit, red blood cell distribution width, mean platelet volume, white blood cell count, heterophils, monocytes, eosinophils, glucose, blood urea nitrogen, creatinine, calcium, magnesium, total protein, albumin, globulin, cholesterol, aspartate aminotransferase, gamma glutamyl transferase, and bicarbonate increased with age. Mean corpuscular hemoglobin concentration, cellular hemoglobin concentration mean, platelets, lymphocytes, phosphorus, albumin/globulin ratio, alkaline phosphatase, anion gap, and calculated osmolality decreased with age. Males had higher hemoglobin, hematocrit, red blood cell count, mean corpuscular hemoglobin concentration, white blood cell count, heterophils, Foa-Kurloff cells, alanine aminotransferase, and bicarbonate and lower mean corpuscular volume, red blood cell distribution width, platelets, mean platelet volume, eosinophils, total protein, albumin, globulin, cholesterol, potassium, anion gap, calculated osmolality, and iron compared to females. Establishing age and sex differences in hematologic and biochemical parameters of Dunkin Hartley guinea pigs provides valuable insight into their physiology to better evaluate diagnostics and experimental results.