Miracle-dz/UniFAR-FTUs huggingface dataset:
Vancosamine. A novel branched chain amino-sugar from the antibiotic vancomycin

Acid hydrolysis of the antibiotic vancomycin from Streptomyces orientalis yields the 3-amino-2,3,6-trideoxy-3-C-methyl-L-lyxo-hexopyranose, vancosamine, the structure of which is assigned on the basis of chemical and spectroscopic studies, particularly n.m. r. spectroscopy.
Parallel processing of natural images by overlapping retinal neuronal ensembles

Even though the retinal microcircuit organization has been described in detail at the single-cell level, little is known about how groups of retinal cells’ coordinated activity encode and process parallel information representing the spatial and temporal structure of changing environmental conditions. To describe the population dynamics of retinal neuronal ensembles, we used microelectrode array recordings that describe hundreds of retinal ganglion cells’ simultaneous activity in response to a short movie captured in the natural environment where our subject develops their visual behaviors. The vectorization of population activity allowed the identification of retinal neuronal ensembles that synchronize to specific segments of natural stimuli. These synchronous retinal neuronal ensembles were reliably activated by the same stimuli at different trials, indicating a robust population response of retinal microcircuits. The generation of asynchronous events required integrating a physiologically meaningful time window larger than 80 ms, demonstrating that retinal neuronal ensembles’ time integration filters non-structured visual information. Interestingly, individual neurons could be part of several ensembles indicating that parallel circuits could encode environmental conditions changes. We conclude that parallel neuronal ensembles could represent the functional unit of retinal computations and propose that the further study of retinal neuronal ensembles could reveal emergent properties of retinal circuits that individual cells’ activity cannot explain.
How human runners regulate footsteps on uneven terrain

Running stably on uneven natural terrain takes skillful control and was critical for human evolution. Even as runners circumnavigate hazardous obstacles such as steep drops, they must contend with uneven ground that is gentler but still destabilizing. We do not know how footsteps are guided based on the uneven topography of the ground and how those choices influence stability. Therefore, we studied human runners on trail-like undulating uneven terrain and measured their energetics, kinematics, ground forces, and stepping patterns. We find that runners do not selectively step on more level ground areas. Instead, the body’s mechanical response, mediated by the control of leg compliance, helps maintain stability without requiring precise regulation of footsteps. Furthermore, their overall kinematics and energy consumption on uneven terrain showed little change from flat ground. These findings may explain how runners remain stable on natural terrain while devoting attention to tasks besides guiding footsteps.
Diffuse optical reconstructions of NIRS data using Maximum Entropy on the Mean

Functional near-infrared spectroscopy (fNIRS) measures the hemoglobin concentration changes associated with neuronal activity. Diffuse optical tomography (DOT) consists in reconstructing the optical density changes measured from scalp channels to the near-infrared light attenuation changes within the cortical regions. In the present study, we adapted a nonlinear source localization method developed and validated in the context of Electro- and Magneto-Encephalography (EEG/MEG): the Maximum Entropy on the Mean (MEM), to solve the inverse problem of DOT reconstruction. We first introduced depth weighting strategy within the MEM framework for DOT reconstruction to avoid biasing the reconstruction results of DOT towards superficial regions. We also proposed a new initialization of the MEM model improving the temporal accuracy of the original MEM framework. To evaluate MEM performance and compare with widely used depth weighted Minimum Norm Estimate (MNE) inverse solution, we applied a realistic simulation scheme which contained 4000 simulations generated by 250 different seeds at different locations and 4 spatial extents ranging from 3 to 40cm2 along the cortical surface. Our results showed that overall MEM provided more accurate DOT reconstructions than MNE. Moreover, we found that MEM was remained particularly robust in low signal-to-noise ratio (SNR) conditions. The proposed method was further illustrated, by comparing to functional Magnetic Resonance Imaging (fMRI) activation maps, on real data involving finger tapping tasks with two different montages. The results showed that MEM provided more accurate HbO and HbR reconstructions in spatial agreement with the fMRI main cluster, when compared to MNE. Highlights We introduced a new NIRS reconstruction method – Maximum Entropy on the Mean. We implemented depth weighting strategy within the MEM framework. We improved the temporal accuracy of the original MEM reconstruction. Performances of MEM and MNE were evaluated with realistic simulations and real data. MEM provided more accurate and robust reconstructions than MNE.
p16-3MR: A Novel Model to Study Cellular Senescence in Cigarette Smoke-Induced Lung Injuries

Cellular senescence and lung aging are associated with the pathogenesis of Chronic Obstructive Pulmonary Disease (COPD). COPD progresses with aging, and chronic smoking is the key susceptibility factor in lung pathological changes concurrent with biological aging. However, these processes involving cigarette smoke (CS)-mediated lung cellular senescence are difficult to distinguish. One of the impediments to study cellular senescence in relation to age-related lung pathologies is the lack of a suitable in vivo model. In view of this, we provide evidence that supports the suitability of p16-3MR mice to study cellular senescence in CS-mediated and age-related lung pathologies. p16-3MR mice has a trimodal reporter fused to the promoter of p16INK4a gene that enables detection, isolation and selective elimination of senescent cells, thus making it a suitable model to study cellular senescence. To determine its suitability in CS-mediated lung pathologies, we exposed young (12-14 months) and old (17-20 months) p16-3MR mice to 30-day CS exposure and studied the expression of senescent genes (p16, p21 and p53) and SASP-associated markers (MMP9, MMP12, PAI-1, and FN-1) in air- and CS-exposed mouse lungs. Our results showed that this model could detect cellular senescence using luminescence and isolate cells undergoing senescence with the help of tissue fluorescence in CS-challenged young and old mice. Our results from the expression of senescence markers and SASP-associated genes in CS-challenged young and old p16-3MR mice were comparable with increased lung cellular senescence and SASP in COPD. We further showed age-dependent alteration in the (i) tissue luminescence and fluorescence, (ii) mRNA and protein expressions of senescent markers and SASP genes, and (iii) SA-β-gal activity in CS-challenged young and old p16-3MR mice as compared to their air controls. Overall, we showed that p16-3MR is a competent model to study cellular senescence in age-related pathologies and could help understand the pathobiology of cellular senescence in lung conditions like COPD and fibrosis.
A “spindle and thread”-mechanism unblocks translation of N-terminally disordered proteins

Protein disorder is a major hurdle for structural biology. A prominent example is the tumour suppressor p53, whose low expression levels and poor conformational stability due to a high degree of disorder pose major challenges to the development of cancer therapeutics. Here, we address these issues by fusing p53 to an engineered spider silk domain termed NT*. The chimeric protein displays highly efficient translation in vitro and in E. coli and is fully active in human cancer cells. The transmission electron microscopy structure and native mass spectrometry reveal that the full-length p53 fusion protein adopts a compact conformation. Molecular dynamics simulations show that the disordered transactivation domain of p53 is wound around the NT* domain via a series of folding events, resulting in a globular structure. We find that expression of B-Raf, another partially disordered cancer target, is similarly enhanced by fusion to NT*. In summary, we demonstrate how inducing co-translational folding via a molecular “spindle and thread” mechanism can overcome poor translation efficiency of partially disordered proteins.
Interaural time difference tuning in the rat inferior colliculus is predictive of behavioral sensitivity

Recent studies have shown that rats are a useful model for binaural cochlear implant (CI) research, with behavioral sensitivity to interaural time differences (ITDs) of CI stimuli which are better than those of human patients. Here, we characterize ITD tuning in the rat inferior colliculus (IC) and explore whether quality of tuning can predict behavioral performance. We recorded IC responses to stimuli of varying pulse rates and envelope types and quantified both mutual information (MI) and neural d’ as measures of ITD sensitivity. Neural d’ values paralleled behavioral ones, declining with increasing click rates or when envelopes changed from rectangular to Hanning windows. While MI values increased with experience, neural d’ did not. However, neural d’ values correlated much better with behavioral performance than MI. Thus, neural d’ appears to be a particularly well suited to predicting how stimulus parameters will impact behavioral performance.
Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. Additionally, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.
Pulsatile contractions and pattern formation in excitable actomyosin cortex

The actin cortex is an active adaptive material, embedded with complex regulatory networks that can sense, generate, and transmit mechanical forces. The cortex exhibits a wide range of dynamic behaviours, from generating pulsatory contractions and travelling waves to forming organised structures. Despite the progress in characterising the biochemical and mechanical components of the actin cortex, the emergent dynamics of this mechanochemical system is poorly understood. Here we develop a reaction-diffusion model for the RhoA signalling network, the upstream regulator for actomyosin assembly and contractility, coupled to an active actomyosin gel, to investigate how the interplay between chemical signalling and mechanical forces regulate stresses and patterns in the cortex. We demonstrate that mechanochemical feedback in the cortex acts to destabilise homogeneous states and robustly generate pulsatile contractions. By tuning active stress in the system, we show that the cortex can generate propagating contraction pulses, form network structures, or exhibit topological turbulence.
Acidogenic Fermentation of Sugarcane Vinasse and Glucose Using Two Different Anaerobic Digestion Inocula

Vinasse is an agroindustrial wastewater obtained at large amounts in countries such as Brazil, which is one of the world greatest sugar and ethanol producers from sugarcane. Despite its most common use is as nutrient for fertirrigation in sugarcane crops nowadays, alternative processing has been intensely sought in last decades for vinasse aiming primarily the production of energy carriers and high-added value chemicals. One of these alternatives is the anaerobic digestion promoted by bacteria, which results in several products of economic importance. In view of these information, this work presents an investigation of acidogenic fermentation by C. acetobutylicum ATCC 824 and C. beijerinckii ATCC 25752 was conducted in batch reactors by using synthetic vinasse and aqueous glucose solution as substrates. Evaluation of effects of microorganism and carbon source was focused mainly on the production of short chain organic acids (SCOAs), although other metabolites, such as ethanol, were also detected. Carbohydrates were effectively consumed by bacteria, so remaining concentrations of sucrose and glucose (Suc and Glu) in both substrates were considerably low at the end of tests. Lactic acid (HLa) was the prevailing metabolite in all experiments, determining the trends observed for total SCOAs content as a function of incubation time, while other acids were generated in much lesser amounts. Moreover, ethanol (EtOH) attained notably higher concentrations in batch reactors containing glucose as substrate, which showed more relevant production of this chemical. Maximum of 14.1 g HLa L−1 was quantified for lactic acid at incubation time 96 h in reactor using synthetic vinasse and C. beijerinckii (VB), linked to a productivity P = 146.46 mg HLa L−1 h−1 and a yield Y = 1108.03 mg HLa (g Sue)−1. For ethanol, maximum was 1.6 g EtOH L−1, occurring in reactor containing glucose and C. acetobutylicum (GA) also at incubation time 90 h, resulting in P = 13.60 mg EtOH L−1 h−1 and Y = 73.04 mg EtOH (g Glu)−1. Finally, kinetic models were adjusted to experimental data of carbohydrate content, lactate concentration and optical density (indicative of microorganism growth), showing good prediction capability as suggested by values of fit quality parameters such as Residual Sum of Squares (RSS) and R2.
Carrier mobilities and process stability of strained Si n- and p-MOSFETs on SiGe virtual substrates

Surface channel strained Si metal–oxide–semiconductor field-effect transistors (MOSFETs) are a leading contender for future high performance complementary metal–oxide–semiconductor (CMOS) applications. The carrier mobility enhancement of these devices is studied as a function of channel strain, and the saturation behavior for n- and p-channel devices is compared. Carrier mobility enhancements of up to 1.8 and 1.6 are achieved for n- and p-channel devices, respectively. The process stability of strained Si MOSFETs is also studied, and carrier mobility enhancement is shown to be robust after well implantation and virtual substrate planarization steps. The effects of high-temperature implant activation anneals are also studied. While no misfit dislocation introduction or strain relaxation is observed in these devices, increased interface state densities or alloy scattering due to Ge interdiffusion are shown to decrease mobility enhancements. Channel thickness effects are also examined for strained Si n-MOSFE.
Relevance of network topology for the dynamics of biological neuronal networks

Complex random networks provide a powerful mathematical framework to study high-dimensional physical and biological systems. Several features of network structure (e.g. degree correlation, average path length, clustering coefficient) are correlated with descriptors of network dynamics and function. However, it is not clear which features of network structure relate to the dynamics of biological neuronal networks (BNNs), characterized by non-linear nodes with high in- and out degrees, but being weakly connected and communicating in an event-driven manner, i.e. only when neurons spike. To better understand the structure-dynamics relationship in BNNs, we analysed the structure and dynamics of > 9,000 BNNs with different sizes and topologies. In addition, we also studied the effect of network degeneration on neuronal network structure and dynamics. Surprisingly, we found that the topological class (random, small-world, scale-free) was not an indicator of the BNNs activity state as quantified by the firing rate, network synchrony and spiking regularity. In fact, we show that different network topologies could result in similar activity dynamics. Furthermore, in most cases, the network activity changes did not depend on the rules according to which neurons or synapses were pruned from the networks. The analysis of dynamics and structure of the networks we studied revealed that the effective synaptic weight (ESW) was the most crucial feature in predicting the statistics of spiking activity in BNNs. ESW also explained why different synapse and neuron pruning strategies resulted in almost identical effects on the network dynamics. Thus, our findings provide new insights into the structure-dynamics relationships in BNNs. Moreover, we argue that network topology and rules by which BNNs degenerate are irrelevant for BNN activity dynamics. Beyond neuroscience, our results suggest that in large networks with non-linear nodes, the effective interaction strength among the nodes, instead of the topological network class, may be a better predictor of the network dynamics and information flow.
Zooming into the genomic vicinity of the major locus for vicine and convicine in faba bean (Vicia faba L.)

The versatility of faba bean (Vicia faba L.) seed as valuable protein feed is hampered by its relatively high level of the compounds vicine and convicine (VC), which are antinutritive factors in poultry and further non-ruminant feed. The objective here was to develop the first-ever genetically low-VC winter faba bean. Hence, the low VC allele vc-, that should be the basis of a known, major locus for VC, need verification and molecular identification and be based on appropriately developed DNA-markers; the low VC feature awaited its transfer into the high-performing winter faba bean germplams. Based on bi-parental F2-families and isogenic lines, we thus developed highly useful SNP markers exploiting transcriptomic data. Furthermore, we fine-mapped and, based on synteny to Medicago truncatula and Cicer arietinum, we identified a candidate gene for the VC locus. A novel, genetically low VC winter faba bean population was bred. The path is now well-prepared for further marker-based breeding progress.
Engineering protease-resistant peptides to inhibit human parainfluenza viral respiratory infection

The lower respiratory tract infections affecting children worldwide are in large part caused by the parainfluenza viruses (HPIVs), particularly HPIV3, along with human metapneumovirus and respiratory syncytial virus, enveloped negative-strand RNA viruses. There are no vaccines for these important human pathogens, and existing treatments have limited or no efficacy. Infection by HPIV is initiated by viral glycoprotein-mediated fusion between viral and host cell membranes. A viral fusion protein (F), once activated in proximity to a target cell, undergoes a series of conformational changes that first extend the trimer subunits to allow insertion of the hydrophobic domains into the target cell membrane, and then refold the trimer into a stable postfusion state, driving the merger of the viral and host cell membranes. Lipopeptides derived from the C-terminal heptad repeat (HRC) domain of HPIV3 F inhibit infection by interfering with the structural transitions of the trimeric F assembly. Clinical application of this strategy, however, requires improving the in vivo stability of antiviral peptides. We show that the HRC peptide backbone can be modified via partial replacement of α-amino acid residues with β-amino acid residues to generate α/β-peptides that retain antiviral activity but are poor protease substrates. Relative to a conventional α-lipopeptide, our best α/β-lipopeptide exhibits improved persistence in vivo and improved anti-HPIV3 antiviral activity in animals.
Chiral compounds of essential oils. Part XI. Simultaneous stereoanalysis of lavandula oil constituents

Enantioselective multidimensional gas chromatography using the column combination Carbowax 20 M/heptakis-(2,3-di-O-acetyl-6-O-tert-butyldimethylsilyl)-β-cyclodextrin in OV 1701-vinyl allows the simultaneous stereodifferentiation of trans- and cis-linalol oxides (furanoid), camphor, octan-3-ol, oct-1-en-3-ol, linalyl acetate, lavandulol, terpinen-4-ol and linalol. The method is applied to commercially available as well as self-prepared essential oils of Lavandula species. Chirality evaluation is discussed in view of quality assessment of these essential oils.
Kinetic Interval Measurement: A Tool to Characterize Thermal Reversion Dynamics of Light-switchable Fluorescent Proteins

Light-switchable proteins like Light-Oxygen-Voltage (LOV) domains can be used to control protein interactions and have been applied in vivo to manipulate cell behavior. The switching between dark and light state of LOV domains depends on temperature or their chemical microenvironment and can be tuned by point mutations. Here, we present a method called Kinetic Interval Measurement (KIM) to quantify the thermal reversion dynamics of light-switchable proteins by using a custom microplate reader. We show that this versatile method can be used to determine the reversion half-life of the excited state of LOV proteins in a reproducible, fast and simple manner consuming only small amounts of protein. The sensitivity of the method allows to report on changes in temperature and imidazole concentration as well as the photoswitching dynamics of LOV proteins in living cells.
Sulfur limitation increases duckweed starch accumulation without compromising growth

Duckweeds contain relatively high levels of starch and are a potential biomass feedstock for biofuel production. Here, the biomass and starch yield of duckweed under three different nutrient-limited conditions were analyzed to investigate possible ways of further increasing the efficiency of starch production. The results showed that sulfur limitation resulted in the highest starch yield, which was 42% and 73% higher than in nitrogen or phosphorus limitation, respectively. The high yield of sulfur-limited duckweed is largely due to the combinations of little effects on biomass and high accumulations of starch. Although nitrogen limitation led to higher starch content (67.4%), it severely reduced biomass production. The photosynthetic performance indicator Fv/Fm was a simple and sensitive indicator of starch content in nutrient-limited duckweed. Taken together, this study demonstrates that sulfur limitation is a simple and efficient way to increase starch yield, highlighting the great potential of duckweed for biofuel production. We report that sulfur limitation is a practical approach to increase starch yields in duckweed without affecting growth or biomass. Highlights Sulfur limitation induces starch production in a duckweed specie. Nitrogen limitation triggers the highest starch content, but limits growth. Sulfur limitation results in the highest starch yield. Fv/Fm is a rapid and robust proxy of starch content in nutrient-limited duckweed.