Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

Significance Enzymes position catalytic and reactant groups in active sites, but motions are also integral to enzyme function. Decades of research have revealed static snapshots for many enzymes, but we know very little about the extents and directions of motions of the residues that make up enzymes and their active sites. We took advantage of emerging crystallographic approaches to provide information about protein conformational ensembles for the enzyme ketosteroid isomerase (KSI). Ensemble analyses indicated limited change in conformational heterogeneity through the enzyme’s reaction cycle and a balance of positioning and flexibility that allows KSI to efficiently catalyze multiple reaction steps. We tested KSI-specific and general models for enzyme catalysis, demonstrating the power of and need for “ensemble–function” interrogation of enzymes. How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.
Modelling live fuel moisture content at leaf and canopy scale under extreme drought using a lumped plant hydraulic model

Water content in living vegetation (or live fuel moisture content, LFMC), is increasingly recognized as a key factor linked to vegetation mortality and wildfire ignition and spread. Most often, empirical indices are used as surrogates for direct LFMC measurements. In this paper, we explore the functional and ecophysiological drivers of LFMC during drought at the leaf and canopy scale using the SurEau-Ecos model, and a three years dataset of leaf and canopy scale measurements on a mature Quercus ilex forest, including an extreme drought. The model is based on forest hydrology and plant hydraulics and allows to simulate temporal variations of water potential and content at a daily time step. At leaf level, it simulates the relationship between water potential and water content by separating the apoplasm and the symplasm. Symplasm water content is modeled using the pressure volume curve theory, and apoplasm water content is modelled using the xylem vulnerability to cavitation. Fuel moisture content was upscaled to the canopy level by accounting for foliage mortality estimated from drought induced cavitation. The model was parameterized either with site-measured traits or using a calibration procedure, and compared with water potential and LFMC measured at leaf level, and NDVI variation measured at canopy level and taken as a surrogate for foliage mortality. At leaf level, LFMC prediction using measured hydraulic traits could be improved by considering year-to-year osmotic adjustments. At canopy level, foliage mortality due to drought induced cavitation was a key driver of LFMC decline during the most extreme drought. A sensitivity analysis showed that parameters driving soil water balance (leaf area index, soil water capacity, and regulation of transpiration) and parameters determining pressure volume curves are key traits driving LFMC dynamics at leaf level. At the canopy level, parameters that drives hydraulic failure were the most sensitive and included, both soil water balance parameters and hydraulic traits (the leaf vulnerability to cavitation) were the main drivers of LFMC decline during extreme drought. We also showed that under normal historic weather conditions, most variation of LFMC are linked to reversible symplasm dehydration, however under future, hotter and dryer conditions, most variations are due to the decline canopy of LFMC driven by foliage mortality.
Influence of herbivory, competition and soil fertility on the abundance of Cirsium arvense in acid grassland

Summary 1. The extent to which the weed Cirsium arvense (creeping thistle) may be controlled by manipulating interspecific competition and herbivory was examined in two factorial experiments in order to identify non-chemical herbicide-based control methods for the weed. 2. In the first experiment, a single spring cultivation of grassland intensively grazed by rabbits led to a 25-fold increase in C. arvense cover within 3 months, the effects of which were still present the following summer. As well as destroying the competing perennial vegetation, cultivation created and dispersed small root fragments (3–5 cm in length) from which almost all shoot recruitment occurred. 3. Fencing the cultivated plots against rabbits decreased the cover of C. arvense because ungrazed regrowth from palatable/grazing intolerant species reduced recruitment of C. arvense seedlings and shoots. Seedling competition, in the form of a wildflower seed mix sown soon after cultivation, reduced C. arvense cover on fenced plots to pre-cultivation levels. 4. In the second experiment, conducted in a permanent grassland, C. arvense shoot densities on plots fenced against rabbits and treated as a hay meadow were about one-eighth of those found on rabbit-grazed plots where competing vegetation was kept short. Adventitious shoot recruitment was greater on soil disturbances such as molehills and rabbit scrapes than in intact vegetation. Seedling recruitment occurred only on soil disturbances such as molehills. 5. Lime and nitrogen fertilizer application to the fenced grassland increased the standing biomass of competing species, which reduced C. arvense shoot density. Outside the fences, rabbit grazing was so concentrated on the competing species of the nitrogen-fertilized and limed areas that C. arvense benefited from competitive release, exhibiting increased shoot density. Cirsium arvense showed pronounced competitive release from grasses, with greater shoot densities where grasses were removed with selective herbicides than where no plant species were removed. 6. Exclusion of insects and molluscs with chemical pesticides had no effect on shoot or seedling recruitment or overall shoot density on cultivated soil or in permanent grassland. 7. It is concluded that combinations of management procedures that encourage interspecific competition, such as sowing crops soon after cultivation and delaying grazing of them, and nitrogen fertilizer application and non- or reduced grazing of intact grasslands, will help reduce C. arvense abundance.
somatosensory areas and forearm muscles in the monkey

Corticomuscular coherence has previously been reported between primary motor cortex (M1) and contralateral muscles. We examined whether such coherence could also be seen from somatosensory areas. Local field potentials (LFPs) were recorded from primary somatosensory cortex (S1; areas 3a and 2) and posterior parietal cortex (PPC; area 5) simultaneously with M1 LFP and forearm EMG activity in two monkeys during an index finger flexion task. Significant beta-band (^20 Hz) corticomuscular coherence was found in all areas investigated. Directed coherence (Granger causality) analysis was used to investigate the direction of effects. Surprisingly, the strongest beta-band directed coherence was in the direction from S1/PPC to muscle; it was much weaker in the ascending direction. Examination of the phase of directed coherence provided estimates of the time delay from cortex to muscle. Delays were longer from M1 (^62 ms for the first dorsal interosseous muscle) than from S1/PPC (^36 ms). We then looked at coherence and directed coherence between M1 and S1 for clues to this discrepancy. Directed coherence showed large beta-band effects from S1/PPC to M1, with smaller directed coherence in the reverse direction. The directed coherence phase suggested a delay of ^40 ms from M1 to S1. Corticomuscular coherence from S1/PPC could involve multiple pathways; the most important is probably common input from M1 to S1/PPC and muscles. If correct, this implies that somatosensory cortex receives oscillatory efference copy information from M1 about the motor command. This could allow sensory inflow to be interpreted in the light of its motor context.
THE AEROBIC SUBMERSION LIMIT OF BAIKAL SEALS, PHOCA SIBIRICA

An aerobic dive limit (ADL), the diving duration beyond which postdive lactate concentration increases above the resting level, has been estimated theoretically for many species. Such calculations have been based on an oxygen store/diving metabolic rate (MR) equation. Until now, an ADL has been determined empirically from measurements of blood lactate concentration only in the Weddell seal, Leptonychotes weddellii. We measured post-submergence plasma lactate concentrations during spontaneous voluntary submersions of three captive adult Baikal seals (Phoca sibirica). Two-phase regression analysis revealed a transition in the lactate concentration – submersion duration relationship after the animal had been diving for 15 min. Data collected in prior studies on oxygen stores and submersion metabolic rates of Baikal seals yielded a calculated aerobic limit of 16 min. As in Weddell seals, the empirically determined aerobic limit was very similar to the theoretical limit. Furthermore, most diving durations reco.
Nafamostat mesylate attenuates the pathophysiologic sequelae of neurovascular ischemia

Nafamostat mesylate, an apparent soi-disant panacea of sorts, is widely used to anticoagulate patients undergoing hemodialysis or cardiopulmonary bypass, mitigate the inflammatory response in patients diagnosed with acute pancreatitis, and reverse the coagulopathy of patients experiencing the commonly preterminal disseminated intravascular coagulation in the Far East. The serine protease inhibitor nafamostat mesylate exhibits significant neuroprotective effects in the setting of neurovascular ischemia. Nafamostat mesylate generates neuroprotective effects by attenuating the enzymatic activity of serine proteases, neuroinflammatory signaling cascades, and the endoplasmic reticulum stress responses, downregulating excitotoxic transient receptor membrane channel subfamily 7 cationic currents, modulating the activity of intracellular signal transduction pathways, and supporting neuronal survival (brain-derived neurotrophic factor/TrkB/ERK1/2/CREB, nuclear factor kappa B. The effects collectively reduce neuronal necrosis and apoptosis and prevent ischemia mediated disruption of blood-brain barrier microarchitecture. Investigational clinical applications of these compounds may mitigate ischemic reperfusion injury in patients undergoing cardiac, hepatic, renal, or intestinal transplant, preventing allograft rejection, and treating solid organ malignancies. Neuroprotective effects mediated by nafamostat mesylate support the wise conduct of randomized prospective controlled trials in Western countries to evaluate the clinical utility of this compound.
Dopamine: an immune transmitter

The dopaminergic system controls several vital central nervous system functions, including the control of movement, reward behaviors and cognition. Alterations of dopaminergic signaling are involved in the pathogenesis of neurodegenerative and psychiatric disorders, in particular Parkinson’s disease, which are associated with a subtle and chronic inflammatory response. A substantial body of evidence has demonstrated the non-neuronal expression of dopamine, its receptors and of the machinery that governs synthesis, secretion and storage of dopamine across several immune cell types. This review aims to summarize current knowledge on the role and expression of dopamine in immune cells. One of the goals is to decipher the complex mechanisms through which these cell types respond to dopamine, in order to address the impact this has on neurodegenerative and psychiatric pathologies such as Parkinson’s disease. A further aim is to illustrate the gaps in our understanding of the physiological roles of dopamine to encourage more targeted research focused on understanding the consequences of aberrant dopamine production on immune regulation. These highlights may prompt scientists in the field to consider alternative functions of this important neurotransmitter when targeting neuroinflammatory/neurodegenerative pathologies.
Bird-dispersal of Phytolacca americana L. and the influence of fruit removal on subsequent fruit development

Characteristics of fruits, seeds, and ripening of Phytolacca americana were studied in New Jersey, USA to assess their importance in the dispersal strategy of this species. Removal by birds was directly related to the percent of ripe fruits available on a raceme. Fruit removal from a raceme resulted in lower fruit pulp and seed weights for fruits developing on the same raceme, but these differences probably do not influence probability for dispersal by birds. We demonstrate that characteristics of the fruit pulp may decrease seed availability for the primary seed predator, Peromyscus leucopus, and increase the time fruits are available for dispersal. We speculate on the significance of the sequential fruiting in Phytolacca and the relationship to availability of dispersal agents and high-lipid fruits. Sequential ripening and protection from predation result in seed dispersal from late August to early December.
Territorial behaviour in an Australian nectar‐feeding bird

Abstract The red wattlebird, a large Australian honey eater,defends feeding territories from other nectar-feeding birds. One such territory decreased in sizeand experienced fewer intruders as the density offlowers increased. Daily energy production fromthe nectar in the territory closely approximated theenergy requirements of the territory holder. Thebird was probably minimizing energetic costsrather than maximizing energy intake. Introduction Nectarivorous birds are excellent subjects forstudying the economics of territoriality. Ter-ritorial behaviour has been investigated inhummingbirds (Stiles & Wolf 1970; Stiles 1971;Wolf & Hainsworth 1971; Gass et al. 1976; Lyonet al. 1977; Kodric-Brown & Brown 1978), sun-birds (Gill & Wolf 1975; Wolf 1975; Pyke 1979)and Hawaiian honeycreepers (Carpenter M Kodric-Brown and Brown 1978: with sun-birds; Gill & Wolf 1975; and with Hawaiianhoneycreepers: Carpenter & MacMillen 1976a). The birds defended areas which provided at leasttheir daily energy requirements.Small, rich territories attracted more intrudersin some cases in hummingbirds (Stiles & Wolf1970, Lyon et ai, 1977). However Gass et al,1976 suggested intruder pressure would beinversely related to richness. Small territorieshave shorter perimeters over which intruders canstray. Small territories should also be easier todefend as intruders are more easily seen, morequickly reached and more rapidly expelled.
Remote ischemic conditioning: the brain's endogenous defense against stroke

Introduction to ischemic conditioning: In 1986, Murray built upon a series of accumulated works to demonstrated that brief ischemic “training” episodes fortified cardiac tissue against impending prolonged infarction (Murry et al., 1986). This discovery altered the dogmatic understanding of ischemia, highlighting that time-dependent tissue compromise during infarction was bimodal, not linear, in nature. Instead of being invariably deleterious, an organ’s response to ischemia is dependent upon both the duration of the infarction as well as adaptions from previous, transient ischemic episodes. During prolonged ischemia, ATPase-dependent ion transport is impaired, disrupting cellular homeostasis to incite calcium overload and volume dysregulation. Tissue reperfusion in turn has paradoxically pathological effects, such as the generation of reactive oxygen species and sequestration of proinflammatory immunocytes in ischemic tissue. Any combination of these accumulative insults following ischemic/reperfusion injury results in wide-spread mitochondrial permeability, cell lysis and death (Kalogeris et al., 2016). Transient ischemia, in contrast, confers a conditioning stimulus protecting against subsequent infarction.
EFFECT OF NaCl ON GELATION CHARACTERISTICS OF ACID- AND ALKALI-TREATED PACIFIC WHITING FISH PROTEIN ISOLATES

The physicochemical properties of gels prepared from Pacific whiting protein isolated at pH 3 and 11 with three concentrations of NaCl were characterized after a pH readjustment to 7.0. The strongest gels were obtained from fish protein isolate (FPI) prepared at pH 11/150-mM NaCl and conventional surimi. The protein solubilities of FPI treatments did not contribute significantly to their gel properties. Surface hydrophobicity and differential scanning calorimetry demonstrated that, in addition to adjusting the pH to 3 or 11, salt addition during protein solubilization and subsequent recovery at the isoelectric point (pI) led to protein denaturation. Rheological study indicated that gelation mechanisms of FPI were identical with the same NaCl concentration regardless of pH. The FPI prepared at pH 3 or 11 with NaCl could be partly refolded at pH 7. Nevertheless, some myosin fragments and actin did not refold. PRACTICAL APPLICATIONS Fish protein isolate (FPI) processing is a new concept for protein recovery using a pH shift. While conventional surimi processing is performed by avoiding protein denaturation, this FPI process is performed chemically by unfolding proteins and subsequent refolding. Since FPI is made with the inclusion of sarcoplasmic proteins, which are removed at the conventional surimi process, it guarantees a significant yield increase. This study revealed that the strongest gels were made from conventional surimi and FPI prepared at pH 11 and 15-mM NaCl. It also confirmed that protein solubility does not support thegelation properties of FPI. Refolding of FPI prepared at extreme pHs (3 or 11) was noted, but in a full scale.
Preoperative Axillary Ultrasound Helps in the Identification of a Limited Nodal Burden in Breast Cancer Patients

Abstract Since the Z0011 trial, the clinical evaluation of axillary status has been redirected to predicting nodal tumor burden rather than nodal metastases. Our study aimed to evaluate the value of clinicopathological factors and axillary ultrasound (US) for the prediction of a high nodal burden (≥3 metastatic lymph nodes) in breast cancer patients. A total of 532 consecutive patients who underwent preoperative axillary US and subsequent surgery for clinical T1–2 breast cancer with a final pathologic analysis were included. Clinical and pathologic variables were retrospectively evaluated. Univariate and multivariate statistical analyses were performed to identify the variables that were associated with a high nodal burden. Among the 532 patients, 110 (20.7%) had a high axillary nodal burden and 422 (79.3%) had a limited nodal burden. The multivariate analysis showed that suspicious axillary US findings (P < 0.001), clinical T2 stage (P = 0.011), the presence of lymphovascular invasion (P < 0.001), and estrogen receptor positivity (P < 0.001) were significantly associated with a high nodal burden. Patients with negative axillary US findings seldom had a high nodal burden, with a negative predictive value of 93.0% (294/316). Patients with suspicious axillary US findings, clinical T2 stage, lymphovascular invasion, and estrogen receptor positivity are more likely to have a high nodal burden, which may provide additional information for the treatment plan of breast cancer patients. Preoperative axillary US helps identify a limited nodal burden in breast cancer patients and has implications for axillary lymph node dissection and adjuvant treatment.
RECENT EXPERIMENTS ON BIRD ORIENTATION

Summary. Pigeons raised in open aviaries show homeward orientation when released 100 or 150 km. away from their home aviary. Some of them (15–20%) actually return. When palisades are placed around the aviaries orientation vanishes. The palisades allow the birds free sight of the sky except for a zone of an elevation of 3° above horizon. Orientation is absent also in pigeons raised in an aviary giving view of a broad sector to the north, i.e. the direction opposite to release. These experiments are being continued. Homing pigeons were subjected to an artificial light/dark change (period 24 hours). If the artificial cycle was out of phase with the natural day/night cycle, the “internal clock” was shifted within three to four days as shown by directional responses. Basically the same deviations are shown by “shifted” pigeons taken away from home and released. What appears to be influenced by shifting is a directional response which must necessarily rest upon a previous determination of position relative to home. This preceding part of the whole orientation performance appears to be unaffected. Orientation is influenced by spatial factors, or factors related to space, of unknown nature. The observed phenomena may be tentatively subdivided into variations due to direction, site of release place, site of loft, and region. Among weather conditions, cloud cover has a significant influence upon homing orientation. Top-class homing flights are less frequent with overcast. Homing ability is subject to an annual fluctuation. Homing is best in August and poorest in January. Parallelity to temperature is obvious throughout the year. Correlation between particular releases and temperatures prevailing at the particular occasions exists only in autumn and winter but not during the rest of the year. A correlation has also been found with interdiurnal barometric change. This correlation is scarcely perceptible at surface level, but significant at the 500 and 200-mb. level. This correlation concerns homing performance as well as correctness of departure directions, but not scatter of departures. So far no cross relations can be established between results attained with the different ways of approach. It is thought that homing ability as shown by the domestic pigeon continues to be a problem of ornithological interest. It is assumed the same ability is possessed by wild species.